From 319bba35c5edfdc6a8425c1c984ca0b886c54470 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Thu, 31 Oct 2024 16:51:19 +0100
Subject: [PATCH 01/46] feat: added tw classes for listbox

---
 apps/tailwind-components/assets/css/main.css | 8 ++++++++
 apps/tailwind-components/tailwind.config.js  | 7 +++++++
 2 files changed, 15 insertions(+)

diff --git a/apps/tailwind-components/assets/css/main.css b/apps/tailwind-components/assets/css/main.css
index 258b7b4a10..6b5787e37e 100644
--- a/apps/tailwind-components/assets/css/main.css
+++ b/apps/tailwind-components/assets/css/main.css
@@ -98,6 +98,9 @@
     --background-color-invalid: var(--color-red-200);
     --background-color-input: var(--color-white);
     --background-color-input-checked: var(--color-yellow-500);
+    --background-color-listbox: var(--color-white);
+    --background-color-listbox-hover: var(--color-gray-100);
+    --background-color-listbox-selected: var(--color-umcg-light-blue);
 
     --text-color-button-primary: var(--color-gray-900);
     --text-color-button-primary-hover: var(--color-gray-900);
@@ -143,6 +146,10 @@
     --text-color-pagination-input: var(--color-blue-800);
     --text-color-pagination-hover: var(--color-white);
     --text-color-footer-link: var(--color-yellow-500);
+    --text-color-listbox: var(--color-black);
+    --text-color-listbox-hover: var(--color-black);
+    --text-color-listbox-selected: var(--color-blue-50);
+    
     
     --text-color-invalid: var(--color-red-500);
     --text-color-valid: var(--color-green-800);
@@ -168,6 +175,7 @@
     --border-color-pagination: var(--color-transparent);
     --border-color-input: var(--color-transparent);
     --border-color-input-inverted: var(--color-gray-600);
+    --border-color-listbox-option: var(--color-gray-100);
 
     --border-radius-3px: 3px;
     --border-radius-50px: 50px;
diff --git a/apps/tailwind-components/tailwind.config.js b/apps/tailwind-components/tailwind.config.js
index d76d8e6b90..a3ca9dc531 100644
--- a/apps/tailwind-components/tailwind.config.js
+++ b/apps/tailwind-components/tailwind.config.js
@@ -153,6 +153,9 @@ module.exports = {
         "disabled": "var(--background-color-disabled)",
         "invalid": "var(--background-color-invalid)",
         "input": "var(--background-color-input)",
+        "listbox": "var(--background-color-listbox)",
+        "listbox-hover": "var(--background-color-listbox-hover)",
+        "listbox-selected": "var(--background-color-listbox-selected)"
       }),
       textColor: ({ theme }) => ({
         "button-primary": "var(--text-color-button-primary)",
@@ -201,6 +204,9 @@ module.exports = {
         "valid": "var(--text-color-valid)",
         "disabled": "var(--text-color-disabled)",
         "required": "var(--text-color-required)",
+        "listbox": "var(--text-color-listbox)",
+        "listbox-hover": "var(--text-color-listbox-hover)",
+        "listbox-selected": "var(--text-color-listbox-selected)",
       }),
       borderColor: ({ theme }) => ({
         "button-primary": "var(--border-color-button-primary)",
@@ -224,6 +230,7 @@ module.exports = {
         "disabled": "var(--border-color-disabled)",
         "input": "var(--border-color-input)",
         "input-inverted": "var(--border-color-input-inverted)",
+        "listbox-option": "var(--border-color-listbox-option)"
       }),
       stroke: ({ theme }) => ({
         "input": "var(--border-color-input)",

From 209e2d983a16a6dac91250a043942b8b0c1e21c8 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Thu, 31 Oct 2024 16:51:37 +0100
Subject: [PATCH 02/46] initial listbox component

---
 .../components/input/Listbox.vue              | 145 ++++++++++++++++++
 .../pages/input/Listbox.story.vue             |  30 ++++
 2 files changed, 175 insertions(+)
 create mode 100644 apps/tailwind-components/components/input/Listbox.vue
 create mode 100644 apps/tailwind-components/pages/input/Listbox.story.vue

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
new file mode 100644
index 0000000000..a52a2da1fb
--- /dev/null
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -0,0 +1,145 @@
+<template>
+  <ul>
+    <li>selection: {{ selectedElemId }}:{{ modelValue }}</li>
+    <li>hover: {{ hoveredOption }}</li>
+    <li>focus: {{ focusedOption }}</li>
+  </ul>
+  <div class="w-full relative">
+    <span :id="`listbox-${id}-label`" class="block mb-3">
+      {{ listboxLabel }}
+    </span>
+    <button
+      :id="`listbox-${id}-toggle`"
+      class="relative h-10 w-full text-left pl-10 bg-listbox border-input text-listbox"
+      :aria-controls="`listbox-${id}-options`"
+      @click="onToggleClick"
+    >
+      <span class="truncate" v-if="modelValue?.label">
+        {{ modelValue.label }}
+      </span>
+      <span v-else-if="modelValue?.value">
+        {{ modelValue.value }}
+      </span>
+      <span class="truncate" v-else>
+        {{ placeholder }}
+      </span>
+      <span
+        class="absolute right-5 top-2"
+        :class="{ 'rotate-180': listboxIsExpanded }"
+        aria-hidden="true"
+      >
+        <BaseIcon name="caret-down" />
+      </span>
+    </button>
+    <ul
+      role="listbox"
+      :id="`listbox-${id}-options`"
+      :aria-expanded="listboxIsExpanded"
+      :aria-activedescendant="selectedElemId"
+      tabindex="0"
+      class="absolute b-0 w-full z-10 bg-listbox"
+      :class="{
+        'hidden shadow-search-input': !listboxIsExpanded,
+      }"
+    >
+      <li
+        v-for="(option, index) in listboxOptions"
+        :id="`listbox-${id}-options-${index}`"
+        :key="index"
+        role="option"
+        :ref="listboxOptionRefs.set"
+        :aria-selected="option.value === modelValue?.value"
+        :data-value="option.value"
+        :data-label="option.label"
+        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option cursor-pointer focus:bg-listbox-hover focus:text-listbox hover:bg-listbox-hover hover:text-listbox"
+        :class="{
+          'bg-listbox-selected text-listbox-selected':
+            option.value === modelValue?.value,
+        }"
+        @click="(event: Event) => onListboxSelection(option, (event.target as HTMLInputElement).id)"
+        @mouseover="onListboxHover(option)"
+        @mouseout="hoveredOption = null"
+        @keypress="(event: KeyboardEvent) => onKeyboardEvent(event.key, option)"
+      >
+        <span
+          aria-hidden="true"
+          :class="{
+            visible: option.value === modelValue?.value,
+          }"
+        >
+          <BaseIcon name="Check" class="text-listbox-selected" :width="16" />
+        </span>
+        <span v-if="(option as IListboxOption).label">
+          {{ (option as IListboxOption).label }}
+        </span>
+        <span v-else>
+          {{ option.value }}
+        </span>
+      </li>
+    </ul>
+  </div>
+</template>
+
+<script lang="ts" setup>
+import { useTemplateRefsList } from "@vueuse/core";
+import { ref } from "vue";
+
+interface IListboxOption {
+  value: string | number | boolean;
+  label?: string;
+}
+
+withDefaults(
+  defineProps<{
+    id: string;
+    listboxLabel: string;
+    listboxOptions: IListboxOption[];
+    required?: boolean;
+    hasError?: boolean;
+    placeholder?: string;
+  }>(),
+  {
+    required: false,
+    hasError: false,
+    placeholder: "Select an option",
+  }
+);
+
+const modelValue = defineModel<IListboxOption>();
+const selectedElemId = ref<string>("");
+const hoveredOption = ref<IListboxOption | null>();
+const focusedOption = ref<IListboxOption | null>();
+const listboxIsExpanded = ref<boolean>(false);
+
+const listboxOptionRefs = useTemplateRefsList<HTMLLIElement>();
+
+function onToggleClick() {
+  listboxIsExpanded.value = !listboxIsExpanded.value;
+  if (listboxIsExpanded.value) {
+    listboxOptionRefs.value[0].focus();
+    focusedOption.value = {
+      value: listboxOptionRefs.value[0].getAttribute("data-value") as string,
+      label: listboxOptionRefs.value[0].getAttribute("data-label") as string,
+    };
+  }
+}
+
+function onListboxSelection(option: IListboxOption, elemId: string) {
+  modelValue.value = option;
+  selectedElemId.value = elemId;
+  listboxIsExpanded.value = false;
+}
+
+function onListboxHover(option: IListboxOption) {
+  hoveredOption.value = option;
+  focusedOption.value = null;
+}
+
+function onListboxFocus(option: IListboxOption) {
+  focusedOption.value = option;
+}
+
+function onKeyboardEvent(key: string, option: IListboxOption | null) {
+  console.log(key);
+}
+</script>
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
new file mode 100644
index 0000000000..915a18d0f1
--- /dev/null
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -0,0 +1,30 @@
+<template>
+  <InputListbox
+    id="pizzaToppings"
+    listboxLabel="Which pizza topping is you favorite?"
+    :listboxOptions="[
+      {
+        value: 'tomatoes',
+        label: 'Roma tomatoes',
+      },
+      {
+        value: 'pepperoni',
+        label: 'Pepperoni',
+      },
+      {
+        value: 'mozzerella',
+        label: 'Fresh mozzerella',
+      },
+      {
+        value: 'chillies',
+        label: 'Chillies',
+      },
+      {
+        value: 'basil',
+        label: 'Fresh basil',
+      },
+    ]"
+  />
+</template>
+
+<script lang="ts" setup></script>

From 4bf9393dbb796f78bce36018c488b669d3b22860 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Fri, 1 Nov 2024 15:08:27 +0100
Subject: [PATCH 03/46] revised listbox classes

---
 apps/tailwind-components/assets/css/main.css | 2 +-
 apps/tailwind-components/tailwind.config.js  | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/apps/tailwind-components/assets/css/main.css b/apps/tailwind-components/assets/css/main.css
index 6b5787e37e..726739346a 100644
--- a/apps/tailwind-components/assets/css/main.css
+++ b/apps/tailwind-components/assets/css/main.css
@@ -149,7 +149,7 @@
     --text-color-listbox: var(--color-black);
     --text-color-listbox-hover: var(--color-black);
     --text-color-listbox-selected: var(--color-blue-50);
-    
+    --text-color-button-input-toggle: var(--color-black);
     
     --text-color-invalid: var(--color-red-500);
     --text-color-valid: var(--color-green-800);
diff --git a/apps/tailwind-components/tailwind.config.js b/apps/tailwind-components/tailwind.config.js
index a3ca9dc531..72a5e81fab 100644
--- a/apps/tailwind-components/tailwind.config.js
+++ b/apps/tailwind-components/tailwind.config.js
@@ -207,6 +207,7 @@ module.exports = {
         "listbox": "var(--text-color-listbox)",
         "listbox-hover": "var(--text-color-listbox-hover)",
         "listbox-selected": "var(--text-color-listbox-selected)",
+        "button-input-toggle": "var(--text-color-button-input-toggle)",
       }),
       borderColor: ({ theme }) => ({
         "button-primary": "var(--border-color-button-primary)",
@@ -238,6 +239,7 @@ module.exports = {
       fill: ({ theme }) => ({
         "input": "var(--background-color-input)",
         "input-checked": "var(--background-color-input-checked)",
+        "listbox-selected": "var(--text-color-listbox-selected)",
       }),
       borderRadius: {
         "3px": "var(--border-radius-3px)",

From 42d7c8ea04fda44fe27d85d28e561fd4c6bacb1e Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Fri, 1 Nov 2024 15:08:56 +0100
Subject: [PATCH 04/46] feat: separated elements into child components

---
 .../components/input/Listbox.vue              | 133 +++++-------------
 .../components/input/Listbox/List.vue         |  28 ++++
 .../components/input/Listbox/ListItem.vue     |  82 +++++++++++
 .../components/input/Listbox/Toggle.vue       |  54 +++++++
 .../pages/input/Listbox.story.vue             |   7 +-
 5 files changed, 207 insertions(+), 97 deletions(-)
 create mode 100644 apps/tailwind-components/components/input/Listbox/List.vue
 create mode 100644 apps/tailwind-components/components/input/Listbox/ListItem.vue
 create mode 100644 apps/tailwind-components/components/input/Listbox/Toggle.vue

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index a52a2da1fb..45fe49b629 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,82 +1,40 @@
 <template>
-  <ul>
-    <li>selection: {{ selectedElemId }}:{{ modelValue }}</li>
+  <ul class="mb-6">
+    <li>selection: {{ modelValue }}</li>
     <li>hover: {{ hoveredOption }}</li>
     <li>focus: {{ focusedOption }}</li>
   </ul>
+
   <div class="w-full relative">
-    <span :id="`listbox-${id}-label`" class="block mb-3">
-      {{ listboxLabel }}
-    </span>
-    <button
+    <InputListboxToggle
       :id="`listbox-${id}-toggle`"
-      class="relative h-10 w-full text-left pl-10 bg-listbox border-input text-listbox"
-      :aria-controls="`listbox-${id}-options`"
-      @click="onToggleClick"
-    >
-      <span class="truncate" v-if="modelValue?.label">
-        {{ modelValue.label }}
-      </span>
-      <span v-else-if="modelValue?.value">
-        {{ modelValue.value }}
-      </span>
-      <span class="truncate" v-else>
-        {{ placeholder }}
-      </span>
-      <span
-        class="absolute right-5 top-2"
-        :class="{ 'rotate-180': listboxIsExpanded }"
-        aria-hidden="true"
-      >
-        <BaseIcon name="caret-down" />
-      </span>
-    </button>
-    <ul
-      role="listbox"
+      :value="modelValue?.value"
+      :label="modelValue?.label"
+      :placeholder="placeholder"
+      :controls="`listbox-${id}-options`"
+      :required="required"
+      :hasError="hasError"
+      @click="openCloseListbox"
+    />
+
+    <InputListboxList
       :id="`listbox-${id}-options`"
-      :aria-expanded="listboxIsExpanded"
-      :aria-activedescendant="selectedElemId"
-      tabindex="0"
-      class="absolute b-0 w-full z-10 bg-listbox"
-      :class="{
-        'hidden shadow-search-input': !listboxIsExpanded,
-      }"
+      :expanded="listboxIsExpanded"
+      :selected-elem-id="modelValue?.elemId"
     >
-      <li
+      <InputListboxListItem
         v-for="(option, index) in listboxOptions"
-        :id="`listbox-${id}-options-${index}`"
         :key="index"
-        role="option"
-        :ref="listboxOptionRefs.set"
-        :aria-selected="option.value === modelValue?.value"
-        :data-value="option.value"
-        :data-label="option.label"
-        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option cursor-pointer focus:bg-listbox-hover focus:text-listbox hover:bg-listbox-hover hover:text-listbox"
-        :class="{
-          'bg-listbox-selected text-listbox-selected':
-            option.value === modelValue?.value,
-        }"
-        @click="(event: Event) => onListboxSelection(option, (event.target as HTMLInputElement).id)"
-        @mouseover="onListboxHover(option)"
-        @mouseout="hoveredOption = null"
-        @keypress="(event: KeyboardEvent) => onKeyboardEvent(event.key, option)"
-      >
-        <span
-          aria-hidden="true"
-          :class="{
-            visible: option.value === modelValue?.value,
-          }"
-        >
-          <BaseIcon name="Check" class="text-listbox-selected" :width="16" />
-        </span>
-        <span v-if="(option as IListboxOption).label">
-          {{ (option as IListboxOption).label }}
-        </span>
-        <span v-else>
-          {{ option.value }}
-        </span>
-      </li>
-    </ul>
+        tabindex="0"
+        :ref="listboxOptionRefs.set" 
+        :listbox-id="`listbox-${id}-options`"
+        :elem-id="`listbox-${id}-options-${index}`"
+        :value="option.value"
+        :label="option.label"
+        :selected="option.value === modelValue?.value"
+        @update:model-value="onSelection"
+      />
+    </InputListboxList>
   </div>
 </template>
 
@@ -85,14 +43,16 @@ import { useTemplateRefsList } from "@vueuse/core";
 import { ref } from "vue";
 
 interface IListboxOption {
+  elemId?: string;
   value: string | number | boolean;
   label?: string;
+  selected?: boolean;
 }
 
 withDefaults(
   defineProps<{
     id: string;
-    listboxLabel: string;
+    listboxLabelId: string;
     listboxOptions: IListboxOption[];
     required?: boolean;
     hasError?: boolean;
@@ -106,40 +66,23 @@ withDefaults(
 );
 
 const modelValue = defineModel<IListboxOption>();
-const selectedElemId = ref<string>("");
 const hoveredOption = ref<IListboxOption | null>();
 const focusedOption = ref<IListboxOption | null>();
 const listboxIsExpanded = ref<boolean>(false);
 
 const listboxOptionRefs = useTemplateRefsList<HTMLLIElement>();
 
-function onToggleClick() {
-  listboxIsExpanded.value = !listboxIsExpanded.value;
-  if (listboxIsExpanded.value) {
-    listboxOptionRefs.value[0].focus();
-    focusedOption.value = {
-      value: listboxOptionRefs.value[0].getAttribute("data-value") as string,
-      label: listboxOptionRefs.value[0].getAttribute("data-label") as string,
-    };
-  }
-}
-
-function onListboxSelection(option: IListboxOption, elemId: string) {
-  modelValue.value = option;
-  selectedElemId.value = elemId;
-  listboxIsExpanded.value = false;
+function openCloseListbox(value: boolean) {
+  listboxIsExpanded.value = value;
+  // if (listboxIsExpanded.value) {
+  //   console.log(listboxOptionRefs.value[0]);
+  // }
 }
 
-function onListboxHover(option: IListboxOption) {
-  hoveredOption.value = option;
-  focusedOption.value = null;
-}
+// onMounted(() => console.dir(listboxOptionRefs.value[0]))
 
-function onListboxFocus(option: IListboxOption) {
-  focusedOption.value = option;
+function onSelection (data: IListboxOption) {
+  modelValue.value = data;
 }
 
-function onKeyboardEvent(key: string, option: IListboxOption | null) {
-  console.log(key);
-}
 </script>
diff --git a/apps/tailwind-components/components/input/Listbox/List.vue b/apps/tailwind-components/components/input/Listbox/List.vue
new file mode 100644
index 0000000000..ce04525d90
--- /dev/null
+++ b/apps/tailwind-components/components/input/Listbox/List.vue
@@ -0,0 +1,28 @@
+<template>
+  <ul
+    :id="id"
+    role="listbox"
+    tabindex="-1"
+    :aria-expanded="expanded"
+    :aria-activedescendant="selectedElemId"
+    class="absolute b-0 w-full z-10 bg-listbox"
+    :class="{
+      'hidden': !expanded,
+    }"
+  >
+    <slot></slot>
+  </ul>
+</template>
+
+<script lang="ts" setup>
+interface IListbox {
+  id: string;
+  expanded: boolean;
+  selectedElemId?: string;
+}
+
+withDefaults(defineProps<IListbox>(), {
+  expanded: false,
+});
+
+</script>
diff --git a/apps/tailwind-components/components/input/Listbox/ListItem.vue b/apps/tailwind-components/components/input/Listbox/ListItem.vue
new file mode 100644
index 0000000000..2e764952f8
--- /dev/null
+++ b/apps/tailwind-components/components/input/Listbox/ListItem.vue
@@ -0,0 +1,82 @@
+<template>
+  <li
+    role="option"
+    :aria-selected="selected"
+    class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option cursor-pointer"
+    :class="{
+      'bg-listbox-selected text-listbox-selected': selected,
+      'hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox': !selected
+    }"
+    @click="emitSelection()"
+    @focus="isFocused = true"
+    @blur="isFocused = false"
+    @keydown="onKeyboardEvent"
+  >
+    <BaseIcon
+      name="Check"
+      class="fill-listbox-selected"
+      :class="selected ? 'visible' : 'invisible'"
+      :width="18"
+    />
+    <span v-if="label">
+      {{ label }}
+    </span>
+    <span v-else>
+      {{ value }}
+    </span>
+  </li>
+</template>
+
+<script lang="ts" setup>
+import { ref } from "vue";
+
+interface IListBoxItemData {
+  value: string | number | boolean;
+  label?: string;
+}
+
+interface IListboxItem extends IListBoxItemData {
+  elemId: string;
+  selected?: boolean;
+}
+
+const props = withDefaults(defineProps<IListboxItem>(), {
+  selected: false,
+});
+
+const modelValue = ref<IListboxItem>({
+  elemId: props.elemId,
+  value: props.value,
+  label: props.label,
+});
+
+const isFocused = ref<boolean>(false);
+
+const emit = defineEmits<{
+  (e: "update:modelValue", option:IListBoxItemData): void;
+  (e: "click", option: IListBoxItemData): void;
+  (e: "focus", value: string): void;
+}>();
+
+function emitSelection() {
+  emit("update:modelValue", modelValue.value);
+}
+
+function onKeyboardEvent (event: KeyboardEvent) {
+  const key = event.key;
+  if (key === 'ArrowDown') {
+    event.preventDefault();
+    console.log('down arrow pressed');
+  } 
+  if (key === 'ArrowUp') {
+    event.preventDefault();
+    console.log('up arrow pressed');
+  }
+  
+  if (key === "Enter") {
+    console.log("new selection")
+    emitSelection();
+  }
+}
+
+</script>
diff --git a/apps/tailwind-components/components/input/Listbox/Toggle.vue b/apps/tailwind-components/components/input/Listbox/Toggle.vue
new file mode 100644
index 0000000000..15c1c52212
--- /dev/null
+++ b/apps/tailwind-components/components/input/Listbox/Toggle.vue
@@ -0,0 +1,54 @@
+<template>
+  <button
+    :id="id"
+    :aria-controls="controls"
+    :aria-expanded="expanded"
+    :aria-required="required"
+    class="flex justify-start items-center h-10 w-full text-left pl-10 border-input bg-input text-button-input-toggle"
+    @click="onClick"
+  >
+    <span class="w-full" v-if="label">
+      {{ label }}
+    </span>
+    <span class="w-full" v-else-if="value">
+      {{ value }}
+    </span>
+    <span class="w-full" v-else>
+      {{ placeholder }}
+    </span>
+    <div class="w-[60px] flex flex-col">
+      <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
+      <BaseIcon :width="18" name="caret-down" class="mx-auto -my-1" />
+    </div>
+  </button>
+</template>
+
+<script lang="ts" setup>
+import { ref } from "vue";
+
+interface IInputToggle {
+  id: string;
+  value?: string | number | boolean;
+  label?: string;
+  placeholder?: string;
+  controls: string;
+  required: boolean;
+  hasError: boolean;
+}
+
+withDefaults(defineProps<IInputToggle>(), {
+  placeholder: "Select an option",
+});
+
+const expanded = ref<boolean>(false);
+
+const emit = defineEmits<{
+  (e: "click", value: boolean): void;
+}>();
+
+function onClick () {
+  expanded.value = !expanded.value;
+  emit("click", expanded.value);
+}
+
+</script>
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index 915a18d0f1..42754fd753 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -1,7 +1,10 @@
 <template>
+  <InputLabel id="pizza-toppings-label" class="block mb-3">
+    <span>Which pizza topping is you favorite?</span>
+  </InputLabel>
   <InputListbox
-    id="pizzaToppings"
-    listboxLabel="Which pizza topping is you favorite?"
+    id="pizza-toppings"
+    listboxLabelId="pizza-toppings-label"
     :listboxOptions="[
       {
         value: 'tomatoes',

From f05673f8ca4582c2e54bb973e45be35720bb95d3 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 5 Nov 2024 15:14:27 +0100
Subject: [PATCH 05/46] temp: reverted to single component

---
 .../components/input/Listbox.vue              | 112 ++++++++++++++----
 .../components/input/Listbox/List.vue         |   5 +-
 .../components/input/Listbox/ListItem.vue     |  45 ++++---
 .../components/input/Listbox/Toggle.vue       |   4 +-
 4 files changed, 113 insertions(+), 53 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index 45fe49b629..15dbf1e81e 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,8 +1,7 @@
 <template>
   <ul class="mb-6">
     <li>selection: {{ modelValue }}</li>
-    <li>hover: {{ hoveredOption }}</li>
-    <li>focus: {{ focusedOption }}</li>
+    <li>focus index: {{ focusIndex }}</li>
   </ul>
 
   <div class="w-full relative">
@@ -17,30 +16,63 @@
       @click="openCloseListbox"
     />
 
-    <InputListboxList
+    <ul
       :id="`listbox-${id}-options`"
-      :expanded="listboxIsExpanded"
-      :selected-elem-id="modelValue?.elemId"
+      role="listbox"
+      tabindex="0"
+      ref="listboxList"
+      :aria-expanded="listboxIsExpanded"
+      :aria-activedescendant="modelValue?.elemId"
+      class="absolute b-0 w-full z-10 bg-listbox"
+      :class="{
+        hidden: !listboxIsExpanded,
+      }"
+      @keydown="onKeyboardEvent"
     >
-      <InputListboxListItem
+      <li
+        v-for="(option, index) in listboxOptions"
+        :ref="listboxOptionRefs.set"
+        role="option"
+        :id="`listbox-${id}-options-${index}`"
+        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option cursor-pointer focus:bg-listbox-hover focus:text-listbox hover:bg-listbox-hover hover:text-listbox"
+        :class="{
+          '!bg-listbox-selected !text-listbox-selected':
+            option.value === modelValue?.value,
+        }"
+        @click="onListOptionClick(option)"
+        @focus="console.log(option.value, ' is focused')"
+      >
+        <BaseIcon
+          name="Check"
+          class="fill-listbox-selected"
+          :class="option.value === modelValue?.value ? 'visible' : 'invisible'"
+          :width="18"
+        />
+        <span v-if="option.label">
+          {{ option.label }}
+        </span>
+        <span v-else>
+          {{ option.value }}
+        </span>
+      </li>
+      <!-- <ListboxListItem
         v-for="(option, index) in listboxOptions"
         :key="index"
-        tabindex="0"
-        :ref="listboxOptionRefs.set" 
+        :ref="listboxOptionRefs.set"
         :listbox-id="`listbox-${id}-options`"
         :elem-id="`listbox-${id}-options-${index}`"
         :value="option.value"
         :label="option.label"
         :selected="option.value === modelValue?.value"
         @update:model-value="onSelection"
-      />
-    </InputListboxList>
+      /> -->
+    </ul>
   </div>
 </template>
 
 <script lang="ts" setup>
 import { useTemplateRefsList } from "@vueuse/core";
-import { ref } from "vue";
+import { ref, useTemplateRef } from "vue";
 
 interface IListboxOption {
   elemId?: string;
@@ -49,7 +81,7 @@ interface IListboxOption {
   selected?: boolean;
 }
 
-withDefaults(
+const props = withDefaults(
   defineProps<{
     id: string;
     listboxLabelId: string;
@@ -66,23 +98,57 @@ withDefaults(
 );
 
 const modelValue = defineModel<IListboxOption>();
-const hoveredOption = ref<IListboxOption | null>();
-const focusedOption = ref<IListboxOption | null>();
 const listboxIsExpanded = ref<boolean>(false);
+const focusIndex = ref<number>(0);
+const listboxListRef = useTemplateRef<HTMLUListElement>("listboxList");
+const listboxOptionRefs = useTemplateRefsList();
 
-const listboxOptionRefs = useTemplateRefsList<HTMLLIElement>();
-
-function openCloseListbox(value: boolean) {
-  listboxIsExpanded.value = value;
-  // if (listboxIsExpanded.value) {
-  //   console.log(listboxOptionRefs.value[0]);
-  // }
+function focusFirstElement() {
+  (listboxOptionRefs.value[0] as HTMLOptionElement).focus();
 }
 
-// onMounted(() => console.dir(listboxOptionRefs.value[0]))
+function openCloseListbox() {
+  listboxIsExpanded.value = !listboxIsExpanded.value;
+  if (listboxIsExpanded.value) {
+    console.log(listboxListRef.value);
+    listboxListRef.value?.focus();
+    focusFirstElement();
+  }
+}
 
-function onSelection (data: IListboxOption) {
+function onListOptionClick(data: IListboxOption) {
   modelValue.value = data;
+  openCloseListbox();
 }
 
+function onKeyboardEvent(event: KeyboardEvent) {
+  const key = event.key;
+  if (key === "ArrowDown") {
+    event.preventDefault();
+    const newIndexValue: number = focusIndex.value + 1;
+    if (newIndexValue > props.listboxOptions.length - 1) {
+      focusIndex.value = props.listboxOptions.length - 1;
+    } else {
+      focusIndex.value = newIndexValue;
+    }
+  }
+  if (key === "ArrowUp") {
+    event.preventDefault();
+    console.log("up arrow pressed");
+    const newIndexValue: number = focusIndex.value - 1;
+    if (newIndexValue < 0) {
+      focusIndex.value = 0;
+    } else {
+      focusIndex.value = newIndexValue;
+    }
+  }
+
+  if (key === "Enter") {
+    console.log("new selection");
+  }
+
+  if (key === "Spacebar" || key === "" || key === " ") {
+    event.preventDefault();
+  }
+}
 </script>
diff --git a/apps/tailwind-components/components/input/Listbox/List.vue b/apps/tailwind-components/components/input/Listbox/List.vue
index ce04525d90..6c43d8ea9f 100644
--- a/apps/tailwind-components/components/input/Listbox/List.vue
+++ b/apps/tailwind-components/components/input/Listbox/List.vue
@@ -2,12 +2,12 @@
   <ul
     :id="id"
     role="listbox"
-    tabindex="-1"
+    tabindex="0"
     :aria-expanded="expanded"
     :aria-activedescendant="selectedElemId"
     class="absolute b-0 w-full z-10 bg-listbox"
     :class="{
-      'hidden': !expanded,
+      hidden: !expanded,
     }"
   >
     <slot></slot>
@@ -24,5 +24,4 @@ interface IListbox {
 withDefaults(defineProps<IListbox>(), {
   expanded: false,
 });
-
 </script>
diff --git a/apps/tailwind-components/components/input/Listbox/ListItem.vue b/apps/tailwind-components/components/input/Listbox/ListItem.vue
index 2e764952f8..e26297761f 100644
--- a/apps/tailwind-components/components/input/Listbox/ListItem.vue
+++ b/apps/tailwind-components/components/input/Listbox/ListItem.vue
@@ -1,16 +1,15 @@
 <template>
   <li
     role="option"
+    tabindex="0"
     :aria-selected="selected"
     class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option cursor-pointer"
     :class="{
       'bg-listbox-selected text-listbox-selected': selected,
-      'hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox': !selected
+      'hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox':
+        !selected,
     }"
     @click="emitSelection()"
-    @focus="isFocused = true"
-    @blur="isFocused = false"
-    @keydown="onKeyboardEvent"
   >
     <BaseIcon
       name="Check"
@@ -38,6 +37,7 @@ interface IListBoxItemData {
 interface IListboxItem extends IListBoxItemData {
   elemId: string;
   selected?: boolean;
+  å;
 }
 
 const props = withDefaults(defineProps<IListboxItem>(), {
@@ -50,33 +50,28 @@ const modelValue = ref<IListboxItem>({
   label: props.label,
 });
 
-const isFocused = ref<boolean>(false);
-
 const emit = defineEmits<{
-  (e: "update:modelValue", option:IListBoxItemData): void;
-  (e: "click", option: IListBoxItemData): void;
-  (e: "focus", value: string): void;
+  (e: "update:modelValue", option: IListBoxItemData): void;
 }>();
 
 function emitSelection() {
   emit("update:modelValue", modelValue.value);
 }
 
-function onKeyboardEvent (event: KeyboardEvent) {
-  const key = event.key;
-  if (key === 'ArrowDown') {
-    event.preventDefault();
-    console.log('down arrow pressed');
-  } 
-  if (key === 'ArrowUp') {
-    event.preventDefault();
-    console.log('up arrow pressed');
-  }
-  
-  if (key === "Enter") {
-    console.log("new selection")
-    emitSelection();
-  }
-}
+// function onKeyboardEvent (event: KeyboardEvent) {
+//   const key = event.key;
+//   if (key === 'ArrowDown') {
+//     event.preventDefault();
+//     console.log('down arrow pressed');
+//   }
+//   if (key === 'ArrowUp') {
+//     event.preventDefault();
+//     console.log('up arrow pressed');
+//   }
 
+//   if (key === "Enter") {
+//     console.log("new selection")
+//     emitSelection();
+//   }
+// }
 </script>
diff --git a/apps/tailwind-components/components/input/Listbox/Toggle.vue b/apps/tailwind-components/components/input/Listbox/Toggle.vue
index 15c1c52212..c03f67ff91 100644
--- a/apps/tailwind-components/components/input/Listbox/Toggle.vue
+++ b/apps/tailwind-components/components/input/Listbox/Toggle.vue
@@ -1,6 +1,7 @@
 <template>
   <button
     :id="id"
+    aria-haspopup="listbox"
     :aria-controls="controls"
     :aria-expanded="expanded"
     :aria-required="required"
@@ -46,9 +47,8 @@ const emit = defineEmits<{
   (e: "click", value: boolean): void;
 }>();
 
-function onClick () {
+function onClick() {
   expanded.value = !expanded.value;
   emit("click", expanded.value);
 }
-
 </script>

From b09d82ad3f6388aaf1513bc8482a09b002abcd09 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Fri, 8 Nov 2024 07:12:34 +0100
Subject: [PATCH 06/46] finalised structure and added initial interactive
 events

---
 .../components/input/Listbox.vue              | 189 ++++++++++--------
 1 file changed, 105 insertions(+), 84 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index 15dbf1e81e..add3ad1952 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,46 +1,61 @@
 <template>
-  <ul class="mb-6">
-    <li>selection: {{ modelValue }}</li>
-    <li>focus index: {{ focusIndex }}</li>
-  </ul>
+  <output class="block w-full mb-6 bg-gray-100 py-2 px-2">
+    {{ focusCounter }}: {{ modelValue }}
+  </output>
 
   <div class="w-full relative">
-    <InputListboxToggle
+    <button
+      ref="listboxToggle"
       :id="`listbox-${id}-toggle`"
-      :value="modelValue?.value"
-      :label="modelValue?.label"
-      :placeholder="placeholder"
-      :controls="`listbox-${id}-options`"
-      :required="required"
-      :hasError="hasError"
+      role="combobox"
+      aria-haspopup="listbox"
+      :aria-controls="`listbox-${id}-options`"
+      :aria-required="required"
+      :aria-expanded="listboxIsExpanded"
+      class="flex justify-start items-center h-10 w-full text-left pl-10 border-input bg-input text-button-input-toggle"
       @click="openCloseListbox"
-    />
+    >
+      <span class="w-full" v-if="modelValue?.label">
+        {{ modelValue.label }}
+      </span>
+      <span class="w-full" v-else-if="modelValue?.value">
+        {{ modelValue.value }}
+      </span>
+      <span class="w-full" v-else>
+        {{ placeholder }}
+      </span>
+      <div class="w-[60px] flex flex-col">
+        <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
+        <BaseIcon :width="18" name="caret-down" class="mx-auto -my-1" />
+      </div>
+    </button>
 
     <ul
       :id="`listbox-${id}-options`"
       role="listbox"
-      tabindex="0"
-      ref="listboxList"
+      ref="listboxListRef"
       :aria-expanded="listboxIsExpanded"
-      :aria-activedescendant="modelValue?.elemId"
       class="absolute b-0 w-full z-10 bg-listbox"
-      :class="{
-        hidden: !listboxIsExpanded,
-      }"
-      @keydown="onKeyboardEvent"
+      :class="{ hidden: !listboxIsExpanded }"
+      tabindex="0"
+      @keydown.space.prevent
+      @keydown.up.prevent="onKeyUp"
+      @keydown.down.prevent="onKeyDown"
     >
       <li
-        v-for="(option, index) in listboxOptions"
-        :ref="listboxOptionRefs.set"
+        v-for="option in listboxOptions"
+        ref="listboxOptionsRef"
+        :id="`listbox-${id}-options-${option.index}`"
         role="option"
-        :id="`listbox-${id}-options-${index}`"
-        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option cursor-pointer focus:bg-listbox-hover focus:text-listbox hover:bg-listbox-hover hover:text-listbox"
+        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-selected focus:text-listbox-selected"
         :class="{
           '!bg-listbox-selected !text-listbox-selected':
             option.value === modelValue?.value,
         }"
-        @click="onListOptionClick(option)"
-        @focus="console.log(option.value, ' is focused')"
+        :aria-selected="option.value === modelValue?.value"
+        @click="(event: Event) => updateModelValue(event, option)"
+        @focus="(event: Event) => updateModelValue(event, option)"
+        @blur="(event: Event) => (event.target as HTMLOptionElement).setAttribute('tabindex', '-1')"
       >
         <BaseIcon
           name="Check"
@@ -55,37 +70,27 @@
           {{ option.value }}
         </span>
       </li>
-      <!-- <ListboxListItem
-        v-for="(option, index) in listboxOptions"
-        :key="index"
-        :ref="listboxOptionRefs.set"
-        :listbox-id="`listbox-${id}-options`"
-        :elem-id="`listbox-${id}-options-${index}`"
-        :value="option.value"
-        :label="option.label"
-        :selected="option.value === modelValue?.value"
-        @update:model-value="onSelection"
-      /> -->
     </ul>
   </div>
 </template>
 
 <script lang="ts" setup>
-import { useTemplateRefsList } from "@vueuse/core";
-import { ref, useTemplateRef } from "vue";
+import { ref, useTemplateRef, nextTick } from "vue";
 
 interface IListboxOption {
-  elemId?: string;
-  value: string | number | boolean;
+  value: string | number | boolean | undefined | null;
   label?: string;
-  selected?: boolean;
+}
+
+interface IInternalListboxOption extends IListboxOption {
+  index: number;
 }
 
 const props = withDefaults(
   defineProps<{
     id: string;
-    listboxLabelId: string;
-    listboxOptions: IListboxOption[];
+    labelId: string;
+    options: IListboxOption[];
     required?: boolean;
     hasError?: boolean;
     placeholder?: string;
@@ -97,58 +102,74 @@ const props = withDefaults(
   }
 );
 
-const modelValue = defineModel<IListboxOption>();
+const focusCounter = ref<number>(0);
 const listboxIsExpanded = ref<boolean>(false);
-const focusIndex = ref<number>(0);
-const listboxListRef = useTemplateRef<HTMLUListElement>("listboxList");
-const listboxOptionRefs = useTemplateRefsList();
+const modelValue = defineModel<IInternalListboxOption>();
+const ulElemRef = useTemplateRef<HTMLUListElement>("listboxListRef");
+const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listboxOptionsRef");
+const btnElemRef = useTemplateRef<HTMLButtonElement>("listboxToggle");
 
-function focusFirstElement() {
-  (listboxOptionRefs.value[0] as HTMLOptionElement).focus();
+const listboxOptions = computed<IInternalListboxOption[]>(() => {
+  const defaultOption: IListboxOption = {
+    value: null,
+    label: props.placeholder,
+  };
+  const data: IListboxOption[] = [defaultOption, ...props.options];
+  return data.map((option: IListboxOption, index: number) => {
+    return { ...option, index: index };
+  });
+});
+
+function counterIsInRange(value: number) {
+  return value <= listboxOptions.value.length - 1 && value >= 0;
 }
 
-function openCloseListbox() {
-  listboxIsExpanded.value = !listboxIsExpanded.value;
-  if (listboxIsExpanded.value) {
-    console.log(listboxListRef.value);
-    listboxListRef.value?.focus();
-    focusFirstElement();
+function updateCounter(value: number) {
+  if (counterIsInRange(value)) {
+    focusCounter.value = value;
+  } else {
+    focusCounter.value = focusCounter.value;
   }
 }
 
-function onListOptionClick(data: IListboxOption) {
-  modelValue.value = data;
-  openCloseListbox();
+function focusListOption() {
+  nextTick(() => {
+    if (olElemRefs.value) {
+      const targetElem = olElemRefs.value[
+        focusCounter.value
+      ] as HTMLOptionElement;
+      targetElem.setAttribute("tabindex", "0");
+      targetElem.focus();
+    }
+  });
 }
 
-function onKeyboardEvent(event: KeyboardEvent) {
-  const key = event.key;
-  if (key === "ArrowDown") {
-    event.preventDefault();
-    const newIndexValue: number = focusIndex.value + 1;
-    if (newIndexValue > props.listboxOptions.length - 1) {
-      focusIndex.value = props.listboxOptions.length - 1;
-    } else {
-      focusIndex.value = newIndexValue;
-    }
-  }
-  if (key === "ArrowUp") {
-    event.preventDefault();
-    console.log("up arrow pressed");
-    const newIndexValue: number = focusIndex.value - 1;
-    if (newIndexValue < 0) {
-      focusIndex.value = 0;
-    } else {
-      focusIndex.value = newIndexValue;
-    }
-  }
+function updateModelValue(event: Event, selection: IInternalListboxOption) {
+  const elemId: string = (event.target as HTMLOptionElement).id;
+  btnElemRef.value?.setAttribute("aria-activedescendant", elemId);
+  modelValue.value = selection;
+  focusCounter.value = selection.index;
+}
 
-  if (key === "Enter") {
-    console.log("new selection");
-  }
+function onKeyUp(event: Event) {
+  const newCounterValue = focusCounter.value - 1;
+  updateCounter(newCounterValue);
+  focusListOption();
+}
+
+function onKeyDown(event: Event) {
+  const newCounterValue = focusCounter.value + 1;
+  updateCounter(newCounterValue);
+  focusListOption();
+}
 
-  if (key === "Spacebar" || key === "" || key === " ") {
-    event.preventDefault();
+function openCloseListbox() {
+  listboxIsExpanded.value = !listboxIsExpanded.value;
+  if (listboxIsExpanded.value && modelValue.value) {
+    updateCounter(modelValue.value.index);
+  } else {
+    updateCounter(0);
   }
+  focusListOption();
 }
 </script>

From be06742af6c20b7230fd0200e7f66ccd8b8f8dd1 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Fri, 8 Nov 2024 11:26:45 +0100
Subject: [PATCH 07/46] feat: added more events; reorganised binding of events

---
 .../components/input/Listbox.vue              | 135 ++++++++++++++----
 1 file changed, 109 insertions(+), 26 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index add3ad1952..c98be54ef1 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -38,25 +38,30 @@
       class="absolute b-0 w-full z-10 bg-listbox"
       :class="{ hidden: !listboxIsExpanded }"
       tabindex="0"
-      @keydown.space.prevent
-      @keydown.up.prevent="onKeyUp"
-      @keydown.down.prevent="onKeyDown"
-    >
+      @keydown="onListboxKeyDown"
+      >
+      <!-- @keydown.space.prevent
+      @keydown.up.prevent="focusPreviousOption"
+      @keydown.down.prevent="focusNextOption"
+      @keydown.escape.prevent="openCloseListbox" -->
       <li
         v-for="option in listboxOptions"
         ref="listboxOptionsRef"
-        :id="`listbox-${id}-options-${option.index}`"
+        :id="option.elemId"
         role="option"
-        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-selected focus:text-listbox-selected"
+        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
         :class="{
-          '!bg-listbox-selected !text-listbox-selected':
-            option.value === modelValue?.value,
+          '!bg-listbox-selected !text-listbox-selected': option.value === modelValue?.value,
         }"
         :aria-selected="option.value === modelValue?.value"
-        @click="(event: Event) => updateModelValue(event, option)"
-        @focus="(event: Event) => updateModelValue(event, option)"
+        @click="updateModelValue(option)"
         @blur="(event: Event) => (event.target as HTMLOptionElement).setAttribute('tabindex', '-1')"
-      >
+        @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
+        >
+        <!-- @keydown.enter.prevent="(event: Event) => updateModelValue(event, option)"
+        @keydown.space.prevent="(event: Event) => updateModelValue(event, option)"
+        @keydown.tab.prevent="(event: Event) => updateModelValue(event, option)" -->
+        <!-- @focus="(event: Event) => updateModelValue(event, option)" -->
         <BaseIcon
           name="Check"
           class="fill-listbox-selected"
@@ -84,6 +89,7 @@ interface IListboxOption {
 
 interface IInternalListboxOption extends IListboxOption {
   index: number;
+  elemId: string;
 }
 
 const props = withDefaults(
@@ -105,7 +111,6 @@ const props = withDefaults(
 const focusCounter = ref<number>(0);
 const listboxIsExpanded = ref<boolean>(false);
 const modelValue = defineModel<IInternalListboxOption>();
-const ulElemRef = useTemplateRef<HTMLUListElement>("listboxListRef");
 const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listboxOptionsRef");
 const btnElemRef = useTemplateRef<HTMLButtonElement>("listboxToggle");
 
@@ -116,7 +121,11 @@ const listboxOptions = computed<IInternalListboxOption[]>(() => {
   };
   const data: IListboxOption[] = [defaultOption, ...props.options];
   return data.map((option: IListboxOption, index: number) => {
-    return { ...option, index: index };
+    return {
+      ...option,
+      index: index,
+      elemId: `listbox-${props.id}-options-${index}`
+    };
   });
 });
 
@@ -128,7 +137,11 @@ function updateCounter(value: number) {
   if (counterIsInRange(value)) {
     focusCounter.value = value;
   } else {
-    focusCounter.value = focusCounter.value;
+    if (value > listboxOptions.value.length - 1) {
+      focusCounter.value = listboxOptions.value.length - 1;
+    } else {
+      focusCounter.value = 0;
+    }
   }
 }
 
@@ -144,32 +157,102 @@ function focusListOption() {
   });
 }
 
-function updateModelValue(event: Event, selection: IInternalListboxOption) {
-  const elemId: string = (event.target as HTMLOptionElement).id;
-  btnElemRef.value?.setAttribute("aria-activedescendant", elemId);
+function updateModelValue(selection: IInternalListboxOption) {
+  btnElemRef.value?.setAttribute("aria-activedescendant", selection.elemId);
   modelValue.value = selection;
   focusCounter.value = selection.index;
+  openCloseListbox();
 }
 
-function onKeyUp(event: Event) {
-  const newCounterValue = focusCounter.value - 1;
+function focusPreviousOption(by: number=1) {
+  const newCounterValue = focusCounter.value - by;
   updateCounter(newCounterValue);
   focusListOption();
 }
 
-function onKeyDown(event: Event) {
-  const newCounterValue = focusCounter.value + 1;
+function focusNextOption(by: number=1) {
+  const newCounterValue = focusCounter.value + by;
   updateCounter(newCounterValue);
   focusListOption();
 }
 
 function openCloseListbox() {
   listboxIsExpanded.value = !listboxIsExpanded.value;
-  if (listboxIsExpanded.value && modelValue.value) {
-    updateCounter(modelValue.value.index);
-  } else {
-    updateCounter(0);
+  if (listboxIsExpanded.value) {
+    if (modelValue.value) {
+      updateCounter(modelValue.value.index);
+    } else {
+      updateCounter(0);
+    }
+    focusListOption();
   }
-  focusListOption();
 }
+
+function onListboxKeyDown (event: KeyboardEvent) {
+  const key = event.key;
+  
+  switch(key) {
+    
+    // focus
+    case "ArrowUp":
+      event.preventDefault();
+      focusPreviousOption();
+      break;
+      
+    case "ArrowDown":
+      event.preventDefault();
+      focusNextOption();
+      break;
+      
+    case "PageUp":
+        event.preventDefault();
+        focusPreviousOption(10);
+        break;
+        
+    case "PageDown":
+      event.preventDefault();
+      focusNextOption(10);
+      break;
+      
+    case "Home":
+      focusCounter.value = 0;
+      focusListOption();
+      break;
+    
+    case "End":
+      focusCounter.value = listboxOptions.value.length - 1;
+      focusListOption();
+      break;
+      
+    // 
+    case "Esc":
+      openCloseListbox();
+      break;
+  }
+}
+
+function onListboxOptionKeyDown (event: KeyboardEvent, option: IInternalListboxOption) {
+  const key: string = event.key;
+  switch (key) {
+    case "Enter":
+      updateModelValue(option);
+      break;
+      
+    case "Spacebar":
+      event.preventDefault();
+      updateModelValue(option);
+      break;
+    
+    // spacebar (for older browser support)
+    case " ":
+      event.preventDefault();
+      updateModelValue(option);
+      break;
+      
+    case "Tab":
+      updateModelValue(option);
+      break;
+  }
+}
+
 </script>

From 97be2b7ec6ca002c1f04e4971be34c4e24aa7ef4 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Fri, 8 Nov 2024 11:27:19 +0100
Subject: [PATCH 08/46] updated example for testing interactivity

---
 .../pages/input/Listbox.story.vue             | 40 ++++++-------------
 1 file changed, 13 insertions(+), 27 deletions(-)

diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index 42754fd753..ffde055184 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -1,33 +1,19 @@
 <template>
-  <InputLabel id="pizza-toppings-label" class="block mb-3">
-    <span>Which pizza topping is you favorite?</span>
+  <InputLabel id="listbox-input-label" class="block mb-3">
+    <span>Select a group assignment</span>
   </InputLabel>
   <InputListbox
-    id="pizza-toppings"
-    listboxLabelId="pizza-toppings-label"
-    :listboxOptions="[
-      {
-        value: 'tomatoes',
-        label: 'Roma tomatoes',
-      },
-      {
-        value: 'pepperoni',
-        label: 'Pepperoni',
-      },
-      {
-        value: 'mozzerella',
-        label: 'Fresh mozzerella',
-      },
-      {
-        value: 'chillies',
-        label: 'Chillies',
-      },
-      {
-        value: 'basil',
-        label: 'Fresh basil',
-      },
-    ]"
+    id="listbox-input"
+    labelId="listbox-input-label"
+    :options="data"
   />
 </template>
 
-<script lang="ts" setup></script>
+<script lang="ts" setup>
+const data = [...Array(26).keys()].map((num: number) => {
+  return {
+    value: num,
+    label: 'Group ' + String.fromCharCode(num + 65)
+  }
+})
+</script>

From 3ddd24a2d2b6ce6337389dfc71ef1192228c644c Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Fri, 8 Nov 2024 11:49:04 +0100
Subject: [PATCH 09/46] ran formatter; added missing files

---
 .../components/input/Listbox.vue              |  52 ++++----
 .../components/input/Listbox/ListItem.vue     |  70 ++---------
 .../components/input/Listbox/Toggle.vue       |  45 +------
 .../components/input/Listbox2.vue             | 118 ++++++++++++++++++
 .../pages/input/Listbox.story.vue             |   6 +-
 5 files changed, 161 insertions(+), 130 deletions(-)
 create mode 100644 apps/tailwind-components/components/input/Listbox2.vue

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index c98be54ef1..aa6e4bfdb4 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -39,7 +39,7 @@
       :class="{ hidden: !listboxIsExpanded }"
       tabindex="0"
       @keydown="onListboxKeyDown"
-      >
+    >
       <!-- @keydown.space.prevent
       @keydown.up.prevent="focusPreviousOption"
       @keydown.down.prevent="focusNextOption"
@@ -51,13 +51,14 @@
         role="option"
         class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
         :class="{
-          '!bg-listbox-selected !text-listbox-selected': option.value === modelValue?.value,
+          '!bg-listbox-selected !text-listbox-selected':
+            option.value === modelValue?.value,
         }"
         :aria-selected="option.value === modelValue?.value"
         @click="updateModelValue(option)"
         @blur="(event: Event) => (event.target as HTMLOptionElement).setAttribute('tabindex', '-1')"
         @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
-        >
+      >
         <!-- @keydown.enter.prevent="(event: Event) => updateModelValue(event, option)"
         @keydown.space.prevent="(event: Event) => updateModelValue(event, option)"
         @keydown.tab.prevent="(event: Event) => updateModelValue(event, option)" -->
@@ -124,7 +125,7 @@ const listboxOptions = computed<IInternalListboxOption[]>(() => {
     return {
       ...option,
       index: index,
-      elemId: `listbox-${props.id}-options-${index}`
+      elemId: `listbox-${props.id}-options-${index}`,
     };
   });
 });
@@ -164,13 +165,13 @@ function updateModelValue(selection: IInternalListboxOption) {
   openCloseListbox();
 }
 
-function focusPreviousOption(by: number=1) {
+function focusPreviousOption(by: number = 1) {
   const newCounterValue = focusCounter.value - by;
   updateCounter(newCounterValue);
   focusListOption();
 }
 
-function focusNextOption(by: number=1) {
+function focusNextOption(by: number = 1) {
   const newCounterValue = focusCounter.value + by;
   updateCounter(newCounterValue);
   focusListOption();
@@ -188,71 +189,72 @@ function openCloseListbox() {
   }
 }
 
-function onListboxKeyDown (event: KeyboardEvent) {
+function onListboxKeyDown(event: KeyboardEvent) {
   const key = event.key;
-  
-  switch(key) {
-    
+
+  switch (key) {
     // focus
     case "ArrowUp":
       event.preventDefault();
       focusPreviousOption();
       break;
-      
+
     case "ArrowDown":
       event.preventDefault();
       focusNextOption();
       break;
-      
+
     case "PageUp":
-        event.preventDefault();
-        focusPreviousOption(10);
-        break;
-        
+      event.preventDefault();
+      focusPreviousOption(10);
+      break;
+
     case "PageDown":
       event.preventDefault();
       focusNextOption(10);
       break;
-      
+
     case "Home":
       focusCounter.value = 0;
       focusListOption();
       break;
-    
+
     case "End":
       focusCounter.value = listboxOptions.value.length - 1;
       focusListOption();
       break;
-      
-    // 
+
+    //
     case "Esc":
       openCloseListbox();
       break;
   }
 }
 
-function onListboxOptionKeyDown (event: KeyboardEvent, option: IInternalListboxOption) {
+function onListboxOptionKeyDown(
+  event: KeyboardEvent,
+  option: IInternalListboxOption
+) {
   const key: string = event.key;
   switch (key) {
     case "Enter":
       updateModelValue(option);
       break;
-      
+
     case "Spacebar":
       event.preventDefault();
       updateModelValue(option);
       break;
-    
+
     // spacebar (for older browser support)
     case " ":
       event.preventDefault();
       updateModelValue(option);
       break;
-      
+
     case "Tab":
       updateModelValue(option);
       break;
   }
 }
-
 </script>
diff --git a/apps/tailwind-components/components/input/Listbox/ListItem.vue b/apps/tailwind-components/components/input/Listbox/ListItem.vue
index e26297761f..65b02360c1 100644
--- a/apps/tailwind-components/components/input/Listbox/ListItem.vue
+++ b/apps/tailwind-components/components/input/Listbox/ListItem.vue
@@ -1,15 +1,11 @@
 <template>
   <li
     role="option"
-    tabindex="0"
     :aria-selected="selected"
-    class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option cursor-pointer"
+    class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
     :class="{
-      'bg-listbox-selected text-listbox-selected': selected,
-      'hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox':
-        !selected,
+      '!bg-listbox-selected !text-listbox-selected': selected,
     }"
-    @click="emitSelection()"
   >
     <BaseIcon
       name="Check"
@@ -17,61 +13,17 @@
       :class="selected ? 'visible' : 'invisible'"
       :width="18"
     />
-    <span v-if="label">
-      {{ label }}
-    </span>
-    <span v-else>
-      {{ value }}
-    </span>
+    <slot></slot>
   </li>
 </template>
 
 <script lang="ts" setup>
-import { ref } from "vue";
-
-interface IListBoxItemData {
-  value: string | number | boolean;
-  label?: string;
-}
-
-interface IListboxItem extends IListBoxItemData {
-  elemId: string;
-  selected?: boolean;
-  å;
-}
-
-const props = withDefaults(defineProps<IListboxItem>(), {
-  selected: false,
-});
-
-const modelValue = ref<IListboxItem>({
-  elemId: props.elemId,
-  value: props.value,
-  label: props.label,
-});
-
-const emit = defineEmits<{
-  (e: "update:modelValue", option: IListBoxItemData): void;
-}>();
-
-function emitSelection() {
-  emit("update:modelValue", modelValue.value);
-}
-
-// function onKeyboardEvent (event: KeyboardEvent) {
-//   const key = event.key;
-//   if (key === 'ArrowDown') {
-//     event.preventDefault();
-//     console.log('down arrow pressed');
-//   }
-//   if (key === 'ArrowUp') {
-//     event.preventDefault();
-//     console.log('up arrow pressed');
-//   }
-
-//   if (key === "Enter") {
-//     console.log("new selection")
-//     emitSelection();
-//   }
-// }
+withDefaults(
+  defineProps<{
+    selected: boolean;
+  }>(),
+  {
+    selected: false,
+  }
+);
 </script>
diff --git a/apps/tailwind-components/components/input/Listbox/Toggle.vue b/apps/tailwind-components/components/input/Listbox/Toggle.vue
index c03f67ff91..a15ae5fcaa 100644
--- a/apps/tailwind-components/components/input/Listbox/Toggle.vue
+++ b/apps/tailwind-components/components/input/Listbox/Toggle.vue
@@ -1,54 +1,13 @@
 <template>
   <button
-    :id="id"
+    role="combobox"
     aria-haspopup="listbox"
-    :aria-controls="controls"
-    :aria-expanded="expanded"
-    :aria-required="required"
     class="flex justify-start items-center h-10 w-full text-left pl-10 border-input bg-input text-button-input-toggle"
-    @click="onClick"
   >
-    <span class="w-full" v-if="label">
-      {{ label }}
-    </span>
-    <span class="w-full" v-else-if="value">
-      {{ value }}
-    </span>
-    <span class="w-full" v-else>
-      {{ placeholder }}
-    </span>
+    <slot></slot>
     <div class="w-[60px] flex flex-col">
       <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
       <BaseIcon :width="18" name="caret-down" class="mx-auto -my-1" />
     </div>
   </button>
 </template>
-
-<script lang="ts" setup>
-import { ref } from "vue";
-
-interface IInputToggle {
-  id: string;
-  value?: string | number | boolean;
-  label?: string;
-  placeholder?: string;
-  controls: string;
-  required: boolean;
-  hasError: boolean;
-}
-
-withDefaults(defineProps<IInputToggle>(), {
-  placeholder: "Select an option",
-});
-
-const expanded = ref<boolean>(false);
-
-const emit = defineEmits<{
-  (e: "click", value: boolean): void;
-}>();
-
-function onClick() {
-  expanded.value = !expanded.value;
-  emit("click", expanded.value);
-}
-</script>
diff --git a/apps/tailwind-components/components/input/Listbox2.vue b/apps/tailwind-components/components/input/Listbox2.vue
new file mode 100644
index 0000000000..3859d895d9
--- /dev/null
+++ b/apps/tailwind-components/components/input/Listbox2.vue
@@ -0,0 +1,118 @@
+<template>
+  <div class="w-full relative">
+    <p>{{ focusCounter }}: {{ modelValue }}</p>
+    <ul
+      role="listbox"
+      ref="listboxRef"
+      class="bg-listbox"
+      tabindex="0"
+      @keydown.space.prevent
+      @keydown.up.prevent="onKeyUp"
+      @keydown.down.prevent="onKeyDown"
+    >
+      <li
+        v-for="(option, index) in options"
+        :id="`listbox-id-option-${index}`"
+        ref="listboxOptionsRef"
+        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-selected focus:text-listbox-selected"
+        :class="{
+          '!bg-listbox-selected !text-listbox-selected':
+            option.value === modelValue?.value,
+        }"
+        :aria-selected="option.value == modelValue?.value"
+        @keydown.tab.prevent
+        @click="(event: Event) => updateModelValue(event, option, index)"
+        @focus="(event: Event) => updateModelValue(event, option, index)"
+        @blur="(event: Event) => (event.target as HTMLOptionElement).setAttribute('tabindex', '-1')"
+      >
+        <BaseIcon
+          name="Check"
+          class="fill-listbox-selected"
+          :class="option.value === modelValue?.value ? 'visible' : 'invisible'"
+          :width="18"
+        />
+        <span>{{ option.value }}</span>
+      </li>
+    </ul>
+  </div>
+</template>
+
+<script setup lang="ts">
+import { ref, onMounted, nextTick, useTemplateRef } from "vue";
+
+interface IListboxOption {
+  elemId?: string;
+  value: string | number | boolean;
+  label?: string;
+  selected?: boolean;
+  focused?: boolean;
+}
+
+const focusCounter = ref<number>(0);
+const listboxRef = useTemplateRef<HTMLUListElement>("listboxRef");
+const listboxOptionsRef =
+  useTemplateRef<HTMLOptionElement[]>("listboxOptionsRef");
+const modelValue = defineModel<IListboxOption>();
+const options = ref<IListboxOption[]>([
+  { value: "tomatoes", label: "Roma tomatoes" },
+  { value: "pepperoni", label: "Pepperoni" },
+  { value: "mozzerella", label: "Fresh mozzerella" },
+  { value: "chillies", label: "Chillies" },
+  { value: "basil", label: "Fresh basil" },
+]);
+
+function counterIsInRange(value: number) {
+  return value <= options.value.length - 1 && value >= 0;
+}
+
+function updateCounter(value: number) {
+  if (counterIsInRange(value)) {
+    focusCounter.value = value;
+  } else {
+    focusCounter.value = focusCounter.value;
+  }
+}
+
+function focusListOption() {
+  nextTick(() => {
+    if (listboxOptionsRef.value) {
+      const targetElem = listboxOptionsRef.value[
+        focusCounter.value
+      ] as HTMLOptionElement;
+      targetElem.setAttribute("tabindex", "0");
+      targetElem.focus();
+    }
+  });
+}
+
+function updateModelValue(
+  event: Event,
+  selection: IListboxOption,
+  index: number
+) {
+  const newSelection: IListboxOption = selection;
+  const elemId: string = (event.target as HTMLOptionElement).id;
+
+  modelValue.value = newSelection;
+  modelValue.value.elemId = elemId;
+  listboxRef.value?.setAttribute("aria-activedescendant", elemId);
+
+  focusCounter.value = index;
+}
+
+function onKeyUp(event: Event) {
+  console.log("key up");
+  const newCounterValue = focusCounter.value - 1;
+  updateCounter(newCounterValue);
+  focusListOption();
+}
+
+function onKeyDown(event: Event) {
+  console.log("key down");
+  const newCounterValue = focusCounter.value + 1;
+  updateCounter(newCounterValue);
+  focusListOption();
+}
+
+onMounted(() => focusListOption());
+</script>
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index ffde055184..b359bca40c 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -13,7 +13,7 @@
 const data = [...Array(26).keys()].map((num: number) => {
   return {
     value: num,
-    label: 'Group ' + String.fromCharCode(num + 65)
-  }
-})
+    label: "Group " + String.fromCharCode(num + 65),
+  };
+});
 </script>

From 6751bfd9c1c8a3e621099c73ee101eab53b19b11 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Mon, 11 Nov 2024 14:19:20 +0000
Subject: [PATCH 10/46] fix: added missing base style

---
 apps/tailwind-components/assets/css/main.css | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apps/tailwind-components/assets/css/main.css b/apps/tailwind-components/assets/css/main.css
index 726739346a..fe759ea234 100644
--- a/apps/tailwind-components/assets/css/main.css
+++ b/apps/tailwind-components/assets/css/main.css
@@ -100,7 +100,7 @@
     --background-color-input-checked: var(--color-yellow-500);
     --background-color-listbox: var(--color-white);
     --background-color-listbox-hover: var(--color-gray-100);
-    --background-color-listbox-selected: var(--color-umcg-light-blue);
+    --background-color-listbox-selected: var(--color-blue-500);
 
     --text-color-button-primary: var(--color-gray-900);
     --text-color-button-primary-hover: var(--color-gray-900);

From 2afd5b513128d04a8ccc0d825d9f50f46a076b49 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Mon, 11 Nov 2024 14:19:39 +0000
Subject: [PATCH 11/46] feat: added/fixed keyboard events

---
 .../components/input/Listbox.vue              | 121 +++++++++++++-----
 1 file changed, 92 insertions(+), 29 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index aa6e4bfdb4..c9e26efee6 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,19 +1,22 @@
 <template>
   <output class="block w-full mb-6 bg-gray-100 py-2 px-2">
-    {{ focusCounter }}: {{ modelValue }}
+    <code>{{ focusCounter }}: {{ modelValue }}</code>
   </output>
 
   <div class="w-full relative">
     <button
-      ref="listboxToggle"
+      ref="listbox-button"
       :id="`listbox-${id}-toggle`"
       role="combobox"
+      :disabled="disabled"
       aria-haspopup="listbox"
       :aria-controls="`listbox-${id}-options`"
       :aria-required="required"
       :aria-expanded="listboxIsExpanded"
-      class="flex justify-start items-center h-10 w-full text-left pl-10 border-input bg-input text-button-input-toggle"
+      :aria-labelledby="labelId"
+      class="flex justify-start items-center h-10 w-full text-left pl-10 border-input bg-input text-button-input-toggle focus:ring-blue-300"
       @click="openCloseListbox"
+      @keydown="onListboxButtonKeyDown"
     >
       <span class="w-full" v-if="modelValue?.label">
         {{ modelValue.label }}
@@ -33,20 +36,19 @@
     <ul
       :id="`listbox-${id}-options`"
       role="listbox"
-      ref="listboxListRef"
+      ref="listbox-ul"
       :aria-expanded="listboxIsExpanded"
-      class="absolute b-0 w-full z-10 bg-listbox"
-      :class="{ hidden: !listboxIsExpanded }"
-      tabindex="0"
+      class="absolute b-0 w-full overflow-y-scroll z-10 bg-listbox"
+      :class="{
+        hidden: !listboxIsExpanded,
+        'h-44': listboxIsExpanded && listboxOptions.length > 5,
+        'shadow-inner': listboxIsExpanded,
+      }"
       @keydown="onListboxKeyDown"
     >
-      <!-- @keydown.space.prevent
-      @keydown.up.prevent="focusPreviousOption"
-      @keydown.down.prevent="focusNextOption"
-      @keydown.escape.prevent="openCloseListbox" -->
       <li
         v-for="option in listboxOptions"
-        ref="listboxOptionsRef"
+        ref="listbox-li"
         :id="option.elemId"
         role="option"
         class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
@@ -55,14 +57,10 @@
             option.value === modelValue?.value,
         }"
         :aria-selected="option.value === modelValue?.value"
-        @click="updateModelValue(option)"
-        @blur="(event: Event) => (event.target as HTMLOptionElement).setAttribute('tabindex', '-1')"
+        @click="onListboxOptionClick(option)"
+        @blur="blurListOption(option)"
         @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
       >
-        <!-- @keydown.enter.prevent="(event: Event) => updateModelValue(event, option)"
-        @keydown.space.prevent="(event: Event) => updateModelValue(event, option)"
-        @keydown.tab.prevent="(event: Event) => updateModelValue(event, option)" -->
-        <!-- @focus="(event: Event) => updateModelValue(event, option)" -->
         <BaseIcon
           name="Check"
           class="fill-listbox-selected"
@@ -101,8 +99,10 @@ const props = withDefaults(
     required?: boolean;
     hasError?: boolean;
     placeholder?: string;
+    disabled?: boolean;
   }>(),
   {
+    disabled: false,
     required: false,
     hasError: false,
     placeholder: "Select an option",
@@ -112,8 +112,9 @@ const props = withDefaults(
 const focusCounter = ref<number>(0);
 const listboxIsExpanded = ref<boolean>(false);
 const modelValue = defineModel<IInternalListboxOption>();
-const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listboxOptionsRef");
-const btnElemRef = useTemplateRef<HTMLButtonElement>("listboxToggle");
+const ulElemRef = useTemplateRef<HTMLUListElement>("listbox-ul");
+const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listbox-li");
+const btnElemRef = useTemplateRef<HTMLButtonElement>("listbox-button");
 
 const listboxOptions = computed<IInternalListboxOption[]>(() => {
   const defaultOption: IListboxOption = {
@@ -149,15 +150,23 @@ function updateCounter(value: number) {
 function focusListOption() {
   nextTick(() => {
     if (olElemRefs.value) {
-      const targetElem = olElemRefs.value[
-        focusCounter.value
-      ] as HTMLOptionElement;
+      const targetElem = olElemRefs.value[focusCounter.value];
       targetElem.setAttribute("tabindex", "0");
       targetElem.focus();
     }
   });
 }
 
+function blurListOption(option: IInternalListboxOption) {
+  nextTick(() => {
+    if (olElemRefs.value) {
+      const targetElem = olElemRefs.value[option.index];
+      targetElem.setAttribute("tabindex", "-1");
+      targetElem.blur();
+    }
+  });
+}
+
 function updateModelValue(selection: IInternalListboxOption) {
   btnElemRef.value?.setAttribute("aria-activedescendant", selection.elemId);
   modelValue.value = selection;
@@ -177,21 +186,63 @@ function focusNextOption(by: number = 1) {
   focusListOption();
 }
 
+function focusListboxButton() {
+  btnElemRef.value?.focus();
+}
+
 function openCloseListbox() {
   listboxIsExpanded.value = !listboxIsExpanded.value;
   if (listboxIsExpanded.value) {
+    ulElemRef.value?.setAttribute("tabindex", "0");
     if (modelValue.value) {
       updateCounter(modelValue.value.index);
     } else {
       updateCounter(0);
     }
     focusListOption();
+  } else {
+    ulElemRef.value?.setAttribute("tabindex", "-1");
   }
 }
 
-function onListboxKeyDown(event: KeyboardEvent) {
+function onListboxButtonKeyDown(event: KeyboardEvent) {
   const key = event.key;
+  switch (key) {
+    case "ArrowUp":
+      event.preventDefault();
+      openCloseListbox();
+      focusPreviousOption();
+      break;
+
+    case "ArrowDown":
+      event.preventDefault();
+      openCloseListbox();
+      break;
+
+    case "Enter":
+      event.preventDefault();
+      openCloseListbox();
+      break;
+
+    case "Space":
+      event.preventDefault();
+      openCloseListbox();
+      break;
+
+    case "Home":
+      focusCounter.value = 0;
+      focusListOption();
+      break;
 
+    case "End":
+      focusCounter.value = listboxOptions.value.length - 1;
+      focusListOption();
+      break;
+  }
+}
+
+function onListboxKeyDown(event: KeyboardEvent) {
+  const key = event.key;
   switch (key) {
     // focus
     case "ArrowUp":
@@ -223,14 +274,14 @@ function onListboxKeyDown(event: KeyboardEvent) {
       focusCounter.value = listboxOptions.value.length - 1;
       focusListOption();
       break;
-
-    //
-    case "Esc":
-      openCloseListbox();
-      break;
   }
 }
 
+function onListboxOptionClick(option: IInternalListboxOption) {
+  updateModelValue(option);
+  focusListboxButton();
+}
+
 function onListboxOptionKeyDown(
   event: KeyboardEvent,
   option: IInternalListboxOption
@@ -238,22 +289,34 @@ function onListboxOptionKeyDown(
   const key: string = event.key;
   switch (key) {
     case "Enter":
+      event.preventDefault();
       updateModelValue(option);
+      focusListboxButton();
       break;
 
     case "Spacebar":
       event.preventDefault();
       updateModelValue(option);
+      focusListboxButton();
       break;
 
     // spacebar (for older browser support)
     case " ":
       event.preventDefault();
       updateModelValue(option);
+      focusListboxButton();
       break;
 
     case "Tab":
       updateModelValue(option);
+      focusListboxButton();
+      break;
+
+    case "Escape":
+      event.preventDefault();
+      blurListOption(option);
+      openCloseListbox();
+      focusListboxButton();
       break;
   }
 }

From f2839b6ee262131447a5e8d1b597255c69f9302c Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 12 Nov 2024 13:15:44 +0000
Subject: [PATCH 12/46] fix: adjusted element identifier pattern

---
 apps/tailwind-components/components/input/Listbox.vue  | 2 +-
 apps/tailwind-components/pages/input/Listbox.story.vue | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index c9e26efee6..b1a48e7966 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -5,8 +5,8 @@
 
   <div class="w-full relative">
     <button
+      :id="id"
       ref="listbox-button"
-      :id="`listbox-${id}-toggle`"
       role="combobox"
       :disabled="disabled"
       aria-haspopup="listbox"
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index b359bca40c..7ec0079ea4 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -1,5 +1,5 @@
 <template>
-  <InputLabel id="listbox-input-label" class="block mb-3">
+  <InputLabel id="listbox-input-label" for="listbox-input" class="block mb-3">
     <span>Select a group assignment</span>
   </InputLabel>
   <InputListbox

From 98f3667d30922176e96171650edfe51951758d7f Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 12 Nov 2024 13:16:11 +0000
Subject: [PATCH 13/46] feat: added e2e test

---
 .../tailwind-components/input/listbox.spec.ts | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 e2e/tests/tailwind-components/input/listbox.spec.ts

diff --git a/e2e/tests/tailwind-components/input/listbox.spec.ts b/e2e/tests/tailwind-components/input/listbox.spec.ts
new file mode 100644
index 0000000000..843bde5d88
--- /dev/null
+++ b/e2e/tests/tailwind-components/input/listbox.spec.ts
@@ -0,0 +1,71 @@
+import { test, expect } from "@playwright/test";
+
+test(
+  "Listbox: button has correct aria attributes @tw-components @tw-forms @tw-listbox",
+  async({ page }) => {
+    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+    const combobox = await page.getByRole("combobox");
+    await expect(combobox).toHaveAttribute("aria-required");
+    await expect(combobox).toHaveAttribute("aria-expanded");
+    await expect(combobox).toHaveAttribute("aria-labelledby");
+    await expect(combobox).toHaveAttribute("role", "combobox");
+    await expect(combobox).toHaveAttribute("aria-haspopup", "listbox");
+  }
+);
+
+test(
+  "Listbox: combox is properly linked to the listbox @tw-components @tw-forms @tw-listbox",
+  async ({ page }) => {
+    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+    const combobox = await page.getByRole("combobox");
+    const listbox = await page.getByRole("listbox");
+    await combobox.click();
+    
+    const comboxId = await combobox.getAttribute("aria-controls");
+    const listboxId = await listbox.getAttribute("id");
+    await expect(comboxId).toEqual(listboxId);   
+  }
+)
+
+test(
+  "Listbox: listbox has is properly labelled @tw-components @tw-forms @tw-listbox",
+  async ({ page }) => {
+    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+    const combobox = await page.getByRole("combobox");
+    const comboxId = await combobox.getAttribute("aria-labelledby");
+    await page.locator(`label[for='${comboxId}']`);
+  }
+)
+
+test(
+  "Listbox: aria expand properties correctly update when expanded @tw-components @tw-forms @tw-listbox",
+  async({ page }) => {
+    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+    const combobox = await page.getByRole("combobox");
+    await expect(combobox).toHaveAttribute("aria-expanded", "false");
+  }
+);
+
+test(
+  "Listbox: placeholder is the first element in the list @tw-components @tw-forms @tw-listbox",
+  async ({ page }) => {
+    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+    const combobox = await page.getByRole("combobox");
+    await combobox.click();
+    const option = await page.getByRole("option").first();
+    await expect(option).toHaveText("Select an option");
+  }
+)
+
+test(
+  "Listbox: list items have the proper attributes @tw-components @tw-forms @tw-listbox",
+  async ({ page }) => {
+    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+    const combobox = await page.getByRole("combobox");
+    combobox.click();
+    await expect(combobox).toHaveAttribute("aria-expanded", "true");
+    for (const option of await page.getByRole("option").all()) { 
+      await expect(option).toHaveAttribute("aria-selected", "false");
+    }
+  }
+)

From b3f55050aeebb12d761b72914266e5b8dfee97e0 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 13 Nov 2024 11:00:49 +0000
Subject: [PATCH 14/46] feat: added additional tw styles; added keyboard
 prevents

---
 apps/tailwind-components/assets/css/main.css  |  2 +
 .../components/input/Listbox.vue              | 29 +++-----
 .../pages/input/Listbox.story.vue             | 69 ++++++++++++++++---
 apps/tailwind-components/tailwind.config.js   |  1 +
 4 files changed, 72 insertions(+), 29 deletions(-)

diff --git a/apps/tailwind-components/assets/css/main.css b/apps/tailwind-components/assets/css/main.css
index 85a95a0c0a..1104c2ee72 100644
--- a/apps/tailwind-components/assets/css/main.css
+++ b/apps/tailwind-components/assets/css/main.css
@@ -180,6 +180,7 @@
     --border-color-input: var(--color-transparent);
     --border-color-input-inverted: var(--color-gray-600);
     --border-color-listbox-option: var(--color-gray-100);
+    --border-color-listbox: var(--border-color-input);
 
     --border-radius-3px: 3px;
     --border-radius-50px: 50px;
@@ -292,6 +293,7 @@
     --border-color-search-input-mobile: var(--color-gray.100);
     --border-color-pagination: var(--color-umcg-dark-blue);
     --border-color-checkbox: #CCCCCC;
+    --border-color-listbox: #CCCCCC;
 
     --border-radius-3px: 3px;
     --border-radius-50px: 50px;
diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index b1a48e7966..62f40a1515 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,8 +1,4 @@
 <template>
-  <output class="block w-full mb-6 bg-gray-100 py-2 px-2">
-    <code>{{ focusCounter }}: {{ modelValue }}</code>
-  </output>
-
   <div class="w-full relative">
     <button
       :id="id"
@@ -14,9 +10,13 @@
       :aria-required="required"
       :aria-expanded="listboxIsExpanded"
       :aria-labelledby="labelId"
-      class="flex justify-start items-center h-10 w-full text-left pl-10 border-input bg-input text-button-input-toggle focus:ring-blue-300"
-      @click="openCloseListbox"
-      @keydown="onListboxButtonKeyDown"
+      class="flex justify-start items-center h-10 w-full text-left pl-10 border bg-input rounded-search-input text-button-input-toggle focus:ring-blue-300"
+      :class="{
+        'border-disabled text-disabled bg-disabled': disabled,
+        'border-invalid text-invalid': hasError,
+      }"
+      @click.prevent="openCloseListbox"
+      @keydown.prevent="onListboxButtonKeyDown"
     >
       <span class="w-full" v-if="modelValue?.label">
         {{ modelValue.label }}
@@ -44,7 +44,7 @@
         'h-44': listboxIsExpanded && listboxOptions.length > 5,
         'shadow-inner': listboxIsExpanded,
       }"
-      @keydown="onListboxKeyDown"
+      @keydown.prevent="onListboxKeyDown"
     >
       <li
         v-for="option in listboxOptions"
@@ -209,23 +209,19 @@ function onListboxButtonKeyDown(event: KeyboardEvent) {
   const key = event.key;
   switch (key) {
     case "ArrowUp":
-      event.preventDefault();
       openCloseListbox();
       focusPreviousOption();
       break;
 
     case "ArrowDown":
-      event.preventDefault();
       openCloseListbox();
       break;
 
     case "Enter":
-      event.preventDefault();
       openCloseListbox();
       break;
 
     case "Space":
-      event.preventDefault();
       openCloseListbox();
       break;
 
@@ -244,24 +240,19 @@ function onListboxButtonKeyDown(event: KeyboardEvent) {
 function onListboxKeyDown(event: KeyboardEvent) {
   const key = event.key;
   switch (key) {
-    // focus
     case "ArrowUp":
-      event.preventDefault();
       focusPreviousOption();
       break;
 
     case "ArrowDown":
-      event.preventDefault();
       focusNextOption();
       break;
 
     case "PageUp":
-      event.preventDefault();
       focusPreviousOption(10);
       break;
 
     case "PageDown":
-      event.preventDefault();
       focusNextOption(10);
       break;
 
@@ -289,20 +280,17 @@ function onListboxOptionKeyDown(
   const key: string = event.key;
   switch (key) {
     case "Enter":
-      event.preventDefault();
       updateModelValue(option);
       focusListboxButton();
       break;
 
     case "Spacebar":
-      event.preventDefault();
       updateModelValue(option);
       focusListboxButton();
       break;
 
     // spacebar (for older browser support)
     case " ":
-      event.preventDefault();
       updateModelValue(option);
       focusListboxButton();
       break;
@@ -313,7 +301,6 @@ function onListboxOptionKeyDown(
       break;
 
     case "Escape":
-      event.preventDefault();
       blurListOption(option);
       openCloseListbox();
       focusListboxButton();
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index 7ec0079ea4..e024e9cbcc 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -1,12 +1,61 @@
 <template>
-  <InputLabel id="listbox-input-label" for="listbox-input" class="block mb-3">
-    <span>Select a group assignment</span>
-  </InputLabel>
-  <InputListbox
-    id="listbox-input"
-    labelId="listbox-input-label"
-    :options="data"
-  />
+  <h2>Listbox component</h2>
+  <p class="mb-2">
+    The <code>InputListbox</code> component is an reimplementation of the
+    <code>InputSelect</code> component. The component functions and behaves in
+    the same manner as the select element, but it allows the component to be
+    styled.
+  </p>
+  <p class="mb-2">
+    The following example demonstrates the use of the listbox components with
+    various configurations.
+  </p>
+  <form class="mb-2 bg-white rounded p-2">
+    <legend>Configure the listbox component</legend>
+    <div class="mb-2">
+      <InputLabel for="listbox-component-state">
+        Select the component state
+      </InputLabel>
+      <InputRadioGroup
+        id="listbox-component-state"
+        v-model="listboxState"
+        :radioOptions="[
+          {
+            value: 'disabled',
+            label: 'Component is disabled',
+          },
+          {
+            value: 'error',
+            label: 'Component has error',
+          },
+        ]"
+        :showClearButton="true"
+      />
+    </div>
+    <div class="mb-2">
+      <InputLabel for="listbox-placeholder">
+        Change the default placeholder text
+      </InputLabel>
+      <InputString id="listbox-placeholder" v-model="listboxPlaceholder" />
+    </div>
+  </form>
+  <div class="mb-2 bg-white rounded p-2">
+    <InputLabel id="listbox-input-label" for="listbox-input" class="block mb-3">
+      <span>Select a group assignment</span>
+    </InputLabel>
+    <InputListbox
+      id="listbox-input"
+      labelId="listbox-input-label"
+      :options="data"
+      v-model="listboxSelection"
+      :hasError="listboxState === 'error'"
+      :disabled="listboxState === 'disabled'"
+      :placeholder="listboxPlaceholder"
+    />
+    <output class="block w-full mt-6 bg-white py-2 px-2">
+      <code>Output: {{ listboxSelection }}</code>
+    </output>
+  </div>
 </template>
 
 <script lang="ts" setup>
@@ -16,4 +65,8 @@ const data = [...Array(26).keys()].map((num: number) => {
     label: "Group " + String.fromCharCode(num + 65),
   };
 });
+
+const listboxState = ref<string>("");
+const listboxSelection = ref();
+const listboxPlaceholder = ref<string>("Select an option");
 </script>
diff --git a/apps/tailwind-components/tailwind.config.js b/apps/tailwind-components/tailwind.config.js
index ae4fa6bd4c..b3a74b83ee 100644
--- a/apps/tailwind-components/tailwind.config.js
+++ b/apps/tailwind-components/tailwind.config.js
@@ -234,6 +234,7 @@ module.exports = {
         "disabled": "var(--border-color-disabled)",
         "input": "var(--border-color-input)",
         "input-inverted": "var(--border-color-input-inverted)",
+        "listbox": "var(--border-color-search-input)",
         "listbox-option": "var(--border-color-listbox-option)"
       }),
       stroke: ({ theme }) => ({

From 1055d918185699a6cee33760c4db585f55bdeacc Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Mon, 18 Nov 2024 09:17:01 +0000
Subject: [PATCH 15/46] fix: corrected input types

---
 .../components/input/Listbox.vue              | 106 +++++++++++-----
 .../components/input/Listbox/List.vue         |  27 ----
 .../components/input/Listbox/ListItem.vue     |  29 -----
 .../components/input/Listbox/Toggle.vue       |  13 --
 .../components/input/Listbox2.vue             | 118 ------------------
 apps/tailwind-components/types/listbox.ts     |  12 ++
 6 files changed, 88 insertions(+), 217 deletions(-)
 delete mode 100644 apps/tailwind-components/components/input/Listbox/List.vue
 delete mode 100644 apps/tailwind-components/components/input/Listbox/ListItem.vue
 delete mode 100644 apps/tailwind-components/components/input/Listbox/Toggle.vue
 delete mode 100644 apps/tailwind-components/components/input/Listbox2.vue
 create mode 100644 apps/tailwind-components/types/listbox.ts

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index 62f40a1515..b6c6d5bdc0 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -18,14 +18,8 @@
       @click.prevent="openCloseListbox"
       @keydown.prevent="onListboxButtonKeyDown"
     >
-      <span class="w-full" v-if="modelValue?.label">
-        {{ modelValue.label }}
-      </span>
-      <span class="w-full" v-else-if="modelValue?.value">
-        {{ modelValue.value }}
-      </span>
-      <span class="w-full" v-else>
-        {{ placeholder }}
+      <span class="w-full">
+        {{ listboxDisplayText }}
       </span>
       <div class="w-[60px] flex flex-col">
         <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
@@ -54,9 +48,9 @@
         class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
         :class="{
           '!bg-listbox-selected !text-listbox-selected':
-            option.value === modelValue?.value,
+            option.value === (modelValue as IListboxOption)?.value || option.value === modelValue,
         }"
-        :aria-selected="option.value === modelValue?.value"
+        :aria-selected="option.value === (modelValue as IListboxOption)?.value || option.value === modelValue"
         @click="onListboxOptionClick(option)"
         @blur="blurListOption(option)"
         @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
@@ -64,7 +58,7 @@
         <BaseIcon
           name="Check"
           class="fill-listbox-selected"
-          :class="option.value === modelValue?.value ? 'visible' : 'invisible'"
+          :class="option.value === (modelValue as IListboxOption)?.value || option.value === modelValue ? 'visible' : 'invisible'"
           :width="18"
         />
         <span v-if="option.label">
@@ -80,22 +74,17 @@
 
 <script lang="ts" setup>
 import { ref, useTemplateRef, nextTick } from "vue";
-
-interface IListboxOption {
-  value: string | number | boolean | undefined | null;
-  label?: string;
-}
-
-interface IInternalListboxOption extends IListboxOption {
-  index: number;
-  elemId: string;
-}
+import type {
+  IListboxValueArray,
+  IListboxOption,
+  IInternalListboxOption,
+} from "../../types/listbox";
 
 const props = withDefaults(
   defineProps<{
     id: string;
     labelId: string;
-    options: IListboxOption[];
+    options: IListboxOption[] | IListboxValueArray[];
     required?: boolean;
     hasError?: boolean;
     placeholder?: string;
@@ -109,19 +98,36 @@ const props = withDefaults(
   }
 );
 
+const sourceDataType = ref<string>("");
+const sourceData = ref<IListboxOption[]>();
 const focusCounter = ref<number>(0);
 const listboxIsExpanded = ref<boolean>(false);
-const modelValue = defineModel<IInternalListboxOption>();
+const modelValue = defineModel<IListboxOption | IListboxValueArray>();
 const ulElemRef = useTemplateRef<HTMLUListElement>("listbox-ul");
 const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listbox-li");
 const btnElemRef = useTemplateRef<HTMLButtonElement>("listbox-button");
+const listboxDisplayText = ref<string>(props.placeholder);
 
-const listboxOptions = computed<IInternalListboxOption[]>(() => {
+function counterIsInRange(value: number) {
+  return value <= listboxOptions.value.length - 1 && value >= 0;
+}
+
+function isIListboxOption(
+  data: IListboxOption[] | IListboxValueArray[]
+): boolean {
+  const testDataValue: IListboxOption | IListboxValueArray = data[0];
+  return (
+    typeof testDataValue === "object" && Object.hasOwn(testDataValue, "value")
+  );
+}
+
+function prepareIListboxOptions(): IInternalListboxOption[] {
   const defaultOption: IListboxOption = {
     value: null,
     label: props.placeholder,
   };
-  const data: IListboxOption[] = [defaultOption, ...props.options];
+  const inputData = sourceData.value as IListboxOption[];
+  const data: IListboxOption[] = [defaultOption, ...inputData];
   return data.map((option: IListboxOption, index: number) => {
     return {
       ...option,
@@ -129,12 +135,27 @@ const listboxOptions = computed<IInternalListboxOption[]>(() => {
       elemId: `listbox-${props.id}-options-${index}`,
     };
   });
-});
+}
 
-function counterIsInRange(value: number) {
-  return value <= listboxOptions.value.length - 1 && value >= 0;
+function asIListboxOption(data: IListboxValueArray[]): IListboxOption[] {
+  return data.map((value: IListboxValueArray): IListboxOption => {
+    return { value: value };
+  });
 }
 
+const listboxOptions = computed<IInternalListboxOption[]>(() => {
+  if (isIListboxOption(props.options)) {
+    sourceDataType.value = "ListboxOptions";
+    sourceData.value = props.options as IListboxOption[];
+  } else {
+    sourceDataType.value = "ListboxValueArray";
+    const inputData = props.options as IListboxValueArray[];
+    const processedData = asIListboxOption(inputData);
+    sourceData.value = processedData as IListboxOption[];
+  }
+  return prepareIListboxOptions();
+});
+
 function updateCounter(value: number) {
   if (counterIsInRange(value)) {
     focusCounter.value = value;
@@ -167,10 +188,31 @@ function blurListOption(option: IInternalListboxOption) {
   });
 }
 
+function updateListboxDisplayText(text: string | undefined | null): string {
+  if (typeof text === "undefined") {
+    return props.placeholder;
+  }
+  return text as string;
+}
+
 function updateModelValue(selection: IInternalListboxOption) {
   btnElemRef.value?.setAttribute("aria-activedescendant", selection.elemId);
-  modelValue.value = selection;
   focusCounter.value = selection.index;
+
+  if (sourceDataType.value === "ListboxOptions") {
+    const selectedOption: IListboxOption = { value: selection.value };
+    if (Object.hasOwn(selection, "label")) {
+      selectedOption.label = selection.label;
+      listboxDisplayText.value = updateListboxDisplayText(selectedOption.label);
+    } else {
+      listboxDisplayText.value = updateListboxDisplayText(selectedOption.value);
+    }
+
+    modelValue.value = selectedOption;
+  } else {
+    modelValue.value = selection.value as IListboxValueArray;
+    listboxDisplayText.value = selection.value as string;
+  }
   openCloseListbox();
 }
 
@@ -195,7 +237,11 @@ function openCloseListbox() {
   if (listboxIsExpanded.value) {
     ulElemRef.value?.setAttribute("tabindex", "0");
     if (modelValue.value) {
-      updateCounter(modelValue.value.index);
+      const startingOption: IInternalListboxOption[] =
+        listboxOptions.value.filter((option: IInternalListboxOption) => {
+          option.value === modelValue.value;
+        });
+      updateCounter(startingOption[0].index);
     } else {
       updateCounter(0);
     }
diff --git a/apps/tailwind-components/components/input/Listbox/List.vue b/apps/tailwind-components/components/input/Listbox/List.vue
deleted file mode 100644
index 6c43d8ea9f..0000000000
--- a/apps/tailwind-components/components/input/Listbox/List.vue
+++ /dev/null
@@ -1,27 +0,0 @@
-<template>
-  <ul
-    :id="id"
-    role="listbox"
-    tabindex="0"
-    :aria-expanded="expanded"
-    :aria-activedescendant="selectedElemId"
-    class="absolute b-0 w-full z-10 bg-listbox"
-    :class="{
-      hidden: !expanded,
-    }"
-  >
-    <slot></slot>
-  </ul>
-</template>
-
-<script lang="ts" setup>
-interface IListbox {
-  id: string;
-  expanded: boolean;
-  selectedElemId?: string;
-}
-
-withDefaults(defineProps<IListbox>(), {
-  expanded: false,
-});
-</script>
diff --git a/apps/tailwind-components/components/input/Listbox/ListItem.vue b/apps/tailwind-components/components/input/Listbox/ListItem.vue
deleted file mode 100644
index 65b02360c1..0000000000
--- a/apps/tailwind-components/components/input/Listbox/ListItem.vue
+++ /dev/null
@@ -1,29 +0,0 @@
-<template>
-  <li
-    role="option"
-    :aria-selected="selected"
-    class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
-    :class="{
-      '!bg-listbox-selected !text-listbox-selected': selected,
-    }"
-  >
-    <BaseIcon
-      name="Check"
-      class="fill-listbox-selected"
-      :class="selected ? 'visible' : 'invisible'"
-      :width="18"
-    />
-    <slot></slot>
-  </li>
-</template>
-
-<script lang="ts" setup>
-withDefaults(
-  defineProps<{
-    selected: boolean;
-  }>(),
-  {
-    selected: false,
-  }
-);
-</script>
diff --git a/apps/tailwind-components/components/input/Listbox/Toggle.vue b/apps/tailwind-components/components/input/Listbox/Toggle.vue
deleted file mode 100644
index a15ae5fcaa..0000000000
--- a/apps/tailwind-components/components/input/Listbox/Toggle.vue
+++ /dev/null
@@ -1,13 +0,0 @@
-<template>
-  <button
-    role="combobox"
-    aria-haspopup="listbox"
-    class="flex justify-start items-center h-10 w-full text-left pl-10 border-input bg-input text-button-input-toggle"
-  >
-    <slot></slot>
-    <div class="w-[60px] flex flex-col">
-      <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
-      <BaseIcon :width="18" name="caret-down" class="mx-auto -my-1" />
-    </div>
-  </button>
-</template>
diff --git a/apps/tailwind-components/components/input/Listbox2.vue b/apps/tailwind-components/components/input/Listbox2.vue
deleted file mode 100644
index 3859d895d9..0000000000
--- a/apps/tailwind-components/components/input/Listbox2.vue
+++ /dev/null
@@ -1,118 +0,0 @@
-<template>
-  <div class="w-full relative">
-    <p>{{ focusCounter }}: {{ modelValue }}</p>
-    <ul
-      role="listbox"
-      ref="listboxRef"
-      class="bg-listbox"
-      tabindex="0"
-      @keydown.space.prevent
-      @keydown.up.prevent="onKeyUp"
-      @keydown.down.prevent="onKeyDown"
-    >
-      <li
-        v-for="(option, index) in options"
-        :id="`listbox-id-option-${index}`"
-        ref="listboxOptionsRef"
-        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-selected focus:text-listbox-selected"
-        :class="{
-          '!bg-listbox-selected !text-listbox-selected':
-            option.value === modelValue?.value,
-        }"
-        :aria-selected="option.value == modelValue?.value"
-        @keydown.tab.prevent
-        @click="(event: Event) => updateModelValue(event, option, index)"
-        @focus="(event: Event) => updateModelValue(event, option, index)"
-        @blur="(event: Event) => (event.target as HTMLOptionElement).setAttribute('tabindex', '-1')"
-      >
-        <BaseIcon
-          name="Check"
-          class="fill-listbox-selected"
-          :class="option.value === modelValue?.value ? 'visible' : 'invisible'"
-          :width="18"
-        />
-        <span>{{ option.value }}</span>
-      </li>
-    </ul>
-  </div>
-</template>
-
-<script setup lang="ts">
-import { ref, onMounted, nextTick, useTemplateRef } from "vue";
-
-interface IListboxOption {
-  elemId?: string;
-  value: string | number | boolean;
-  label?: string;
-  selected?: boolean;
-  focused?: boolean;
-}
-
-const focusCounter = ref<number>(0);
-const listboxRef = useTemplateRef<HTMLUListElement>("listboxRef");
-const listboxOptionsRef =
-  useTemplateRef<HTMLOptionElement[]>("listboxOptionsRef");
-const modelValue = defineModel<IListboxOption>();
-const options = ref<IListboxOption[]>([
-  { value: "tomatoes", label: "Roma tomatoes" },
-  { value: "pepperoni", label: "Pepperoni" },
-  { value: "mozzerella", label: "Fresh mozzerella" },
-  { value: "chillies", label: "Chillies" },
-  { value: "basil", label: "Fresh basil" },
-]);
-
-function counterIsInRange(value: number) {
-  return value <= options.value.length - 1 && value >= 0;
-}
-
-function updateCounter(value: number) {
-  if (counterIsInRange(value)) {
-    focusCounter.value = value;
-  } else {
-    focusCounter.value = focusCounter.value;
-  }
-}
-
-function focusListOption() {
-  nextTick(() => {
-    if (listboxOptionsRef.value) {
-      const targetElem = listboxOptionsRef.value[
-        focusCounter.value
-      ] as HTMLOptionElement;
-      targetElem.setAttribute("tabindex", "0");
-      targetElem.focus();
-    }
-  });
-}
-
-function updateModelValue(
-  event: Event,
-  selection: IListboxOption,
-  index: number
-) {
-  const newSelection: IListboxOption = selection;
-  const elemId: string = (event.target as HTMLOptionElement).id;
-
-  modelValue.value = newSelection;
-  modelValue.value.elemId = elemId;
-  listboxRef.value?.setAttribute("aria-activedescendant", elemId);
-
-  focusCounter.value = index;
-}
-
-function onKeyUp(event: Event) {
-  console.log("key up");
-  const newCounterValue = focusCounter.value - 1;
-  updateCounter(newCounterValue);
-  focusListOption();
-}
-
-function onKeyDown(event: Event) {
-  console.log("key down");
-  const newCounterValue = focusCounter.value + 1;
-  updateCounter(newCounterValue);
-  focusListOption();
-}
-
-onMounted(() => focusListOption());
-</script>
diff --git a/apps/tailwind-components/types/listbox.ts b/apps/tailwind-components/types/listbox.ts
new file mode 100644
index 0000000000..df0f5fcfe1
--- /dev/null
+++ b/apps/tailwind-components/types/listbox.ts
@@ -0,0 +1,12 @@
+
+export type IListboxValueArray = string;
+
+export interface IListboxOption {
+  value: string | undefined | null;
+  label?: string;
+}
+
+export interface IInternalListboxOption extends IListboxOption {
+  index: number;
+  elemId: string;
+}

From 21010e93eb14f3a1e70bf7aba8b2f8fea8683774 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Mon, 18 Nov 2024 09:17:24 +0000
Subject: [PATCH 16/46] chore: finialised story

---
 .../pages/input/Listbox.story.vue             | 80 +++++++++++++------
 1 file changed, 57 insertions(+), 23 deletions(-)

diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index e024e9cbcc..2300d8787b 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -1,18 +1,42 @@
 <template>
-  <h2>Listbox component</h2>
-  <p class="mb-2">
-    The <code>InputListbox</code> component is an reimplementation of the
-    <code>InputSelect</code> component. The component functions and behaves in
-    the same manner as the select element, but it allows the component to be
-    styled.
-  </p>
-  <p class="mb-2">
-    The following example demonstrates the use of the listbox components with
-    various configurations.
-  </p>
-  <form class="mb-2 bg-white rounded p-2">
-    <legend>Configure the listbox component</legend>
-    <div class="mb-2">
+  <article
+    aria-labelledby="listbox-component-title"
+    class="[&>p]:mt-3 [&_p]:mb-4"
+  >
+    <h2 id="listbox-component-title" class="text-heading-2xl">
+      Listbox component
+    </h2>
+    <p>
+      The <code>InputListbox</code> component an alternative to the
+      <code>InputSelect</code> component. This component functions and behaves
+      in the same manner as the select element, but it allows the component to
+      be styled with greater detail. The component is flexible in that it allows
+      for multiple input types. Options can be generated from an array of values
+      (string, number, boolean) or as an array of objects that follow the
+      <code>IListboxOption</code> type (<code
+        >[{value: "...", label: "..."},...]</code
+      >). The return value will always match the input type. When passing data
+      into the component, you must also supply the listbox type. There are two
+      types to use.
+    </p>
+    <ul class="pl-6 mb-4 list-disc">
+      <li>
+        <code>IListboxValueArray</code>: an array of values (as strings, or
+        string[]). For now, this component only supports string arrays.
+      </li>
+      <li>
+        <code>IListboxOption</code>: an array of objects that have a value and a
+        label key.(<code>[{value: "...", label: "..."},...]</code>).
+      </li>
+    </ul>
+    <p>
+      The following examples demonstrate the use of the listbox components and
+      the various configurations that area allowed.
+    </p>
+  </article>
+  <form class="mb-4 bg-white rounded p-4">
+    <legend class="mb-2">Configure the listbox component</legend>
+    <div class="mb-4">
       <InputLabel for="listbox-component-state">
         Select the component state
       </InputLabel>
@@ -32,21 +56,21 @@
         :showClearButton="true"
       />
     </div>
-    <div class="mb-2">
+    <div class="mb-4">
       <InputLabel for="listbox-placeholder">
         Change the default placeholder text
       </InputLabel>
       <InputString id="listbox-placeholder" v-model="listboxPlaceholder" />
     </div>
   </form>
-  <div class="mb-2 bg-white rounded p-2">
+  <div class="mb-2 bg-white rounded p-4">
     <InputLabel id="listbox-input-label" for="listbox-input" class="block mb-3">
       <span>Select a group assignment</span>
     </InputLabel>
     <InputListbox
       id="listbox-input"
       labelId="listbox-input-label"
-      :options="data"
+      :options="optionsAsValueArrays"
       v-model="listboxSelection"
       :hasError="listboxState === 'error'"
       :disabled="listboxState === 'disabled'"
@@ -59,12 +83,22 @@
 </template>
 
 <script lang="ts" setup>
-const data = [...Array(26).keys()].map((num: number) => {
-  return {
-    value: num,
-    label: "Group " + String.fromCharCode(num + 65),
-  };
-});
+import { ref } from "vue";
+import type { IListboxValueArray, IListboxOption } from "../../types/listbox";
+
+// as ListboxOption
+const letters = [...Array(26).keys()].map((num) =>
+  String.fromCharCode(num + 65)
+);
+
+const optionsWithLabelsData = ref<IListboxOption[]>(
+  letters.map((letter: string) => {
+    return { value: letter, label: "Group" + letter };
+  })
+);
+
+// as Listbox Array
+const optionsAsValueArrays = ref<IListboxValueArray[]>(letters);
 
 const listboxState = ref<string>("");
 const listboxSelection = ref();

From 4db42b00ad589b9808d46b94716a0727b21a6339 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 19 Nov 2024 10:18:44 +0000
Subject: [PATCH 17/46] fix: set selected value focus when menu opens

---
 apps/tailwind-components/components/input/Listbox.vue | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index b6c6d5bdc0..8262fe064f 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -107,6 +107,7 @@ const ulElemRef = useTemplateRef<HTMLUListElement>("listbox-ul");
 const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listbox-li");
 const btnElemRef = useTemplateRef<HTMLButtonElement>("listbox-button");
 const listboxDisplayText = ref<string>(props.placeholder);
+const startingCounter = ref<number>(0);
 
 function counterIsInRange(value: number) {
   return value <= listboxOptions.value.length - 1 && value >= 0;
@@ -198,6 +199,7 @@ function updateListboxDisplayText(text: string | undefined | null): string {
 function updateModelValue(selection: IInternalListboxOption) {
   btnElemRef.value?.setAttribute("aria-activedescendant", selection.elemId);
   focusCounter.value = selection.index;
+  startingCounter.value = selection.index;
 
   if (sourceDataType.value === "ListboxOptions") {
     const selectedOption: IListboxOption = { value: selection.value };
@@ -237,11 +239,7 @@ function openCloseListbox() {
   if (listboxIsExpanded.value) {
     ulElemRef.value?.setAttribute("tabindex", "0");
     if (modelValue.value) {
-      const startingOption: IInternalListboxOption[] =
-        listboxOptions.value.filter((option: IInternalListboxOption) => {
-          option.value === modelValue.value;
-        });
-      updateCounter(startingOption[0].index);
+      updateCounter(startingCounter.value);
     } else {
       updateCounter(0);
     }

From 76c92044cbe463acc02a028c27cf37cb571bf877 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 19 Nov 2024 10:19:05 +0000
Subject: [PATCH 18/46] docs: added option to switch data types in story

---
 .../pages/input/Listbox.story.vue             | 103 +++++++++++-------
 1 file changed, 66 insertions(+), 37 deletions(-)

diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index 2300d8787b..f9314fc5e3 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -34,73 +34,102 @@
       the various configurations that area allowed.
     </p>
   </article>
-  <form class="mb-4 bg-white rounded p-4">
-    <legend class="mb-2">Configure the listbox component</legend>
-    <div class="mb-4">
-      <InputLabel for="listbox-component-state">
-        Select the component state
-      </InputLabel>
-      <InputRadioGroup
-        id="listbox-component-state"
-        v-model="listboxState"
-        :radioOptions="[
-          {
-            value: 'disabled',
-            label: 'Component is disabled',
-          },
-          {
-            value: 'error',
-            label: 'Component has error',
-          },
-        ]"
-        :showClearButton="true"
-      />
+  <form class="mb-6 bg-white rounded p-4">
+    <legend class="mb-2 text-heading-lg">
+      Configure the listbox component
+    </legend>
+    <div class="flex flex-row flex-wrap justify-center items-start gap-4">
+      <div class="p-2 grow">
+        <InputLabel for="listbox-data-type" class="pl-0">
+          <span>Select the input data type</span>
+        </InputLabel>
+        <InputRadioGroup
+          id="listbox-data-type"
+          v-model="listboxDataType"
+          :radio-options="[
+            { value: 'string', label: 'String array' },
+            { value: 'array', label: 'Array of options' },
+          ]"
+        />
+      </div>
+      <div class="p-2 grow">
+        <InputLabel for="listbox-component-state" class="pl-0">
+          Change the component state
+        </InputLabel>
+        <InputRadioGroup
+          id="listbox-component-state"
+          v-model="listboxState"
+          :radioOptions="[
+            {
+              value: 'disabled',
+              label: 'Disabled: disable interactivity with the component',
+            },
+            {
+              value: 'error',
+              label: 'Error: simulate an instance where an error occurred',
+            },
+          ]"
+          :showClearButton="true"
+        />
+      </div>
     </div>
-    <div class="mb-4">
+    <div class="bg-white p-2 grow">
       <InputLabel for="listbox-placeholder">
         Change the default placeholder text
       </InputLabel>
       <InputString id="listbox-placeholder" v-model="listboxPlaceholder" />
     </div>
   </form>
-  <div class="mb-2 bg-white rounded p-4">
-    <InputLabel id="listbox-input-label" for="listbox-input" class="block mb-3">
+  <div class="mb-2 bg-white rounded p-6">
+    <h3 class="text-heading-lg mb-2">Listbox example</h3>
+    <InputLabel
+      id="listbox-input-label"
+      for="listbox-input"
+      class="block mb-3 pl-0"
+    >
       <span>Select a group assignment</span>
     </InputLabel>
     <InputListbox
       id="listbox-input"
       labelId="listbox-input-label"
-      :options="optionsAsValueArrays"
+      :options="listboxData"
       v-model="listboxSelection"
       :hasError="listboxState === 'error'"
       :disabled="listboxState === 'disabled'"
       :placeholder="listboxPlaceholder"
     />
-    <output class="block w-full mt-6 bg-white py-2 px-2">
-      <code>Output: {{ listboxSelection }}</code>
+    <output class="block w-full mt-6 bg-gray-100 py-3 px-2 pl-6">
+      <code
+        >Output {{ listboxDataType === "true" ? "Value" : "Object" }}:
+        {{ listboxSelection }}</code
+      >
     </output>
   </div>
 </template>
 
 <script lang="ts" setup>
-import { ref } from "vue";
+import { ref, computed } from "vue";
 import type { IListboxValueArray, IListboxOption } from "../../types/listbox";
 
 // as ListboxOption
-const letters = [...Array(26).keys()].map((num) =>
+const letters: string[] = [...Array(26).keys()].map((num) =>
   String.fromCharCode(num + 65)
 );
 
-const optionsWithLabelsData = ref<IListboxOption[]>(
-  letters.map((letter: string) => {
-    return { value: letter, label: "Group" + letter };
-  })
-);
-
-// as Listbox Array
-const optionsAsValueArrays = ref<IListboxValueArray[]>(letters);
+const lettersWithLabels: IListboxOption[] = letters.map((letter: string) => {
+  return { value: letter, label: `Group ${letter}` };
+});
 
 const listboxState = ref<string>("");
 const listboxSelection = ref();
 const listboxPlaceholder = ref<string>("Select an option");
+const listboxDataType = ref<string>("string");
+
+const listboxData = computed<IListboxOption[] | IListboxValueArray[]>(() => {
+  if (listboxDataType.value === "string") {
+    return letters as IListboxValueArray[];
+  } else {
+    return lettersWithLabels as IListboxOption[];
+  }
+});
 </script>

From b00813724d2e4bf4ecb239f26075bcbf82ce90c0 Mon Sep 17 00:00:00 2001
From: Harm Brugge <harmbrugge@gmail.com>
Date: Thu, 21 Nov 2024 09:18:43 +0100
Subject: [PATCH 19/46] fix: when setting isOidcEnabled is false override env
 variable (#4403)

* When OIDC setting is available use it

* provide an error state if parameters are missing

* Load db settings in security config

* Show error message when setting oidc to true when settings are incomplete

---------

Co-authored-by: Morris Swertz <m.a.swertz@rug.nl>
---
 .../src/components/admin/ManageSettings.vue   | 17 ++++--
 .../org/molgenis/emx2/sql/SqlDatabase.java    | 59 +++++++++++++++----
 .../emx2/web/MolgenisSessionManager.java      |  3 +
 .../molgenis/emx2/web/MolgenisWebservice.java |  6 +-
 .../emx2/web/SecurityConfigFactory.java       |  7 ++-
 .../emx2/web/controllers/OIDCController.java  | 16 ++---
 6 files changed, 78 insertions(+), 30 deletions(-)

diff --git a/apps/central/src/components/admin/ManageSettings.vue b/apps/central/src/components/admin/ManageSettings.vue
index 2270da2f9b..45e5b4aea2 100644
--- a/apps/central/src/components/admin/ManageSettings.vue
+++ b/apps/central/src/components/admin/ManageSettings.vue
@@ -1,5 +1,6 @@
 <template>
   <div>
+    <MessageError v-if="graphqlError">{{ graphqlError }}</MessageError>
     <h3>Manage system settings</h3>
 
     <table class="table table-hover table-bordered bg-white">
@@ -74,6 +75,7 @@ import {
   InputText,
   ButtonAlt,
   ButtonAction,
+  MessageError,
 } from "molgenis-components";
 
 export default {
@@ -87,6 +89,7 @@ export default {
     InputText,
     ButtonAlt,
     ButtonAction,
+    MessageError,
   },
   data() {
     return {
@@ -138,6 +141,7 @@ export default {
       this.showModal = true;
     },
     async createSetting() {
+      this.graphqlError = null;
       const createMutation = gql`
         mutation change($settings: [MolgenisSettingsInput]) {
           change(settings: $settings) {
@@ -153,11 +157,14 @@ export default {
         },
       };
 
-      await request("graphql", createMutation, variables).catch((e) => {
-        console.error(e);
-      });
-      this.fetchSettings();
-      this.showModal = false;
+      try {
+        await request("graphql", createMutation, variables);
+        this.fetchSettings();
+        this.showModal = false;
+      } catch (e) {
+        this.graphqlError =
+          e.response?.errors?.[0]?.message || "An error occurred.";
+      }
     },
     async deleteSetting() {
       const deleteMutation = gql`
diff --git a/backend/molgenis-emx2-sql/src/main/java/org/molgenis/emx2/sql/SqlDatabase.java b/backend/molgenis-emx2-sql/src/main/java/org/molgenis/emx2/sql/SqlDatabase.java
index 2660273b4e..479840f5a2 100644
--- a/backend/molgenis-emx2-sql/src/main/java/org/molgenis/emx2/sql/SqlDatabase.java
+++ b/backend/molgenis-emx2-sql/src/main/java/org/molgenis/emx2/sql/SqlDatabase.java
@@ -52,8 +52,7 @@ public class SqlDatabase extends HasSettings<Database> implements Database {
   private String initialAdminPassword =
       (String)
           EnvironmentProperty.getParameter(Constants.MOLGENIS_ADMIN_PW, ADMIN_PW_DEFAULT, STRING);
-  private final Boolean isOidcEnabled =
-      EnvironmentProperty.getParameter(Constants.MOLGENIS_OIDC_CLIENT_ID, null, STRING) != null;
+  private Boolean isOidcEnabled = false;
   private static String postgresUser =
       (String)
           EnvironmentProperty.getParameter(
@@ -179,10 +178,7 @@ public void init() { // setup default stuff
       // get the settings
       clearCache();
 
-      if (getSetting(Constants.IS_OIDC_ENABLED) == null) {
-        // use environment property unless overridden in settings
-        this.setSetting(Constants.IS_OIDC_ENABLED, String.valueOf(isOidcEnabled));
-      }
+      initOidc();
 
       String instanceId = getSetting(Constants.MOLGENIS_INSTANCE_ID);
       if (instanceId == null) {
@@ -230,6 +226,38 @@ public void init() { // setup default stuff
     }
   }
 
+  private void initOidc() {
+    // oidc settings takes priority over env variables
+    String isOidcEnabledSetting = getSetting(Constants.IS_OIDC_ENABLED);
+    if (isOidcEnabledSetting != null) {
+      this.isOidcEnabled = Boolean.parseBoolean(isOidcEnabledSetting);
+    } else {
+      Object envSetting =
+          EnvironmentProperty.getParameter(Constants.MOLGENIS_OIDC_CLIENT_ID, null, STRING);
+      if (envSetting != null) {
+        this.setSetting(Constants.IS_OIDC_ENABLED, "true");
+        this.isOidcEnabled = true;
+      }
+    }
+    if (!this.isOidcEnabled) return;
+
+    // check if OIDC settings are complete otherwise log error and set to false
+    if (!isValidOidcSettings()) {
+      setSetting(
+          Constants.IS_OIDC_ENABLED,
+          "error: Environment OIDC settings are incomplete. Fix and then set again to true");
+    }
+  }
+
+  private boolean isValidOidcSettings() {
+    Object oidcClientId =
+        EnvironmentProperty.getParameter(Constants.MOLGENIS_OIDC_CLIENT_ID, null, STRING);
+    Object clientSecret =
+        EnvironmentProperty.getParameter(Constants.MOLGENIS_OIDC_CLIENT_SECRET, null, STRING);
+
+    return clientSecret != null && oidcClientId != null;
+  }
+
   @Override
   public void setListener(DatabaseListener listener) {
     this.listener = listener;
@@ -402,14 +430,21 @@ public SchemaInfo getSchemaInfo(String schemaName) {
 
   @Override
   public Database setSettings(Map<String, String> settings) {
-    if (isAdmin()) {
-      super.setSettings(settings);
-      MetadataUtils.saveDatabaseSettings(jooq, getSettings());
-      // force all sessions to reload
-      this.listener.afterCommit();
-    } else {
+    if (!isAdmin()) {
       throw new MolgenisException("Insufficient rights to create database level setting");
     }
+    if (settings.containsKey(Constants.IS_OIDC_ENABLED)) {
+      String isOidcEnabledSetting = settings.get(Constants.IS_OIDC_ENABLED);
+      if (Boolean.parseBoolean(isOidcEnabledSetting) && !isValidOidcSettings()) {
+        throw new MolgenisException("OIDC environment setting are incomplete");
+      }
+    }
+
+    super.setSettings(settings);
+    MetadataUtils.saveDatabaseSettings(jooq, getSettings());
+    // force all sessions to reload
+    this.listener.afterCommit();
+
     return this;
   }
 
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisSessionManager.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisSessionManager.java
index 4120fea14d..b3fa17b866 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisSessionManager.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisSessionManager.java
@@ -1,5 +1,7 @@
 package org.molgenis.emx2.web;
 
+import static org.molgenis.emx2.web.MolgenisWebservice.oidcController;
+
 import jakarta.servlet.http.HttpServletRequest;
 import jakarta.servlet.http.HttpSessionEvent;
 import jakarta.servlet.http.HttpSessionListener;
@@ -77,6 +79,7 @@ public String findUsedAuthTokenKey(HttpServletRequest request) {
    * this method is used to reset cache of all sessions, necessary when for example metadata changes
    */
   public void clearAllCaches() {
+    oidcController.reloadConfig();
     for (MolgenisSession session : sessions.values()) {
       session.clearCache();
     }
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisWebservice.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisWebservice.java
index e6e9b2a1b7..dc3b184ebe 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisWebservice.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisWebservice.java
@@ -29,8 +29,8 @@ public class MolgenisWebservice {
   static final Logger logger = LoggerFactory.getLogger(MolgenisWebservice.class);
   private static final String ROBOTS_TXT = "robots.txt";
   private static final String USER_AGENT_ALLOW = "User-agent: *\nAllow: /";
-  static MolgenisSessionManager sessionManager;
-  static OIDCController oidcController;
+  public static MolgenisSessionManager sessionManager;
+  public static OIDCController oidcController;
 
   private MolgenisWebservice() {
     // hide constructor
@@ -39,7 +39,7 @@ private MolgenisWebservice() {
   public static void start(int port) {
 
     sessionManager = new MolgenisSessionManager();
-    oidcController = new OIDCController(sessionManager, new SecurityConfigFactory().build());
+    oidcController = new OIDCController();
     Javalin app =
         Javalin.create(
                 config -> {
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/SecurityConfigFactory.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/SecurityConfigFactory.java
index 7bf3c734da..84f8bbd0b3 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/SecurityConfigFactory.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/SecurityConfigFactory.java
@@ -13,9 +13,8 @@
 
 public class SecurityConfigFactory {
 
-  private String oidcClientId =
-      (String) EnvironmentProperty.getParameter(Constants.MOLGENIS_OIDC_CLIENT_ID, null, STRING);
-  private String oidcClientSecret =
+  private String oidcClientId;
+  private final String oidcClientSecret =
       (String)
           EnvironmentProperty.getParameter(Constants.MOLGENIS_OIDC_CLIENT_SECRET, null, STRING);
   public static String OIDC_CLIENT_NAME =
@@ -39,6 +38,8 @@ public class SecurityConfigFactory {
 
   public Config build() {
     final OidcConfiguration oidcConfiguration = new OidcConfiguration();
+    oidcClientId =
+        (String) EnvironmentProperty.getParameter(Constants.MOLGENIS_OIDC_CLIENT_ID, null, STRING);
     oidcConfiguration.setClientId(oidcClientId);
     oidcConfiguration.setSecret(oidcClientSecret);
     oidcConfiguration.setDiscoveryURI(oidcDiscoveryURI);
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/controllers/OIDCController.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/controllers/OIDCController.java
index 665e4d2e9b..c69ee39df5 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/controllers/OIDCController.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/controllers/OIDCController.java
@@ -1,6 +1,6 @@
 package org.molgenis.emx2.web.controllers;
 
-import static java.util.Objects.requireNonNull;
+import static org.molgenis.emx2.web.MolgenisWebservice.sessionManager;
 import static org.molgenis.emx2.web.SecurityConfigFactory.OIDC_CLIENT_NAME;
 
 import io.javalin.http.Context;
@@ -9,7 +9,7 @@
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.MolgenisException;
 import org.molgenis.emx2.web.JavalinCustomHttpActionAdapter;
-import org.molgenis.emx2.web.MolgenisSessionManager;
+import org.molgenis.emx2.web.SecurityConfigFactory;
 import org.pac4j.core.config.Config;
 import org.pac4j.core.context.session.SessionStore;
 import org.pac4j.core.engine.CallbackLogic;
@@ -31,16 +31,18 @@ public class OIDCController {
 
   private static final Logger logger = LoggerFactory.getLogger(OIDCController.class);
 
-  private final MolgenisSessionManager sessionManager;
-  private final Config securityConfig;
+  private Config securityConfig;
   private final SessionStore sessionStore;
 
-  public OIDCController(MolgenisSessionManager sessionManager, Config securityConfig) {
-    this.sessionManager = requireNonNull(sessionManager);
-    this.securityConfig = requireNonNull(securityConfig);
+  public OIDCController() {
+    this.securityConfig = new SecurityConfigFactory().build();
     this.sessionStore = FindBest.sessionStore(null, securityConfig, JEESessionStore.INSTANCE);
   }
 
+  public void reloadConfig() {
+    this.securityConfig = new SecurityConfigFactory().build();
+  }
+
   public void handleLoginRequest(Context ctx) {
     final JavalinWebContext context = new JavalinWebContext(ctx);
     sessionStore.set(context, Pac4jConstants.REQUESTED_URL, ctx.queryParams("redirect"));

From ffca17ffd886d6efc6db0fc1a7ed9130a6afa4b8 Mon Sep 17 00:00:00 2001
From: Morris Swertz <m.a.swertz@rug.nl>
Date: Thu, 21 Nov 2024 09:40:28 +0100
Subject: [PATCH 20/46] build: reduce preview resource requirements (#4507)

---
 helm-chart/templates/deployment.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/helm-chart/templates/deployment.yaml b/helm-chart/templates/deployment.yaml
index a2758ae421..947b7696d3 100644
--- a/helm-chart/templates/deployment.yaml
+++ b/helm-chart/templates/deployment.yaml
@@ -27,7 +27,7 @@ spec:
             limits:
               memory: "2Gi"
             requests:
-              memory: "500Mi"
+              memory: "256Mi"
           ports:
             - containerPort: 8080
           env:
@@ -74,9 +74,9 @@ spec:
             - max_locks_per_transaction=1024
           resources:
             limits:
-              memory: "1Gi"
+              memory: "512Mi"
             requests:
-              memory: "256Mi"
+              memory: "128Mi"
           env:
             - name: POSTGRES_DB
               value: {{ .Values.postgres.name }}
@@ -102,9 +102,9 @@ spec:
           imagePullPolicy: {{ .Values.image.pullPolicy }}
           resources:
             limits:
-              memory: "1Gi"
+              memory: "128Mi"
             requests:
-              memory: "256Mi"
+              memory: "64Mi"
           ports:
             - containerPort: 3000
           env:

From 63fdd731c23cc4196a92eeb60c7fb3614765f38f Mon Sep 17 00:00:00 2001
From: BrendaHijmans <42644481+BrendaHijmans@users.noreply.github.com>
Date: Thu, 21 Nov 2024 10:27:16 +0100
Subject: [PATCH 21/46] fix(catalogue): add UMCG template loader (#4466)

---
 apps/central/src/components/SchemaCreateModal.vue      |  1 +
 .../java/org/molgenis/emx2/datamodels/DataModels.java  |  3 ++-
 .../datacatalogue_cohortstaging/Contacts.csv           |  4 ++--
 data/_profiles/UMCGCohortsStaging.yaml                 | 10 +++++++---
 4 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/apps/central/src/components/SchemaCreateModal.vue b/apps/central/src/components/SchemaCreateModal.vue
index 2b289b655c..87e18bd6e5 100644
--- a/apps/central/src/components/SchemaCreateModal.vue
+++ b/apps/central/src/components/SchemaCreateModal.vue
@@ -141,6 +141,7 @@ export default {
         "DATA_CATALOGUE",
         "DATA_CATALOGUE_COHORT_STAGING",
         "DATA_CATALOGUE_NETWORK_STAGING",
+        "UMCG_COHORT_STAGING",
         "UMCU_COHORTS_STAGING",
         "RD3",
         "JRC_COMMON_DATA_ELEMENTS",
diff --git a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/DataModels.java b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/DataModels.java
index fbd1c652f8..e2a7cfabc0 100644
--- a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/DataModels.java
+++ b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/DataModels.java
@@ -9,10 +9,11 @@
 public class DataModels {
 
   public enum Profile {
+    DATA_CATALOGUE("_profiles/DataCatalogue.yaml"),
     DATA_CATALOGUE_COHORT_STAGING("_profiles/CohortsStaging.yaml"),
     DATA_CATALOGUE_NETWORK_STAGING("_profiles/NetworksStaging.yaml"),
     DATA_CATALOGUE_AGGREGATES("_profiles/DataCatalogueAggregates.yaml"),
-    DATA_CATALOGUE("_profiles/DataCatalogue.yaml"),
+    UMCG_COHORT_STAGING("_profiles/UMCGCohortsStaging.yaml"),
     UMCU_COHORTS_STAGING("_profiles/UMCUCohorts.yaml"),
     FAIR_DATA_HUB("_profiles/FAIRDataHub.yaml"),
     RD3("_profiles/RD3.yaml"),
diff --git a/data/_demodata/applications/datacatalogue_cohortstaging/Contacts.csv b/data/_demodata/applications/datacatalogue_cohortstaging/Contacts.csv
index c0b98331f0..ff647fdd14 100644
--- a/data/_demodata/applications/datacatalogue_cohortstaging/Contacts.csv
+++ b/data/_demodata/applications/datacatalogue_cohortstaging/Contacts.csv
@@ -1,2 +1,2 @@
-resource,role,first name,last name,prefix,initials,title,organisation,email,orcid,homepage,photo,photo_filename,expertise
-testCohort,"Principal Investigator,Primary contact",Morris,Swertz,,,,UMCG,m.a.swertz@rug.nl,0000-0002-0979-3401,https://www.rug.nl/staff/m.a.swertz/,,,edit
+resource,role,first name,last name,prefix,initials,title,organisation,email,orcid,homepage,photo,photo_filename,expertise,statement of consent personal data,statement of consent email
+testCohort,"Principal Investigator,Primary contact",Morris,Swertz,,,,UMCG,m.a.swertz@rug.nl,0000-0002-0979-3401,https://www.rug.nl/staff/m.a.swertz/,,,edit,TRUE,TRUE
diff --git a/data/_profiles/UMCGCohortsStaging.yaml b/data/_profiles/UMCGCohortsStaging.yaml
index 47cdb4a596..605f2dc771 100644
--- a/data/_profiles/UMCGCohortsStaging.yaml
+++ b/data/_profiles/UMCGCohortsStaging.yaml
@@ -1,13 +1,17 @@
 ---
-name: Staging area for filling out UMCG cohort metadata
+name: UMCGCohortsStaging
+description: "Staging area for filling out UMCG cohort metadata"
 
 profileTags: UMCGCohortsStaging
 
-# demoData: _demodata/applications/datacatalogue
+demoData: _demodata/applications/datacatalogue_cohortstaging
 
 #settings: _settings/datacatalogue
 
 # special options
-# setViewPermission: anonymous
 ontologiesToFixedSchema: CatalogueOntologies
 setFixedSchemaViewPermission: anonymous
+firstCreateSchemasIfMissing:
+  - name: UMCG
+    profile: _profiles/DataCatalogue.yaml
+    importDemoData: false
\ No newline at end of file

From fbc31c0c4e2f08c562ea64aeebe2c83b8d60a29c Mon Sep 17 00:00:00 2001
From: Sander van den Hoek <svandenhoek@users.noreply.github.com>
Date: Thu, 21 Nov 2024 15:00:19 +0100
Subject: [PATCH 22/46] fixed example hyperlinks to be valid (#4508)

---
 apps/molgenis-components/src/components/forms/FormInput.vue | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/apps/molgenis-components/src/components/forms/FormInput.vue b/apps/molgenis-components/src/components/forms/FormInput.vue
index d2e979bd63..debc318890 100644
--- a/apps/molgenis-components/src/components/forms/FormInput.vue
+++ b/apps/molgenis-components/src/components/forms/FormInput.vue
@@ -523,9 +523,9 @@ export default {
         emailValue: "bla@molgenis.org",
         emailValueInplace: "bla@molgenis.org",
         emailValueArray: ["bla@molgenis.org", "asd@molgenis.org"],
-        hyperlinkValue: "www.molgenis.org",
-        hyperlinkValueInplace: "www.molgenis.org",
-        hyperlinkValueArray: ["www.molgenis.org", "molgenis.org"],
+        hyperlinkValue: "https://molgenis.org",
+        hyperlinkValueInplace: "https://molgenis.org",
+        hyperlinkValueArray: ["https://molgenis.org", "https://www.molgenis.org"],
         ontologyValue: null,
         ontologyArrayValue: [],
         dateValue: null,

From 97b0e5d6a6265ad0dfda40d6e7abf17425cdadcc Mon Sep 17 00:00:00 2001
From: dtroelofsprins <57137088+dtroelofsprins@users.noreply.github.com>
Date: Thu, 21 Nov 2024 15:55:55 +0100
Subject: [PATCH 23/46] feat(directory): molgenis-emx2-directory-client (#3863)

* Initial commit: copy of molgenis-py-bbmri-eric

* chore: adjust tool setup files

* chore: rename some modules and classes and fix imports

* chore: rename tool name folder

* chore: change import paths

* chore: update molgenis-emx2-pyclient

* chore: change email and project URLs

* feat: EMX2 version of the publish script

* chore: fix tests

* chore: added additional packages to setup.cfg

* chore: working example file to run the package

* fix: import pyhandle from forked git repo to solve incompatibility with latest pyclient version

* chore(directory): new version of PYHANDLE available

* chore: remove commented out code

---------

Co-authored-by: Hessel Haagsma <h.haagsma@umcg.nl>
---
 tools/directory/.coveragerc                   |  29 +
 tools/directory/.gitignore                    |  59 ++
 tools/directory/.isort.cfg                    |   3 +
 tools/directory/.pre-commit-config.yaml       |  35 +
 tools/directory/AUTHORS.md                    |   3 +
 tools/directory/CHANGELOG.md                  |   3 +
 tools/directory/LICENSE.txt                   | 165 +++++
 tools/directory/Pipfile                       |  18 +
 tools/directory/Pipfile.lock                  | 674 ++++++++++++++++++
 tools/directory/README.md                     |  76 ++
 tools/directory/dev/dev.py                    |  64 ++
 tools/directory/pyproject.toml                |   9 +
 tools/directory/setup.cfg                     | 120 ++++
 tools/directory/setup.py                      |  21 +
 .../directory_client/__init__.py              |  16 +
 .../directory_client/categories.py            | 235 ++++++
 .../directory_client/directory.py             | 149 ++++
 .../directory_client/directory_client.py      | 461 ++++++++++++
 .../molgenis_emx2/directory_client/errors.py  |  78 ++
 .../molgenis_emx2/directory_client/model.py   | 419 +++++++++++
 .../directory_client/model_fitting.py         | 168 +++++
 .../directory_client/pid_manager.py           | 143 ++++
 .../directory_client/pid_service.py           | 228 ++++++
 .../molgenis_emx2/directory_client/printer.py |  79 ++
 .../directory_client/publication_preparer.py  |  74 ++
 .../directory_client/publisher.py             | 134 ++++
 .../molgenis_emx2/directory_client/stager.py  | 110 +++
 .../directory_client/transformer.py           | 204 ++++++
 .../molgenis_emx2/directory_client/utils.py   |  23 +
 .../directory_client/validation.py            | 145 ++++
 tools/directory/tests/__init__.py             |   0
 tools/directory/tests/conftest.py             | 129 ++++
 tools/directory/tests/resources/__init__.py   |   0
 .../directory/tests/resources/also_known.json |  14 +
 tools/directory/tests/resources/biobanks.json |  43 ++
 .../tests/resources/collections.json          |  64 ++
 tools/directory/tests/resources/facts.json    |  11 +
 tools/directory/tests/resources/networks.json |  19 +
 tools/directory/tests/resources/persons.json  |  14 +
 tools/directory/tests/test_categories.py      | 193 +++++
 tools/directory/tests/test_directory.py       | 123 ++++
 tools/directory/tests/test_errors.py          |  97 +++
 tools/directory/tests/test_model.py           | 115 +++
 tools/directory/tests/test_model_fitting.py   | 122 ++++
 tools/directory/tests/test_pid_manager.py     | 118 +++
 tools/directory/tests/test_pid_service.py     | 103 +++
 tools/directory/tests/test_printer.py         | 158 ++++
 .../tests/test_publication_preparer.py        | 175 +++++
 tools/directory/tests/test_publisher.py       | 122 ++++
 tools/directory/tests/test_stager.py          | 200 ++++++
 tools/directory/tests/test_transformer.py     | 299 ++++++++
 tools/directory/tests/test_utils.py           |  24 +
 tools/directory/tests/test_validator.py       | 144 ++++
 tools/directory/tox.ini                       |  63 ++
 54 files changed, 6295 insertions(+)
 create mode 100644 tools/directory/.coveragerc
 create mode 100644 tools/directory/.gitignore
 create mode 100644 tools/directory/.isort.cfg
 create mode 100644 tools/directory/.pre-commit-config.yaml
 create mode 100644 tools/directory/AUTHORS.md
 create mode 100644 tools/directory/CHANGELOG.md
 create mode 100644 tools/directory/LICENSE.txt
 create mode 100644 tools/directory/Pipfile
 create mode 100644 tools/directory/Pipfile.lock
 create mode 100644 tools/directory/README.md
 create mode 100644 tools/directory/dev/dev.py
 create mode 100644 tools/directory/pyproject.toml
 create mode 100644 tools/directory/setup.cfg
 create mode 100644 tools/directory/setup.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/__init__.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/categories.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/directory.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/directory_client.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/errors.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/model.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/model_fitting.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/pid_manager.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/pid_service.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/printer.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/publication_preparer.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/publisher.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/stager.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/transformer.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/utils.py
 create mode 100644 tools/directory/src/molgenis_emx2/directory_client/validation.py
 create mode 100644 tools/directory/tests/__init__.py
 create mode 100644 tools/directory/tests/conftest.py
 create mode 100644 tools/directory/tests/resources/__init__.py
 create mode 100644 tools/directory/tests/resources/also_known.json
 create mode 100644 tools/directory/tests/resources/biobanks.json
 create mode 100644 tools/directory/tests/resources/collections.json
 create mode 100644 tools/directory/tests/resources/facts.json
 create mode 100644 tools/directory/tests/resources/networks.json
 create mode 100644 tools/directory/tests/resources/persons.json
 create mode 100644 tools/directory/tests/test_categories.py
 create mode 100644 tools/directory/tests/test_directory.py
 create mode 100644 tools/directory/tests/test_errors.py
 create mode 100644 tools/directory/tests/test_model.py
 create mode 100644 tools/directory/tests/test_model_fitting.py
 create mode 100644 tools/directory/tests/test_pid_manager.py
 create mode 100644 tools/directory/tests/test_pid_service.py
 create mode 100644 tools/directory/tests/test_printer.py
 create mode 100644 tools/directory/tests/test_publication_preparer.py
 create mode 100644 tools/directory/tests/test_publisher.py
 create mode 100644 tools/directory/tests/test_stager.py
 create mode 100644 tools/directory/tests/test_transformer.py
 create mode 100644 tools/directory/tests/test_utils.py
 create mode 100644 tools/directory/tests/test_validator.py
 create mode 100644 tools/directory/tox.ini

diff --git a/tools/directory/.coveragerc b/tools/directory/.coveragerc
new file mode 100644
index 0000000000..a405b17a9f
--- /dev/null
+++ b/tools/directory/.coveragerc
@@ -0,0 +1,29 @@
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = directory_client
+data_file = reports/.coverage
+# omit = bad_file.py
+
+[paths]
+source =
+    src
+    */site-packages/
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
diff --git a/tools/directory/.gitignore b/tools/directory/.gitignore
new file mode 100644
index 0000000000..bdef33627d
--- /dev/null
+++ b/tools/directory/.gitignore
@@ -0,0 +1,59 @@
+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+.DS_Store
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+.vscode
+tags
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.coverage.*
+.tox
+junit*.xml
+coverage.xml
+.pytest_cache/
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/api/*
+docs/_rst/*
+docs/_build/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+.venv*/
+.conda*/
+
+# env variables
+*.env
+*.env.local
+
+!CHANGELOG.md
diff --git a/tools/directory/.isort.cfg b/tools/directory/.isort.cfg
new file mode 100644
index 0000000000..b2911975f6
--- /dev/null
+++ b/tools/directory/.isort.cfg
@@ -0,0 +1,3 @@
+[settings]
+profile = black
+known_first_party = molgenis-emx2
diff --git a/tools/directory/.pre-commit-config.yaml b/tools/directory/.pre-commit-config.yaml
new file mode 100644
index 0000000000..6644c1a5ba
--- /dev/null
+++ b/tools/directory/.pre-commit-config.yaml
@@ -0,0 +1,35 @@
+exclude: '^docs/conf.py'
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-xml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+      - id: mixed-line-ending
+        args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+      - id: black
+        language_version: python3
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
+    hooks:
+      - id: flake8
+        args: [--config, tools/directory/setup.cfg]
diff --git a/tools/directory/AUTHORS.md b/tools/directory/AUTHORS.md
new file mode 100644
index 0000000000..fb26b49418
--- /dev/null
+++ b/tools/directory/AUTHORS.md
@@ -0,0 +1,3 @@
+# Contributors
+
+* Dieuwke Roelofs-Prins < https://github.com/dtroelofsprins >
diff --git a/tools/directory/CHANGELOG.md b/tools/directory/CHANGELOG.md
new file mode 100644
index 0000000000..595f693476
--- /dev/null
+++ b/tools/directory/CHANGELOG.md
@@ -0,0 +1,3 @@
+# Changelog
+## Version 1.0.0 (development)
+- EMX2 version of the Python tooling for a BBMRI Biobank Directory
diff --git a/tools/directory/LICENSE.txt b/tools/directory/LICENSE.txt
new file mode 100644
index 0000000000..65c5ca88a6
--- /dev/null
+++ b/tools/directory/LICENSE.txt
@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
diff --git a/tools/directory/Pipfile b/tools/directory/Pipfile
new file mode 100644
index 0000000000..a4ebb1a028
--- /dev/null
+++ b/tools/directory/Pipfile
@@ -0,0 +1,18 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+molgenis-emx2-directory-client = {editable = true, path = "."}
+
+[dev-packages]
+pytest = "*"
+setuptools = "*"
+pytest-cov = "*"
+tox = "*"
+python-dotenv = "*"
+flake8 = "*"
+
+[requires]
+python_version = "3.10"
diff --git a/tools/directory/Pipfile.lock b/tools/directory/Pipfile.lock
new file mode 100644
index 0000000000..2b3b129603
--- /dev/null
+++ b/tools/directory/Pipfile.lock
@@ -0,0 +1,674 @@
+{
+    "_meta": {
+        "hash": {
+            "sha256": "5876b04a2087efd2fbf3e9731974fbf1e0bfe4dc60c105377c72a3e35d3c5eea"
+        },
+        "pipfile-spec": 6,
+        "requires": {
+            "python_version": "3.10"
+        },
+        "sources": [
+            {
+                "name": "pypi",
+                "url": "https://pypi.org/simple",
+                "verify_ssl": true
+            }
+        ]
+    },
+    "default": {
+        "certifi": {
+            "hashes": [
+                "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8",
+                "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==2024.8.30"
+        },
+        "charset-normalizer": {
+            "hashes": [
+                "sha256:0099d79bdfcf5c1f0c2c72f91516702ebf8b0b8ddd8905f97a8aecf49712c621",
+                "sha256:0713f3adb9d03d49d365b70b84775d0a0d18e4ab08d12bc46baa6132ba78aaf6",
+                "sha256:07afec21bbbbf8a5cc3651aa96b980afe2526e7f048fdfb7f1014d84acc8b6d8",
+                "sha256:0b309d1747110feb25d7ed6b01afdec269c647d382c857ef4663bbe6ad95a912",
+                "sha256:0d99dd8ff461990f12d6e42c7347fd9ab2532fb70e9621ba520f9e8637161d7c",
+                "sha256:0de7b687289d3c1b3e8660d0741874abe7888100efe14bd0f9fd7141bcbda92b",
+                "sha256:1110e22af8ca26b90bd6364fe4c763329b0ebf1ee213ba32b68c73de5752323d",
+                "sha256:130272c698667a982a5d0e626851ceff662565379baf0ff2cc58067b81d4f11d",
+                "sha256:136815f06a3ae311fae551c3df1f998a1ebd01ddd424aa5603a4336997629e95",
+                "sha256:14215b71a762336254351b00ec720a8e85cada43b987da5a042e4ce3e82bd68e",
+                "sha256:1db4e7fefefd0f548d73e2e2e041f9df5c59e178b4c72fbac4cc6f535cfb1565",
+                "sha256:1ffd9493de4c922f2a38c2bf62b831dcec90ac673ed1ca182fe11b4d8e9f2a64",
+                "sha256:2006769bd1640bdf4d5641c69a3d63b71b81445473cac5ded39740a226fa88ab",
+                "sha256:20587d20f557fe189b7947d8e7ec5afa110ccf72a3128d61a2a387c3313f46be",
+                "sha256:223217c3d4f82c3ac5e29032b3f1c2eb0fb591b72161f86d93f5719079dae93e",
+                "sha256:27623ba66c183eca01bf9ff833875b459cad267aeeb044477fedac35e19ba907",
+                "sha256:285e96d9d53422efc0d7a17c60e59f37fbf3dfa942073f666db4ac71e8d726d0",
+                "sha256:2de62e8801ddfff069cd5c504ce3bc9672b23266597d4e4f50eda28846c322f2",
+                "sha256:2f6c34da58ea9c1a9515621f4d9ac379871a8f21168ba1b5e09d74250de5ad62",
+                "sha256:309a7de0a0ff3040acaebb35ec45d18db4b28232f21998851cfa709eeff49d62",
+                "sha256:35c404d74c2926d0287fbd63ed5d27eb911eb9e4a3bb2c6d294f3cfd4a9e0c23",
+                "sha256:3710a9751938947e6327ea9f3ea6332a09bf0ba0c09cae9cb1f250bd1f1549bc",
+                "sha256:3d59d125ffbd6d552765510e3f31ed75ebac2c7470c7274195b9161a32350284",
+                "sha256:40d3ff7fc90b98c637bda91c89d51264a3dcf210cade3a2c6f838c7268d7a4ca",
+                "sha256:425c5f215d0eecee9a56cdb703203dda90423247421bf0d67125add85d0c4455",
+                "sha256:43193c5cda5d612f247172016c4bb71251c784d7a4d9314677186a838ad34858",
+                "sha256:44aeb140295a2f0659e113b31cfe92c9061622cadbc9e2a2f7b8ef6b1e29ef4b",
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+                "sha256:707b82d19e65c9bd28b81dde95249b07bf9f5b90ebe1ef17d9b57473f8a64b7b",
+                "sha256:7706f5850360ac01d80c89bcef1640683cc12ed87f42579dab6c5d3ed6888613",
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+                "sha256:6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==0.7.0"
+        },
+        "packaging": {
+            "hashes": [
+                "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759",
+                "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==24.2"
+        },
+        "platformdirs": {
+            "hashes": [
+                "sha256:357fb2acbc885b0419afd3ce3ed34564c13c9b95c89360cd9563f73aa5e2b907",
+                "sha256:73e575e1408ab8103900836b97580d5307456908a03e92031bab39e4554cc3fb"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==4.3.6"
+        },
+        "pluggy": {
+            "hashes": [
+                "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1",
+                "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==1.5.0"
+        },
+        "pycodestyle": {
+            "hashes": [
+                "sha256:46f0fb92069a7c28ab7bb558f05bfc0110dac69a0cd23c61ea0040283a9d78b3",
+                "sha256:6838eae08bbce4f6accd5d5572075c63626a15ee3e6f842df996bf62f6d73521"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==2.12.1"
+        },
+        "pyflakes": {
+            "hashes": [
+                "sha256:1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f",
+                "sha256:84b5be138a2dfbb40689ca07e2152deb896a65c3a3e24c251c5c62489568074a"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==3.2.0"
+        },
+        "pyproject-api": {
+            "hashes": [
+                "sha256:3d7d347a047afe796fd5d1885b1e391ba29be7169bd2f102fcd378f04273d228",
+                "sha256:77b8049f2feb5d33eefcc21b57f1e279636277a8ac8ad6b5871037b243778496"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==1.8.0"
+        },
+        "pytest": {
+            "hashes": [
+                "sha256:70b98107bd648308a7952b06e6ca9a50bc660be218d53c257cc1fc94fda10181",
+                "sha256:a6853c7375b2663155079443d2e45de913a911a11d669df02a50814944db57b2"
+            ],
+            "index": "pypi",
+            "markers": "python_version >= '3.8'",
+            "version": "==8.3.3"
+        },
+        "pytest-cov": {
+            "hashes": [
+                "sha256:eee6f1b9e61008bd34975a4d5bab25801eb31898b032dd55addc93e96fcaaa35",
+                "sha256:fde0b595ca248bb8e2d76f020b465f3b107c9632e6a1d1705f17834c89dcadc0"
+            ],
+            "index": "pypi",
+            "markers": "python_version >= '3.9'",
+            "version": "==6.0.0"
+        },
+        "python-dotenv": {
+            "hashes": [
+                "sha256:e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca",
+                "sha256:f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a"
+            ],
+            "index": "pypi",
+            "markers": "python_version >= '3.8'",
+            "version": "==1.0.1"
+        },
+        "setuptools": {
+            "hashes": [
+                "sha256:8199222558df7c86216af4f84c30e9b34a61d8ba19366cc914424cdbd28252f6",
+                "sha256:ce74b49e8f7110f9bf04883b730f4765b774ef3ef28f722cce7c273d253aaf7d"
+            ],
+            "markers": "python_version >= '3.9'",
+            "version": "==75.6.0"
+        },
+        "tomli": {
+            "hashes": [
+                "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8",
+                "sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391"
+            ],
+            "markers": "python_version < '3.11'",
+            "version": "==2.1.0"
+        },
+        "tox": {
+            "hashes": [
+                "sha256:452bc32bb031f2282881a2118923176445bac783ab97c874b8770ab4c3b76c38",
+                "sha256:86075e00e555df6e82e74cfc333917f91ecb47ffbc868dcafbd2672e332f4a2c"
+            ],
+            "index": "pypi",
+            "markers": "python_version >= '3.8'",
+            "version": "==4.23.2"
+        },
+        "typing-extensions": {
+            "hashes": [
+                "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d",
+                "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"
+            ],
+            "markers": "python_version < '3.11'",
+            "version": "==4.12.2"
+        },
+        "virtualenv": {
+            "hashes": [
+                "sha256:142c6be10212543b32c6c45d3d3893dff89112cc588b7d0879ae5a1ec03a47ba",
+                "sha256:f11f1b8a29525562925f745563bfd48b189450f61fb34c4f9cc79dd5aa32a1f4"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==20.27.1"
+        }
+    }
+}
diff --git a/tools/directory/README.md b/tools/directory/README.md
new file mode 100644
index 0000000000..b97abe4dd9
--- /dev/null
+++ b/tools/directory/README.md
@@ -0,0 +1,76 @@
+# molgenis-emx2-directory-client
+
+MOLGENIS EMX2 Python tooling for a BBMRI Biobank Directory
+
+## Description
+This library contains tools for the MOLGENIS EMX2 BBMRI Biobank Directory that help with
+staging and publishing the data of the national nodes. **Staging** is the process of copying
+data from a national node's external server (for example [BBMRI-NL](https://catalogue.bbmri.nl/menu/main/home)) to
+the staging area on the Directory server. Not all national nodes have external servers; these
+do not need to be staged. **Publishing** is the process of copying and combining the data from the staging areas
+to the public combined tables of the Directory.
+
+## Usage
+
+These tools can be used as a library in a script. Start by installing the library with
+`pip install molgenis-emx2-directory-client`.
+
+For an example of how to use this library to stage and publish nodes, see [`dev.py`](dev/dev.py).
+
+If you just want to retrieve the data of a node for another purpose, you can use the `DirectorySession`
+and `ExternalServerSession` directly:
+
+```python
+from molgenis.bbmri_eric.bbmri_client import DirectorySession, ExternalServerSession
+from molgenis.bbmri_eric.model import NodeData
+
+# Get the staging and published data of NL from the directory
+session = EricSession(url="<DIRECTORY_URL")
+nl = session.get_external_node("NL")
+nl_staging_data: NodeData = session.get_staging_node_data(nl)
+nl_published_data: NodeData = session.get_published_node_data(nl)
+
+# Get the data from the external server of NL
+external_session = ExternalServerSession(nl)
+nl_external_data: NodeData = external_session.get_node_data()
+
+# Now you can use the NodeData objects as you wish
+for person in nl_external_data.persons.rows:
+    print(person)
+```
+
+
+## For developers
+This project uses [pre-commit](https://pre-commit.com/) and [pipenv](https://pypi.org/project/pipenv/) for the development workflow.
+
+Install pre-commit and pipenv if you haven't already:
+```
+pip install pre-commit
+pip install pipenv
+```
+
+Install the git commit hooks:
+```
+pre-commit install
+```
+
+Create an environment and install the package including all (dev) dependencies:
+```
+pipenv install --dev
+```
+
+Enter the environment:
+```
+pipenv shell
+```
+
+Build and run the tests:
+```
+tox
+```
+
+
+## Note
+
+This project has been set up using PyScaffold 4.0.2. For details and usage
+information on PyScaffold see https://pyscaffold.org/.
diff --git a/tools/directory/dev/dev.py b/tools/directory/dev/dev.py
new file mode 100644
index 0000000000..ea74ea9021
--- /dev/null
+++ b/tools/directory/dev/dev.py
@@ -0,0 +1,64 @@
+"""
+Example usage file meant for development. Make sure you have an .env file and a
+pyhandle_creds.json file in this folder.
+"""
+
+import asyncio
+import logging
+import os
+
+from dotenv import load_dotenv
+from tools.directory.src.molgenis_emx2.directory_client.directory import Directory
+from tools.directory.src.molgenis_emx2.directory_client.directory_client import (
+    DirectorySession,
+)
+from tools.directory.src.molgenis_emx2.directory_client.pid_service import PidService
+
+# Get credentials from .env
+load_dotenv()
+
+target = os.getenv("TARGET")
+username = os.getenv("USERNAME")
+password = os.getenv("PASSWORD")
+directory_schema = os.getenv("DIRECTORY")
+
+
+async def sync_directory():
+    # Set up the logger
+    logging.basicConfig(level="INFO", format=" %(levelname)s: %(name)s: %(message)s")
+    logging.getLogger("requests").setLevel(logging.WARNING)
+    logging.getLogger("urllib3").setLevel(logging.WARNING)
+
+    # Login to the directory with a DirectorySession
+    with DirectorySession(url=target, schema=directory_schema) as session:
+        # Apply the 'signin' method with the username and password
+        session.signin(username, password)
+
+        # Get the nodes you want to work with
+        # When staging a node the .env file should include a "node"_user="token"
+        # with view permissions on the external staging area
+        nodes_to_stage = session.get_external_nodes(["NL"])
+        nodes_to_publish = session.get_nodes()
+
+        # Create PidService
+        pid_service = PidService.from_credentials("pyhandle_creds.json")
+        print(f"Script runs on server {pid_service.base_url}")
+        # Use the DummyPidService if testing without interacting with a handle server
+        # pid_service = DummyPidService()
+        # Use the NoOpPidService if you want to turn off the PID features completely
+        # pid_service = NoOpPidService()
+
+        # Instantiate the Directory class and do some work
+        directory = Directory(session, pid_service)
+        staging_report = await directory.stage_external_nodes(nodes_to_stage)
+        publishing_report = await directory.publish_nodes(nodes_to_publish)
+
+        if staging_report.has_errors():
+            raise ValueError("Some nodes did not publish correctly")
+
+        if publishing_report.has_errors():
+            raise ValueError("Some nodes did not publish correctly")
+
+
+if __name__ == "__main__":
+    asyncio.run(sync_directory())
diff --git a/tools/directory/pyproject.toml b/tools/directory/pyproject.toml
new file mode 100644
index 0000000000..f6e0481642
--- /dev/null
+++ b/tools/directory/pyproject.toml
@@ -0,0 +1,9 @@
+[build-system]
+# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
+requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+# See configuration details in https://github.com/pypa/setuptools_scm
+root = "../../"
+version_scheme = "no-guess-dev"
diff --git a/tools/directory/setup.cfg b/tools/directory/setup.cfg
new file mode 100644
index 0000000000..0651bb160d
--- /dev/null
+++ b/tools/directory/setup.cfg
@@ -0,0 +1,120 @@
+# http://setuptools.readthedocs.io/en/latest/setuptools.html#configuring-setup-using-setup-cfg-files
+
+[metadata]
+name = molgenis-emx2-directory-client
+description = MOLGENIS EMX2 Python tooling for a BBMRI Biobank Directory
+author = Dieuwke Roelofs-Prins
+author_email = support@molgenis.org
+license = LGPL-3.0-only
+long_description = file: README.md
+long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
+url = https://github.com/molgenis/molgenis-emx2/tools/directory/
+project_urls =
+    Source = https://github.com/molgenis/molgenis-emx2/tools/directory
+
+# Change if running only on Windows, Mac or Linux (comma-separated)
+platforms = any
+
+# Add here all kinds of additional classifiers as defined under
+# https://pypi.python.org/pypi?%3Aaction=list_classifiers
+classifiers =
+    License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+    Programming Language :: Python
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.10
+
+[options]
+zip_safe = False
+packages = find_namespace:
+include_package_data = True
+package_dir =
+    =src
+
+# Require a min/specific Python version (comma-separated conditions)
+python_requires = >=3.10
+
+# Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
+# Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
+# new major versions. This works if the required packages follow Semantic Versioning.
+# For more information, check out https://semver.org/.
+install_requires =
+    dataclasses
+    molgenis-emx2-pyclient>=11.23.0
+    requests>=2.21.0
+    unidecode
+    pyhandle>=1.3.1
+
+
+[options.packages.find]
+where = src
+exclude =
+    tests
+
+[options.extras_require]
+# Add here test requirements (semicolon/line-separated)
+testing =
+    setuptools
+    pytest
+    pytest-cov
+    pytest-asyncio
+    pytest-mock
+
+[tool:pytest]
+# Specify command line options as you would do when invoking pytest directly.
+# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
+# in order to write a coverage file that can be read by Jenkins.
+# CAUTION: --cov flags may prohibit setting breakpoints while debugging.
+#          Comment those flags to avoid this py.test issue.
+addopts =
+    --cov molgenis_emx2.directory_client --cov-report term-missing
+    --verbose
+    --junitxml junit.xml
+asyncio_default_fixture_loop_scope="function"
+norecursedirs =
+    dist
+    build
+    .tox
+testpaths = tests
+# Use pytest markers to select/deselect specific tests
+# markers =
+#     slow: mark tests as slow (deselect with '-m "not slow"')
+#     system: mark end-to-end system tests
+
+[bdist_wheel]
+# Use this option if your package is pure-python
+universal = 1
+
+[devpi:upload]
+# Options for the devpi: PyPI server and packaging tool
+# VCS export must be deactivated since we are using setuptools-scm
+no_vcs = 1
+formats = bdist_wheel
+
+[flake8]
+# Some sane defaults for the code style checker flake8
+max_line_length = 88
+extend_ignore = E203, W503
+# ^  Black-compatible
+#    E203 and W503 have edge cases handled by black
+exclude =
+    .tox
+    build
+    dist
+    .eggs
+    docs/conf.py
+
+[bumpversion]
+commit = False
+tag = True
+tag_name = {new_version}
+
+[pyscaffold]
+# PyScaffold's parameters when the project was created.
+# This will be used when updating. Do not change!
+version = 4.0.2
+package = directory_client
+extensions =
+    markdown
+    namespace
+    pre_commit
+namespace = molgenis-emx2
diff --git a/tools/directory/setup.py b/tools/directory/setup.py
new file mode 100644
index 0000000000..f46fff2e66
--- /dev/null
+++ b/tools/directory/setup.py
@@ -0,0 +1,21 @@
+"""
+    Setup file for molgenis-emx2-directory-client
+    Use setup.cfg to configure your project.
+
+    This file was generated with PyScaffold 4.0.2.
+    PyScaffold helps you to put up the scaffold of your new Python project.
+    Learn more under: https://pyscaffold.org/
+"""
+from setuptools import setup
+
+if __name__ == "__main__":
+    try:
+        setup(use_scm_version={"version_scheme": "no-guess-dev"})
+    except:  # noqa
+        print(
+            "\n\nAn error occurred while building the project, "
+            "please ensure you have the most updated version of setuptools, "
+            "setuptools_scm and wheel with:\n"
+            "   pip install -U setuptools setuptools_scm wheel\n\n"
+        )
+        raise
diff --git a/tools/directory/src/molgenis_emx2/directory_client/__init__.py b/tools/directory/src/molgenis_emx2/directory_client/__init__.py
new file mode 100644
index 0000000000..77ac61d71e
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/__init__.py
@@ -0,0 +1,16 @@
+import sys
+
+if sys.version_info[:2] >= (3, 8):
+    # noinspection PyCompatibility
+    from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
+else:
+    # noinspection PyUnresolvedReferences
+    from importlib_metadata import PackageNotFoundError, version  # pragma: no cover
+
+try:
+    dist_name = "molgenis-emx2-directory-client"
+    __version__ = version(dist_name)
+except PackageNotFoundError:  # pragma: no cover
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError
diff --git a/tools/directory/src/molgenis_emx2/directory_client/categories.py b/tools/directory/src/molgenis_emx2/directory_client/categories.py
new file mode 100644
index 0000000000..b661539b7b
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/categories.py
@@ -0,0 +1,235 @@
+from copy import deepcopy
+from enum import Enum
+from typing import List, Set
+
+from .model import OntologyTable
+
+
+class Category(Enum):
+    """
+    Enum of Collection Categories with identifiers found in the Categories table.
+    """
+
+    AUTOIMMUNE = "autoimmune"
+    CARDIOVASCULAR = "cardiovascular"
+    COVID19 = "covid19"
+    INFECTIOUS = "infectious"
+    METABOLIC = "metabolic"
+    NERVOUS_SYSTEM = "nervous_system"
+    ONCOLOGY = "oncology"
+    PAEDIATRICS = "paediatrics"
+    POPULATION = "population"
+    RARE_DISEASE = "rare_disease"
+
+
+class AgeUnit(Enum):
+    """
+    Enum of age units with identifiers found in the AgeUnits table.
+    """
+
+    DAY = "DAY"
+    WEEK = "WEEK"
+    MONTH = "MONTH"
+    YEAR = "YEAR"
+
+
+AUTOIMMUNE_TERMS = {
+    "urn:miriam:icd:B20",
+    # "D50-D89",
+    "urn:miriam:icd:D50-D53",
+    "urn:miriam:icd:D55-D59",
+    "urn:miriam:icd:D60-D64",
+    "urn:miriam:icd:D65-D69",
+    "urn:miriam:icd:D70-D77",
+    # "urn:miriam:icd:D71",
+    "urn:miriam:icd:D80-D89",
+    "urn:miriam:icd:E06.3",
+    "urn:miriam:icd:K90.0",
+    "urn:miriam:icd:M06",
+    "urn:miriam:icd:M35.9",
+    "urn:miriam:icd:M45",
+    "urn:miriam:icd:K75",
+}
+
+CARDIOVASCULAR_TERMS = {
+    "urn:miriam:icd:IX",
+}
+
+COVID_TERMS = {
+    "urn:miriam:icd:U07.1",
+    "urn:miriam:icd:U07.2",
+    "urn:miriam:icd:U08",
+    "urn:miriam:icd:U09",
+    "urn:miriam:icd:U09.9",
+    "urn:miriam:icd:U10",
+    "urn:miriam:icd:U10.9",
+    "urn:miriam:icd:U11",
+    "urn:miriam:icd:U11.9",
+    "urn:miriam:icd:U12",
+    "urn:miriam:icd:U12.9",
+}
+
+INFECTIOUS_TERMS = {
+    "urn:miriam:icd:I",
+    "urn:miriam:icd:J09-J18",
+    "urn:miriam:icd:U07.1",
+    "urn:miriam:icd:U07.2",
+    "urn:miriam:icd:U08",
+    "urn:miriam:icd:U09",
+    "urn:miriam:icd:U09.9",
+    "urn:miriam:icd:U10",
+    "urn:miriam:icd:U10.9",
+    "urn:miriam:icd:U11",
+    "urn:miriam:icd:U11.9",
+    "urn:miriam:icd:U12",
+    "urn:miriam:icd:U12.9",
+}
+
+METABOLIC_TERMS = {
+    # E00-E89
+    # if E90 can be included: "urn:miriam:icd:IV",
+    "urn:miriam:icd:E00-E07",
+    "urn:miriam:icd:E10-E14",
+    "urn:miriam:icd:E15-E16",
+    "urn:miriam:icd:E20-E35",
+    "urn:miriam:icd:E40-E46",
+    "urn:miriam:icd:E50-E64",
+    "urn:miriam:icd:E65-E68",
+    "urn:miriam:icd:E70",
+    "urn:miriam:icd:E71",
+    "urn:miriam:icd:E72",
+    "urn:miriam:icd:E73",
+    "urn:miriam:icd:E74",
+    "urn:miriam:icd:E75",
+    "urn:miriam:icd:E76",
+    "urn:miriam:icd:E77",
+    "urn:miriam:icd:E78",
+    "urn:miriam:icd:E79",
+    "urn:miriam:icd:E80",
+    "urn:miriam:icd:E83",
+    "urn:miriam:icd:E84",
+    "urn:miriam:icd:E85",
+    "urn:miriam:icd:E86",
+    "urn:miriam:icd:E87",
+    "urn:miriam:icd:E88",
+    "urn:miriam:icd:E89",
+}
+
+NERVOUS_SYSTEM_TERMS = {
+    # G00-G99
+    "urn:miriam:icd:VI",
+}
+
+ONCOLOGY_TERMS = {
+    # "urn:miriam:icd:C00-D49",
+    "urn:miriam:icd:II",
+}
+
+PAEDIATRIC_AGE_LIMIT = {
+    AgeUnit.DAY: 365 * 18,
+    AgeUnit.WEEK: 52 * 18,
+    AgeUnit.MONTH: 12 * 18,
+    AgeUnit.YEAR: 18,
+}
+
+POPULATION_TERMS = {
+    "urn:miriam:icd:Z00",
+}
+
+
+class CategoryMapper:
+    def __init__(self, diseases: OntologyTable):
+        self.diseases = diseases
+
+    def map(self, collection: dict) -> List[str]:
+        """
+        Maps data from a collection to a list of categories that the collection belongs
+        to.
+        :param collection: the collection to map
+        :return: a list of categories
+        """
+        categories = []
+
+        self._map_paediatric(collection, categories)
+        self._map_diseases(collection, categories)
+        self._map_collection_types(collection, categories)
+
+        return list(set(categories))
+
+    @classmethod
+    def _map_paediatric(cls, collection: dict, categories: List[str]):
+        unit = collection.get("age_unit", None)
+        if unit:
+            low = collection.get("age_low", None)
+            high = collection.get("age_high", None)
+
+            if (
+                low is not None
+                and high is not None
+                and ((low == 0 and high == 0) or (low > high))
+            ):
+                return
+
+            age_limit = PAEDIATRIC_AGE_LIMIT[AgeUnit[unit]]
+            if high is not None and (high < age_limit):
+                categories.append(Category.PAEDIATRICS.value)
+            if low is not None and (low < age_limit):
+                # categories.append(Category.PAEDIATRIC_INCLUDED.value)
+                categories.append(Category.PAEDIATRICS.value)
+
+    @classmethod
+    def _map_collection_types(cls, collection: dict, categories: List[str]):
+        if "RD" in collection.get("type", []):
+            categories.append(Category.RARE_DISEASE.value)
+        if "BIRTH_COHORT" in collection.get("type", []):
+            categories.append(Category.PAEDIATRICS.value)
+        if "CASE_CONTROL" in collection.get(
+            "type", []
+        ) or "POPULATION_BASED" in collection.get("type", []):
+            categories.append(Category.POPULATION.value)
+
+    def _map_diseases(self, collection: dict, categories: List[str]):
+        diagnoses = deepcopy(collection.get("diagnosis_available", []))
+        if diagnoses:
+            if self.diseases.matching_attrs:
+                matching_diagnoses = self.diseases.get_matching_ontologies(diagnoses)
+                diagnoses.extend(matching_diagnoses)
+                diagnoses = set(diagnoses)
+
+            if self._contains_descendant_of(diagnoses, AUTOIMMUNE_TERMS):
+                categories.append(Category.AUTOIMMUNE.value)
+
+            if self._contains_descendant_of(diagnoses, CARDIOVASCULAR_TERMS):
+                categories.append(Category.CARDIOVASCULAR.value)
+
+            if self._contains_descendant_of(diagnoses, COVID_TERMS):
+                categories.append(Category.COVID19.value)
+
+            if self._contains_descendant_of(diagnoses, INFECTIOUS_TERMS):
+                categories.append(Category.INFECTIOUS.value)
+
+            if self._contains_descendant_of(diagnoses, METABOLIC_TERMS):
+                categories.append(Category.METABOLIC.value)
+
+            if self._contains_descendant_of(diagnoses, NERVOUS_SYSTEM_TERMS):
+                categories.append(Category.NERVOUS_SYSTEM.value)
+
+            if self._contains_descendant_of(diagnoses, ONCOLOGY_TERMS):
+                categories.append(Category.ONCOLOGY.value)
+
+            if self._contains_descendant_of(diagnoses, POPULATION_TERMS):
+                categories.append(Category.POPULATION.value)
+
+            if self._contains_orphanet(diagnoses):
+                categories.append(Category.RARE_DISEASE.value)
+
+    def _contains_orphanet(self, diagnoses: List[str]) -> bool:
+        for diagnosis in diagnoses:
+            term = self.diseases.rows_by_id.get(diagnosis, None)
+            if term and term.get("codesystem", "") == "orphanet":
+                return True
+
+    def _contains_descendant_of(self, diagnoses: List[str], terms: Set[str]):
+        for diagnosis in diagnoses:
+            if self.diseases.is_descendant_of_any(diagnosis, terms):
+                return True
diff --git a/tools/directory/src/molgenis_emx2/directory_client/directory.py b/tools/directory/src/molgenis_emx2/directory_client/directory.py
new file mode 100644
index 0000000000..efc3e14da3
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/directory.py
@@ -0,0 +1,149 @@
+from typing import List, Optional
+
+from .directory_client import AttributesRequest, DirectorySession
+from .errors import DirectoryError, ErrorReport, requests_error_handler
+from .model import ExternalServerNode, Node
+from .pid_manager import PidManagerFactory
+from .pid_service import BasePidService
+from .printer import Printer
+from .publication_preparer import PublicationPreparer
+from .publisher import Publisher, PublishingState
+from .stager import Stager
+
+
+class Directory:
+    """
+    Main class for doing operations on the BBMRI Biobank Directory.
+    """
+
+    def __init__(
+        self, session: DirectorySession, pid_service: Optional[BasePidService] = None
+    ):
+        """
+        :param session: an authenticated session with a BBMRI Biobank Directory.
+        :param pid_service: a configured PidService, required for publishing. When no
+        PidService is provided, nodes can only be staged.
+        """
+        self.session = session
+        self.printer = Printer()
+        self.stager = Stager(self.session, self.printer)
+        self.pid_service: Optional[BasePidService] = pid_service
+        if pid_service:
+            self.pid_manager = PidManagerFactory.create(self.pid_service, self.printer)
+            self.preparator = PublicationPreparer(
+                self.printer, self.pid_manager, self.session
+            )
+            self.publisher = Publisher(self.session, self.printer, self.pid_manager)
+
+    async def stage_external_nodes(
+        self, nodes: List[ExternalServerNode]
+    ) -> ErrorReport:
+        """
+        Stages all data from the provided external nodes in the BBMRI Biobank Directory.
+
+        Parameters:
+            nodes (List[ExternalServerNode]): The list of external nodes to stage
+        """
+        report = ErrorReport(nodes)
+        for node in nodes:
+            self.printer.print_node_title(node)
+            try:
+                await self._stage_node(node, report)
+            except DirectoryError as e:
+                self.printer.print_error(e)
+                report.add_node_error(node, e)
+
+        self.printer.print_summary(report)
+        return report
+
+    async def publish_nodes(self, nodes: List[Node]) -> ErrorReport:
+        """
+        Publishes data from the provided nodes to the tables in the Directory.
+
+        Parameters:
+            nodes (List[Node]): The list of nodes to publish
+        """
+        if not self.pid_service:
+            raise ValueError("A PID service is required to publish nodes")
+
+        report = ErrorReport(nodes)
+        try:
+            state = self._init_state(nodes, report)
+        except DirectoryError as e:
+            self.printer.print_error(e)
+            report.set_global_error(e)
+        else:
+            await self._prepare_nodes(nodes, state)
+            await self._publish_nodes(state)
+
+        self.printer.print_summary(report)
+        return report
+
+    @requests_error_handler
+    def _init_state(self, nodes: List[Node], report: ErrorReport) -> PublishingState:
+        self.printer.print_header("⚙️ Preparation")
+
+        self.printer.print("📦 Retrieving existing published data")
+        published_data = self.session.get_published_data(
+            nodes,
+            AttributesRequest(
+                persons=["id", "national_node"],
+                networks=["id", "national_node"],
+                also_known_in=["id", "national_node"],
+                biobanks=["id", "pid", "name", "national_node", "withdrawn"],
+                collections=["id", "national_node"],
+                facts=["id", "national_node"],
+            ),
+        )
+
+        self.printer.print("📦 Retrieving quality information")
+        quality_info = self.session.get_quality_info()
+
+        self.printer.print("📦 Retrieving data of node EU")
+        eu_node_data = self.session.get_staging_node_data(self.session.get_node("EU"))
+
+        self.printer.print("📦 Retrieving disease ontologies")
+        diseases = self.session.get_ontology(
+            "DiseaseTypes",
+            matching_attrs=["exact_mapping", "ntbt_mapping"],
+        )
+
+        return PublishingState(
+            existing_data=published_data,
+            quality_info=quality_info,
+            eu_node_data=eu_node_data,
+            diseases=diseases,
+            nodes=nodes,
+            report=report,
+        )
+
+    async def _prepare_nodes(self, nodes, state):
+        for node in nodes:
+            self.printer.print_node_title(node)
+            try:
+                if isinstance(node, ExternalServerNode):
+                    await self._stage_node(node, state.report)
+                node_data = self.preparator.prepare(node, state)
+                state.data_to_publish.merge(node_data)
+            except DirectoryError as e:
+                self.printer.print_error(e)
+                state.existing_data.remove_node_rows(node)
+                state.report.add_node_error(node, e)
+
+    async def _publish_nodes(self, state: PublishingState):
+        self.printer.print_header(
+            f"🎁 Publishing node{'s' if len(state.nodes) > 1 else ''}"
+        )
+        try:
+            await self.publisher.publish(state)
+        except DirectoryError as e:
+            self.printer.print_error(e)
+            state.report.set_global_error(e)
+
+    @requests_error_handler
+    async def _stage_node(self, node: ExternalServerNode, report: ErrorReport):
+        self.printer.print(f"📥 Staging data of node {node.code}")
+        with self.printer.indentation():
+            warnings = await self.stager.stage(node)
+            if warnings:
+                report.add_node_warnings(node, warnings)
diff --git a/tools/directory/src/molgenis_emx2/directory_client/directory_client.py b/tools/directory/src/molgenis_emx2/directory_client/directory_client.py
new file mode 100644
index 0000000000..cb7443bc8e
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/directory_client.py
@@ -0,0 +1,461 @@
+import csv
+import io
+import os
+import tempfile
+from collections import defaultdict
+from dataclasses import asdict, dataclass
+from pathlib import Path
+from typing import List
+from zipfile import ZipFile
+
+import pandas as pd
+from molgenis_emx2_pyclient import Client as Session
+from molgenis_emx2_pyclient.exceptions import NoSuchSchemaException
+from molgenis_emx2_pyclient.metadata import NoSuchTableException, Schema
+from molgenis_emx2_pyclient.metadata import Table as MetaTable
+
+from .errors import MolgenisRequestError
+from .model import (
+    DirectoryData,
+    ExternalServerNode,
+    MixedData,
+    Node,
+    NodeData,
+    OntologyTable,
+    QualityInfo,
+    Source,
+    Table,
+    TableMeta,
+    TableType,
+)
+from .utils import create_csv
+
+
+@dataclass
+class AttributesRequest:
+    persons: List[str]
+    networks: List[str]
+    also_known_in: List[str]
+    biobanks: List[str]
+    collections: List[str]
+    facts: List[str]
+
+
+class MolgenisImportError(MolgenisRequestError):
+    pass
+
+
+class DirectorySession(Session):
+    """
+    A session with a BBMRI Biobank Directory. Contains methods to get national nodes,
+    their (staging) data and quality information.
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.directory_schema = self.default_schema
+
+    NODES_TABLE = "NationalNodes"
+    ONTOLOGY_SCHEMA = "DirectoryOntologies"
+
+    def get(
+        self,
+        table: str,
+        query_filter: str = None,
+        schema: str = None,
+        as_df: bool = False,
+    ) -> list | pd.DataFrame:
+        """
+        Copy of the EMX2 pyclient get, with change in how list of dicts is returned
+        Retrieves data from a schema and returns as a list of dictionaries or as
+        a pandas DataFrame (as pandas is used to parse the response).
+
+        :param schema: name of a schema
+        :type schema: str
+        :param query_filter: the query to filter the output
+        :type query_filter: str
+        :param table: the name of the table
+        :type table: str
+        :param as_df: if True, the response will be returned as a
+                      pandas DataFrame. Otherwise, a recordset will be returned.
+        :type as_df: bool
+
+        :returns: list of dictionaries, status message or data frame
+        :rtype: list | pd.DataFrame
+        """
+        current_schema = schema
+        if current_schema is None:
+            current_schema = self.default_schema
+
+        if current_schema not in self.schema_names:
+            raise NoSuchSchemaException(f"Schema {current_schema!r} not available.")
+
+        if not self._table_in_schema(table, current_schema):
+            raise NoSuchTableException(
+                f"Table {table!r} not found " f"in schema {current_schema!r}."
+            )
+
+        schema_metadata: Schema = self.get_schema_metadata(current_schema)
+        table_id = schema_metadata.get_table(by="name", value=table).id
+
+        filter_part = self._prepare_filter(query_filter, table, schema)
+        query_url = f"{self.url}/{current_schema}/api/csv/{table_id}{filter_part}"
+        response = self.session.get(url=query_url)
+
+        self._validate_graphql_response(
+            response=response,
+            fallback_error_message=f"Failed to retrieve "
+            f"data from {current_schema}::{table!r}.\n"
+            f"Status code: {response.status_code}.",
+        )
+
+        response_data = pd.read_csv(io.BytesIO(response.content), keep_default_na=False)
+
+        if not as_df:
+            response_data = []
+            data = response.content.decode("utf-8").strip()
+            with io.StringIO(data) as infile:
+                reader = csv.DictReader(infile, quotechar='"')
+                for rec in reader:
+                    response_data.append(rec)
+
+            response_data = self._reset_data_types(
+                response_data, schema_metadata.get_table(by="name", value=table)
+            )
+        return response_data
+
+    def get_table_meta(
+        self,
+        table_name: str,
+        schema: str = None,
+    ):
+        schema_meta = self.get_schema_metadata(schema)
+        for table in schema_meta.tables:
+            if table.name == table_name:
+                return table.columns
+        raise MolgenisRequestError(f"Unknown table: {table_name}")
+
+    def get_ontology(
+        self,
+        entity_type_id: str,
+        matching_attrs: List[str] | None = None,
+        parent_attr: str = "parent",
+    ) -> OntologyTable:
+        """
+        Retrieves an ontology table.
+        :param entity_type_id: the identifier of the table
+        :param parent_attr: the name of the attribute that contains the parent relation
+        :param matching_attrs: a list with the relevant level or levels of the
+                               "matching" ontology code columns
+        :return: an OntologyTable
+        """
+        matching_attrs = matching_attrs if matching_attrs else []
+
+        rows = self.get(
+            schema=self.ONTOLOGY_SCHEMA,
+            table=entity_type_id,
+        )
+
+        meta = TableMeta(
+            meta=self.get_table_meta(
+                schema=self.ONTOLOGY_SCHEMA, table_name=entity_type_id
+            )
+        )
+        return OntologyTable.of(meta, rows, parent_attr, matching_attrs)
+
+    def get_quality_info(self) -> QualityInfo:
+        """
+        Retrieves the quality information identifiers for biobanks and collections.
+        :return: a QualityInfo object
+        """
+
+        biobank_qualities = self.get(
+            table="QualityInfoBiobanks",
+        )
+        collection_qualities = self.get(
+            table="QualityInfoCollections",
+        )
+
+        bb_qual = defaultdict(list)
+        bb_level = defaultdict(list)
+        coll_qual = defaultdict(list)
+        coll_level = defaultdict(list)
+        for row in biobank_qualities:
+            bb_qual[row["biobank"]].append(row["id"])
+            bb_level[row["biobank"]].append(row["assess_level_bio"])
+        for row in collection_qualities:
+            coll_qual[row["collection"]].append(row["id"])
+            coll_level[row["collection"]].append(row["assess_level_col"])
+
+        return QualityInfo(
+            biobanks=bb_qual,
+            collections=coll_qual,
+            biobank_levels=bb_level,
+            collection_levels=coll_level,
+        )
+
+    def get_node(self, code: str) -> Node:
+        """
+        Retrieves a single Node object from the national nodes table.
+        :param code: node to get by code
+        :return: Node object
+        """
+        nodes = self.get(table=self.NODES_TABLE, query_filter=f"id == {code}")
+        self._validate_codes([code], nodes)
+        return self._to_nodes(nodes)[0]
+
+    def get_nodes(self, codes: List[str] = None) -> List[Node]:
+        """
+        Retrieves a list of Node objects from the national nodes table. Will return
+        all nodes or some nodes if 'codes' is specified.
+        :param codes: nodes to get by code
+        :return: list of Node objects
+        """
+        if codes:
+            nodes = self.get(table=self.NODES_TABLE, query_filter=f"id == {codes}")
+        else:
+            nodes = self.get(table=self.NODES_TABLE)
+
+        if codes:
+            self._validate_codes(codes, nodes)
+        return self._to_nodes(nodes)
+
+    def get_external_node(self, code: str) -> ExternalServerNode:
+        """
+        Retrieves a single ExternalServerNode object from the national nodes table.
+        :param code: node to get by code
+        :return: ExternalServerNode object
+        """
+        df_nodes = self.get(
+            table=self.NODES_TABLE, query_filter=f"id == {code}", as_df=True
+        )
+        df_nodes = df_nodes.loc[df_nodes["dns"] != ""]
+        nodes = df_nodes.to_dict("records")
+
+        self._validate_codes([code], nodes)
+        return self._to_nodes(nodes)[0]
+
+    def get_external_nodes(self, codes: List[str] = None) -> List[ExternalServerNode]:
+        """
+        Retrieves a list of ExternalServerNode objects from the national nodes table.
+        Will return all nodes or some nodes if 'codes' is specified.
+        :param codes: nodes to get by code
+        :return: list of ExternalServerNode objects
+        """
+        if codes:
+            df_nodes = self.get(
+                table=self.NODES_TABLE, query_filter=f"id == {codes}", as_df=True
+            )
+        else:
+            df_nodes = self.get(table=self.NODES_TABLE, as_df=True)
+
+        df_nodes = df_nodes.loc[df_nodes["dns"] != ""]
+        nodes = df_nodes.to_dict("records")
+
+        if codes:
+            self._validate_codes(codes, nodes)
+        return self._to_nodes(nodes)
+
+    @staticmethod
+    def _validate_codes(codes: List[str], nodes: List[dict]):
+        """Raises a KeyError if a requested node code was not found."""
+        retrieved_codes = {node["id"] for node in nodes}
+        for code in codes:
+            if code not in retrieved_codes:
+                raise KeyError(f"Unknown code: {code}")
+
+    @staticmethod
+    def _to_nodes(nodes: List[dict]):
+        """Maps rows to Node or ExternalServerNode objects."""
+        result = list()
+        for node in nodes:
+            if "dns" not in node:
+                result.append(
+                    Node(
+                        code=node["id"],
+                        description=node["description"],
+                        date_end=node.get("date_end"),
+                    )
+                )
+            else:
+                result.append(
+                    ExternalServerNode(
+                        code=node["id"],
+                        description=node["description"],
+                        date_end=node.get("date_end"),
+                        url=node["dns"],
+                        token=os.getenv(f"{node['id']}_user"),
+                    )
+                )
+
+        return result
+
+    @staticmethod
+    def _reset_data_types(data: List, meta: MetaTable):
+        for row in data:
+            bools = meta.get_columns(by="columnType", value="BOOL")
+            bools = [i.name for i in bools]
+            ints = meta.get_columns(by="columnType", value="INT")
+            ints = [column.name for column in ints]
+            arrays = meta.get_columns(by="columnType", value="REF_ARRAY")
+            arrays.extend(meta.get_columns(by="columnType", value="ONTOLOGY_ARRAY"))
+            arrays = [column.name for column in arrays]
+            for column in [column.name for column in meta.columns]:
+                if column not in row:
+                    continue
+                if column in arrays:
+                    if not row[column]:
+                        row[column] = []
+                    else:
+                        row[column] = row[column].split(",")
+                if not row[column] and type(row[column]) is not list:
+                    del row[column]
+                    continue
+                if column in ints:
+                    row[column] = int(row[column])
+                if column in bools and type(row[column]) is str:
+                    row[column] = eval(row[column].capitalize())
+        return data
+
+    def get_staging_node_data(self, node: Node) -> NodeData:
+        """
+        Gets the six tables that belong to a single node's staging area.
+
+        :param Node node: the node to get the staging data for
+        :return: a NodeData object
+        """
+        tables = dict()
+        for table_type in TableType.get_import_order():
+            id_ = node.get_staging_id(table_type)
+            meta = TableMeta(
+                meta=self.get_table_meta(schema=node.get_schema_id(), table_name=id_)
+            )
+
+            tables[table_type.value] = Table.of(
+                table_type=table_type,
+                meta=meta,
+                rows=self.get(schema=node.get_schema_id(), table=id_),
+            )
+
+        return NodeData.from_dict(node=node, source=Source.STAGING, tables=tables)
+
+    def get_published_node_data(self, node: Node) -> NodeData:
+        """
+        Gets the six tables that belong to a single node from the published tables.
+        Filters the rows based on the national_node field.
+
+        :param Node node: the node to get the published data for
+        :return: a NodeData object
+        """
+        tables = dict()
+        for table_type in TableType.get_import_order():
+            id_ = table_type.base_id
+            meta = TableMeta(
+                self.get_table_meta(schema=self.directory_schema, table_name=id_)
+            )
+
+            tables[table_type.value] = Table.of(
+                table_type=table_type,
+                meta=meta,
+                rows=self.get(
+                    table=id_, query_filter=f"national_node.id == {node.code}"
+                ),
+            )
+
+        return NodeData.from_dict(node=node, source=Source.PUBLISHED, tables=tables)
+
+    def get_published_data(
+        self, nodes: List[Node], attributes: AttributesRequest
+    ) -> MixedData:
+        """
+        Gets the six tables that belong to one or more nodes from the Directory tables.
+        Filters the rows based on the national_node field.
+
+        :param List[Node] nodes: the node(s) to get the Directory data for
+        :param AttributesRequest attributes: the attributes to get for each table
+        :return: a DirectoryData object
+        """
+
+        if len(nodes) == 0:
+            raise ValueError("No nodes provided")
+
+        attributes = asdict(attributes)
+        codes = [node.code for node in nodes]
+        tables = dict()
+        for table_type in TableType.get_import_order():
+            id_ = table_type.base_id
+            meta = TableMeta(
+                self.get_table_meta(schema=self.directory_schema, table_name=id_)
+            )
+            attrs = attributes[table_type.value]
+            data = []
+            for code in codes:
+                p_code = self.get(table=id_, query_filter=f"national_node.id == {code}")
+                data.extend(p_code)
+            rows = []
+            for row in data:
+                rows.append(dict(filter(lambda x: x[0] in attrs, row.items())))
+
+            tables[table_type.value] = Table.of(
+                table_type=table_type, meta=meta, rows=rows
+            )
+
+        return MixedData.from_mixed_dict(source=Source.PUBLISHED, tables=tables)
+
+    async def upload_data(self, schema: str, data: DirectoryData):
+        """
+        Converts the six tables of a DirectoryData object to CSV, bundles them in
+        a ZIP archive and imports them through the import API.
+        :param schema: database where data should be uploaded into
+        :param data: a DirectoryData object
+        """
+        with tempfile.TemporaryDirectory() as tmpdir:
+            archive_name = f"{tmpdir}/directory_data.zip"
+            with ZipFile(archive_name, "w") as archive:
+                for table in data.import_order:
+                    file_name = f"{table.full_name}.csv"
+                    file_path = f"{tmpdir}/{file_name}"
+                    create_csv(table.rows, file_path, table.meta.attributes)
+                    archive.write(file_path, file_name)
+
+            await self.upload_file(schema=schema, file_path=Path(archive_name))
+
+
+class ExternalServerSession(DirectorySession):
+    """
+    A session with a national node's external server (for example BBMRI-NL).
+    """
+
+    def __init__(self, node: ExternalServerNode):
+        super().__init__(url=node.url, token=node.token)
+        self.node = node
+
+    def get_node_data(self) -> NodeData:
+        """
+        Gets the six tables of this node's external server.
+
+        :return: a NodeData object
+        """
+
+        tables = dict()
+        for table_type in TableType.get_import_order():
+            id_ = self.node.get_staging_id(table_type)
+            schema_meta = self.get_schema_metadata(self.node.get_schema_id())
+            try:
+                schema_meta.get_table(by="name", value=id_)
+                meta = TableMeta(
+                    self.get_table_meta(
+                        schema=self.node.get_schema_id(), table_name=id_
+                    )
+                )
+                tables[table_type.value] = Table.of(
+                    table_type=table_type,
+                    meta=meta,
+                    rows=self.get(schema=self.node.get_schema_id(), table=id_),
+                )
+            except NoSuchTableException:
+                tables[table_type.value] = Table.of_placeholder(table_type)
+
+        return NodeData.from_dict(
+            node=self.node, source=Source.EXTERNAL_SERVER, tables=tables
+        )
diff --git a/tools/directory/src/molgenis_emx2/directory_client/errors.py b/tools/directory/src/molgenis_emx2/directory_client/errors.py
new file mode 100644
index 0000000000..81c85f8d40
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/errors.py
@@ -0,0 +1,78 @@
+from collections import defaultdict
+from dataclasses import dataclass, field
+from typing import DefaultDict, List, Optional
+
+import requests
+
+from .model import Node
+
+
+@dataclass(frozen=True)
+class DirectoryWarning:
+    """
+    Class that contains a warning message. Use this when a problem occurs that
+    shouldn't cancel the current action (for example staging or publishing).
+    """
+
+    message: str
+
+
+class DirectoryError(Exception):
+    """
+    Raise this exception when an error occurs that we can not recover from.
+    """
+
+    pass
+
+
+@dataclass
+class ErrorReport:
+    """
+    Summary object. Stores errors and warnings that occur during staging or publishing.
+    """
+
+    nodes: List[Node]
+    node_errors: DefaultDict[Node, DirectoryError] = field(
+        default_factory=lambda: defaultdict(list)
+    )
+    node_warnings: DefaultDict[Node, List[DirectoryWarning]] = field(
+        default_factory=lambda: defaultdict(list)
+    )
+    error: Optional[DirectoryError] = None
+
+    def add_node_error(self, node: Node, error: DirectoryError):
+        self.node_errors[node] = error
+
+    def add_node_warnings(self, node: Node, warnings: List[DirectoryWarning]):
+        if warnings:
+            self.node_warnings[node].extend(warnings)
+
+    def set_global_error(self, error: DirectoryError):
+        self.error = error
+
+    def has_errors(self) -> bool:
+        return len(self.node_errors) > 0 or self.error
+
+    def has_warnings(self) -> bool:
+        return len(self.node_warnings) > 0
+
+
+class MolgenisRequestError(Exception):
+    def __init__(self, error, response=False):
+        self.message = error
+        if response:
+            self.response = response
+
+
+def requests_error_handler(func):
+    """
+    Decorator that catches RequestExceptions and wraps them in a DirectoryError.
+    """
+
+    def inner_function(*args, **kwargs):
+        try:
+            return func(*args, **kwargs)
+        except (requests.exceptions.RequestException, MolgenisRequestError) as e:
+            raise DirectoryError("Request failed") from e
+
+    return inner_function
diff --git a/tools/directory/src/molgenis_emx2/directory_client/model.py b/tools/directory/src/molgenis_emx2/directory_client/model.py
new file mode 100644
index 0000000000..e250297123
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/model.py
@@ -0,0 +1,419 @@
+import os
+import typing
+from abc import ABC
+from collections import OrderedDict
+from copy import deepcopy
+from dataclasses import dataclass, field
+from enum import Enum
+from typing import Dict, List, Set
+
+from .utils import to_ordered_dict
+
+
+class TableType(Enum):
+    """Enum representing the six tables each national node has."""
+
+    PERSONS = "persons"
+    ALSO_KNOWN = "also_known_in"
+    NETWORKS = "networks"
+    BIOBANKS = "biobanks"
+    COLLECTIONS = "collections"
+    FACTS = "facts"
+
+    @classmethod
+    def get_import_order(cls) -> List["TableType"]:
+        return [type_ for type_ in cls]
+
+    @property
+    def base_id(self) -> str:
+        if self.value == "facts":
+            table = "collectionFacts"
+        elif self.value == "also_known_in":
+            table = "alsoKnownIn"
+        else:
+            table = self.value
+
+        return table[0].upper() + table[1:]
+
+
+@dataclass(frozen=True)
+class TableMeta:
+    """Convenient wrapper for the output of the metadata API."""
+
+    meta: dict
+    id_attribute: str = field(init=False)
+
+    def __post_init__(self):
+        for attribute in self.meta:
+            if attribute.get("key") == 1:
+                object.__setattr__(self, "id_attribute", attribute.name)
+
+    @property
+    def id(self):
+        return self.meta[0].get("table")
+
+    @property
+    def attributes(self):
+        return [attr.name for attr in self.meta]
+
+    @property
+    def one_to_manys(self) -> List[str]:
+        one_to_manys = []
+        for attribute in self.meta["attributes"]["items"]:
+            if attribute["data"]["type"] == "onetomany":
+                one_to_manys.append(attribute["data"]["name"])
+        return one_to_manys
+
+    @property
+    def hyperlinks(self) -> List[str]:
+        hyperlinks = []
+        for attribute in self.meta:
+            if attribute.get("columnType") == "hyperlink":
+                hyperlinks.append(attribute.name)
+        return hyperlinks
+
+
+@dataclass(frozen=True)
+class BaseTable(ABC):
+    """
+    Simple representation of a MOLGENIS table. The rows should be in the uploadable
+    format. (See utils.py)
+    """
+
+    rows_by_id: "typing.OrderedDict[str, dict]"
+    meta: TableMeta
+
+    @property
+    def rows(self) -> List[dict]:
+        return list(self.rows_by_id.values())
+
+    @property
+    def full_name(self) -> str:
+        return self.meta.id
+
+
+@dataclass(frozen=True)
+class Table(BaseTable):
+    """
+    Simple representation of a BBMRI ERIC node table.
+    """
+
+    type: TableType
+
+    @staticmethod
+    def of(table_type: TableType, meta: TableMeta, rows: List[dict]) -> "Table":
+        """Factory method that takes a list of rows instead of an OrderedDict of
+        ids/rows."""
+        return Table(
+            rows_by_id=to_ordered_dict(rows, meta.id_attribute),
+            meta=meta,
+            type=table_type,
+        )
+
+    @staticmethod
+    def of_empty(table_type: TableType, meta: TableMeta):
+        return Table(rows_by_id=OrderedDict(), meta=meta, type=table_type)
+
+    @staticmethod
+    def of_placeholder(table_type: TableType):
+        meta = {
+            "id": table_type.base_id,
+            "attributes": {"items": [{"data": {"name": "id", "idAttribute": True}}]},
+        }
+        return Table.of_empty(
+            table_type=table_type,
+            meta=TableMeta(meta=meta),
+        )
+
+
+@dataclass(frozen=True)
+class OntologyTable(BaseTable):
+    """
+    Simple representation of an ontology table where the parent/child relations are
+    persisted with self-references.
+    """
+
+    parent_attr: str
+    matching_attrs: List[str] | None = None
+
+    def get_matching_ontologies(self, ontologies: List[str]) -> Set[str]:
+        """
+        Will add matching ontologies with the specified level(s) of confidence to the
+        list of ontologies
+
+        :param ontologies: a list with the current ontologies
+        :return: a list with the current ontologies extended with matching ontologies,
+        if available.
+        """
+        matching_ontologies = []
+        for attr in self.matching_attrs:
+            for ontology in ontologies:
+                try:
+                    matching_ontologies.extend(self.rows_by_id[ontology][attr])
+                except KeyError:
+                    pass
+
+        return set(matching_ontologies)
+
+    def is_descendant_of_any(self, descendant_id: str, ancestor_ids: Set[str]) -> bool:
+        """
+        Will walk from the descendant up through the parents until it finds one of the
+        provided ancestors, or return False if it reaches an element without a parent.
+        Will also return True if the descendant_id itself is in de ancestor_ids.
+
+        :param descendant_id: the id of the descendant
+        :param ancestor_ids: the ids of the ancestors
+        :return: True if the descendant_id is a descendant of any of the ancestor_ids
+        """
+        current = self.rows_by_id[descendant_id]
+        while True and current["codesystem"] != "orphanet":
+            if current[self.meta.id_attribute] in ancestor_ids:
+                return True
+            if not current[self.parent_attr]:
+                return False
+            if len(current[self.parent_attr]) == 1:
+                current = self.rows_by_id[current[self.parent_attr][0]]
+            else:
+                raise TypeError("More than one ICD-10 parent")
+
+    @staticmethod
+    def of(
+        meta: TableMeta,
+        rows: List[dict],
+        parent_attr: str,
+        matching_attrs: List[str] | None = None,
+    ) -> "OntologyTable":
+        """Factory method that takes a list of rows instead of an OrderedDict of
+        ids/rows."""
+        matching_attrs = matching_attrs if matching_attrs else []
+        return OntologyTable(
+            rows_by_id=to_ordered_dict(rows, meta.id_attribute),
+            meta=meta,
+            parent_attr=parent_attr,
+            matching_attrs=matching_attrs,
+        )
+
+
+@dataclass(frozen=True)
+class Node:
+    """Represents a single national node in a BBMRI Biobank Directory."""
+
+    code: str
+    description: str | None = None
+    date_end: str | None = None
+
+    _classifiers = {
+        TableType.PERSONS: "contactID",
+        TableType.NETWORKS: "networkID",
+        TableType.ALSO_KNOWN: "akiID",
+        TableType.BIOBANKS: "ID",
+        TableType.COLLECTIONS: "ID",
+        TableType.FACTS: "factID",
+    }
+
+    def get_schema_id(self) -> str:
+        return f"{os.getenv('SCHEMA_PREFIX')}-{self.code}"
+
+    @staticmethod
+    def get_staging_id(table_type: TableType) -> str:
+        """
+        Returns the identifier of a node's staging table.
+
+        :param TableType table_type: the table to get the staging id of
+        :return: the id of the staging table
+        """
+        if table_type.value == "facts":
+            table = "collectionFacts"
+        elif table_type.value == "also_known_in":
+            table = "alsoKnownIn"
+        else:
+            table = table_type.value
+
+        return table[0].upper() + table[1:]
+
+    def get_id_prefix(self, table_type: TableType) -> str:
+        """
+        Each table has a specific prefix for the identifiers of its rows. This prefix is
+        based on the node's code and the classifier of the table.
+
+        :param TableType table_type: the table to get the id prefix for
+        :return: the id prefix
+        """
+        classifier = self._classifiers[table_type]
+        return f"bbmri-eric:{classifier}:{self.code}_"
+
+    @classmethod
+    def get_eu_id_prefix(cls, table_type: TableType) -> str:
+        """
+        Some nodes can refer to rows in the EU node. These rows have an EU prefix, and
+        it's based on the classifier of the table.
+
+        :param TableType table_type: the table to get the EU id prefix for
+        :return: the EU id prefix
+        """
+
+        classifier = cls._classifiers[table_type]
+        return f"bbmri-eric:{classifier}:EU_"
+
+    @staticmethod
+    def of(code: str):
+        return Node(code, None, None)
+
+    def __eq__(self, other: object) -> bool:
+        if isinstance(other, Node):
+            return self.code == other.code
+        return False
+
+    def __hash__(self):
+        return hash(self.code)
+
+
+@dataclass(frozen=True)
+class ExternalServerNode(Node):
+    """Represents a node that has an external server on which its data is hosted."""
+
+    url: str | None = None
+    token: str | None = None
+
+
+class Source(Enum):
+    EXTERNAL_SERVER = "external_server"
+    STAGING = "staging"
+    PUBLISHED = "published"
+    TRANSFORMED = "transformed"
+
+
+@dataclass
+class DirectoryData(ABC):
+    """Abstract base class for containers storing rows from the six Directory tables:
+    persons, networks, also_known_in, biobanks, collections and facts."""
+
+    source: Source
+    persons: Table
+    also_known_in: Table
+    networks: Table
+    biobanks: Table
+    collections: Table
+    facts: Table
+    table_by_type: Dict[TableType, Table] = field(init=False)
+
+    def __post_init__(self):
+        self.table_by_type = {
+            TableType.PERSONS: self.persons,
+            TableType.NETWORKS: self.networks,
+            TableType.ALSO_KNOWN: self.also_known_in,
+            TableType.BIOBANKS: self.biobanks,
+            TableType.COLLECTIONS: self.collections,
+            TableType.FACTS: self.facts,
+        }
+
+    @property
+    def import_order(self) -> List[Table]:
+        return [
+            self.persons,
+            self.networks,
+            self.also_known_in,
+            self.biobanks,
+            self.collections,
+            self.facts,
+        ]
+
+
+@dataclass
+class NodeData(DirectoryData):
+    """Container object storing the six tables of a single node."""
+
+    node: Node
+
+    @staticmethod
+    def from_dict(node: Node, source: Source, tables: Dict[str, Table]) -> "NodeData":
+        return NodeData(node=node, source=source, **tables)
+
+    def convert_to_staging(self) -> "NodeData":
+        """
+        The metadata of an external node is the same as the metadata of its staging
+        area. This method copies an external server's NodeData and changes only the
+        table identifiers to point to the staging area's identifiers.
+        """
+        if self.source != Source.EXTERNAL_SERVER:
+            raise ValueError("data isn't from an external server")
+
+        tables = dict()
+        for table in self.import_order:
+            metadata = deepcopy(table.meta.meta)
+            # metadata["id"] = self.node.get_staging_id(table.type)
+            tables[table.type.value] = Table(
+                table.rows_by_id, TableMeta(metadata), table.type
+            )
+
+        return NodeData(node=self.node, source=Source.STAGING, **tables)
+
+
+class MixedData(DirectoryData):
+    """Container object storing the six tables with mixed origins, for example from
+    the combined tables or from multiple staging areas."""
+
+    @staticmethod
+    def from_mixed_dict(source: Source, tables: Dict[str, Table]) -> "MixedData":
+        return MixedData(source=source, **tables)
+
+    def merge(self, other_data: DirectoryData):
+        self.persons.rows_by_id.update(other_data.persons.rows_by_id)
+        self.networks.rows_by_id.update(other_data.networks.rows_by_id)
+        self.also_known_in.rows_by_id.update(other_data.also_known_in.rows_by_id)
+        self.biobanks.rows_by_id.update(other_data.biobanks.rows_by_id)
+        self.collections.rows_by_id.update(other_data.collections.rows_by_id)
+        self.facts.rows_by_id.update(other_data.facts.rows_by_id)
+
+    def remove_node_rows(self, node: Node):
+        for table in self.import_order:
+            ids_to_remove = [
+                row["id"] for row in table.rows if row["national_node"] == node.code
+            ]
+            all(table.rows_by_id.pop(id_) for id_ in ids_to_remove)
+
+    def copy_empty(self) -> "MixedData":
+        return MixedData(
+            source=self.source,
+            persons=Table.of_empty(TableType.PERSONS, self.persons.meta),
+            networks=Table.of_empty(TableType.NETWORKS, self.networks.meta),
+            also_known_in=Table.of_empty(TableType.ALSO_KNOWN, self.also_known_in.meta),
+            biobanks=Table.of_empty(TableType.BIOBANKS, self.biobanks.meta),
+            collections=Table.of_empty(TableType.COLLECTIONS, self.collections.meta),
+            facts=Table.of_empty(TableType.FACTS, self.facts.meta),
+        )
+
+
+@dataclass(frozen=True)
+class QualityInfo:
+    """
+    Stores the quality information for biobanks and collections.
+    """
+
+    biobanks: Dict[str, List[str]]
+    """Dictionary of biobank ids and their quality ids"""
+
+    biobank_levels: Dict[str, List[str]]
+    """Dictionary of biobank ids and their assessment levels"""
+
+    collections: Dict[str, List[str]]
+    """Dictionary of collection ids and their quality ids"""
+
+    collection_levels: Dict[str, List[str]]
+    """Dictionary of collection ids and their assessment levels"""
+
+    def get_qualities(self, table_type: TableType) -> Dict[str, List[str]]:
+        if table_type == TableType.BIOBANKS:
+            return self.biobanks
+        elif table_type == TableType.COLLECTIONS:
+            return self.collections
+        else:
+            return dict()
+
+    def get_levels(self, table_type: TableType) -> Dict[str, List[str]]:
+        if table_type == TableType.BIOBANKS:
+            return self.biobank_levels
+        elif table_type == TableType.COLLECTIONS:
+            return self.collection_levels
+        else:
+            return dict()
diff --git a/tools/directory/src/molgenis_emx2/directory_client/model_fitting.py b/tools/directory/src/molgenis_emx2/directory_client/model_fitting.py
new file mode 100644
index 0000000000..2f594dae31
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/model_fitting.py
@@ -0,0 +1,168 @@
+from collections import OrderedDict
+
+from unidecode import unidecode
+
+from .errors import DirectoryWarning
+from .model import NodeData, Table, TableType
+from .printer import Printer
+from .utils import to_ordered_dict
+
+
+class ModelFitter:
+    """
+    Sometimes, model changes are implemented in the published Directory tables, but
+    can't be implemented yet in all staging areas because action
+    (adjustment of local databases, API calls, etc.) from the national nodes is needed.
+    This class contains temporary solutions to transform the staging areas data
+    according to the published model. If the models of all staging areas are equal to
+    the Directory model this class shouldn't contain any methods.
+    """
+
+    def __init__(
+        self,
+        node_data: NodeData,
+        printer: Printer,
+    ):
+        self.node_data = node_data
+        self.printer = printer
+
+        self.warnings = []
+
+    def fit_model(self):
+        """
+        Transforms the data of a node according to the published model:
+        1. Merges biobank 'covid19biobank' values into 'capabilities'
+        2. Moves biobank and collection head information to persons
+        """
+        self._merge_covid19_capabilities()
+        self._move_heads_to_persons()
+        return self.warnings
+
+    def _add_warning(self, message: str):
+        self.printer.print_warning(DirectoryWarning(message), indent=1)
+        self.warnings.append(message)
+
+    def _merge_covid19_capabilities(self):
+        """
+        Merges each biobank's 'covid19biobank' column into its 'capabilities' column and
+        then removes it.
+        """
+        self.printer.print("Merging 'covid19biobank' into 'capabilities'")
+
+        covid = "covid19biobank"
+        caps = "capabilities"
+        for biobank in self.node_data.biobanks.rows:
+            if covid in biobank and biobank[covid]:
+                self._add_warning(
+                    f"Biobank {biobank['id']} uses deprecated {covid}' "
+                    f"column. Use '{caps}' instead."
+                )
+
+                if not biobank[caps]:
+                    biobank[caps] = []
+
+                biobank[caps] = list(
+                    OrderedDict.fromkeys(biobank[caps] + biobank[covid])
+                )
+
+            biobank.pop(covid, None)
+
+    def _move_heads_to_persons(self):
+        """
+        Moves the head information in the biobank and collection tables to persons and
+        adds the person ID to the biobank and collection tables.
+        """
+        self.printer.print("Moving heads to persons")
+        self._move_heads_for_table(self.node_data.biobanks)
+        self._move_heads_for_table(self.node_data.collections)
+
+    def _move_heads_for_table(self, table: Table):
+        """
+        1. Checks if the head already exists as a person
+        2a. If not, creates a new person
+        2b. If so, updates person information (f.e. add the role)
+        3. Fills the 'head' column with person ID
+        4. Removes the redundant 'head' columns.
+        """
+        head_columns = [
+            "head_title_before_name",
+            "head_firstname",
+            "head_lastname",
+            "head_title_after_name",
+            "head_role",
+        ]
+
+        for row in table.rows:
+            if set(row.keys()).isdisjoint(set(head_columns)):
+                continue
+
+            if "head" in row.keys():
+                self._add_warning(
+                    f"{table.type.value.capitalize()[:-1]} has a head ID. "
+                    "But still includes deprecated 'head' columns."
+                )
+
+            else:
+                self._add_warning(
+                    f"{table.type.value.capitalize()[:-1]} {row['id']} uses "
+                    "deprecated 'head' columns. Move head info to persons instead."
+                )
+
+                # Add head id to the table
+                row["head"] = self._add_head(row, table)
+
+            for column in head_columns:
+                row.pop(column, None)
+
+    def _add_head(self, data, table):
+        if {"head_lastname", "head_firstname"}.issubset(set(data.keys())):
+            person_id = self._check_person(data)
+            if not person_id:
+                self._add_warning(
+                    f"Add {data['head_firstname']} {data['head_lastname']} to persons "
+                )
+                person_id = self._create_person(data)
+            return person_id
+
+        self._add_warning(
+            f"{table.type.value.capitalize()[:-1]} {data['id']} has head"
+            " info without first and/or last name"
+        )
+
+        return None
+
+    def _check_person(self, data):
+        # A head exists if the combination of first- and last name exists in persons
+        for person in self.node_data.persons.rows:
+            if (
+                person.get("last_name", "NN").lower().replace(" ", "")
+                == data["head_lastname"].lower().replace(" ", "")
+                and person.get("first_name", "NN").lower().strip()
+                == data["head_firstname"].lower().strip()
+            ):
+                if "role" in person and person["role"] and data.get("head_role"):
+                    roles = person["role"].split(" and ")
+                    roles.append(data.get("head_role").strip())
+                    person["role"] = " and ".join(set(roles))
+                else:
+                    person["role"] = data.get("head_role")
+                return person["id"]
+
+        return None
+
+    def _create_person(self, data):
+        prefix = self.node_data.node.get_id_prefix(TableType.PERSONS)
+        person = dict()
+        person["id"] = prefix + data.get("head_lastname").lower().replace(" ", "")
+        person["id"] = unidecode(person["id"])
+        person["title_before_name"] = data.get("head_title_before_name")
+        person["first_name"] = data.get("head_firstname")
+        person["last_name"] = data.get("head_lastname")
+        person["title_after_name"] = data.get("head_title_after_name")
+        person["role"] = data.get("head_role")
+        person["email"] = "UNKNOWN@" + self.node_data.node.code
+        person["country"] = data.get("country")
+        person["national_node"] = self.node_data.node.code
+        self.node_data.persons.rows_by_id.update(to_ordered_dict([person], "id"))
+
+        return person["id"]
diff --git a/tools/directory/src/molgenis_emx2/directory_client/pid_manager.py b/tools/directory/src/molgenis_emx2/directory_client/pid_manager.py
new file mode 100644
index 0000000000..fa73d2c43b
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/pid_manager.py
@@ -0,0 +1,143 @@
+from abc import ABC, abstractmethod
+from typing import List
+
+from .errors import DirectoryWarning
+from .model import Table
+from .pid_service import BasePidService, NoOpPidService, Status
+from .printer import Printer
+
+
+class BasePidManager(ABC):
+    @abstractmethod
+    def assign_biobank_pids(self, biobanks: Table) -> List[DirectoryWarning]:
+        pass
+
+    @abstractmethod
+    def update_biobank_pids(self, biobanks: Table, existing_biobanks: Table):
+        pass
+
+    @abstractmethod
+    def terminate_biobanks(self, biobank_pids: List[str]):
+        pass
+
+
+class PidManager(BasePidManager):
+    """
+    This class is responsible for managing PIDs of BBMRI Biobank Directory entities:
+    assignment, updates and status changes are done here.
+    """
+
+    def __init__(self, pid_service: BasePidService, printer: Printer):
+        self.pid_service = pid_service
+        self.printer = printer
+        self.biobank_url_prefix = pid_service.base_url + "#/biobank/"
+
+    def assign_biobank_pids(self, biobanks: Table) -> List[DirectoryWarning]:
+        """
+        Registers and assigns a new PID for biobanks that have an empty "pid" attribute.
+        Make sure to enrich the table with existing PIDs before using this method.
+        """
+        warnings = []
+        for biobank in biobanks.rows:
+            if "pid" not in biobank:
+                biobank["pid"] = self._register_biobank_pid(
+                    biobank["id"], biobank["name"], warnings
+                )
+                if biobank.get("withdrawn", False):
+                    self.pid_service.set_status(biobank["pid"], Status.WITHDRAWN)
+                    self.printer.print(
+                        f"Set STATUS of {biobank['pid']} to {Status.WITHDRAWN.value}"
+                    )
+
+        return warnings
+
+    def update_biobank_pids(self, biobanks: Table, existing_biobanks: Table):
+        """
+        Detects changes in biobanks and updates their PIDs accordingly.
+        """
+        existing_biobanks = existing_biobanks.rows_by_id
+        for biobank in biobanks.rows:
+            id_ = biobank["id"]
+            if id_ in existing_biobanks:
+                if biobank["name"] != existing_biobanks.get(biobank["id"])["name"]:
+                    self._update_biobank_name(biobank["pid"], biobank["name"])
+                if (
+                    biobank.get("withdrawn", False)
+                    != existing_biobanks.get(biobank["id"])["withdrawn"]
+                ):
+                    self._update_withdrawn_status(biobank["pid"], biobank["withdrawn"])
+
+    def terminate_biobanks(self, biobank_pids: List[str]):
+        """
+        Sets the STATUS of a PID into TERMINATED.
+        """
+        for biobank_pid in biobank_pids:
+            self.pid_service.set_status(biobank_pid, Status.TERMINATED)
+            self.printer.print(
+                f"Set STATUS of {biobank_pid} to {Status.TERMINATED.value}"
+            )
+
+    def _register_biobank_pid(
+        self, biobank_id: str, biobank_name: str, warnings: List[DirectoryWarning]
+    ) -> str:
+        """
+        Registers a PID for a new biobank. If one or more PIDs for this biobank already
+        exist, warnings will be shown.
+        """
+        url = self.biobank_url_prefix + biobank_id
+        existing_pids = self.pid_service.reverse_lookup(url)
+
+        if existing_pids:
+            pid = existing_pids[0]
+            warning = DirectoryWarning(
+                f'PID(s) already exist for new biobank "{biobank_name}": '
+                f"{str(existing_pids)}. Please check the PID's contents!"
+            )
+            self.printer.print_warning(warning)
+            warnings.append(warning)
+        else:
+            pid = self.pid_service.register_pid(url=url, name=biobank_name)
+            self.printer.print(f'Registered {pid} for new biobank "{biobank_name}"')
+
+        return pid
+
+    def _update_biobank_name(self, pid: str, name: str):
+        self.pid_service.set_name(pid, name)
+        self.printer.print(f'Updated NAME of {pid} to "{name}"')
+
+    def _update_withdrawn_status(self, pid: str, withdrawn: bool):
+        if withdrawn:
+            self.pid_service.set_status(pid, Status.WITHDRAWN)
+            self.printer.print(f"Set STATUS of {pid} to {Status.WITHDRAWN.value}")
+        if not withdrawn:
+            self.pid_service.remove_status(pid)
+            self.printer.print(f"Remove WITHDRAWN STATUS of {pid}")
+
+
+class NoOpPidManager(BasePidManager):
+    """
+    This implementation does nothing. It's used to turn off all PID features.
+    """
+
+    def assign_biobank_pids(self, biobanks: Table) -> List[DirectoryWarning]:
+        return []
+
+    def update_biobank_pids(self, biobanks: Table, existing_biobanks: Table):
+        pass
+
+    def terminate_biobanks(self, biobank_pids: List[str]):
+        pass
+
+
+class PidManagerFactory:
+    """
+    Returns an implementation of BasePidManager based on the BasePidService that is
+    provided.
+    """
+
+    @staticmethod
+    def create(pid_service: BasePidService, printer: Printer) -> BasePidManager:
+        if type(pid_service) is NoOpPidService:
+            return NoOpPidManager()
+        else:
+            return PidManager(pid_service, printer)
diff --git a/tools/directory/src/molgenis_emx2/directory_client/pid_service.py b/tools/directory/src/molgenis_emx2/directory_client/pid_service.py
new file mode 100644
index 0000000000..48b0323ffb
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/pid_service.py
@@ -0,0 +1,228 @@
+import secrets
+from abc import ABCMeta, abstractmethod
+from enum import Enum
+from typing import List, Optional
+from urllib.parse import quote
+
+from pyhandle.client.resthandleclient import RESTHandleClient
+from pyhandle.clientcredentials import PIDClientCredentials
+from pyhandle.handleclient import PyHandleClient
+from pyhandle.handleexceptions import (
+    HandleAuthenticationError,
+    HandleNotFoundException,
+    HandleSyntaxError,
+)
+
+from .errors import DirectoryError
+
+
+class Status(Enum):
+    TERMINATED = "TERMINATED"
+    MERGED = "MERGED"
+    WITHDRAWN = "Withdrawn from the BBMRI-ERIC Directory"
+
+
+def pyhandle_error_handler(func):
+    """
+    Decorator that catches PyHandleExceptions and wraps them in a DirectoryError.
+    """
+
+    def inner_function(*args, **kwargs):
+        try:
+            return func(*args, **kwargs)
+        except HandleAuthenticationError as e:
+            raise DirectoryError("Handle authentication failed") from e
+        except HandleNotFoundException as e:
+            raise DirectoryError(f"Handle not found on handle server: {e.handle}")
+        except HandleSyntaxError as e:
+            raise DirectoryError(f"Handle has incorrect syntax: {e.handle}")
+
+    return inner_function
+
+
+class BasePidService(metaclass=ABCMeta):
+    service_prefix = "1."
+
+    base_url: str
+
+    @abstractmethod
+    def reverse_lookup(self, url: str) -> Optional[List[str]]:
+        pass
+
+    @abstractmethod
+    def register_pid(self, url: str, name: str) -> str:
+        pass
+
+    @abstractmethod
+    def set_name(self, pid: str, new_name: str):
+        pass
+
+    @abstractmethod
+    def set_status(self, pid: str, status: Status):
+        pass
+
+    @abstractmethod
+    def remove_status(self, pid: str):
+        pass
+
+    @staticmethod
+    def generate_pid(prefix: str) -> str:
+        """
+        Generates a new PID. Uses a cryptographically secure random, 12 digit
+        hexadecimal number separated by hyphens every 4 digits (example: 6ed7-328b-2793)
+        Has been tested to have <1 collisions every 10 million ids. PIDs of the
+        Directory are also prefixed with "1.".
+        """
+        id_ = secrets.token_hex(6)
+        return f"{prefix}/{BasePidService.service_prefix}{id_[:4]}-{id_[4:8]}-{id_[8:]}"
+
+
+class PidService(BasePidService):
+    """
+    Low level service for interacting with the handle server.
+    """
+
+    def __init__(self, client: RESTHandleClient, prefix: str, base_url: str):
+        self.client = client
+        self.prefix = prefix
+        self.base_url = base_url.rstrip("/") + "/"
+
+    @staticmethod
+    def from_credentials(credentials_json: str, base_url: str = None) -> "PidService":
+        """
+        Factory method to create a PidService from a credentials JSON file. The
+        credentials file should have the following contents:
+
+        {
+          "handle_server_url": "...",
+          "private_key": "...",
+          "certificate_only": "...",
+          "client": "rest",
+          "prefix": "...",
+          "reverselookup_username": "...",
+          "reverselookup_password": "...",
+          "server_url": "..." <- optional
+        }
+
+        :param base_url: the base URL to which the PIDs will link
+        :param credentials_json: a full path to the credentials file
+        :return: a PidService
+        """
+        credentials = PIDClientCredentials.load_from_JSON(credentials_json)
+
+        if not base_url:
+            try:
+                base_url = credentials.get_config()["server_url"]
+            except KeyError:
+                raise ValueError("server_url missing in credentials file")
+
+        return PidService(
+            PyHandleClient("rest").instantiate_with_credentials(credentials),
+            credentials.get_prefix(),
+            base_url,
+        )
+
+    @pyhandle_error_handler
+    def reverse_lookup(self, url: str) -> Optional[List[str]]:
+        """
+        Looks for handles with this url.
+
+        :param url: the URL to look up
+        :raise: EricError if insufficient permissions for reverse lookup
+        :return: a (potentially empty) list of PIDs
+        """
+        url = quote(url)
+        pids = self.client.search_handle(URL=url, prefix=self.prefix)
+
+        if pids is None:
+            raise DirectoryError("Insufficient permissions for reverse lookup")
+
+        return pids
+
+    @pyhandle_error_handler
+    def register_pid(self, url: str, name: str) -> str:
+        """
+        Generates a new PID and registers it with a URL and a NAME field.
+
+        :param url: the URL for the handle
+        :param name: the NAME for the handle
+        :return: the generated PID
+        """
+        pid = self.generate_pid(self.prefix)
+        return self.client.register_handle(handle=pid, location=url, NAME=name)
+
+    @pyhandle_error_handler
+    def set_name(self, pid: str, new_name: str):
+        """
+        Sets the NAME field of an existing PID. Adds the field if it doesn't exist.
+
+        :param pid: the PID to change the NAME of
+        :param new_name: the new value for the NAME field
+        """
+        self.client.modify_handle_value(pid, NAME=new_name)
+
+    @pyhandle_error_handler
+    def set_status(self, pid: str, status: Status):
+        """
+        Sets the STATUS field of an existing PID. Adds the field if it doesn't exist.
+
+        :param pid: the PID to change the STATUS of
+        :param status: a Status enum
+        """
+        self.client.modify_handle_value(pid, STATUS=status.value)
+
+    @pyhandle_error_handler
+    def remove_status(self, pid: str):
+        """
+        Removes the STATUS field of an existing PID.
+
+        :param pid: the PID to remove the STATUS field of
+        """
+        self.client.delete_handle_value(pid, "STATUS")
+
+
+class DummyPidService(BasePidService):
+    """
+    This dummy implementation can be used to test publishing without actually
+    interacting with a Handle server. It will create fake PIDs.
+    """
+
+    def __init__(self):
+        self.base_url = "FAKE-SERVER/"
+
+    def reverse_lookup(self, url: str) -> Optional[List[str]]:
+        pass
+
+    def register_pid(self, url: str, name: str) -> str:
+        return self.generate_pid("FAKE-PREFIX")
+
+    def set_name(self, pid: str, new_name: str):
+        pass
+
+    def set_status(self, pid: str, status: Status):
+        pass
+
+    def remove_status(self, pid: str):
+        pass
+
+
+class NoOpPidService(BasePidService):
+    """
+    The NoOpPidService does completely nothing. It can be used as a feature toggle:
+    using this implementation will turn off all PID features.
+    """
+
+    def reverse_lookup(self, url: str) -> Optional[List[str]]:
+        pass
+
+    def register_pid(self, url: str, name: str) -> str:
+        pass
+
+    def set_name(self, pid: str, new_name: str):
+        pass
+
+    def set_status(self, pid: str, status: Status):
+        pass
+
+    def remove_status(self, pid: str):
+        pass
diff --git a/tools/directory/src/molgenis_emx2/directory_client/printer.py b/tools/directory/src/molgenis_emx2/directory_client/printer.py
new file mode 100644
index 0000000000..99e3d36ea4
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/printer.py
@@ -0,0 +1,79 @@
+from contextlib import contextmanager
+
+from .errors import DirectoryError, DirectoryWarning, ErrorReport
+from .model import Node
+
+
+class Printer:
+    """
+    Simple printer that keeps track of indentation levels. Also has utility methods
+    for printing some Directory objects.
+    """
+
+    def __init__(self):
+        self.indents = 0
+
+    def indent(self):
+        self.indents += 1
+
+    def dedent(self):
+        self.indents = max(0, self.indents - 1)
+
+    def reset_indent(self):
+        self.indents = 0
+
+    def print(self, value: str = None, indent: int = 0):
+        self.indents += indent
+        if value:
+            print(f"{'    ' * self.indents}{value}")
+        else:
+            print()
+        self.indents -= indent
+
+    def print_node_title(self, node: Node):
+        self.print_header(f"🌍 Node {node.code} ({node.description})")
+
+    def print_header(self, text: str):
+        title = f"{text}"
+        border = "=" * (len(title) + 1)
+        self.reset_indent()
+        self.print()
+        self.print(border)
+        self.print(title)
+        self.print(border)
+
+    def print_error(self, error: DirectoryError):
+        message = str(error)
+        if error.__cause__:
+            message += f" - Cause: {str(error.__cause__)}"
+        self.print(f"❌ {message}")
+
+    def print_warning(self, warning: DirectoryWarning, indent: int = 0):
+        self.print(f"⚠️ {warning.message}", indent)
+
+    def print_summary(self, report: ErrorReport):
+        self.reset_indent()
+        self.print()
+        self.print("==========")
+        self.print("📋 Summary")
+        self.print("==========")
+
+        for node in report.nodes:
+            if node in report.node_errors or report.error:
+                message = f"❌ Node {node.code} failed"
+                if node in report.node_warnings:
+                    message += f" with {len(report.node_warnings[node])} warning(s)"
+            elif node in report.node_warnings:
+                message = (
+                    f"⚠️ Node {node.code} finished successfully with "
+                    f"{len(report.node_warnings[node])} warning(s)"
+                )
+            else:
+                message = f"✅ Node {node.code} finished successfully"
+            self.print(message)
+
+    @contextmanager
+    def indentation(self):
+        self.indent()
+        yield
+        self.dedent()
diff --git a/tools/directory/src/molgenis_emx2/directory_client/publication_preparer.py b/tools/directory/src/molgenis_emx2/directory_client/publication_preparer.py
new file mode 100644
index 0000000000..2b040d58aa
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/publication_preparer.py
@@ -0,0 +1,74 @@
+from .directory_client import DirectorySession
+from .errors import ErrorReport, requests_error_handler
+from .model import Node, NodeData
+from .model_fitting import ModelFitter
+from .pid_manager import BasePidManager
+from .printer import Printer
+from .publisher import PublishingState
+from .transformer import Transformer
+from .validation import Validator
+
+
+class PublicationPreparer:
+    """Prepares nodes for publishing."""
+
+    def __init__(
+        self, printer: Printer, pid_manager: BasePidManager, session: DirectorySession
+    ):
+        self.printer = printer
+        self.pid_manager = pid_manager
+        self.session = session
+
+    @requests_error_handler
+    def prepare(self, node: Node, state: PublishingState) -> NodeData:
+        node_data = self._get_node_data(node)
+        self._validate_node(node_data, state.report)
+        self._fit_node_model(node_data, state.report)
+        self._transform_node(node_data, state)
+        self._manage_node_pids(node_data, state)
+        return node_data
+
+    def _validate_node(self, node_data: NodeData, report: ErrorReport):
+        self.printer.print(f"🔎 Validating staged data of node {node_data.node.code}")
+        with self.printer.indentation():
+            warnings = Validator(node_data, self.printer).validate()
+            if warnings:
+                report.add_node_warnings(node_data.node, warnings)
+
+    def _fit_node_model(self, node_data: NodeData, report: ErrorReport):
+        self.printer.print(
+            f"⟺ Align staged data of node {node_data.node.code} "
+            f"with the published model"
+        )
+        with self.printer.indentation():
+            warnings = ModelFitter(node_data, self.printer).fit_model()
+            if warnings:
+                report.add_node_warnings(node_data.node, warnings)
+
+    def _transform_node(self, node_data: NodeData, state: PublishingState):
+        self.printer.print("✏️ Preparing staged data for publishing")
+        with self.printer.indentation():
+            warnings = Transformer(
+                node_data=node_data,
+                quality=state.quality_info,
+                printer=self.printer,
+                existing_biobanks=state.existing_data.biobanks,
+                eu_node_data=state.eu_node_data,
+                diseases=state.diseases,
+            ).transform()
+            if warnings:
+                state.report.add_node_warnings(node_data.node, warnings)
+
+    def _manage_node_pids(self, node_data: NodeData, state: PublishingState):
+        self.printer.print("🆔 Managing PIDs")
+        with self.printer.indentation():
+            warnings = self.pid_manager.assign_biobank_pids(node_data.biobanks)
+            self.pid_manager.update_biobank_pids(
+                node_data.biobanks, state.existing_data.biobanks
+            )
+            if warnings:
+                state.report.add_node_warnings(node_data.node, warnings)
+
+    def _get_node_data(self, node: Node) -> NodeData:
+        self.printer.print(f"📦 Retrieving staged data of node {node.code}")
+        return self.session.get_staging_node_data(node)
diff --git a/tools/directory/src/molgenis_emx2/directory_client/publisher.py b/tools/directory/src/molgenis_emx2/directory_client/publisher.py
new file mode 100644
index 0000000000..91bef813a2
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/publisher.py
@@ -0,0 +1,134 @@
+from dataclasses import dataclass, field
+from typing import List
+
+from .directory_client import DirectorySession
+from .errors import DirectoryError, DirectoryWarning, ErrorReport, MolgenisRequestError
+from .model import (
+    MixedData,
+    Node,
+    NodeData,
+    OntologyTable,
+    QualityInfo,
+    Source,
+    Table,
+    TableType,
+)
+from .pid_manager import BasePidManager
+from .printer import Printer
+
+
+@dataclass
+class PublishingState:
+    existing_data: MixedData
+    eu_node_data: NodeData
+    quality_info: QualityInfo
+    nodes: List[Node]
+    report: ErrorReport
+    diseases: OntologyTable
+    data_to_publish: MixedData = field(init=False)
+
+    def __post_init__(self):
+        self.data_to_publish = self.existing_data.copy_empty()
+        self.data_to_publish.source = Source.TRANSFORMED
+
+
+class Publisher:
+    """
+    This class is responsible for copying data from the staging areas to the combined
+    public tables.
+    """
+
+    def __init__(
+        self,
+        session: DirectorySession,
+        printer: Printer,
+        pid_manager: BasePidManager,
+    ):
+        self.session = session
+        self.printer = printer
+        self.pid_manager = pid_manager
+
+    async def publish(self, state: PublishingState):
+        """
+        Copies staging data to the combined tables. This happens in two phases:
+        1. New/existing rows are upserted in the Directory tables
+        2. Removed rows are deleted from the Directory tables
+        """
+        self.printer.print("💾 Saving new and updated data to Directory tables")
+        with self.printer.indentation():
+            await self._upsert_data(state)
+
+        self.printer.print("🧼 Cleaning up removed data in Directory tables")
+        with self.printer.indentation():
+            self._delete_data(state)
+
+    async def _upsert_data(self, state):
+        try:
+            await self.session.upload_data(
+                schema=self.session.directory_schema, data=state.data_to_publish
+            )
+        except MolgenisRequestError as e:
+            raise DirectoryError("Error importing data to combined tables") from e
+
+    def _delete_data(self, state):
+        for table in reversed(state.data_to_publish.import_order):
+            try:
+                with self.printer.indentation():
+                    self._delete_rows(
+                        table, state.existing_data.table_by_type[table.type], state
+                    )
+            except MolgenisRequestError as e:
+                raise DirectoryError(
+                    f"Error deleting rows from {table.type.base_id}"
+                ) from e
+
+    def _delete_rows(self, table: Table, existing_table: Table, state: PublishingState):
+        """
+        Deletes rows from a combined table that are not present in the staging area's
+        table. If a row is referenced from the quality info tables, it is not deleted
+        but a warning will be raised.
+
+        :param Table table: the staging area's table
+        :param Table existing_table: the existing rows
+        """
+        # Compare the ids from staging and production to see what was deleted
+        staging_ids = table.rows_by_id.keys()
+        production_ids = set(existing_table.rows_by_id.keys())
+        deleted_ids = production_ids.difference(staging_ids)
+
+        # Remove ids that we are not allowed to delete
+        undeletable_ids = state.quality_info.get_qualities(table.type).keys()
+        deletable_ids = deleted_ids.difference(undeletable_ids)
+
+        # For deleted biobanks, update the handle
+        if table.type == TableType.BIOBANKS:
+            self.pid_manager.terminate_biobanks(
+                [existing_table.rows_by_id[id_].get("pid") for id_ in deletable_ids]
+            )
+
+        # Actually delete the rows in the combined table
+        if deletable_ids:
+            ids_dict = [{table.meta.id_attribute: id_} for id_ in deletable_ids]
+            self.printer.print(
+                f"Deleting {len(deletable_ids)} row(s) in {table.type.base_id}"
+            )
+            self.session.delete_records(table=table.type.base_id, data=ids_dict)
+            for id_ in deletable_ids:
+                with self.printer.indentation():
+                    code = existing_table.rows_by_id[id_]["national_node"]
+                    warning = DirectoryWarning(f"ID {id_} is deleted")
+                    self.printer.print_warning(warning)
+                    state.report.add_node_warnings(Node.of(code), [warning])
+
+        # Show warning for every id that we prevented deletion of
+        if deleted_ids != deletable_ids:
+            for id_ in undeletable_ids:
+                if id_ in deleted_ids:
+                    warning = DirectoryWarning(
+                        f"Prevented the deletion of a row that is referenced from "
+                        f"the quality info: {table.type.value} {id_}."
+                    )
+                    self.printer.print_warning(warning)
+
+                    code = existing_table.rows_by_id[id_]["national_node"]
+                    state.report.add_node_warnings(Node.of(code), [warning])
diff --git a/tools/directory/src/molgenis_emx2/directory_client/stager.py b/tools/directory/src/molgenis_emx2/directory_client/stager.py
new file mode 100644
index 0000000000..4009268a5b
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/stager.py
@@ -0,0 +1,110 @@
+from typing import List
+
+from .directory_client import (
+    DirectorySession,
+    ExternalServerSession,
+    NoSuchTableException,
+)
+from .errors import DirectoryError, DirectoryWarning, requests_error_handler
+from .model import ExternalServerNode, NodeData, TableType
+from .printer import Printer
+
+
+class Stager:
+    """
+    This class is responsible for copying data from a node with an external server to
+    its staging area in the BBMRI Biobank Directory.
+    """
+
+    def __init__(self, session: DirectorySession, printer: Printer):
+        self.session = session
+        self.printer = printer
+
+        self.warnings: List[DirectoryWarning] = list()
+
+    @requests_error_handler
+    async def stage(self, node: ExternalServerNode):
+        """
+        Stages all data from the provided external node in the Directory.
+        """
+        self.warnings = []
+        source_data = self._get_source_data(node)
+        self._clear_staging_area(node)
+        await self._import_node(source_data)
+
+        return self.warnings
+
+    def _get_source_data(self, node: ExternalServerNode) -> NodeData:
+        """
+        Gets a node's data from an external server.
+        First check if:
+        - the session has the right permissions
+        - and if all tables are available
+        """
+        self.printer.print(f"📦 Retrieving node's data from {node.url}")
+        source_session = ExternalServerSession(node=node)
+        self._check_permissions(source_session)
+        self._check_tables(source_session)
+        return source_session.get_node_data()
+
+    @staticmethod
+    def _check_permissions(session: ExternalServerSession):
+        """
+        Check if the session has the necessary permissions
+        """
+        # In stead of this method try except around source_session with schema parameter
+        schemas = [schema.name for schema in session.schemas]
+        if session.node.get_schema_id() not in schemas:
+            raise DirectoryError(
+                "The session user has invalid permissions\n       Please check the "
+                "token and permissions of this user"
+            )
+
+    def _check_tables(self, session: ExternalServerSession):
+        """
+        Check if all tables are available on the external server
+        """
+        schema_meta = session.get_schema_metadata(session.node.get_schema_id())
+        for table_type in TableType.get_import_order():
+            id_ = session.node.get_staging_id(table_type)
+            try:
+                schema_meta.get_table(by="name", value=id_)
+            except NoSuchTableException:
+                warning = DirectoryWarning(
+                    f"Node {session.node.code} has no {table_type.value} table"
+                )
+                self.printer.print_warning(warning, indent=1)
+                self.warnings.append(warning)
+
+    def _clear_staging_area(self, node: ExternalServerNode):
+        """
+        Deletes all data in the staging area of an external node.
+        """
+        self.printer.print(f"🔥 Clearing staging area of {node.code}")
+        for table_type in reversed(TableType.get_import_order()):
+            # If truncate table is available this workaround can be removed
+            df_data = self.session.get(
+                schema=node.get_schema_id(),
+                table=node.get_staging_id(table_type),
+                as_df=True,
+            )
+            if len(df_data) > 0:
+                ids = df_data["id"].to_frame().to_dict("records")
+                self.session.delete_records(
+                    schema=node.get_schema_id(),
+                    table=node.get_staging_id(table_type),
+                    data=ids,
+                )
+
+    async def _import_node(self, source_data: NodeData):
+        """
+        Imports an external node's data to its staging area.
+        """
+        self.printer.print(
+            f"💾 Saving data to the staging area of {source_data.node.code}"
+        )
+
+        await self.session.upload_data(
+            schema=source_data.node.get_schema_id(),
+            data=source_data.convert_to_staging(),
+        )
diff --git a/tools/directory/src/molgenis_emx2/directory_client/transformer.py b/tools/directory/src/molgenis_emx2/directory_client/transformer.py
new file mode 100644
index 0000000000..c4398affa9
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/transformer.py
@@ -0,0 +1,204 @@
+from datetime import date
+
+from .categories import CategoryMapper
+from .errors import DirectoryWarning
+from .model import Node, NodeData, OntologyTable, QualityInfo, Table
+from .printer import Printer
+
+
+class Transformer:
+    """
+    The published Directory tables have a few extra attributes that the staging tables
+    do not have. This class is responsible for adding those attributes so the staging
+    tables can be published correctly.
+    """
+
+    def __init__(
+        self,
+        node_data: NodeData,
+        quality: QualityInfo,
+        printer: Printer,
+        existing_biobanks: Table,
+        eu_node_data: NodeData,
+        diseases: OntologyTable,
+    ):
+        self.node_data = node_data
+        self.quality = quality
+        self.printer = printer
+        self.existing_biobanks = existing_biobanks.rows_by_id
+        self.eu_node_data = eu_node_data
+        self.category_mapper = CategoryMapper(diseases)
+
+        self.warnings = []
+
+    def transform(self):
+        """
+        Transforms the data of a node:
+        1. Adds the national node code to all rows
+        2. Sets the withdrawn column to True for all rows of a withdrawn national nodes
+        3. Replaces a node's EU rows with the data from node EU's staging area
+        4. Sets the commercial use boolean in collections
+        5. Sets the quality info field for biobanks and collections
+        6. Adds PIDs to biobanks
+        7. Add biobank labels (biobank name) to collections
+        8. Adds the combined networks' ids to collections
+        9. Adds the combined qualities to collections
+        10. Sets the collections' categories
+
+        """
+        self._set_national_node_code()
+        self._set_withdrawn()
+        self._replace_eu_rows()
+        self._set_commercial_use_bool()
+        self._set_quality_info()
+        self._set_biobank_pids()
+        self._set_biobank_labels()
+        self._set_combined_networks()
+        self._set_combined_qualities()
+        self._set_collection_categories()
+        return self.warnings
+
+    def _set_commercial_use_bool(self):
+        """
+        Takes the data of a Node and sets the commercial_use boolean of all collections
+        based on a set of criteria.
+        """
+
+        self.printer.print("Setting 'commercial_use' booleans")
+        for collection in self.node_data.collections.rows:
+
+            def is_true(row: dict, attr: str):
+                # if the value is not entered, it is also considered true
+                return attr not in row or row[attr] is True
+
+            biobank_id = collection["biobank"]
+            biobank = self.node_data.biobanks.rows_by_id[biobank_id]
+
+            collection["commercial_use"] = is_true(
+                biobank, "collaboration_commercial"
+            ) and is_true(collection, "collaboration_commercial")
+
+    def _set_national_node_code(self):
+        """
+        Adds the national node code to each row of every table of a node.
+        """
+        self.printer.print("Adding national node codes")
+        for table in self.node_data.import_order:
+            for row in table.rows:
+                row["national_node"] = self.node_data.node.code
+
+    def _set_quality_info(self):
+        """
+        Adds the one_to_many "quality" field to the biobank and collection tables based
+        on the quality info tables.
+        """
+        self.printer.print("Adding quality information")
+        self._set_quality_for_table(self.node_data.biobanks)
+        self._set_quality_for_table(self.node_data.collections)
+
+    def _set_quality_for_table(self, table: Table):
+        for row in table.rows:
+            qualities = self.quality.get_qualities(table.type)
+            quality_ids = qualities.get(row["id"], [])
+            if quality_ids:
+                row["quality"] = quality_ids
+
+    def _set_biobank_pids(self):
+        """
+        Adds the PIDs for existing biobanks.
+        """
+        self.printer.print("Adding existing PIDs to biobanks")
+        for biobank in self.node_data.biobanks.rows:
+            biobank_id = biobank["id"]
+            if biobank_id in self.existing_biobanks:
+                existing_biobank = self.existing_biobanks[biobank_id]
+                if "pid" in existing_biobank:
+                    biobank["pid"] = existing_biobank["pid"]
+
+    def _replace_eu_rows(self):
+        """
+        Replaces a node's EU networks and persons with data from the EU staging node.
+        """
+        node_data = self.node_data
+        node = node_data.node
+        if node.code == "EU":
+            return
+
+        self.printer.print("Replacing EU networks and persons")
+        self._replace_rows(node, node_data.persons, self.eu_node_data.persons)
+        self._replace_rows(node, node_data.networks, self.eu_node_data.networks)
+
+    def _replace_rows(self, node: Node, table: Table, eu_table: Table):
+        eu_prefix = node.get_eu_id_prefix(table.type)
+        for network in table.rows:
+            id_ = network["id"]
+            if id_.startswith(eu_prefix):
+                if id_ in eu_table.rows_by_id:
+                    table.rows_by_id[id_] = eu_table.rows_by_id[id_]
+
+                    # overwrite EU code that was added in previous enrichment step
+                    table.rows_by_id[id_]["national_node"] = self.eu_node_data.node.code
+                else:
+                    warning = DirectoryWarning(
+                        f"{id_} is not present in {eu_table.type.base_id}"
+                    )
+                    self.printer.print_warning(warning, indent=1)
+                    self.warnings.append(warning)
+
+    def _set_biobank_labels(self):
+        """
+        For every collection of the Node, adds the `biobank_label` field, with the
+        name of its biobank
+        """
+        self.printer.print("Adding biobank labels")
+        for collection in self.node_data.collections.rows:
+            biobank = self.node_data.biobanks.rows_by_id[collection["biobank"]]
+            collection["biobank_label"] = biobank["name"]
+
+    def _set_combined_networks(self):
+        """
+        For every collection of the Node, adds to the `combined_network` field, the
+        union of the networks of the collection itself and the ones of its biobank.
+        """
+        self.printer.print("Adding combined networks")
+        for collection in self.node_data.collections.rows:
+            biobank = self.node_data.biobanks.rows_by_id[collection["biobank"]]
+            collection["combined_network"] = list(
+                set(biobank["network"] + collection["network"])
+            )
+
+    def _set_combined_qualities(self):
+        """
+        For every collection of the Node, adds to the `combined_quality` field, the
+        union of the qualities of the collection itself and the ones of its biobank.
+        """
+        self.printer.print("Adding combined qualities")
+
+        bb_levels = self.quality.get_levels(self.node_data.biobanks.type)
+        coll_levels = self.quality.get_levels(self.node_data.collections.type)
+        for collection in self.node_data.collections.rows:
+            biobank = self.node_data.biobanks.rows_by_id[collection["biobank"]]
+            bb_level = bb_levels.get(biobank["id"], [])
+            coll_level = coll_levels.get(collection["id"], [])
+            collection["combined_quality"] = list(set(bb_level + coll_level))
+
+    def _set_collection_categories(self):
+        """
+        Sets the 'categories' field of each collection based on the collection values.
+        """
+        self.printer.print("Setting collection categories")
+        for collection in self.node_data.collections.rows:
+            collection["categories"] = self.category_mapper.map(collection)
+
+    def _set_withdrawn(self):
+        """
+        Adds withdrawn is True to each row of every table of a node that is withdrawn
+        """
+        self.printer.print("Marking withdrawn national nodes")
+        for table in self.node_data.import_order:
+            if (
+                self.node_data.node.date_end
+                and self.node_data.node.date_end <= date.today().strftime("%Y-%m-%d")
+            ):
+                for row in table.rows:
+                    row["withdrawn"] = True
diff --git a/tools/directory/src/molgenis_emx2/directory_client/utils.py b/tools/directory/src/molgenis_emx2/directory_client/utils.py
new file mode 100644
index 0000000000..0eade0ef4c
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/utils.py
@@ -0,0 +1,23 @@
+import csv
+from collections import OrderedDict
+from typing import List
+
+
+def to_ordered_dict(rows: List[dict], id_attribute: str) -> OrderedDict:
+    rows_by_id = OrderedDict()
+    for row in rows:
+        rows_by_id[row[id_attribute]] = row
+    return rows_by_id
+
+
+def create_csv(table: List[dict], file_name: str, meta_attributes: List[str]):
+    with open(file_name, "w", encoding="utf-8") as fp:
+        writer = csv.DictWriter(
+            fp, fieldnames=meta_attributes, quoting=csv.QUOTE_ALL, extrasaction="ignore"
+        )
+        writer.writeheader()
+        for row in table:
+            for key, value in row.items():
+                if isinstance(value, list):
+                    row[key] = ",".join(value)
+            writer.writerow(row)
diff --git a/tools/directory/src/molgenis_emx2/directory_client/validation.py b/tools/directory/src/molgenis_emx2/directory_client/validation.py
new file mode 100644
index 0000000000..e5e91a899a
--- /dev/null
+++ b/tools/directory/src/molgenis_emx2/directory_client/validation.py
@@ -0,0 +1,145 @@
+import re
+from typing import List, Set
+
+from .errors import DirectoryWarning
+from .model import NodeData, Table, TableType
+from .printer import Printer
+
+
+class Validator:
+    """
+    This class is responsible for validating the data in a single node. Validation
+    consists of:
+    1. Checking the validity of all identifiers
+    2. Checking if there are rows that reference rows with invalid identifiers
+    3. Checking the validity of ages
+    4. Checking the validity of hyperlinks
+    """
+
+    ALLOWS_EU_PREFIXES = {TableType.PERSONS, TableType.NETWORKS}
+    HYPERLINK_REGEX = (
+        r"^((https?):\/\/)(www.)?[-a-zA-Z0-9@:%._\\+~#?&//=]{2,256}\."
+        r"[a-z]{2,6}\b([-a-zA-Z0-9@:%._\\+~#?&//=]*)\/?$|^$/"
+    )
+
+    def __init__(self, node_data: NodeData, printer: Printer):
+        self.printer = printer
+        self.node_data = node_data
+        self.invalid_ids: Set[str] = set()
+        self.warnings: List[DirectoryWarning] = list()
+
+    def validate(self) -> List[DirectoryWarning]:
+        for table in self.node_data.import_order:
+            self._validate_ids(table)
+            self._validate_hyperlinks(table)
+
+        self._validate_networks()
+        self._validate_biobanks()
+        self._validate_collections()
+
+        return self.warnings
+
+    def _validate_ids(self, table: Table):
+        for row in table.rows:
+            id_ = row["id"]
+            self._validate_id_prefix(id_, table)
+            self._validate_id_chars(id_, table)
+
+    def _validate_hyperlinks(self, table: Table):
+        for row in table.rows:
+            for column in list(set(table.meta.hyperlinks).intersection(row.keys())):
+                if not re.match(self.HYPERLINK_REGEX, row[column]):
+                    self._warn(
+                        f"{table.type.value.capitalize()[:-1]} {row['id']} "
+                        f"has an invalid {column}: {row[column]}"
+                    )
+
+    def _validate_networks(self):
+        for network in self.node_data.networks.rows:
+            self._validate_xref(network, "contact")
+            self._validate_mref(network, "parent_network")
+
+    def _validate_biobanks(self):
+        for biobank in self.node_data.biobanks.rows:
+            self._validate_xref(biobank, "contact")
+            self._validate_mref(biobank, "network")
+            self._validate_mref(biobank, "also_known_in")
+
+    def _validate_collections(self):
+        for collection in self.node_data.collections.rows:
+            self._validate_xref(collection, "contact")
+            self._validate_xref(collection, "biobank")
+            self._validate_xref(collection, "parent_collection")
+            self._validate_mref(collection, "networks")
+            self._validate_mref(collection, "also_known_in")
+            self._validate_ages(
+                collection,
+            )
+
+    def _validate_ages(self, collection: dict):
+        low = collection.get("age_low", None)
+        high = collection.get("age_high", None)
+        unit = collection.get("age_unit", None)
+
+        if low == 0 and high == 0:
+            self._warn(
+                f"Collection {collection['id']} has invalid ages: age_low = 0 and "
+                f"age_high = 0"
+            )
+
+        if (low is not None or high is not None) and not unit:
+            self._warn(
+                f"Collection {collection['id']} has age_low/age_high without age_unit"
+            )
+
+        if low is not None and high is not None and (low > high):
+            self._warn(
+                f"Collection {collection['id']} has invalid ages: age_low > age_high"
+            )
+
+    def _validate_xref(self, row: dict, ref_attr: str):
+        if ref_attr in row:
+            self._validate_ref(row, row[ref_attr])
+
+    def _validate_mref(self, row: dict, mref_attr: str):
+        if mref_attr in row:
+            for ref_id in row[mref_attr]:
+                self._validate_ref(row, ref_id)
+
+    def _validate_ref(self, row: dict, ref_id: str):
+        if ref_id in self.invalid_ids:
+            warning = DirectoryWarning(f"{row['id']} references invalid id: {ref_id}")
+            self.printer.print_warning(warning)
+            self.warnings.append(warning)
+
+    def _validate_id_prefix(self, id_: str, table: Table):
+        node = self.node_data.node
+
+        prefix = node.get_id_prefix(table.type)
+        if table.type in self.ALLOWS_EU_PREFIXES:
+            eu_prefix = node.get_eu_id_prefix(table.type)
+            if not id_.startswith((prefix, eu_prefix)):
+                self._warn(
+                    f"{id_} in entity: {table.full_name} does not start with {prefix} "
+                    f"or {eu_prefix}"
+                )
+                self.invalid_ids.add(id_)
+        else:
+            if not id_.startswith(prefix):
+                self._warn(
+                    f"{id_} in entity: {table.full_name} does not start with {prefix}"
+                )
+                self.invalid_ids.add(id_)
+
+    def _validate_id_chars(self, id_: str, table: Table):
+        if not re.search("^[A-Za-z0-9-_:]+$", id_):
+            self._warn(
+                f"{id_} in entity: {table.full_name} contains"
+                f" invalid characters. Only alphanumerics and -_: are allowed."
+            )
+            self.invalid_ids.add(id_)
+
+    def _warn(self, message: str):
+        warning = DirectoryWarning(message)
+        self.printer.print_warning(warning)
+        self.warnings.append(warning)
diff --git a/tools/directory/tests/__init__.py b/tools/directory/tests/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/tools/directory/tests/conftest.py b/tools/directory/tests/conftest.py
new file mode 100644
index 0000000000..9730e53d64
--- /dev/null
+++ b/tools/directory/tests/conftest.py
@@ -0,0 +1,129 @@
+import json
+import os
+from importlib import resources
+from typing import List
+from unittest.mock import AsyncMock, MagicMock
+
+import pytest
+
+from molgenis_emx2.directory_client.model import (
+    Node,
+    NodeData,
+    Source,
+    Table,
+    TableType,
+)
+
+
+def get_data(table_type) -> List[dict]:
+    file_name = table_type + ".json"
+    file = open(str(resources.files("tests.resources") / file_name), "r")
+
+    data = json.load(file)
+    file.close()
+    return data
+
+
+@pytest.fixture
+def node_data() -> NodeData:
+    """
+    Reads json files with the six data sources and
+    returns NodeData to test with.
+    """
+    persons_meta = MagicMock()
+    persons_meta.id = "eu_bbmri_eric_NL_persons"
+    persons_meta.id_attribute = "id"
+    persons = Table.of(
+        TableType.PERSONS,
+        persons_meta,
+        get_data("persons"),
+    )
+
+    networks_meta = MagicMock()
+    networks_meta.id = "eu_bbmri_eric_NL_networks"
+    networks_meta.id_attribute = "id"
+    networks = Table.of(
+        TableType.NETWORKS,
+        networks_meta,
+        get_data("networks"),
+    )
+
+    also_known_meta = MagicMock()
+    also_known_meta.id = "eu_bbmri_eric_NL_also_known_in"
+    also_known_meta.id_attribute = "id"
+    also_known = Table.of(
+        TableType.ALSO_KNOWN,
+        also_known_meta,
+        get_data("also_known"),
+    )
+
+    biobanks_meta = MagicMock()
+    biobanks_meta.id = "eu_bbmri_eric_NL_biobanks"
+    biobanks_meta.id_attribute = "id"
+    biobanks_meta.hyperlinks = ["url"]
+    biobanks = Table.of(
+        TableType.BIOBANKS,
+        biobanks_meta,
+        get_data("biobanks"),
+    )
+
+    collection_meta = MagicMock()
+    collection_meta.id = "eu_bbmri_eric_NL_collections"
+    collection_meta.id_attribute = "id"
+    collections = Table.of(
+        TableType.COLLECTIONS,
+        collection_meta,
+        get_data("collections"),
+    )
+
+    facts_meta = MagicMock()
+    facts_meta.id = "eu_bbmri_eric_NL_facts"
+    facts_meta.id_attribute = "id"
+    facts = Table.of(
+        TableType.FACTS,
+        facts_meta,
+        get_data("facts"),
+    )
+
+    return NodeData.from_dict(
+        Node("NL", "NL"),
+        Source.STAGING,
+        {
+            TableType.PERSONS.value: persons,
+            TableType.NETWORKS.value: networks,
+            TableType.ALSO_KNOWN.value: also_known,
+            TableType.BIOBANKS.value: biobanks,
+            TableType.COLLECTIONS.value: collections,
+            TableType.FACTS.value: facts,
+        },
+    )
+
+
+@pytest.fixture
+def async_session() -> AsyncMock:
+    session = AsyncMock()
+    session.url = "url"
+    session.directory_schema = "BBMRI-ERIC"
+    return session
+
+
+@pytest.fixture
+def session() -> MagicMock:
+    session = MagicMock()
+    session.url = "url"
+    return session
+
+
+@pytest.fixture
+def printer() -> MagicMock:
+    return MagicMock()
+
+
+@pytest.fixture
+def pid_service() -> MagicMock:
+    service = MagicMock()
+    service.base_url = "url/"
+    return service
+
+
+os.environ["SCHEMA_PREFIX"] = "BBMRI"
diff --git a/tools/directory/tests/resources/__init__.py b/tools/directory/tests/resources/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/tools/directory/tests/resources/also_known.json b/tools/directory/tests/resources/also_known.json
new file mode 100644
index 0000000000..aef60b5fb9
--- /dev/null
+++ b/tools/directory/tests/resources/also_known.json
@@ -0,0 +1,14 @@
+[
+  {
+    "id": "bbmri-eric:akiID:BE_invalid_node_code",
+    "name_system": "eucan-connect",
+    "pid": "A-eucan-connect",
+    "url": "https:/eucan-connect.eu/A"
+  },
+  {
+    "id": "bbmri-eric:akiID:NL_001",
+    "name_system": "eucan-connect",
+    "pid": "001-eucan-connect",
+    "url": "https:/eucan-connect.eu/001"
+  }
+]
diff --git a/tools/directory/tests/resources/biobanks.json b/tools/directory/tests/resources/biobanks.json
new file mode 100644
index 0000000000..02e97df73e
--- /dev/null
+++ b/tools/directory/tests/resources/biobanks.json
@@ -0,0 +1,43 @@
+[
+  {
+    "id": "bbmri-eric:ID:NL_valid-biobankID-1",
+    "contact": "bbmri-eric:contactID:NL_valid-personID-1",
+    "also_known_in": ["bbmri-eric:akiID:BE_invalid_node_code"],
+    "head_firstname": "Jan",
+    "head_lastname": "Janssen",
+    "head_role": "Director",
+    "country": "NL",
+    "url": "https://valid_url.nl"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_valid:biobankID-2",
+    "contact": "bbmri-eric:ID:NL_invalid_person_classifier",
+    "network": ["bbmri-eric:networkID:NL_valid-networkID-1"],
+    "head_title_before_name": "Dr",
+    "head_firstname": "Piet",
+    "head_lastname": "Geluk",
+    "head_role": "Principal Investigator",
+    "country": "NL",
+    "url": "www.invalid@url.nl"
+  },
+  {"id": "bbmri-eric:test:NL_invalid_biobank_classifier"},
+  {
+    "id": "bbmri-eric:ID:BE_invalid_node_code",
+    "network": [
+      "bbmri-eric:network:NL_valid-networkID-1",
+      "bbmri-eric:ID:NL_invalid_network_classifier"
+    ]
+  },
+  {
+    "id": "bbmri-eric:ID:NL_test_quality_biobank1"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_test_quality_biobank2"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_test_quality_biobank3"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_biobank_noQual"
+  }
+]
diff --git a/tools/directory/tests/resources/collections.json b/tools/directory/tests/resources/collections.json
new file mode 100644
index 0000000000..fae91f6523
--- /dev/null
+++ b/tools/directory/tests/resources/collections.json
@@ -0,0 +1,64 @@
+[
+  {
+    "id": "bbmri-eric:ID:NL_valid-collectionID-1",
+    "contact": "bbmri-eric:contactID:NL_valid-personID-1",
+    "biobank": "bbmri-eric:ID:NL_valid-biobankID-1",
+    "also_known_in": ["bbmri-eric:akiID:BE_invalid_node_code"],
+    "head_firstname": "Jan",
+    "head_lastname": "Janssen",
+    "head_role": "Director",
+    "country": "NL"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_valid:collectionID-2",
+    "contact": "bbmri-eric:ID:NL_invalid_person_classifier",
+    "networks": ["bbmri-eric:network:NL_valid-networkID-1"],
+    "biobank": "bbmri-eric:test:NL_invalid_biobank_classifier",
+    "parent_collection": "bbmri-eric:collection:NL_invalid_collection_classifier",
+    "title_before_name": "Dr",
+    "head_firstname": "Piet",
+    "head_lastname": "Geluk",
+    "head_role": "Collection head",
+    "country": "NL"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_valid:collectionID-3",
+    "biobank": "bbmri-eric:ID:NL_valid:biobankID-2",
+    "head_title_before_name": "Prof",
+    "head_firstname": "Bart",
+    "head_lastname": "de Vries",
+    "head_role": "Principal Investigator",
+    "head_title_after_name": "Msc",
+    "country": "NL"
+  },
+  {
+    "id": "bbmri-eric:collection:NL_invalid_collection_classifier",
+    "biobank": "bbmri-eric:ID:NL_valid-biobankID-1"
+  },
+  {
+    "id": "bbmri-eric:ID:BE_invalid_node_code:collectionID",
+    "biobank": "bbmri-eric:ID:NL_valid-biobankID-1",
+    "networks": [
+      "bbmri-eric:network:NL_valid-networkID-1",
+      "bbmri-eric:ID:NL_invalid_network_classifier"
+    ],
+    "parent_collection": "bbmri-eric:ID:NL_valid-collectionID-1"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_bb1:collection:test_quality1",
+    "biobank": "bbmri-eric:ID:NL_biobank_noQual"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_bb1:collection:test_quality2",
+    "biobank": "bbmri-eric:ID:NL_test_quality_biobank2"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_bb3:collection:test_quality3",
+    "biobank": "bbmri-eric:ID:NL_test_quality_biobank3"
+  },
+  {
+    "id": "bbmri-eric:ID:NL_bb1:collection:test_noQual",
+    "biobank": "bbmri-eric:ID:NL_test_quality_biobank1"
+
+  }
+]
diff --git a/tools/directory/tests/resources/facts.json b/tools/directory/tests/resources/facts.json
new file mode 100644
index 0000000000..2ff3225476
--- /dev/null
+++ b/tools/directory/tests/resources/facts.json
@@ -0,0 +1,11 @@
+[
+  {
+    "id": "bbmri-eric:factID:NL_valid-factID",
+    "collection": "bbmri-eric:ID:NL_valid-collectionID-1"
+  },
+  {
+    "id": "bbmri-eric:NL_invalid:factsID",
+    "collection": "bbmri-eric:ID:NL_valid:collectionID-2"
+  }
+
+]
diff --git a/tools/directory/tests/resources/networks.json b/tools/directory/tests/resources/networks.json
new file mode 100644
index 0000000000..62d9db1da0
--- /dev/null
+++ b/tools/directory/tests/resources/networks.json
@@ -0,0 +1,19 @@
+[
+  {
+    "id": "bbmri-eric:networkID:NL_valid-networkID-1",
+    "contact": "bbmri-eric:contactID:NL_valid-personID-1"
+  },
+  {
+    "id": "bbmri-eric:networkID:NL_valid:networkID-2",
+    "contact": "bbmri-eric:ID:NL_invalid_person_classifier",
+    "parent_network": ["bbmri-eric:network:NL_valid-networkID-1"]
+  },
+  {"id": "bbmri-eric:ID:NL_invalid_network_classifier"},
+  {
+    "id": "bbmri-eric:networkID:BE_invalid_node_code",
+    "parent_network": [
+      "bbmri-eric:network:NL_valid-networkID-1",
+      "bbmri-eric:ID:NL_invalid_network_classifier"
+    ]
+  }
+]
diff --git a/tools/directory/tests/resources/persons.json b/tools/directory/tests/resources/persons.json
new file mode 100644
index 0000000000..430e6c45fe
--- /dev/null
+++ b/tools/directory/tests/resources/persons.json
@@ -0,0 +1,14 @@
+[{
+  "id": "bbmri-eric:contactID:NL_valid-personID-1",
+  "title_before_name": "Dr",
+  "first_name": "Jan",
+  "last_name": "Janssen",
+  "title_after_name": "MSc",
+  "email": "jan.janssen@test.nl",
+  "country": "NL"
+},
+  {"id": "bbmri-eric:contactID:NL_valid:personID-2"},
+  {"id": "bbmri-eric:ID:NL_invalid_person_classifier"},
+  {"id": "bbmri-eric:contactID:EU_invalid_node_code"},
+  {"id": "bbmri-eric:contactID:NL_invalid_illegal_characters#$&"}
+]
diff --git a/tools/directory/tests/test_categories.py b/tools/directory/tests/test_categories.py
new file mode 100644
index 0000000000..08e897d507
--- /dev/null
+++ b/tools/directory/tests/test_categories.py
@@ -0,0 +1,193 @@
+from typing import List
+from unittest.mock import MagicMock
+
+import pytest
+
+from molgenis_emx2.directory_client.categories import Category, CategoryMapper
+from molgenis_emx2.directory_client.model import OntologyTable
+
+
+@pytest.fixture
+def mapper():
+    return CategoryMapper(MagicMock())
+
+
+@pytest.fixture
+def disease_ontology() -> OntologyTable:
+    meta = MagicMock()
+    meta.id_attribute = "id"
+    return OntologyTable.of(
+        meta,
+        [
+            {"id": "urn:miriam:icd:T18.5", "parent": [], "codesystem": "ICD-10"},
+            {"id": "urn:miriam:icd:II", "parent": [], "codesystem": "ICD-10"},
+            {
+                "id": "urn:miriam:icd:C97",
+                "parent": ["urn:miriam:icd:II"],
+                "codesystem": "ICD-10",
+                "exact_mapping": ["ORPHA:93969"],
+            },
+            {"id": "urn:miriam:icd:U09", "parent": [], "codesystem": "ICD-10"},
+            {
+                "id": "urn:miriam:icd:U09.9",
+                "parent": ["urn:miriam:icd:U09"],
+                "codesystem": "ICD-10",
+                "ntbt_mapping": ["ORPHA:93969"],
+            },
+            {
+                "id": "urn:miriam:icd:D69.6",
+                "parent": ["urn:miriam:icd:D69"],
+                "codesystem": "ICD-10",
+            },
+            {
+                "id": "urn:miriam:icd:D69",
+                "parent": ["urn:miriam:icd:D65-D69"],
+                "codesystem": "ICD-10",
+            },
+            {
+                "id": "urn:miriam:icd:I05-I09",
+                "parent": ["urn:miriam:icd:IX"],
+                "codesystem": "ICD-10",
+            },
+            {"id": "urn:miriam:icd:IX", "parent": [], "codesystem": "ICD-10"},
+            {"id": "urn:miriam:icd:U07.1", "parent": [], "codesystem": "ICD-10"},
+            {
+                "id": "urn:miriam:icd:I05",
+                "parent": ["urn:miriam:icd:I05-I09"],
+                "codesystem": "ICD-10",
+            },
+            {"id": "urn:miriam:icd:D65-D69", "parent": [], "codesystem": "ICD-10"},
+            {
+                "id": "urn:miriam:icd:E43",
+                "parent": ["urn:miriam:icd:E40-E46"],
+                "codesystem": "ICD-10",
+            },
+            {"id": "urn:miriam:icd:E40-E46", "parent": [], "codesystem": "ICD-10"},
+            {
+                "id": "urn:miriam:icd:G32",
+                "parent": ["urn:miriam:icd:G30-G32"],
+                "codesystem": "ICD-10",
+            },
+            {
+                "id": "urn:miriam:icd:G30-G32",
+                "parent": ["urn:miriam:icd:VI"],
+                "codesystem": "ICD-10",
+            },
+            {"id": "urn:miriam:icd:VI", "parent": [], "codesystem": "ICD-10"},
+            {
+                "id": "urn:miriam:icd:Z00.5",
+                "parent": ["urn:miriam:icd:Z00"],
+                "codesystem": "ICD-10",
+            },
+            {"id": "urn:miriam:icd:Z00", "parent": [], "codesystem": "ICD-10"},
+            {"id": "ORPHA:93969", "parent": [], "codesystem": "orphanet"},
+        ],
+        "parent",
+        ["exact_mapping", "ntbt_mapping"],
+    )
+
+
+@pytest.mark.parametrize(
+    "collection,expected",
+    [
+        (dict(), []),
+        ({"age_unit": "WEEK"}, []),
+        ({"age_high": 8}, []),
+        ({"age_high": 8, "age_unit": "YEAR"}, [Category.PAEDIATRICS.value]),
+        ({"age_high": 365 * 18 + 1, "age_unit": "DAY"}, []),
+        ({"age_high": 365 * 18 - 1, "age_unit": "DAY"}, [Category.PAEDIATRICS.value]),
+        ({"age_high": 52 * 18 + 1, "age_unit": "WEEK"}, []),
+        ({"age_high": 52 * 18 - 1, "age_unit": "WEEK"}, [Category.PAEDIATRICS.value]),
+        ({"age_high": 12 * 18 + 1, "age_unit": "MONTH"}, []),
+        ({"age_high": 12 * 18 - 1, "age_unit": "MONTH"}, [Category.PAEDIATRICS.value]),
+        ({"age_low": 0, "age_high": 0, "age_unit": "YEAR"}, []),
+        ({"age_low": 10, "age_high": 1, "age_unit": "YEAR"}, []),
+        (
+            {"age_low": 0, "age_high": 20, "age_unit": "YEAR"},
+            [Category.PAEDIATRICS.value],
+        ),
+        ({"age_low": 18, "age_high": 40, "age_unit": "YEAR"}, []),
+    ],
+)
+def test_map_paediatric(mapper, collection: dict, expected: List[str]):
+    categories = []
+    mapper._map_paediatric(collection, categories)
+    assert categories == expected
+
+
+@pytest.mark.parametrize(
+    "collection,expected",
+    [
+        (dict(), []),
+        ({"diagnosis_available": ["urn:miriam:icd:T18.5"]}, []),
+        ({"diagnosis_available": ["ORPHA:93969"]}, [Category.RARE_DISEASE.value]),
+        (
+            {"diagnosis_available": ["urn:miriam:icd:C97"]},
+            [Category.ONCOLOGY.value, Category.RARE_DISEASE.value],
+        ),
+        (
+            {"diagnosis_available": ["urn:miriam:icd:U09.9"]},
+            [
+                Category.COVID19.value,
+                Category.INFECTIOUS.value,
+                Category.RARE_DISEASE.value,
+            ],
+        ),
+        (
+            {
+                "diagnosis_available": [
+                    "urn:miriam:icd:U09",
+                    "urn:miriam:icd:T18.5",
+                    "ORPHA:93969",
+                ]
+            },
+            [
+                Category.COVID19.value,
+                Category.INFECTIOUS.value,
+                Category.RARE_DISEASE.value,
+            ],
+        ),
+        (
+            {"diagnosis_available": ["urn:miriam:icd:D69.6"]},
+            [Category.AUTOIMMUNE.value],
+        ),
+        (
+            {"diagnosis_available": ["urn:miriam:icd:I05"]},
+            [Category.CARDIOVASCULAR.value],
+        ),
+        (
+            {"diagnosis_available": ["urn:miriam:icd:U07.1"]},
+            [Category.COVID19.value, Category.INFECTIOUS.value],
+        ),
+        ({"diagnosis_available": ["urn:miriam:icd:E43"]}, [Category.METABOLIC.value]),
+        (
+            {"diagnosis_available": ["urn:miriam:icd:G32"]},
+            [Category.NERVOUS_SYSTEM.value],
+        ),
+        (
+            {"diagnosis_available": ["urn:miriam:icd:Z00.5"]},
+            [Category.POPULATION.value],
+        ),
+    ],
+)
+def test_map_diseases(mapper, disease_ontology, collection: dict, expected: List[str]):
+    mapper.diseases = disease_ontology
+    categories = []
+    mapper._map_diseases(collection, categories)
+    assert categories == expected
+
+
+@pytest.mark.parametrize(
+    "collection,expected",
+    [
+        (dict(), []),
+        ({"type": ["DISEASE_SPECIFIC"]}, []),
+        ({"type": ["RD"]}, [Category.RARE_DISEASE.value]),
+        ({"type": ["BIRTH_COHORT"]}, [Category.PAEDIATRICS.value]),
+        ({"type": ["CASE_CONTROL", "POPULATION_BASED"]}, [Category.POPULATION.value]),
+    ],
+)
+def test_map_collection_types(mapper, collection: dict, expected: List[str]):
+    categories = []
+    mapper._map_collection_types(collection, categories)
+    assert categories == expected
diff --git a/tools/directory/tests/test_directory.py b/tools/directory/tests/test_directory.py
new file mode 100644
index 0000000000..f3e5668939
--- /dev/null
+++ b/tools/directory/tests/test_directory.py
@@ -0,0 +1,123 @@
+from typing import List
+from unittest.mock import AsyncMock, MagicMock, call, patch
+
+import pytest
+
+from molgenis_emx2.directory_client.directory import Directory
+from molgenis_emx2.directory_client.errors import DirectoryError, ErrorReport
+from molgenis_emx2.directory_client.model import ExternalServerNode, Node
+from molgenis_emx2.directory_client.publisher import PublishingState
+
+pytest_plugins = ("pytest_asyncio",)
+
+
+@pytest.fixture
+def report_init():
+    with patch("molgenis_emx2.directory_client.directory.ErrorReport") as report_mock:
+        yield report_mock
+
+
+@pytest.fixture
+def eric(async_session, printer, pid_service) -> Directory:
+    eric = Directory(async_session, pid_service)
+    eric.printer = printer
+    eric.stager = AsyncMock()
+    eric.preparator = MagicMock()
+    eric.pid_manager = MagicMock()
+    eric.publisher = AsyncMock()
+    return eric
+
+
+@pytest.mark.asyncio
+async def test_stage_external_nodes(eric):
+    error = DirectoryError("error")
+    eric.stager.stage.side_effect = [None, error]
+    nl = ExternalServerNode("NL", "will succeed", None, "url.nl")
+    be = ExternalServerNode("BE", "will fail", None, "url.be")
+
+    report = await eric.stage_external_nodes([nl, be])
+
+    assert eric.printer.print_node_title.mock_calls == [call(nl), call(be)]
+    assert eric.stager.stage.mock_calls == [call(nl), call(be)]
+    assert nl not in report.node_errors
+    assert report.node_errors[be] == error
+    eric.printer.print_summary.assert_called_once_with(report)
+
+
+@pytest.mark.asyncio
+async def test_publish_node_staging_fails(eric, async_session, report_init):
+    nl = ExternalServerNode("NL", "Netherlands", None, "url")
+    state = _setup_state([nl], eric, report_init)
+
+    error = DirectoryError("error")
+    eric.stager.stage.side_effect = error
+
+    report = await eric.publish_nodes([nl])
+
+    eric.printer.print_node_title.assert_called_once_with(nl)
+    eric.stager.stage.assert_called_with(nl)
+    assert not async_session.get_published_node_data.called
+    assert not eric.preparator.prepare.called
+    assert await eric.publisher.publish.called_with(state)
+    assert len(state.data_to_publish.biobanks.rows_by_id) == 0
+    assert report.node_errors[nl] == error
+    eric.printer.print_summary.assert_called_once_with(report)
+
+
+@pytest.mark.asyncio
+async def test_publish_node_prepare_fails(eric, report_init):
+    nl = ExternalServerNode("NL", "Netherlands", None, "url")
+    state = _setup_state([nl], eric, report_init)
+
+    error = DirectoryError("error")
+    eric.preparator.prepare.side_effect = error
+
+    report = await eric.publish_nodes([nl])
+
+    eric.printer.print_node_title.assert_called_once_with(nl)
+    eric.stager.stage.assert_called_with(nl)
+    assert await eric.publisher.publish.called_with(state)
+    assert report.node_errors[nl] == error
+    eric.printer.print_summary.assert_called_once_with(report)
+
+
+@pytest.mark.asyncio
+async def test_publish_nodes(eric, report_init):
+    no = Node("NO", "succeeds", None)
+    nl = ExternalServerNode("NL", "fails during publishing", None, "url")
+    state = _setup_state([no, nl], eric, report_init)
+
+    error = DirectoryError("error")
+    eric.publisher.publish.side_effect = error
+    eric.stager.stage.return_value = []
+
+    report = await eric.publish_nodes([no, nl])
+
+    assert eric.printer.print_node_title.mock_calls == [call(no), call(nl)]
+    eric.stager.stage.assert_has_calls([call(nl)])
+    eric.preparator.prepare.assert_has_calls(
+        [call(no, state), call(nl, state)], any_order=True
+    )
+    eric.publisher.publish.assert_called_with(state)
+    assert len(report.node_errors) == 0
+    assert report.error == error
+    assert len(report.node_warnings[nl]) == 0
+    eric.printer.print_summary.assert_called_once_with(report)
+
+
+# noinspection PyProtectedMember
+def _setup_state(nodes: List[Node], eric: Directory, report_init):
+    report = ErrorReport(nodes)
+    report_init.return_value = report
+
+    state = PublishingState(
+        existing_data=MagicMock(),
+        eu_node_data=MagicMock(),
+        quality_info=MagicMock(),
+        nodes=nodes,
+        report=report,
+        diseases=MagicMock(),
+    )
+    eric._init_state = MagicMock()
+    eric._init_state.return_value = state
+    return state
diff --git a/tools/directory/tests/test_errors.py b/tools/directory/tests/test_errors.py
new file mode 100644
index 0000000000..fe43c07387
--- /dev/null
+++ b/tools/directory/tests/test_errors.py
@@ -0,0 +1,97 @@
+import pytest
+import requests.exceptions
+
+from molgenis_emx2.directory_client.errors import (
+    DirectoryError,
+    DirectoryWarning,
+    ErrorReport,
+    requests_error_handler,
+)
+from molgenis_emx2.directory_client.model import Node
+
+
+def test_warning():
+    warning = DirectoryWarning("test")
+    assert warning.message == "test"
+
+
+def test_error():
+    error = DirectoryError("test")
+    assert str(error) == "test"
+
+
+def test_error_report():
+    a = Node("A", "A", None)
+    b = Node("B", "B", None)
+    report = ErrorReport([a, b])
+    warning = DirectoryWarning("warning")
+    error = DirectoryError("error")
+
+    assert not report.has_errors()
+    assert not report.has_warnings()
+
+    report.add_node_error(a, error)
+
+    assert report.node_errors[a] == error
+    assert b not in report.node_errors
+    assert report.has_errors()
+    assert not report.has_warnings()
+
+    report.add_node_warnings(b, [warning, warning])
+
+    assert report.node_warnings[b] == [warning, warning]
+    assert a not in report.node_warnings
+    assert report.has_errors()
+    assert report.has_warnings()
+
+
+def test_error_report_global_error():
+    report = ErrorReport([])
+    assert not report.has_errors()
+    report.set_global_error(DirectoryError())
+    assert report.has_errors()
+
+
+def test_requests_error_handler():
+    exception = requests.exceptions.ConnectionError()
+
+    @requests_error_handler
+    def raising_function():
+        raise exception
+
+    with pytest.raises(DirectoryError) as exception_info:
+        raising_function()
+
+    assert exception_info.value.__cause__ == exception
+
+
+# def test_molgenisrequesterror(session):
+#     def get_table_meta(self, table_name: str,  schema: str = None, ):
+#         schema_meta = self.get_schema_metadata(schema)
+#         for table in schema_meta.tables:
+#             if table.name == table_name:
+#                 return table.columns
+#         raise MolgenisRequestError(f"Unknown table: {table_name}")
+#
+#
+#     with pytest.raises(DirectoryError) as e:
+#         await stager.stage(node)
+#
+#     assert str(e.value) == (
+#         "The session user has invalid permissions\n       "
+#         "Please check the token and permissions of this user"
+#     )
+
+#
+#
+#
+# exception = requests.exceptions.ConnectionError()
+#
+# @requests_error_handler
+# def raising_function():
+#     raise exception
+#
+# with pytest.raises(MolgenisRequestError) as exception_info:
+#    raise MolgenisRequestError("error")
+#
+# assert exception_info.value.__cause__ == exception
diff --git a/tools/directory/tests/test_model.py b/tools/directory/tests/test_model.py
new file mode 100644
index 0000000000..4e4ea52692
--- /dev/null
+++ b/tools/directory/tests/test_model.py
@@ -0,0 +1,115 @@
+# noinspection PyProtectedMember
+from unittest.mock import MagicMock
+
+from molgenis_emx2.directory_client.model import (
+    ExternalServerNode,
+    Node,
+    NodeData,
+    Source,
+    Table,
+    TableType,
+)
+
+
+def test_table_type_order():
+    assert TableType.get_import_order() == [
+        TableType.PERSONS,
+        TableType.ALSO_KNOWN,
+        TableType.NETWORKS,
+        TableType.BIOBANKS,
+        TableType.COLLECTIONS,
+        TableType.FACTS,
+    ]
+
+
+def test_table_type_base_ids():
+    assert TableType.PERSONS.base_id == "Persons"
+    assert TableType.ALSO_KNOWN.base_id == "AlsoKnownIn"
+    assert TableType.NETWORKS.base_id == "Networks"
+    assert TableType.BIOBANKS.base_id == "Biobanks"
+    assert TableType.COLLECTIONS.base_id == "Collections"
+    assert TableType.FACTS.base_id == "CollectionFacts"
+
+
+def test_table_factory_method():
+    row1 = {"id": "1"}
+    row2 = {"id": "2"}
+    rows = [row1, row2]
+
+    meta = MagicMock()
+    meta.id_attribute = "id"
+
+    table = Table.of(TableType.PERSONS, meta, rows)
+
+    assert table.rows_by_id["2"] == row2
+    assert table.rows[0] == row1
+    assert table.rows[1] == row2
+
+
+def test_node_staging_id():
+    node = Node("NL", "NL", None)
+
+    assert node.get_staging_id(TableType.PERSONS) == "Persons"
+    assert node.get_staging_id(TableType.NETWORKS) == "Networks"
+    assert node.get_staging_id(TableType.BIOBANKS) == "Biobanks"
+    assert node.get_staging_id(TableType.COLLECTIONS) == "Collections"
+    assert node.get_staging_id(TableType.FACTS) == "CollectionFacts"
+
+
+def test_node_id_prefix():
+    node = Node("BE", "BE", None)
+
+    assert node.get_id_prefix(TableType.PERSONS) == "bbmri-eric:contactID:BE_"
+    assert node.get_id_prefix(TableType.NETWORKS) == "bbmri-eric:networkID:BE_"
+    assert node.get_id_prefix(TableType.BIOBANKS) == "bbmri-eric:ID:BE_"
+    assert node.get_id_prefix(TableType.COLLECTIONS) == "bbmri-eric:ID:BE_"
+    assert node.get_id_prefix(TableType.FACTS) == "bbmri-eric:factID:BE_"
+
+
+def test_node_eu_id_prefix():
+    node = Node("BE", "BE", None)
+
+    assert node.get_eu_id_prefix(TableType.PERSONS) == "bbmri-eric:contactID:EU_"
+    assert node.get_eu_id_prefix(TableType.NETWORKS) == "bbmri-eric:networkID:EU_"
+    assert node.get_eu_id_prefix(TableType.BIOBANKS) == "bbmri-eric:ID:EU_"
+    assert node.get_eu_id_prefix(TableType.COLLECTIONS) == "bbmri-eric:ID:EU_"
+    assert node.get_eu_id_prefix(TableType.FACTS) == "bbmri-eric:factID:EU_"
+
+
+def test_external_server_node():
+    node = ExternalServerNode("NL", description="NL", date_end=None, url="test.nl")
+
+    assert node.get_staging_id(TableType.PERSONS) == "Persons"
+    assert node.url == "test.nl"
+
+
+def test_node_data_order():
+    meta = MagicMock()
+    meta.id_attribute = "id"
+    persons = Table.of(TableType.PERSONS, meta, [{"id": "1"}])
+    networks = Table.of(TableType.NETWORKS, meta, [{"id": "1"}])
+    also_known_in = Table.of(TableType.ALSO_KNOWN, meta, [{"id": "1"}])
+    biobanks = Table.of(TableType.BIOBANKS, meta, [{"id": "1"}])
+    collections = Table.of(TableType.COLLECTIONS, meta, [{"id": "1"}])
+    facts = Table.of(TableType.FACTS, meta, [{"id": "1"}])
+    node = Node("NL", "NL")
+
+    node_data = NodeData(
+        node=node,
+        source=Source.STAGING,
+        persons=persons,
+        networks=networks,
+        also_known_in=also_known_in,
+        biobanks=biobanks,
+        collections=collections,
+        facts=facts,
+    )
+
+    assert node_data.import_order == [
+        persons,
+        networks,
+        also_known_in,
+        biobanks,
+        collections,
+        facts,
+    ]
diff --git a/tools/directory/tests/test_model_fitting.py b/tools/directory/tests/test_model_fitting.py
new file mode 100644
index 0000000000..2190f06c86
--- /dev/null
+++ b/tools/directory/tests/test_model_fitting.py
@@ -0,0 +1,122 @@
+from unittest.mock import MagicMock
+
+import pytest
+
+from molgenis_emx2.directory_client.model_fitting import ModelFitter
+
+
+@pytest.fixture
+def model_fitter():
+    return ModelFitter(
+        node_data=MagicMock(),
+        printer=MagicMock(),
+    )
+
+
+def test_merge_covid19_capabilities(model_fitter):
+    node_data = MagicMock()
+    node_data.biobanks.rows = [
+        {"id": "0"},
+        {"id": "1", "covid19biobank": None, "capabilities": None},
+        {"id": "2", "covid19biobank": None, "capabilities": ["a", "b"]},
+        {"id": "3", "covid19biobank": ["c"], "capabilities": ["a", "b"]},
+        {"id": "4", "covid19biobank": ["c"], "capabilities": None},
+        {"id": "5", "covid19biobank": ["a"], "capabilities": ["a", "b"]},
+    ]
+    model_fitter.node_data = node_data
+
+    model_fitter._merge_covid19_capabilities()
+
+    assert node_data.biobanks.rows == [
+        {"id": "0"},
+        {"id": "1", "capabilities": None},
+        {"id": "2", "capabilities": ["a", "b"]},
+        {"id": "3", "capabilities": ["a", "b", "c"]},
+        {"id": "4", "capabilities": ["c"]},
+        {"id": "5", "capabilities": ["a", "b"]},
+    ]
+
+
+def test_move_head_info(node_data, model_fitter):
+    model_fitter.node_data = node_data
+
+    model_fitter._move_heads_to_persons()
+
+    assert (
+        node_data.persons.rows_by_id["bbmri-eric:contactID:NL_valid-personID-1"]["role"]
+        == "Director"
+    )
+    # Separate checks as person has two roles and order differs per run
+
+    assert (
+        node_data.persons.rows_by_id["bbmri-eric:contactID:" "NL_geluk"][
+            "title_before_name"
+        ]
+        == "Dr"
+    )
+    assert (
+        node_data.persons.rows_by_id["bbmri-eric:contactID:NL_geluk"]["first_name"]
+        == "Piet"
+    )
+    assert (
+        node_data.persons.rows_by_id["bbmri-eric:contactID:NL_geluk"]["last_name"]
+        == "Geluk"
+    )
+    assert (
+        node_data.persons.rows_by_id["bbmri-eric:contactID:NL_geluk"]["email"]
+        == "UNKNOWN@NL"
+    )
+    assert (
+        node_data.persons.rows_by_id["bbmri-eric:contactID:NL_geluk"]["country"] == "NL"
+    )
+    assert (
+        node_data.persons.rows_by_id["bbmri-eric:contactID:" "NL_geluk"][
+            "national_node"
+        ]
+        == "NL"
+    )
+    assert (
+        set(
+            node_data.persons.rows_by_id["bbmri-eric:contactID:NL_geluk"]["role"].split(
+                " and "
+            )
+        )
+    ) == set("Collection head and Principal Investigator".split(" and "))
+    assert node_data.persons.rows_by_id["bbmri-eric:contactID:NL_devries"] == {
+        "id": "bbmri-eric:contactID:NL_devries",
+        "title_after_name": "Msc",
+        "title_before_name": "Prof",
+        "first_name": "Bart",
+        "last_name": "de Vries",
+        "email": "UNKNOWN@NL",
+        "role": "Principal Investigator",
+        "country": "NL",
+        "national_node": "NL",
+    }
+
+    assert (
+        node_data.biobanks.rows_by_id["bbmri-eric:ID:NL_valid-biobankID-1"]["head"]
+        == "bbmri-eric:contactID:NL_valid-personID-1"
+    )
+    assert (
+        node_data.biobanks.rows_by_id["bbmri-eric:ID:NL_valid:biobankID-2"]["head"]
+        == "bbmri-eric:contactID:NL_geluk"
+    )
+    assert (
+        node_data.collections.rows_by_id["bbmri-eric:ID:" "NL_valid-collectionID-1"][
+            "head"
+        ]
+        == "bbmri-eric:contactID:NL_valid-personID-1"
+    )
+    assert (
+        node_data.collections.rows_by_id["bbmri-eric:ID:" "NL_valid:collectionID-2"][
+            "head"
+        ]
+        == "bbmri-eric:contactID:NL_geluk"
+    )
+    assert (
+        node_data.collections.rows_by_id["bbmri-eric:ID:" "NL_valid:collectionID-3"][
+            "head"
+        ]
+        == "bbmri-eric:contactID:NL_devries"
+    )
diff --git a/tools/directory/tests/test_pid_manager.py b/tools/directory/tests/test_pid_manager.py
new file mode 100644
index 0000000000..2f1eee11c7
--- /dev/null
+++ b/tools/directory/tests/test_pid_manager.py
@@ -0,0 +1,118 @@
+from unittest import mock
+from unittest.mock import MagicMock, call
+
+import pytest
+
+from molgenis_emx2.directory_client.model import Table, TableType
+from molgenis_emx2.directory_client.pid_manager import (
+    NoOpPidManager,
+    PidManager,
+    PidManagerFactory,
+)
+from molgenis_emx2.directory_client.pid_service import (
+    DummyPidService,
+    NoOpPidService,
+    Status,
+)
+from molgenis_emx2.directory_client.printer import Printer
+
+
+@pytest.fixture
+def pid_manager(pid_service, printer):
+    return PidManager(pid_service, printer)
+
+
+def test_assign_biobank_pids(pid_manager, pid_service):
+    biobank_meta = MagicMock()
+    biobank_meta.id_attribute = "id"
+    biobanks = Table.of(
+        table_type=TableType.BIOBANKS,
+        meta=biobank_meta,
+        rows=[
+            {"id": "b1", "name": "biobank1", "pid": "pid1"},
+            {"id": "b2", "name": "biobank2"},
+            {"id": "b3", "name": "biobank3"},
+            {"id": "b4", "name": "biobank4", "withdrawn": True},
+        ],
+    )
+
+    pid_service.reverse_lookup.side_effect = [[], ["pid3"], []]
+    pid_service.register_pid.return_value = None
+
+    warnings = pid_manager.assign_biobank_pids(biobanks)
+
+    pid_service.register_pid.assert_has_calls(
+        [
+            call(url="url/#/biobank/b2", name="biobank2"),
+            call(url="url/#/biobank/b4", name="biobank4"),
+        ]
+    )
+
+    pid_service.set_status.assert_called_with(None, Status.WITHDRAWN)
+
+    assert len(warnings) == 1
+    assert (
+        warnings[0].message
+        == "PID(s) already exist for new biobank \"biobank3\": ['pid3']. Please check "
+        "the PID's contents!"
+    )
+
+
+def test_update_biobank_pids(pid_manager, pid_service):
+    biobank_meta = MagicMock()
+    biobank_meta.id_attribute = "id"
+    biobanks = Table.of(
+        table_type=TableType.BIOBANKS,
+        meta=biobank_meta,
+        rows=[
+            {"id": "b1", "name": "biobank1", "pid": "pid1"},
+            {"id": "b2", "name": "biobank2_renamed", "pid": "pid2"},
+            {"id": "b3", "name": "biobank3", "pid": "pid3", "withdrawn": True},
+            {"id": "b4", "name": "biobank4", "pid": "pid4", "withdrawn": False},
+        ],
+    )
+
+    existing_biobanks = Table.of(
+        table_type=TableType.BIOBANKS,
+        meta=biobank_meta,
+        rows=[
+            {"id": "b1", "name": "biobank1", "pid": "pid1", "withdrawn": False},
+            {"id": "b2", "name": "biobank2", "pid": "pid2", "withdrawn": False},
+            {"id": "b3", "name": "biobank3", "pid": "pid3", "withdrawn": False},
+            {"id": "b4", "name": "biobank4", "pid": "pid4", "withdrawn": True},
+        ],
+    )
+
+    pid_manager.update_biobank_pids(biobanks, existing_biobanks)
+
+    pid_service.set_name.assert_called_with("pid2", "biobank2_renamed")
+    pid_service.set_status.assert_called_with("pid3", Status.WITHDRAWN)
+    pid_service.remove_status.assert_called_with("pid4")
+
+
+def test_terminate_biobanks(pid_manager, pid_service):
+    pid_manager.terminate_biobanks(["pid1", "pid2"])
+    assert pid_service.set_status.mock_calls == [
+        mock.call("pid1", Status.TERMINATED),
+        mock.call("pid2", Status.TERMINATED),
+    ]
+
+
+def test_noop_pid_manager():
+    noop = NoOpPidManager()
+
+    assert noop.assign_biobank_pids(MagicMock()) == []
+    assert noop.update_biobank_pids(MagicMock(), MagicMock()) is None
+    assert noop.terminate_biobanks(MagicMock()) is None
+
+
+def test_pid_manager_factory():
+    noop_pid_service = NoOpPidService()
+    dummy_pid_service = DummyPidService()
+    printer = Printer()
+
+    manager1 = PidManagerFactory.create(noop_pid_service, printer)
+    manager2 = PidManagerFactory.create(dummy_pid_service, printer)
+
+    assert type(manager1) == NoOpPidManager
+    assert type(manager2) == PidManager
diff --git a/tools/directory/tests/test_pid_service.py b/tools/directory/tests/test_pid_service.py
new file mode 100644
index 0000000000..ee6f271844
--- /dev/null
+++ b/tools/directory/tests/test_pid_service.py
@@ -0,0 +1,103 @@
+from unittest import mock
+from unittest.mock import MagicMock
+
+import pytest
+
+from molgenis_emx2.directory_client.errors import DirectoryError
+from molgenis_emx2.directory_client.pid_service import (
+    DummyPidService,
+    NoOpPidService,
+    PidService,
+    Status,
+)
+
+
+@pytest.fixture
+def handle_client() -> MagicMock:
+    return MagicMock()
+
+
+@pytest.fixture
+def pid_service(handle_client) -> PidService:
+    return PidService(handle_client, "test", "test.nl")
+
+
+def test_reverse_lookup(pid_service, handle_client):
+    handle_client.search_handle.return_value = ["pid1", "pid2"]
+
+    result = pid_service.reverse_lookup("my_url")
+
+    handle_client.search_handle.assert_called_with(URL="my_url", prefix="test")
+    assert result == ["pid1", "pid2"]
+
+
+def test_reverse_lookup_no_auth(pid_service, handle_client):
+    handle_client.search_handle.return_value = None
+
+    with pytest.raises(DirectoryError) as e:
+        pid_service.reverse_lookup("my_url")
+
+    assert str(e.value) == "Insufficient permissions for reverse lookup"
+
+
+def test_register_pid(pid_service: PidService, handle_client):
+    handle_client.register_handle.return_value = "test/pid"
+
+    with mock.patch.object(PidService, "generate_pid") as generate_pid_mock:
+        generate_pid_mock.return_value = "test/pid"
+        result = pid_service.register_pid("url", "biobank1")
+
+    handle_client.register_handle.assert_called_with(
+        handle="test/pid", location="url", NAME="biobank1"
+    )
+    assert result == "test/pid"
+
+
+def test_set_name(pid_service: PidService, handle_client):
+    pid_service.set_name("pid1", "new_name")
+    handle_client.modify_handle_value.assert_called_with("pid1", NAME="new_name")
+
+
+def test_set_status(pid_service: PidService, handle_client):
+    pid_service.set_status("pid1", Status.TERMINATED)
+    handle_client.modify_handle_value.assert_called_with("pid1", STATUS="TERMINATED")
+
+
+def test_remove_status(pid_service: PidService, handle_client):
+    pid_service.remove_status("pid1")
+    handle_client.delete_handle_value.assert_called_with("pid1", "STATUS")
+
+
+def test_generate_pid(pid_service: PidService):
+    pid = pid_service.generate_pid("test")
+
+    pid = pid.replace("-", "")
+    prefix, suffix = pid.split("/1.")
+
+    assert prefix == "test"
+    try:
+        int(suffix, 16)
+    except ValueError:
+        pytest.fail("Couldn't parse hex id as int")
+
+
+def test_dummy_service():
+    dummy = DummyPidService()
+
+    assert dummy.register_pid("", "").startswith("FAKE-PREFIX/1.")
+    assert dummy.reverse_lookup("") is None
+
+
+def test_noop_service():
+    noop = NoOpPidService()
+
+    assert noop.register_pid("", "") is None
+    assert noop.reverse_lookup("") is None
+
+
+def test_base_url(handle_client):
+    service1 = PidService(handle_client, "test", "test1.nl")
+    service2 = PidService(handle_client, "test", "test2.nl")
+
+    assert service1.base_url == "test1.nl/"
+    assert service2.base_url == "test2.nl/"
diff --git a/tools/directory/tests/test_printer.py b/tools/directory/tests/test_printer.py
new file mode 100644
index 0000000000..aad04246b1
--- /dev/null
+++ b/tools/directory/tests/test_printer.py
@@ -0,0 +1,158 @@
+import textwrap
+
+from molgenis_emx2.directory_client.errors import (
+    DirectoryError,
+    DirectoryWarning,
+    ErrorReport,
+)
+from molgenis_emx2.directory_client.model import Node
+from molgenis_emx2.directory_client.printer import Printer
+
+
+def test_indentation(capsys):
+    expected = textwrap.dedent(
+        """\
+        line1
+            line2
+                line3
+                line4
+            line5
+        """
+    )
+
+    printer = Printer()
+    printer.print("line1")
+    printer.indent()
+    printer.print("line2")
+    printer.indent()
+    printer.print("line3")
+    printer.dedent()
+    printer.print("line4", 1)
+    printer.print("line5")
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
+
+
+def test_reset_indent(capsys):
+    expected = textwrap.dedent(
+        """\
+                line1
+        line2
+        """
+    )
+
+    printer = Printer()
+    printer.indent()
+    printer.indent()
+    printer.print("line1")
+    printer.reset_indent()
+    printer.print("line2")
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
+
+
+def test_print_node_title(capsys):
+    node = Node("NL", "Netherlands")
+    expected = textwrap.dedent(
+        """\
+
+        ========================
+        🌍 Node NL (Netherlands)
+        ========================
+        """
+    )
+
+    printer = Printer()
+    printer.print_node_title(node)
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
+
+
+def test_print_error_with_cause(capsys):
+    expected = "❌ this is the message - Cause: this is the cause\n"
+
+    try:
+        raise DirectoryError("this is the message") from ValueError("this is the cause")
+    except DirectoryError as e:
+        Printer().print_error(e)
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
+
+
+def test_print_error_without_cause(capsys):
+    expected = "❌ this is the message\n"
+
+    try:
+        raise DirectoryError("this is the message")
+    except DirectoryError as e:
+        Printer().print_error(e)
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
+
+
+def test_print_warning(capsys):
+    expected = "⚠️ this is the message\n"
+    warning = DirectoryWarning("this is the message")
+
+    Printer().print_warning(warning)
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
+
+
+def test_print_summary(capsys):
+    expected = textwrap.dedent(
+        """\
+
+        ==========
+        📋 Summary
+        ==========
+        ✅ Node A finished successfully
+        ❌ Node B failed
+        ❌ Node C failed with 1 warning(s)
+        ⚠️ Node D finished successfully with 2 warning(s)
+        """
+    )
+
+    a = Node("A", "success", None)
+    b = Node("B", "error", None)
+    c = Node("C", "error and warnings", None)
+    d = Node("D", "success with warnings", None)
+    nodes = [a, b, c, d]
+    report = ErrorReport(nodes)
+    warning = DirectoryWarning("warning")
+    error = DirectoryError("error")
+    report.add_node_warnings(c, [warning])
+    report.add_node_warnings(d, [warning, warning])
+    report.add_node_error(b, error)
+    report.add_node_error(c, error)
+
+    Printer().print_summary(report)
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
+
+
+def test_with_indentation(capsys):
+    expected = textwrap.dedent(
+        """\
+        line1
+            line2
+        line3
+        """
+    )
+
+    printer = Printer()
+
+    printer.print("line1")
+    with printer.indentation():
+        printer.print("line2")
+    printer.print("line3")
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
diff --git a/tools/directory/tests/test_publication_preparer.py b/tools/directory/tests/test_publication_preparer.py
new file mode 100644
index 0000000000..e22abcd360
--- /dev/null
+++ b/tools/directory/tests/test_publication_preparer.py
@@ -0,0 +1,175 @@
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from molgenis_emx2.directory_client.errors import DirectoryWarning, ErrorReport
+from molgenis_emx2.directory_client.model import Node
+from molgenis_emx2.directory_client.publication_preparer import PublicationPreparer
+
+
+@pytest.fixture
+def validator_init():
+    with (
+        patch(
+            "molgenis_emx2.directory_client.publication_preparer.Validator"
+        ) as validator_mock
+    ):
+        yield validator_mock
+
+
+@pytest.fixture
+def model_fitter_init():
+    with patch(
+        "molgenis_emx2.directory_client.publication_preparer.ModelFitter"
+    ) as model_fitter_mock:
+        yield model_fitter_mock
+
+
+@pytest.fixture
+def transformer_init():
+    with patch(
+        "molgenis_emx2.directory_client.publication_preparer.Transformer"
+    ) as transformer_mock:
+        yield transformer_mock
+
+
+@pytest.fixture
+def pid_manager():
+    return MagicMock()
+
+
+@pytest.fixture
+def preparer(session, printer, pid_manager):
+    return PublicationPreparer(printer, pid_manager, session)
+
+
+def test_prepare(preparer, session):
+    validate_func = MagicMock()
+    preparer._validate_node = validate_func
+    model_fitter_func = MagicMock()
+    preparer._fit_node_model = model_fitter_func
+    transform_func = MagicMock()
+    preparer._transform_node = transform_func
+    manage_pids_func = MagicMock()
+    preparer._manage_node_pids = manage_pids_func
+    nl = Node.of("NL")
+    state = MagicMock()
+    report = MagicMock()
+    state.report = report
+    node_data = MagicMock()
+    session.get_staging_node_data.return_value = node_data
+
+    preparer.prepare(nl, state)
+
+    session.get_staging_node_data.assert_called_with(nl)
+    validate_func.assert_called_with(node_data, report)
+    model_fitter_func.assert_called_with(node_data, report)
+    transform_func.assert_called_with(node_data, state)
+    manage_pids_func.assert_called_with(node_data, state)
+
+
+def test_validate(preparer: PublicationPreparer, validator_init, printer):
+    validator = MagicMock()
+    validator_init.return_value = validator
+    node_data = MagicMock()
+    report = MagicMock()
+
+    preparer._validate_node(node_data, report)
+
+    validator_init.assert_called_with(node_data, printer)
+    assert validator.validate.called
+
+
+def test_validate_warnings(preparer: PublicationPreparer, validator_init, printer):
+    validator = MagicMock()
+    validator_init.return_value = validator
+    warning = DirectoryWarning("warning")
+    validator.validate.return_value = [warning]
+    node_data = MagicMock()
+    nl = Node.of("NL")
+    node_data.node = nl
+    report: ErrorReport = ErrorReport([nl])
+
+    preparer._validate_node(node_data, report)
+
+    assert report.node_warnings[nl] == [warning]
+
+
+def test_model_fitting(preparer: PublicationPreparer, model_fitter_init):
+    model_fitter = MagicMock()
+    model_fitter_init.return_value = model_fitter
+
+    preparer._fit_node_model(MagicMock(), MagicMock())
+
+    assert model_fitter_init.called
+    assert model_fitter.fit_model.called
+
+
+def test_model_fitting_warnings(preparer: PublicationPreparer, model_fitter_init):
+    model_fitter = MagicMock()
+    model_fitter_init.return_value = model_fitter
+    warning = DirectoryWarning("warning")
+    model_fitter.fit_model.return_value = [warning]
+    node_data = MagicMock()
+    nl = Node.of("NL")
+    node_data.node = nl
+    state = MagicMock()
+    state.report = ErrorReport(nl)
+
+    preparer._fit_node_model(node_data, state.report)
+
+    assert state.report.node_warnings[nl] == [warning]
+
+
+def test_transform(preparer: PublicationPreparer, transformer_init):
+    transformer = MagicMock()
+    transformer_init.return_value = transformer
+
+    preparer._transform_node(MagicMock(), MagicMock())
+
+    assert transformer_init.called
+    assert transformer.transform.called
+
+
+def test_transform_warnings(preparer: PublicationPreparer, transformer_init, printer):
+    transformer = MagicMock()
+    transformer_init.return_value = transformer
+    warning = DirectoryWarning("warning")
+    transformer.transform.return_value = [warning]
+    node_data = MagicMock()
+    nl = Node.of("NL")
+    node_data.node = nl
+    state = MagicMock()
+    state.report = ErrorReport(nl)
+
+    preparer._transform_node(node_data, state)
+
+    assert state.report.node_warnings[nl] == [warning]
+
+
+def test_manage_pids(preparer, transformer_init, pid_manager):
+    biobanks = MagicMock()
+    node_data = MagicMock()
+    node_data.biobanks = biobanks
+    existing_biobanks = MagicMock()
+    state = MagicMock()
+    state.existing_data.biobanks = existing_biobanks
+
+    preparer._manage_node_pids(node_data, state)
+
+    pid_manager.assign_biobank_pids.assert_called_with(biobanks)
+    pid_manager.update_biobank_pids.assert_called_with(biobanks, existing_biobanks)
+
+
+def test_manage_pids_warning(preparer, transformer_init, pid_manager):
+    nl = Node.of("NL")
+    node_data = MagicMock()
+    node_data.node = nl
+    state = MagicMock()
+    state.report = ErrorReport([nl])
+    warning = DirectoryWarning("warning")
+    pid_manager.assign_biobank_pids.return_value = [warning]
+
+    preparer._manage_node_pids(node_data, state)
+
+    assert state.report.node_warnings[nl] == [warning]
diff --git a/tools/directory/tests/test_publisher.py b/tools/directory/tests/test_publisher.py
new file mode 100644
index 0000000000..5f762af7f6
--- /dev/null
+++ b/tools/directory/tests/test_publisher.py
@@ -0,0 +1,122 @@
+from unittest import mock
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from molgenis_emx2.directory_client.errors import DirectoryWarning, ErrorReport
+from molgenis_emx2.directory_client.model import (
+    MixedData,
+    Node,
+    NodeData,
+    QualityInfo,
+    Source,
+    Table,
+    TableType,
+)
+from molgenis_emx2.directory_client.publisher import Publisher, PublishingState
+
+pytest_plugins = ("pytest_asyncio",)
+
+
+@pytest.fixture
+def pid_manager_factory():
+    with patch(
+        "molgenis_emx2.directory_client.publisher.PidManagerFactory"
+    ) as pid_manager_factory_mock:
+        yield pid_manager_factory_mock
+
+
+@pytest.fixture
+def async_publisher(async_session, printer, pid_service) -> Publisher:
+    return Publisher(async_session, printer, pid_service)
+
+
+@pytest.fixture
+def publisher(session, printer, pid_service) -> Publisher:
+    return Publisher(session, printer, pid_service)
+
+
+@pytest.mark.asyncio
+async def test_publish(async_publisher, async_session):
+    async_publisher._delete_rows = MagicMock()
+
+    state = PublishingState(
+        nodes=[Node.of("NL"), Node.of("BE")],
+        existing_data=MixedData(
+            source=Source.TRANSFORMED,
+            persons=Table.of_empty(TableType.PERSONS, MagicMock()),
+            networks=Table.of_empty(TableType.NETWORKS, MagicMock()),
+            also_known_in=Table.of_empty(TableType.ALSO_KNOWN, MagicMock()),
+            biobanks=Table.of_empty(TableType.BIOBANKS, MagicMock()),
+            collections=Table.of_empty(TableType.COLLECTIONS, MagicMock()),
+            facts=Table.of_empty(TableType.FACTS, MagicMock()),
+        ),
+        eu_node_data=MagicMock(),
+        quality_info=MagicMock(),
+        report=MagicMock(),
+        diseases=MagicMock(),
+    )
+
+    await async_publisher.publish(state)
+
+    async_session.upload_data.assert_called_with(
+        schema=async_session.directory_schema, data=state.data_to_publish
+    )
+    assert async_publisher._delete_rows.mock_calls == [
+        mock.call(state.data_to_publish.facts, state.existing_data.facts, state),
+        mock.call(
+            state.data_to_publish.collections, state.existing_data.collections, state
+        ),
+        mock.call(state.data_to_publish.biobanks, state.existing_data.biobanks, state),
+        mock.call(
+            state.data_to_publish.also_known_in,
+            state.existing_data.also_known_in,
+            state,
+        ),
+        mock.call(state.data_to_publish.networks, state.existing_data.networks, state),
+        mock.call(state.data_to_publish.persons, state.existing_data.persons, state),
+    ]
+
+
+def test_delete_rows(publisher, pid_service, node_data: NodeData, session):
+    biobank_meta = MagicMock()
+    biobank_meta.id_attribute = "id"
+    existing_biobanks_table = Table.of(
+        table_type=TableType.BIOBANKS,
+        meta=biobank_meta,
+        rows=[
+            {
+                "id": "bbmri-eric:ID:NL_valid-biobankID-1",
+                "pid": "pid1",
+                "national_node": "NL",
+            },
+            {"id": "delete_this_row", "pid": "pid2", "national_node": "NL"},
+            {"id": "undeletable_id", "pid": "pid3", "national_node": "NL"},
+        ],
+    )
+
+    state: PublishingState = MagicMock()
+    state.quality_info = QualityInfo(
+        biobanks={"undeletable_id": ["quality"]},
+        collections={},
+        biobank_levels={},
+        collection_levels={},
+    )
+
+    state.report = ErrorReport([node_data.node])
+
+    warning1 = DirectoryWarning("ID delete_this_row is deleted")
+
+    warning2 = DirectoryWarning(
+        "Prevented the deletion of a row that is referenced from "
+        "the quality info: biobanks undeletable_id."
+    )
+
+    publisher._delete_rows(node_data.biobanks, existing_biobanks_table, state)
+
+    publisher.pid_manager.terminate_biobanks.assert_called_with(["pid2"])
+    session.delete_records.assert_called_with(
+        table="Biobanks", data=[{"id": "delete_this_row"}]
+    )
+
+    assert state.report.node_warnings[node_data.node] == [warning1, warning2]
diff --git a/tools/directory/tests/test_stager.py b/tools/directory/tests/test_stager.py
new file mode 100644
index 0000000000..a824f18ba0
--- /dev/null
+++ b/tools/directory/tests/test_stager.py
@@ -0,0 +1,200 @@
+from http import HTTPStatus
+from unittest import mock
+from unittest.mock import AsyncMock, MagicMock, patch
+
+import pandas as pd
+import pytest
+from molgenis_emx2_pyclient.metadata import Schema
+
+from molgenis_emx2.directory_client.directory_client import DirectorySession
+from molgenis_emx2.directory_client.errors import DirectoryError, DirectoryWarning
+from molgenis_emx2.directory_client.model import ExternalServerNode, NodeData
+from molgenis_emx2.directory_client.printer import Printer
+from molgenis_emx2.directory_client.stager import Stager
+
+pytest_plugins = "pytest_asyncio"
+
+
+@pytest.fixture
+def external_server_init():
+    with (
+        patch(
+            "molgenis_emx2.directory_client.stager.ExternalServerSession"
+        ) as ext_session_mock
+    ):
+        yield ext_session_mock
+
+
+@pytest.fixture
+def directory_server_init():
+    with (
+        patch(
+            "molgenis_emx2.directory_client.stager.DirectorySession"
+        ) as dir_session_mock
+    ):
+        yield dir_session_mock
+
+
+@pytest.mark.asyncio
+async def test_stager(mocker):
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client."
+        "DirectorySession._validate_url",
+        return_value=HTTPStatus(200),
+    )
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client.DirectorySession._"
+        "validate_graphql_response",
+        return_value=HTTPStatus(200),
+    )
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client.DirectorySession.get_schemas",
+        return_value=[
+            Schema(id="BBMRI-NL", name="None-NL", label="BBMRI-ERIC", description="")
+        ],
+    )
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client.DirectorySession."
+        "set_schema",
+        return_value=["BBMRI-NL"],
+    )
+
+    stager = Stager(DirectorySession("https://url.nl", "BBMRI-NL"), Printer())
+    source_data = MagicMock()
+    stager._clear_staging_area = MagicMock(name="_clear_staging_area")
+    stager._import_node = AsyncMock(name="_import_node")
+    stager._get_source_data = MagicMock(name="_get_mock_data")
+    stager._get_source_data.return_value = source_data
+    node = ExternalServerNode("NL", "NL", url="url")
+
+    await stager.stage(node)
+
+    stager._get_source_data.assert_called_with(node)
+    stager._clear_staging_area.assert_called_with(node)
+    stager._import_node.assert_called_with(source_data)
+
+
+def test_get_source_data(external_server_init):
+    node_data = MagicMock()
+    node = ExternalServerNode("NL", "Netherlands", url="url")
+
+    source_session_mock_instance = external_server_init.return_value
+    source_session_mock_instance.schemas = [
+        Schema(id="BBMRI-NL", name="BBMRI-NL", label="BBMRI-NL", description="")
+    ]
+    source_session_mock_instance.node.get_schema_id.return_value = "BBMRI-NL"
+    source_session_mock_instance.get_node_data.return_value = node_data
+
+    source_data = Stager(MagicMock(), Printer())._get_source_data(node)
+
+    external_server_init.assert_called_with(node=node)
+    assert source_data == node_data
+
+
+@pytest.mark.asyncio
+async def test_check_permissions(external_server_init):
+    node = ExternalServerNode("NL", "Netherlands", url="url.nl", token="stager_token")
+    session = external_server_init.return_value
+    session.schemas = [
+        Schema(id="BBMRI-ERIC", name="BBMRI-ERIC", label="BBMRI-ERIC", description="")
+    ]
+    session.node = node
+    stager = Stager(MagicMock(), Printer())
+
+    with pytest.raises(DirectoryError) as e:
+        await stager.stage(node)
+
+    assert str(e.value) == (
+        "The session user has invalid permissions\n       "
+        "Please check the token and permissions of this user"
+    )
+
+
+@pytest.mark.asyncio
+async def test_check_tables(mocker, external_server_init):
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client.DirectorySession."
+        "get_schema_metadata"
+    )
+    node = ExternalServerNode(
+        "NL", "Netherlands", url="https://url.nl", token="stager_token"
+    )
+    session = external_server_init.return_value
+    session.node = node
+    session.get_schema_metadata.return_value = Schema(
+        id="BBMRI-NL", name="BBMRI-NL", label="BBMRI-NL", description="", tables=[]
+    )
+    eric_session = AsyncMock(DirectorySession)
+    eric_session.get.return_value = pd.DataFrame({})
+
+    stager = Stager(eric_session, Printer())
+    stager._check_permissions = MagicMock()
+
+    warnings = await stager.stage(node)
+
+    external_server_init.assert_called_with(node=node)
+
+    # Can't get this to work:
+    # assert session.get_schema_metadata.get_tables.call_count == 6
+    assert session.get_schema_metadata.call_count == 1
+
+    assert warnings[0] == DirectoryWarning("Node NL has no persons table")
+    assert warnings[1] == DirectoryWarning("Node NL has no also_known_in table")
+    assert warnings[2] == DirectoryWarning("Node NL has no networks table")
+    assert warnings[3] == DirectoryWarning("Node NL has no biobanks table")
+    assert warnings[4] == DirectoryWarning("Node NL has no collections table")
+    assert warnings[5] == DirectoryWarning("Node NL has no facts table")
+
+
+def test_clear_staging_area(mocker):
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client.DirectorySession."
+        "_validate_url",
+        return_value=HTTPStatus(200),
+    )
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client.DirectorySession."
+        "_validate_graphql_response",
+        return_value=HTTPStatus(200),
+    )
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client.DirectorySession."
+        "get_schemas",
+        return_value=[
+            Schema(id="BBMRI-NL", name="None-NL", label="BBMRI-ERIC", description="")
+        ],
+    )
+    mocker.patch(
+        "molgenis_emx2.directory_client.directory_client.DirectorySession."
+        "set_schema",
+        return_value=["BBMRI-NL"],
+    )
+    session = DirectorySession("https://url.nl", "BBMRI-NL")
+    session.get = MagicMock()
+    session.get.return_value = pd.DataFrame([{"id": "All"}])
+    session.delete_records = MagicMock(name="delete")
+    node = ExternalServerNode("NL", "Netherlands", url="url.nl")
+
+    Stager(session, Printer())._clear_staging_area(node)
+
+    assert session.delete_records.mock_calls == [
+        mock.call(schema="BBMRI-NL", table="CollectionFacts", data=[{"id": "All"}]),
+        mock.call(schema="BBMRI-NL", table="Collections", data=[{"id": "All"}]),
+        mock.call(schema="BBMRI-NL", table="Biobanks", data=[{"id": "All"}]),
+        mock.call(schema="BBMRI-NL", table="Networks", data=[{"id": "All"}]),
+        mock.call(schema="BBMRI-NL", table="AlsoKnownIn", data=[{"id": "All"}]),
+        mock.call(schema="BBMRI-NL", table="Persons", data=[{"id": "All"}]),
+    ]
+
+
+@pytest.mark.asyncio
+async def test_import_node(async_session, external_server_init):
+    node_data: NodeData = MagicMock()
+    converted_data = MagicMock()
+    node_data.convert_to_staging.return_value = converted_data
+
+    await Stager(async_session, Printer())._import_node(node_data)
+
+    async_session.upload_data.assert_called_with(
+        schema=node_data.node.get_schema_id(), data=converted_data
+    )
diff --git a/tools/directory/tests/test_transformer.py b/tools/directory/tests/test_transformer.py
new file mode 100644
index 0000000000..066a531d96
--- /dev/null
+++ b/tools/directory/tests/test_transformer.py
@@ -0,0 +1,299 @@
+from unittest.mock import MagicMock, call
+
+import pytest
+
+from molgenis_emx2.directory_client.errors import DirectoryWarning
+from molgenis_emx2.directory_client.model import Node, QualityInfo, Table, TableType
+from molgenis_emx2.directory_client.transformer import Transformer
+
+
+@pytest.fixture
+def transformer():
+    return Transformer(
+        node_data=MagicMock(),
+        quality=MagicMock(),
+        printer=MagicMock(),
+        existing_biobanks=MagicMock(),
+        eu_node_data=MagicMock(),
+        diseases=MagicMock(),
+    )
+
+
+def test_transformer_node_codes(node_data, transformer):
+    for table in node_data.import_order:
+        assert "national_node" not in table.rows[0]
+
+    transformer.node_data = node_data
+    transformer._set_national_node_code()
+
+    for table in node_data.import_order:
+        assert table.rows[0]["national_node"] == "NL"
+
+
+def test_transformer_not_withdrawn(node_data, transformer):
+    for table in node_data.import_order:
+        assert "withdrawn" not in table.rows[0]
+
+    transformer.node_data = node_data
+    transformer._set_withdrawn()
+
+    for table in node_data.import_order:
+        assert "withdrawn" not in table.rows[0]
+
+
+def test_transformer_withdrawn(node_data, transformer):
+    node_data.node = Node("NL", "NL", "20200101")
+    for table in node_data.import_order:
+        assert "withdrawn" not in table.rows[0]
+
+    transformer.node_data = node_data
+    transformer._set_withdrawn()
+
+    for table in node_data.import_order:
+        assert table.rows[0]["withdrawn"]
+
+
+def test_transformer_commercial_use(transformer):
+    node_data = MagicMock()
+    node_data.collections.rows = [
+        {"biobank": "biobank1", "collaboration_commercial": True},
+        {"biobank": "biobank1", "collaboration_commercial": False},
+        {"biobank": "biobank1"},
+        {"biobank": "biobank2", "collaboration_commercial": True},
+        {"biobank": "biobank2", "collaboration_commercial": False},
+        {"biobank": "biobank2"},
+        {"biobank": "biobank3", "collaboration_commercial": True},
+        {"biobank": "biobank3", "collaboration_commercial": False},
+        {"biobank": "biobank3"},
+    ]
+    node_data.biobanks.rows_by_id = {
+        "biobank1": dict(),
+        "biobank2": {"collaboration_commercial": True},
+        "biobank3": {"collaboration_commercial": False},
+    }
+
+    transformer.node_data = node_data
+    transformer._set_commercial_use_bool()
+
+    assert node_data.collections.rows[0]["commercial_use"] is True
+    assert node_data.collections.rows[1]["commercial_use"] is False
+    assert node_data.collections.rows[2]["commercial_use"] is True
+    assert node_data.collections.rows[3]["commercial_use"] is True
+    assert node_data.collections.rows[4]["commercial_use"] is False
+    assert node_data.collections.rows[5]["commercial_use"] is True
+    assert node_data.collections.rows[6]["commercial_use"] is False
+    assert node_data.collections.rows[7]["commercial_use"] is False
+    assert node_data.collections.rows[8]["commercial_use"] is False
+
+
+def test_transformer_quality(node_data, transformer):
+    q_info = QualityInfo(
+        biobanks={
+            "bbmri-eric:ID:NL_test_quality_biobank1": ["quality1", "quality2"],
+            "bbmri-eric:ID:NL_test_quality_biobank2": ["quality3"],
+        },
+        biobank_levels={},
+        collections={"bbmri-eric:ID:NL_bb1:collection:test_quality1": ["quality1"]},
+        collection_levels={},
+    )
+    transformer.node_data = node_data
+    transformer.quality = q_info
+
+    transformer._set_quality_info()
+
+    assert node_data.biobanks.rows_by_id["bbmri-eric:ID:NL_test_quality_biobank1"][
+        "quality"
+    ] == ["quality1", "quality2"]
+    assert (
+        "quality"
+        not in node_data.biobanks.rows_by_id["bbmri-eric:ID:NL_biobank_noQual"]
+    )
+    assert node_data.biobanks.rows_by_id["bbmri-eric:ID:NL_test_quality_biobank2"][
+        "quality"
+    ] == ["quality3"]
+    assert node_data.collections.rows_by_id[
+        "bbmri-eric:ID:NL_bb1:collection:test_quality1"
+    ]["quality"] == ["quality1"]
+    assert (
+        "quality"
+        not in node_data.collections.rows_by_id[
+            "bbmri-eric:ID:NL_bb1:collection:test_noQual"
+        ]
+    )
+
+
+def test_transformer_replace_eu_rows_skip_eu(transformer):
+    eu = Node("EU", "Europe", None)
+    node_data = MagicMock()
+    node_data.node = eu
+    transformer.node_data = node_data
+    transformer._replace_rows = MagicMock()
+
+    transformer._replace_eu_rows()
+
+    transformer._replace_rows.assert_not_called()
+
+
+def test_transformer_replace_eu_rows(transformer):
+    cy = Node("CY", "Cyprus", None)
+    eu = Node("EU", "Europe", None)
+
+    node_data = MagicMock()
+    eu_node_data = MagicMock()
+
+    persons_meta = MagicMock()
+    persons_meta.id_attribute = "id"
+    persons = Table.of(
+        TableType.PERSONS,
+        persons_meta,
+        [
+            {"id": "bbmri-eric:contactID:CY_person1", "name": "person1"},
+            {"id": "bbmri-eric:contactID:EU_person2", "name": "should be overwritten"},
+            {"id": "bbmri-eric:contactID:EU_person4", "name": "person4"},
+        ],
+    )
+
+    eu_persons_meta = MagicMock()
+    eu_persons_meta.id_attribute = "id"
+    eu_persons = Table.of(
+        TableType.PERSONS,
+        eu_persons_meta,
+        [
+            {"id": "bbmri-eric:contactID:EU_person2", "name": "person2"},
+            {"id": "bbmri-eric:contactID:EU_person3", "name": "person3"},
+        ],
+    )
+
+    node_data.node = cy
+    eu_node_data.node = eu
+    transformer.node_data = node_data
+    transformer.eu_node_data = eu_node_data
+
+    transformer._replace_rows(cy, persons, eu_persons)
+
+    assert persons.rows_by_id["bbmri-eric:contactID:EU_person2"]["name"] == "person2"
+    assert transformer.warnings == [
+        DirectoryWarning(
+            message="bbmri-eric:contactID:EU_person4 is not present in Persons"
+        )
+    ]
+
+
+def test_transformer_set_biobank_labels(transformer):
+    node_data = MagicMock()
+    node_data.collections.rows = [
+        {"biobank": "biobank1", "name": "Collections1"},
+        {"biobank": "biobank2", "name": "Collections2"},
+    ]
+    node_data.biobanks.rows_by_id = {
+        "biobank1": {"name": "BIOBANK1"},
+        "biobank2": {"name": ""},
+    }
+    transformer.node_data = node_data
+
+    transformer._set_biobank_labels()
+
+    assert node_data.collections.rows[0]["biobank_label"] == "BIOBANK1"
+
+    assert node_data.collections.rows[1]["biobank_label"] == ""
+
+
+def test_transformer_create_combined_networks(transformer):
+    node_data = MagicMock()
+    node_data.collections.rows = [
+        {"biobank": "biobank1", "network": []},
+        {"biobank": "biobank2", "network": ["network1"]},
+        {"biobank": "biobank3", "network": ["network2"]},
+        {"biobank": "biobank4", "network": []},
+        {"biobank": "biobank5", "network": ["network1", "network2"]},
+        {"biobank": "biobank6", "network": []},
+    ]
+    node_data.biobanks.rows_by_id = {
+        "biobank1": {"network": ["network1", "network2"]},
+        "biobank2": {"network": []},
+        "biobank3": {"network": ["network1"]},
+        "biobank4": {"network": ["network2"]},
+        "biobank5": {"network": []},
+        "biobank6": {"network": []},
+    }
+    transformer.node_data = node_data
+
+    transformer._set_combined_networks()
+
+    assert set(node_data.collections.rows[0]["combined_network"]) == {
+        "network1",
+        "network2",
+    }
+    assert set(node_data.collections.rows[1]["combined_network"]) == {"network1"}
+    assert set(node_data.collections.rows[2]["combined_network"]) == {
+        "network1",
+        "network2",
+    }
+    assert set(node_data.collections.rows[3]["combined_network"]) == {"network2"}
+    assert set(node_data.collections.rows[4]["combined_network"]) == {
+        "network1",
+        "network2",
+    }
+    assert set(node_data.collections.rows[5]["combined_network"]) == set()
+
+
+def test_transformer_combined_quality(node_data, transformer):
+    q_info = QualityInfo(
+        biobanks={},
+        biobank_levels={
+            "bbmri-eric:ID:NL_test_quality_biobank1": ["level_bio1", "level_bio2"],
+            "bbmri-eric:ID:NL_test_quality_biobank2": ["level_bio3"],
+            "bbmri-eric:ID:NL_test_quality_biobank3": ["level_bio_col"],
+        },
+        collections={},
+        collection_levels={
+            "bbmri-eric:ID:NL_bb1:collection:test_quality1": ["level_col5"],
+            "bbmri-eric:ID:NL_bb1:collection:test_quality2": ["level_col2"],
+            "bbmri-eric:ID:NL_bb3:collection:test_quality3": ["level_bio_col"],
+        },
+    )
+    transformer.node_data = node_data
+    transformer.quality = q_info
+
+    transformer._set_combined_qualities()
+
+    assert (
+        "combined_quality"
+        not in node_data.biobanks.rows_by_id["bbmri-eric:ID:NL_biobank_noQual"]
+    )
+    assert sorted(
+        node_data.collections.rows_by_id["bbmri-eric:ID:NL_bb1:collection:test_noQual"][
+            "combined_quality"
+        ]
+    ) == sorted(["level_bio1", "level_bio2"])
+    assert sorted(
+        node_data.collections.rows_by_id[
+            "bbmri-eric:ID:NL_bb1:collection:test_quality2"
+        ]["combined_quality"]
+    ) == sorted(["level_col2", "level_bio3"])
+    assert node_data.collections.rows_by_id[
+        "bbmri-eric:ID:NL_bb1:collection:test_quality1"
+    ]["combined_quality"] == ["level_col5"]
+    assert node_data.collections.rows_by_id[
+        "bbmri-eric:ID:NL_bb3:collection:test_quality3"
+    ]["combined_quality"] == ["level_bio_col"]
+    assert (
+        node_data.collections.rows_by_id["bbmri-eric:ID:NL_valid-collectionID-1"][
+            "combined_quality"
+        ]
+        == []
+    )
+
+
+def test_map_categories(transformer):
+    node_data = MagicMock()
+    collection1 = MagicMock()
+    collection2 = MagicMock()
+    node_data.collections.rows = [collection1, collection2]
+    category_mapper = MagicMock()
+    transformer.node_data = node_data
+    transformer.category_mapper = category_mapper
+
+    transformer._set_collection_categories()
+
+    category_mapper.map.assert_has_calls([call(collection1), call(collection2)])
diff --git a/tools/directory/tests/test_utils.py b/tools/directory/tests/test_utils.py
new file mode 100644
index 0000000000..17b61b8be3
--- /dev/null
+++ b/tools/directory/tests/test_utils.py
@@ -0,0 +1,24 @@
+import pytest
+
+from molgenis_emx2.directory_client import utils
+
+
+@pytest.fixture
+def rows():
+    return [
+        {
+            "id": "collA",
+            "parent_collection": "collB",
+            "sub_collections": [],
+        },
+        {
+            "id": "collB",
+            "sub_collections": ["collA"],
+        },
+    ]
+
+
+def test_to_ordered_dict(rows):
+    rows_by_id = utils.to_ordered_dict(rows, "id")
+    assert rows_by_id["collA"]["parent_collection"] == "collB"
+    assert rows_by_id["collB"]["sub_collections"] == ["collA"]
diff --git a/tools/directory/tests/test_validator.py b/tools/directory/tests/test_validator.py
new file mode 100644
index 0000000000..c03e6f1048
--- /dev/null
+++ b/tools/directory/tests/test_validator.py
@@ -0,0 +1,144 @@
+from typing import List
+from unittest.mock import MagicMock
+
+import pytest
+
+from molgenis_emx2.directory_client.errors import DirectoryWarning
+from molgenis_emx2.directory_client.printer import Printer
+from molgenis_emx2.directory_client.validation import Validator
+
+
+@pytest.fixture
+def validator() -> Validator:
+    return Validator(MagicMock(), MagicMock())
+
+
+def test_validate_id(node_data):
+    validator = Validator(node_data, Printer())
+
+    warnings = validator.validate()
+
+    assert warnings == [
+        DirectoryWarning(
+            message="bbmri-eric:ID:NL_invalid_person_classifier in entity: "
+            "eu_bbmri_eric_NL_persons does not start with "
+            "bbmri-eric:contactID:NL_ or bbmri-eric:contactID:EU_"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:contactID:NL_invalid_illegal_characters#$& in entity: "
+            "eu_bbmri_eric_NL_persons contains invalid characters. Only "
+            "alphanumerics and -_: are allowed."
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:NL_invalid_network_classifier in entity: "
+            "eu_bbmri_eric_NL_networks does not start with "
+            "bbmri-eric:networkID:NL_ or bbmri-eric:networkID:EU_"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:networkID:BE_invalid_node_code in entity: "
+            "eu_bbmri_eric_NL_networks does not start with "
+            "bbmri-eric:networkID:NL_ or bbmri-eric:networkID:EU_"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:akiID:BE_invalid_node_code in entity: "
+            "eu_bbmri_eric_NL_also_known_in does not start with "
+            "bbmri-eric:akiID:NL_"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:test:NL_invalid_biobank_classifier in entity: "
+            "eu_bbmri_eric_NL_biobanks does not start with bbmri-eric:ID:NL_"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:BE_invalid_node_code in entity: "
+            "eu_bbmri_eric_NL_biobanks does not start with bbmri-eric:ID:NL_"
+        ),
+        DirectoryWarning(
+            message="Biobank bbmri-eric:ID:NL_valid:biobankID-2 has an invalid url: "
+            "www.invalid@url.nl"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:collection:NL_invalid_collection_classifier in entity: "
+            "eu_bbmri_eric_NL_collections does not start with bbmri-eric:ID:NL_"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:BE_invalid_node_code:collectionID in entity: "
+            "eu_bbmri_eric_NL_collections does not start with bbmri-eric:ID:NL_"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:NL_invalid:factsID in entity: "
+            "eu_bbmri_eric_NL_facts does not start with bbmri-eric:factID:NL_"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:networkID:NL_valid:networkID-2 references invalid id: "
+            "bbmri-eric:ID:NL_invalid_person_classifier"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:networkID:BE_invalid_node_code references invalid id: "
+            "bbmri-eric:ID:NL_invalid_network_classifier"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:NL_valid-biobankID-1 references invalid id: "
+            "bbmri-eric:akiID:BE_invalid_node_code"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:NL_valid:biobankID-2 references invalid id: "
+            "bbmri-eric:ID:NL_invalid_person_classifier"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:BE_invalid_node_code references invalid id: "
+            "bbmri-eric:ID:NL_invalid_network_classifier"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:NL_valid-collectionID-1 references invalid id: "
+            "bbmri-eric:akiID:BE_invalid_node_code"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:NL_valid:collectionID-2 references invalid id: "
+            "bbmri-eric:ID:NL_invalid_person_classifier"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:NL_valid:collectionID-2 references invalid id: "
+            "bbmri-eric:test:NL_invalid_biobank_classifier"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:NL_valid:collectionID-2 references invalid id: "
+            "bbmri-eric:collection:NL_invalid_collection_classifier"
+        ),
+        DirectoryWarning(
+            message="bbmri-eric:ID:BE_invalid_node_code:collectionID references "
+            "invalid id: bbmri-eric:ID:NL_invalid_network_classifier"
+        ),
+    ]
+
+
+@pytest.mark.parametrize(
+    "collection,expected",
+    [
+        (dict(), []),
+        ({"id": "0", "age_low": 0, "age_unit": "YEAR"}, []),
+        (
+            {"id": "2", "age_low": 5},
+            [DirectoryWarning("Collection 2 has age_low/age_high without age_unit")],
+        ),
+        (
+            {"id": "3", "age_low": 0, "age_high": 0, "age_unit": "YEAR"},
+            [
+                DirectoryWarning(
+                    "Collection 3 has invalid ages: age_low = 0 and age_high = " "0"
+                )
+            ],
+        ),
+        (
+            {"id": "4", "age_low": 40, "age_high": 20},
+            [
+                DirectoryWarning("Collection 4 has age_low/age_high without age_unit"),
+                DirectoryWarning("Collection 4 has invalid ages: age_low > age_high"),
+            ],
+        ),
+    ],
+)
+def test_validate_collection_ages(
+    validator: Validator, collection: dict, expected: List[DirectoryWarning]
+):
+    validator._validate_ages(collection)
+    assert validator.warnings == expected
diff --git a/tools/directory/tox.ini b/tools/directory/tox.ini
new file mode 100644
index 0000000000..880b604bd0
--- /dev/null
+++ b/tools/directory/tox.ini
@@ -0,0 +1,63 @@
+# Tox configuration file
+# Read more under https://tox.readthedocs.org/
+
+[tox]
+minversion = 3.15
+envlist = default
+
+
+[testenv]
+description = invoke pytest to run automated tests
+isolated_build = True
+setenv =
+    TOXINIDIR = {toxinidir}
+passenv =
+    HOME
+extras =
+    testing
+commands =
+    pytest --junitxml=reports/junit.xml --cov=src --cov-report xml:reports/coverage.xml {posargs}
+
+
+[testenv:{clean,build}]
+description =
+    Build (or clean) the package in isolation according to instructions in:
+    https://setuptools.readthedocs.io/en/latest/build_meta.html#how-to-use-it
+    https://github.com/pypa/pep517/issues/91
+    https://github.com/pypa/build
+# NOTE: build is still experimental, please refer to the links for updates/issues
+skip_install = True
+changedir = {toxinidir}
+deps =
+    build: build[virtualenv]
+commands =
+    clean: python -c 'from shutil import rmtree; rmtree("build", True); rmtree("dist", True)'
+    build: python -m build .
+# By default `build` produces wheels, you can also explicitly use the flags `--sdist` and `--wheel`
+
+
+[testenv:{docs,doctests}]
+description = invoke sphinx-build to build the docs/run doctests
+setenv =
+    DOCSDIR = {toxinidir}/docs
+    BUILDDIR = {toxinidir}/docs/_build
+    docs: BUILD = html
+    doctests: BUILD = doctest
+deps =
+    -r {toxinidir}/docs/requirements.txt
+    # ^  requirements.txt shared with Read The Docs
+commands =
+    sphinx-build -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs}
+
+
+[testenv:publish]
+description =
+    Publish the package you have been developing to a package index server.
+    By default, it uses testpypi. If you really want to publish your package
+    to be publicly accessible in PyPI, use the `-- --repository pypi` option.
+skip_install = True
+changedir = {toxinidir}
+deps = twine
+commands =
+    python -m twine check dist/*
+    python -m twine upload {posargs:--repository testpypi} dist/*

From c3bd9b06171355ffd078ad621be94b371ec65d76 Mon Sep 17 00:00:00 2001
From: Sander van den Hoek <svandenhoek@users.noreply.github.com>
Date: Thu, 21 Nov 2024 18:07:52 +0100
Subject: [PATCH 24/46] feat(RDF): Every `ColumnType` should now be correctly
 converted to RDF (#4323)

* Moved namespace creation to own method + enum

* auto-formatting

* simplified code

* minor renames for more clarity

* Split ColumnType mapping knowledge to separate class

* auto-formatting

* Adjusted for equals check

* Fixed empty values check

* Added email fix

* Fix to copy old behavior

* Added some notes

* Created dedicated function for String methods to remove some initially needed castings.

* Minor javadoc changes

* Added a test that validates if all ColumnTypes are covered by a mapper

* reverted an accidental change

* auto-formatting

* Split RDF row generating into separate functions

* added baseURL validation to ColumnTypeRdfMapper

* Fixed UUIDs being represented as Strings

* concept version of testing all ColumnType conversions

* Enabled previously failing test code

* fixed a test

* fixed a bug for datetime_array

* Updated tests

* Fixed ColumnType.FILE IRI

* ColumnType.HEAD correct implementation/test

* Fixed test to check correctly for REFBACK (non-query retrieval excludes REFBACK values)

* Updated test comments

* JSONB_ARRAY now not included in RDF output

* fixed comment

* Added some basic file metadata for ColumnType.FILE

* Added missing drop schema in test

* Added test to validate if refback is in RDF output

* Fixed a bug regarding composite keys

* Added missing drop schema in testing

* auto-formatting

* auto-formatting

* Revert "auto-formatting" -> in class unrelated to this PR

This reverts commit 4f5d0ce0a725d3b501b2ee7d235ff0954c0afa02.

* fixes AUTO_ID (uses Snowflake ID, not UUID)
---
 .../emx2/rdf/ColumnTypeRdfMapper.java         | 316 +++++++++++++
 .../molgenis/emx2/rdf/DefaultNamespace.java   |  36 ++
 .../org/molgenis/emx2/rdf/RDFService.java     | 442 +++++++-----------
 .../emx2/rdf/ColumnTypeRdfMapperTest.java     | 428 +++++++++++++++++
 .../java/org/molgenis/emx2/rdf/RDFTest.java   |  88 ++++
 .../src/test/resources/testfiles/molgenis.png | Bin 0 -> 37458 bytes
 6 files changed, 1042 insertions(+), 268 deletions(-)
 create mode 100644 backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java
 create mode 100644 backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/DefaultNamespace.java
 create mode 100644 backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapperTest.java
 create mode 100644 backend/molgenis-emx2-rdf/src/test/resources/testfiles/molgenis.png

diff --git a/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java b/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java
new file mode 100644
index 0000000000..353ed53ebc
--- /dev/null
+++ b/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java
@@ -0,0 +1,316 @@
+package org.molgenis.emx2.rdf;
+
+import static java.util.Map.entry;
+import static org.eclipse.rdf4j.model.util.Values.literal;
+
+import com.google.common.net.UrlEscapers;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
+import java.util.*;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import org.eclipse.rdf4j.model.IRI;
+import org.eclipse.rdf4j.model.Namespace;
+import org.eclipse.rdf4j.model.Value;
+import org.eclipse.rdf4j.model.base.CoreDatatype;
+import org.eclipse.rdf4j.model.util.Values;
+import org.molgenis.emx2.*;
+import org.molgenis.emx2.utils.TypeUtils;
+import org.molgenis.emx2.utils.URIUtils;
+
+/**
+ * Used for functionalities that are {@link ColumnType} specific. This includes:
+ *
+ * <ul>
+ *   <li>Retrieving the appropiate {@link CoreDatatype.XSD}
+ *   <li>The method for extracting the {@link Value}'s for that specific {@link ColumnType} usable
+ *       for generating the RDF
+ * </ul>
+ */
+public class ColumnTypeRdfMapper {
+  // Needed in some cases for Values retrieval.
+  private final String baseURL;
+
+  // All ColumnType mappings.
+  // mapping.keySet() should be equal to ColumnType.values()
+  private static final Map<ColumnType, RdfColumnType> mapping =
+      Map.ofEntries(
+          // SIMPLE
+          entry(ColumnType.BOOL, RdfColumnType.BOOLEAN),
+          entry(ColumnType.BOOL_ARRAY, RdfColumnType.BOOLEAN),
+          entry(ColumnType.UUID, RdfColumnType.UUID),
+          entry(ColumnType.UUID_ARRAY, RdfColumnType.UUID),
+          entry(ColumnType.FILE, RdfColumnType.FILE),
+
+          // STRING
+          entry(ColumnType.STRING, RdfColumnType.STRING),
+          entry(ColumnType.STRING_ARRAY, RdfColumnType.STRING),
+          entry(ColumnType.TEXT, RdfColumnType.STRING),
+          entry(ColumnType.TEXT_ARRAY, RdfColumnType.STRING),
+
+          // NUMERIC
+          entry(ColumnType.INT, RdfColumnType.INT),
+          entry(ColumnType.INT_ARRAY, RdfColumnType.INT),
+          entry(ColumnType.LONG, RdfColumnType.LONG),
+          entry(ColumnType.LONG_ARRAY, RdfColumnType.LONG),
+          entry(ColumnType.DECIMAL, RdfColumnType.DECIMAL),
+          entry(ColumnType.DECIMAL_ARRAY, RdfColumnType.DECIMAL),
+          entry(ColumnType.DATE, RdfColumnType.DATE),
+          entry(ColumnType.DATE_ARRAY, RdfColumnType.DATE),
+          entry(ColumnType.DATETIME, RdfColumnType.DATETIME),
+          entry(ColumnType.DATETIME_ARRAY, RdfColumnType.DATETIME),
+          entry(ColumnType.PERIOD, RdfColumnType.DURATION),
+          entry(ColumnType.PERIOD_ARRAY, RdfColumnType.DURATION),
+
+          // COMPOSITE
+          entry(ColumnType.JSONB, RdfColumnType.STRING),
+          entry(ColumnType.JSONB_ARRAY, RdfColumnType.SKIP), // Unsupported.
+
+          // RELATIONSHIP
+          entry(ColumnType.REF, RdfColumnType.REFERENCE),
+          entry(ColumnType.REF_ARRAY, RdfColumnType.REFERENCE),
+          entry(ColumnType.REFBACK, RdfColumnType.REFERENCE),
+
+          // LAYOUT and other constants
+          entry(ColumnType.HEADING, RdfColumnType.SKIP), // Should not be in RDF output.
+
+          // format flavors that extend a baseType
+          entry(ColumnType.AUTO_ID, RdfColumnType.STRING),
+          entry(ColumnType.ONTOLOGY, RdfColumnType.ONTOLOGY),
+          entry(ColumnType.ONTOLOGY_ARRAY, RdfColumnType.ONTOLOGY),
+          entry(ColumnType.EMAIL, RdfColumnType.EMAIL),
+          entry(ColumnType.EMAIL_ARRAY, RdfColumnType.EMAIL),
+          entry(ColumnType.HYPERLINK, RdfColumnType.URI),
+          entry(ColumnType.HYPERLINK_ARRAY, RdfColumnType.URI));
+
+  public ColumnTypeRdfMapper(String baseURL) {
+    String baseUrlTrim = baseURL.trim();
+    this.baseURL = baseUrlTrim.endsWith("/") ? baseUrlTrim : baseUrlTrim + "/";
+  }
+
+  /** Retrieve all {@link ColumnType}{@code 's} which have a mapping available. */
+  static Set<ColumnType> getMapperKeys() {
+    return mapping.keySet();
+  }
+
+  public static CoreDatatype.XSD getCoreDataType(Column column) {
+    return getCoreDataType(column.getColumnType());
+  }
+
+  public static CoreDatatype.XSD getCoreDataType(ColumnType columnType) {
+    return mapping.get(columnType).getCoreDatatype();
+  }
+
+  /**
+   * Returns the output for the defined cell:
+   *
+   * <ul>
+   *   <li>If {@link ColumnType} should not be represented in RDF, returns an empty {@link Set}
+   *   <li>If field is empty, returns an empty {@link Set}
+   *   <li>If field has value(s), returns a filled {@link Set}
+   * </ul>
+   */
+  public Set<Value> retrieveValues(final Row row, final Column column) {
+    if (row.getString(column.getName()) == null) {
+      return Set.of();
+    }
+    return mapping.get(column.getColumnType()).retrieveValues(baseURL, row, column);
+  }
+
+  private enum RdfColumnType {
+    BOOLEAN(CoreDatatype.XSD.BOOLEAN) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrieval(row.getBooleanArray(column.getName()), Values::literal);
+      }
+    },
+    UUID(CoreDatatype.XSD.ANYURI) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrievalString(
+            row.getStringArray(column.getName()), (i) -> URIUtils.encodedIRI("urn:uuid:" + i));
+      }
+    },
+    STRING(CoreDatatype.XSD.STRING) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrievalString(row.getStringArray(column.getName()), Values::literal);
+      }
+    },
+    INT(CoreDatatype.XSD.INT) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrieval(row.getIntegerArray(column.getName()), Values::literal);
+      }
+    },
+    LONG(CoreDatatype.XSD.LONG) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrieval(row.getLongArray(column.getName()), Values::literal);
+      }
+    },
+    DECIMAL(CoreDatatype.XSD.DECIMAL) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrieval(row.getDecimalArray(column.getName()), Values::literal);
+      }
+    },
+    DATE(CoreDatatype.XSD.DATE) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrieval(
+            row.getDateArray(column.getName()), (i) -> literal(i.toString(), getCoreDatatype()));
+      }
+    },
+    DATETIME(CoreDatatype.XSD.DATETIME) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrieval(
+            row.getDateTimeArray(column.getName()),
+            (i) -> literal(dateTimeFormatter.format((LocalDateTime) i), getCoreDatatype()));
+      }
+    },
+    DURATION(CoreDatatype.XSD.DURATION) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrieval(row.getPeriodArray(column.getName()), Values::literal);
+      }
+    },
+
+    URI(CoreDatatype.XSD.ANYURI) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrievalString(row.getStringArray(column.getName()), URIUtils::encodedIRI);
+      }
+    },
+    EMAIL(CoreDatatype.XSD.ANYURI) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrievalString(
+            row.getStringArray(column.getName()), (i) -> URIUtils.encodedIRI("mailto:" + i));
+      }
+    },
+    FILE(CoreDatatype.XSD.ANYURI) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        final String schemaPath =
+            UrlEscapers.urlPathSegmentEscaper().escape(column.getSchemaName());
+        final String tablePath = UrlEscapers.urlPathSegmentEscaper().escape(column.getTableName());
+        final String columnPath = UrlEscapers.urlPathSegmentEscaper().escape(column.getName());
+        final String fileName =
+            UrlEscapers.urlPathSegmentEscaper().escape(row.getString(column.getName()));
+        return Set.of(
+            Values.iri(
+                baseURL
+                    + schemaPath
+                    + "/api/file/"
+                    + tablePath
+                    + "/"
+                    + columnPath
+                    + "/"
+                    + fileName));
+      }
+    },
+    REFERENCE(CoreDatatype.XSD.ANYURI) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        final TableMetadata target = column.getRefTable();
+        final String rootTableName =
+            UrlEscapers.urlPathSegmentEscaper().escape(target.getRootTable().getIdentifier());
+        final Namespace ns = getSchemaNamespace(baseURL, target.getRootTable().getSchema());
+
+        final Set<IRI> iris = new HashSet<>();
+        final Map<Integer, Map<String, String>> items = new HashMap<>();
+        for (final Reference reference : column.getReferences()) {
+          final String localColumn = reference.getName();
+          final String targetColumn = reference.getRefTo();
+          if (column.isArray()) {
+            final String[] values = row.getStringArray(localColumn);
+            if (values != null) {
+              for (int i = 0; i < values.length; i++) {
+                var keyValuePairs = items.getOrDefault(i, new LinkedHashMap<>());
+                keyValuePairs.put(targetColumn, values[i]);
+                items.put(i, keyValuePairs);
+              }
+            }
+          } else {
+            final String value = row.getString(localColumn);
+            if (value != null) {
+              var keyValuePairs = items.getOrDefault(0, new LinkedHashMap<>());
+              keyValuePairs.put(targetColumn, value);
+              items.put(0, keyValuePairs);
+            }
+          }
+        }
+
+        for (final var item : items.values()) {
+          PrimaryKey key = new PrimaryKey(item);
+          iris.add(Values.iri(ns, rootTableName + "?" + key.getEncodedValue()));
+        }
+        return Set.copyOf(iris);
+      }
+    },
+    ONTOLOGY(CoreDatatype.XSD.ANYURI) {
+      // TODO: Implement Ontology behavior where it also returns ontologyTermURI as Value.
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return RdfColumnType.REFERENCE.retrieveValues(baseURL, row, column);
+      }
+    },
+    SKIP(CoreDatatype.XSD.STRING) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return Set.of();
+      }
+    };
+
+    private static final DateTimeFormatter dateTimeFormatter =
+        DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss");
+
+    private final CoreDatatype.XSD coreDatatype;
+
+    public CoreDatatype.XSD getCoreDatatype() {
+      return coreDatatype;
+    }
+
+    RdfColumnType(CoreDatatype.XSD coreDatatype) {
+      this.coreDatatype = coreDatatype;
+    }
+
+    // TODO: Fix code duplicity with RDFService.
+    private static Namespace getSchemaNamespace(final String baseURL, final SchemaMetadata schema) {
+      final String schemaName = UrlEscapers.urlPathSegmentEscaper().escape(schema.getName());
+      final String url = baseURL + schemaName + "/api/rdf/";
+      final String prefix = TypeUtils.convertToPascalCase(schema.getName());
+      return Values.namespace(prefix, url);
+    }
+
+    /**
+     * Generic retrieval function. Can be used for {@link Values#literal(Object)} or any custom
+     * function which outputs a {@link Value}.
+     */
+    private static Set<Value> basicRetrieval(Object[] object, Function<Object, Value> function) {
+      return Arrays.stream(object)
+          .map(value -> (Value) function.apply(value))
+          .collect(Collectors.toSet());
+    }
+
+    /**
+     * Similar to {@link #basicRetrieval(Object[], Function)}, but with some changes:
+     *
+     * <ul>
+     *   <li>Enforces {@link Values#literal(String)} to be called when using it as {@code function}
+     *       parameter
+     *   <li>Removes the need for casting in custom functions that require a {@link String} as input
+     * </ul>
+     */
+    private static Set<Value> basicRetrievalString(
+        String[] object, Function<String, Value> function) {
+      return Arrays.stream(object)
+          .map(value -> (Value) function.apply(value))
+          .collect(Collectors.toSet());
+    }
+
+    abstract Set<Value> retrieveValues(final String baseURL, final Row row, final Column column);
+  }
+}
diff --git a/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/DefaultNamespace.java b/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/DefaultNamespace.java
new file mode 100644
index 0000000000..09178ebd66
--- /dev/null
+++ b/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/DefaultNamespace.java
@@ -0,0 +1,36 @@
+package org.molgenis.emx2.rdf;
+
+import java.util.Arrays;
+import java.util.stream.Stream;
+import org.eclipse.rdf4j.model.Namespace;
+import org.eclipse.rdf4j.model.impl.SimpleNamespace;
+
+public enum DefaultNamespace {
+  RDF("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#"),
+  RDFS("rdfs", "http://www.w3.org/2000/01/rdf-schema#"),
+  XSD("xsd", "http://www.w3.org/2001/XMLSchema#"),
+  OWL("owl", "http://www.w3.org/2002/07/owl#"),
+  SIO("sio", "http://semanticscience.org/resource/"),
+  QB("qb", "http://purl.org/linked-data/cube#"),
+  SKOS("skos", "http://www.w3.org/2004/02/skos/core#"),
+  DCTERMS("dcterms", "http://purl.org/dc/terms/"),
+  DCAT("dcat", "http://www.w3.org/ns/dcat#"),
+  FOAF("foaf", "http://xmlns.com/foaf/0.1/"),
+  VCARD("vcard", "http://www.w3.org/2006/vcard/ns#"),
+  ORG("org", "http://www.w3.org/ns/org#"),
+  FDP("fdp-o", "https://w3id.org/fdp/fdp-o#");
+
+  private final Namespace namespace;
+
+  public Namespace getNamespace() {
+    return namespace;
+  }
+
+  DefaultNamespace(String prefix, String namespace) {
+    this.namespace = new SimpleNamespace(prefix, namespace);
+  }
+
+  public static Stream<Namespace> streamAll() {
+    return Arrays.stream(DefaultNamespace.values()).map(DefaultNamespace::getNamespace);
+  }
+}
diff --git a/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RDFService.java b/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RDFService.java
index b3d948a848..e74e9f278a 100644
--- a/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RDFService.java
+++ b/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RDFService.java
@@ -4,9 +4,10 @@
 import static org.molgenis.emx2.Constants.MG_TABLECLASS;
 import static org.molgenis.emx2.FilterBean.f;
 import static org.molgenis.emx2.Operator.EQUALS;
-import static org.molgenis.emx2.utils.URIUtils.*;
+import static org.molgenis.emx2.SelectColumn.s;
 
 import com.google.common.net.UrlEscapers;
+import java.io.IOException;
 import java.io.OutputStream;
 import java.nio.charset.StandardCharsets;
 import java.time.format.DateTimeFormatter;
@@ -16,7 +17,6 @@
 import org.eclipse.rdf4j.model.Model;
 import org.eclipse.rdf4j.model.Namespace;
 import org.eclipse.rdf4j.model.Value;
-import org.eclipse.rdf4j.model.base.CoreDatatype;
 import org.eclipse.rdf4j.model.util.ModelBuilder;
 import org.eclipse.rdf4j.model.util.Values;
 import org.eclipse.rdf4j.model.vocabulary.*;
@@ -46,19 +46,6 @@ public class RDFService {
   private static final DateTimeFormatter dateTimeFormatter =
       DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss");
   public static final IRI LDP_CONTAINS = Values.iri("http://www.w3.org/ns/ldp#contains");
-  public static final String NAMESPACE_RDF = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
-  public static final String NAMESPACE_RDFS = "http://www.w3.org/2000/01/rdf-schema#";
-  public static final String NAMESPACE_XSD = "http://www.w3.org/2001/XMLSchema#";
-  public static final String NAMESPACE_OWL = "http://www.w3.org/2002/07/owl#";
-  public static final String NAMESPACE_SIO = "http://semanticscience.org/resource/";
-  public static final String NAMESPACE_QB = "http://purl.org/linked-data/cube#";
-  public static final String NAMESPACE_SKOS = "http://www.w3.org/2004/02/skos/core#";
-  public static final String NAMESPACE_DCTERMS = "http://purl.org/dc/terms/";
-  public static final String NAMESPACE_DCAT = "http://www.w3.org/ns/dcat#";
-  public static final String NAMESPACE_FOAF = "http://xmlns.com/foaf/0.1/";
-  public static final String NAMESPACE_VCARD = "http://www.w3.org/2006/vcard/ns#";
-  public static final String NAMESPACE_ORG = "http://www.w3.org/ns/org#";
-  public static final String NAMESPACE_FDP = "https://w3id.org/fdp/fdp-o#";
   public static final IRI IRI_DATABASE_TABLE =
       Values.iri("http://semanticscience.org/resource/SIO_000754");
   public static final IRI IRI_DATASET_CLASS =
@@ -86,15 +73,19 @@ public class RDFService {
   public static final IRI IRI_CODED_VALUE_DATATYPE =
       Values.iri("http://purl.obolibrary.org/obo/NCIT_C95637");
 
-  /** SIO:000750 = database */
+  /** SIO:SIO_000750 = database */
   public static final IRI IRI_DATABASE =
       Values.iri("http://semanticscience.org/resource/SIO_000750");
 
+  /** SIO:SIO_000396 = file */
+  public static final IRI IRI_FILE = Values.iri("http://semanticscience.org/resource/SIO_000396");
+
   public static final IRI IRI_MOLGENIS = Values.iri("https://molgenis.org");
   public static final String ONTOLOGY_TERM_URI = "ontologyTermURI";
 
   private final WriterConfig config;
   private final RDFFormat rdfFormat;
+  private final ColumnTypeRdfMapper mapper;
 
   /**
    * The baseURL is the URL at which MOLGENIS is deployed, include protocol and port (if deviating
@@ -113,11 +104,9 @@ public class RDFService {
   public RDFService(final String baseURL, final String rdfAPIPath, final RDFFormat format) {
     // Ensure that the base URL has a trailing "/" so we can use it easily to
     // construct URL paths.
-    if (baseURL.trim().endsWith("/")) {
-      this.baseURL = baseURL.trim();
-    } else {
-      this.baseURL = baseURL.trim() + "/";
-    }
+    String baseUrlTrim = baseURL.trim();
+    this.baseURL = baseUrlTrim.endsWith("/") ? baseUrlTrim : baseUrlTrim + "/";
+    this.mapper = new ColumnTypeRdfMapper(this.baseURL);
     this.rdfFormat = format == null ? RDFFormat.TURTLE : format;
 
     this.config = new WriterConfig();
@@ -158,29 +147,8 @@ public void describeAsRDF(
     try {
       final ModelBuilder builder = new ModelBuilder();
 
-      // Defines if all used schemas have a custom_rdf setting.
-      boolean allIncludeCustomRdf = true;
-      // Define the schemas at the start of the document.
-      for (final Schema schema : schemas) {
-        final Namespace ns = getSchemaNamespace(schema);
-        builder.setNamespace(ns);
-        // Adds custom RDF to model.
-        if (schema.hasSetting(SETTING_CUSTOM_RDF)) {
-          addModelToBuilder(
-              builder,
-              Rio.parse(
-                  IOUtils.toInputStream(
-                      schema.getSettingValue(SETTING_CUSTOM_RDF), StandardCharsets.UTF_8),
-                  RDFFormat.TURTLE));
-        } else {
-          allIncludeCustomRdf = false;
-        }
-      }
-
-      // If any of the used schemas do not have custom_rdf set, adds the default ones.
-      if (!allIncludeCustomRdf) {
-        addDefaultPrefixes(builder);
-      }
+      // (custom) namespaces & custom rdf
+      buildgenericRdf(builder, schemas);
 
       if (table == null) {
         describeRoot(builder);
@@ -245,25 +213,42 @@ private boolean processInheritedTable(
     return false;
   }
 
-  private void addModelToBuilder(ModelBuilder builder, Model model) {
-    model.getNamespaces().forEach(builder::setNamespace);
-    model.forEach(e -> builder.add(e.getSubject(), e.getPredicate(), e.getObject()));
+  /**
+   * Processes all schemas for custom namespaces/RDF.
+   *
+   * @param builder
+   * @param schemas
+   * @throws IOException
+   */
+  private void buildgenericRdf(ModelBuilder builder, Schema[] schemas) throws IOException {
+    // Defines if all used schemas have a custom_rdf setting.
+    boolean allIncludeCustomRdf = true;
+    // Define the schemas at the start of the document.
+    for (final Schema schema : schemas) {
+      final Namespace ns = getSchemaNamespace(schema);
+      builder.setNamespace(ns);
+      // Adds custom RDF to model.
+      if (schema.hasSetting(SETTING_CUSTOM_RDF)) {
+        addModelToBuilder(
+            builder,
+            Rio.parse(
+                IOUtils.toInputStream(
+                    schema.getSettingValue(SETTING_CUSTOM_RDF), StandardCharsets.UTF_8),
+                RDFFormat.TURTLE));
+      } else {
+        allIncludeCustomRdf = false;
+      }
+    }
+
+    // If any of the used schemas do not have custom_rdf set, adds the default ones.
+    if (!allIncludeCustomRdf) {
+      DefaultNamespace.streamAll().forEach(builder::setNamespace);
+    }
   }
 
-  private void addDefaultPrefixes(ModelBuilder builder) {
-    builder.setNamespace("rdf", NAMESPACE_RDF);
-    builder.setNamespace("rdfs", NAMESPACE_RDFS);
-    builder.setNamespace("xsd", NAMESPACE_XSD);
-    builder.setNamespace("owl", NAMESPACE_OWL);
-    builder.setNamespace("sio", NAMESPACE_SIO);
-    builder.setNamespace("qb", NAMESPACE_QB);
-    builder.setNamespace("skos", NAMESPACE_SKOS);
-    builder.setNamespace("dcterms", NAMESPACE_DCTERMS);
-    builder.setNamespace("dcat", NAMESPACE_DCAT);
-    builder.setNamespace("foaf", NAMESPACE_FOAF);
-    builder.setNamespace("vcard", NAMESPACE_VCARD);
-    builder.setNamespace("org", NAMESPACE_ORG);
-    builder.setNamespace("fdp-o", NAMESPACE_FDP);
+  private void addModelToBuilder(ModelBuilder builder, Model model) {
+    model.getNamespaces().forEach(builder::setNamespace); // namespaces
+    model.forEach(e -> builder.add(e.getSubject(), e.getPredicate(), e.getObject())); // triples
   }
 
   public WriterConfig getConfig() {
@@ -424,7 +409,7 @@ private void describeColumn(final ModelBuilder builder, final Column column) {
         builder.add(subject, RDF.TYPE, OWL.OBJECTPROPERTY);
       } else {
         builder.add(subject, RDF.TYPE, OWL.DATATYPEPROPERTY);
-        builder.add(subject, RDFS.RANGE, columnTypeToXSD(column.getColumnType()));
+        builder.add(subject, RDFS.RANGE, ColumnTypeRdfMapper.getCoreDataType(column));
       }
     }
     builder.add(subject, RDFS.LABEL, column.getName());
@@ -457,34 +442,6 @@ private void describeColumn(final ModelBuilder builder, final Column column) {
     }
   }
 
-  private CoreDatatype.XSD columnTypeToXSD(final ColumnType columnType) {
-    return switch (columnType) {
-      case BOOL, BOOL_ARRAY -> CoreDatatype.XSD.BOOLEAN;
-      case DATE, DATE_ARRAY -> CoreDatatype.XSD.DATE;
-      case DATETIME, DATETIME_ARRAY -> CoreDatatype.XSD.DATETIME;
-      case DECIMAL, DECIMAL_ARRAY -> CoreDatatype.XSD.DECIMAL;
-      case EMAIL,
-              EMAIL_ARRAY,
-              HEADING,
-              JSONB,
-              JSONB_ARRAY,
-              STRING,
-              STRING_ARRAY,
-              TEXT,
-              TEXT_ARRAY,
-              UUID,
-              UUID_ARRAY,
-              AUTO_ID ->
-          CoreDatatype.XSD.STRING;
-      case FILE, HYPERLINK, HYPERLINK_ARRAY, ONTOLOGY, ONTOLOGY_ARRAY, REF, REF_ARRAY, REFBACK ->
-          CoreDatatype.XSD.ANYURI;
-      case INT, INT_ARRAY -> CoreDatatype.XSD.INT;
-      case LONG, LONG_ARRAY -> CoreDatatype.XSD.LONG;
-      case PERIOD, PERIOD_ARRAY -> CoreDatatype.XSD.DURATION;
-      default -> throw new MolgenisException("ColumnType not mapped: " + columnType);
-    };
-  }
-
   /**
    * Write the rows to RDF
    *
@@ -492,83 +449,117 @@ private CoreDatatype.XSD columnTypeToXSD(final ColumnType columnType) {
    * @param table the table for which to fetch the rows
    * @param rowId optional rowId
    */
-  public void rowsToRdf(final ModelBuilder builder, Table table, final String rowId) {
+  public void rowsToRdf(final ModelBuilder builder, final Table table, final String rowId) {
     final IRI tableIRI = getTableIRI(table);
-    for (final Row row : getRows(table, rowId)) {
-      IRI subject = getIriForRow(row, table.getMetadata());
-
-      if (table.getMetadata().getTableType() == TableType.ONTOLOGIES) {
-        builder.add(subject, RDF.TYPE, IRI_CODED_VALUE_DATATYPE);
-        builder.add(subject, RDF.TYPE, OWL.CLASS);
-        builder.add(subject, RDF.TYPE, SKOS.CONCEPT);
-        builder.add(subject, RDFS.SUBCLASSOF, tableIRI);
-        builder.add(subject, SKOS.IN_SCHEME, tableIRI);
-        if (row.getString("name") != null) {
-          builder.add(subject, RDFS.LABEL, Values.literal(row.getString("name")));
-          builder.add(subject, SKOS.PREF_LABEL, Values.literal(row.getString("name")));
-        }
-        if (row.getString("label") != null) {
-          builder.add(subject, RDFS.LABEL, Values.literal(row.getString("label")));
-          builder.add(subject, SKOS.ALT_LABEL, Values.literal(row.getString("name")));
-        }
-        if (row.getString("code") != null) {
-          builder.add(subject, SKOS.NOTATION, Values.literal(row.getString("code")));
-        }
-        if (row.getString("codesystem") != null) {
-          builder.add(
-              subject, IRI_CONTROLLED_VOCABULARY, Values.literal(row.getString("codesystem")));
-        }
-        if (row.getString("definition") != null) {
-          builder.add(subject, SKOS.DEFINITION, Values.literal(row.getString("definition")));
-        }
-        if (row.getString(ONTOLOGY_TERM_URI) != null) {
-          builder.add(subject, OWL.SAMEAS, Values.iri(row.getString(ONTOLOGY_TERM_URI)));
-        }
-        if (row.getString("parent") != null) {
-          List<IRI> parents = getIriValue(row, table.getMetadata().getColumn("parent"));
-          for (var parent : parents) {
-            builder.add(subject, RDFS.SUBCLASSOF, parent);
-          }
-        }
-      } else {
-        builder.add(subject, RDF.TYPE, tableIRI);
-        builder.add(subject, RDF.TYPE, IRI_OBSERVATION);
-        if (table.getMetadata().getSemantics() != null) {
-          for (String semantics : table.getMetadata().getSemantics()) {
-            builder.add(subject, RDF.TYPE, iri(semantics));
+    final List<Row> rows = getRows(table, rowId);
+    switch (table.getMetadata().getTableType()) {
+      case ONTOLOGIES ->
+          rows.forEach(
+              row -> ontologyRowToRdf(builder, table, tableIRI, row, getIriForRow(row, table)));
+      case DATA ->
+          rows.forEach(
+              row -> dataRowToRdf(builder, table, tableIRI, row, rowId, getIriForRow(row, table)));
+      default -> throw new MolgenisException("Cannot convert unsupported TableType to RDF");
+    }
+  }
+
+  private void ontologyRowToRdf(
+      final ModelBuilder builder,
+      final Table table,
+      final IRI tableIRI,
+      final Row row,
+      final IRI subject) {
+    builder.add(subject, RDF.TYPE, IRI_CODED_VALUE_DATATYPE);
+    builder.add(subject, RDF.TYPE, OWL.CLASS);
+    builder.add(subject, RDF.TYPE, SKOS.CONCEPT);
+    builder.add(subject, RDFS.SUBCLASSOF, tableIRI);
+    builder.add(subject, SKOS.IN_SCHEME, tableIRI);
+    if (row.getString("name") != null) {
+      builder.add(subject, RDFS.LABEL, Values.literal(row.getString("name")));
+      builder.add(subject, SKOS.PREF_LABEL, Values.literal(row.getString("name")));
+    }
+    if (row.getString("label") != null) {
+      builder.add(subject, RDFS.LABEL, Values.literal(row.getString("label")));
+      builder.add(subject, SKOS.ALT_LABEL, Values.literal(row.getString("name")));
+    }
+    if (row.getString("code") != null) {
+      builder.add(subject, SKOS.NOTATION, Values.literal(row.getString("code")));
+    }
+    if (row.getString("codesystem") != null) {
+      builder.add(subject, IRI_CONTROLLED_VOCABULARY, Values.literal(row.getString("codesystem")));
+    }
+    if (row.getString("definition") != null) {
+      builder.add(subject, SKOS.DEFINITION, Values.literal(row.getString("definition")));
+    }
+    if (row.getString(ONTOLOGY_TERM_URI) != null) {
+      builder.add(subject, OWL.SAMEAS, Values.iri(row.getString(ONTOLOGY_TERM_URI)));
+    }
+    if (row.getString("parent") != null) {
+      Set<Value> parents = mapper.retrieveValues(row, table.getMetadata().getColumn("parent"));
+      for (var parent : parents) {
+        builder.add(subject, RDFS.SUBCLASSOF, parent);
+      }
+    }
+  }
+
+  private void dataRowToRdf(
+      final ModelBuilder builder,
+      Table table,
+      final IRI tableIRI,
+      final Row row,
+      final String rowId,
+      final IRI subject) {
+    builder.add(subject, RDF.TYPE, tableIRI);
+    builder.add(subject, RDF.TYPE, IRI_OBSERVATION);
+    if (table.getMetadata().getSemantics() != null) {
+      for (String semantics : table.getMetadata().getSemantics()) {
+        builder.add(subject, RDF.TYPE, iri(semantics));
+      }
+    }
+    builder.add(subject, IRI_DATASET_PREDICATE, tableIRI);
+    builder.add(subject, RDFS.LABEL, Values.literal(getLabelForRow(row, table.getMetadata())));
+    // via rowId might be subclass
+    if (rowId != null) {
+      // because row IRI point to root tables we need to find actual subclass table to ensure we
+      // get all columns
+      table = getSubclassTableForRowBasedOnMgTableclass(table, row);
+    }
+    for (final Column column : table.getMetadata().getColumns()) {
+      // Exclude the system columns that refer to specific users
+      if (column.isSystemAddUpdateByUserColumn()) {
+        continue;
+      }
+      IRI columnIRI = getColumnIRI(column);
+      for (final Value value : mapper.retrieveValues(row, column)) {
+        if (column.getSemantics() != null) {
+          for (String semantics : column.getSemantics()) {
+            builder.add(subject.stringValue(), semantics, value);
+            //                builder.add(
+            //                    // subject, Values.iri(semantics), value);
+            //                    subject, Values.iri(semantics.split(":")[0],
+            // semantics.split(":")[1]), value);
           }
         }
-        builder.add(subject, IRI_DATASET_PREDICATE, tableIRI);
-        builder.add(subject, RDFS.LABEL, Values.literal(getLabelForRow(row, table.getMetadata())));
-        // via rowId might be subclass
-        if (rowId != null) {
-          // because row IRI point to root tables we need to find actual subclass table to ensure we
-          // get all columns
-          table = getSubclassTableForRowBasedOnMgTableclass(table, row);
+        builder.add(subject, columnIRI, value);
+        if (column.getColumnType().equals(ColumnType.HYPERLINK)
+            || column.getColumnType().equals(ColumnType.HYPERLINK_ARRAY)) {
+          var resource = Values.iri(value.stringValue());
+          builder.add(resource, RDFS.LABEL, Values.literal(value.stringValue()));
         }
-        for (final Column column : table.getMetadata().getColumns()) {
-          // Exclude the system columns that refer to specific users
-          if (column.isSystemAddUpdateByUserColumn()) {
-            continue;
-          }
-          IRI columnIRI = getColumnIRI(column);
-          for (final Value value : formatValue(row, column)) {
-            if (column.getSemantics() != null) {
-              for (String semantics : column.getSemantics()) {
-                builder.add(subject.stringValue(), semantics, value);
-                //                builder.add(
-                //                    // subject, Values.iri(semantics), value);
-                //                    subject, Values.iri(semantics.split(":")[0],
-                // semantics.split(":")[1]), value);
-              }
-            }
-            builder.add(subject, columnIRI, value);
-            if (column.getColumnType().equals(ColumnType.HYPERLINK)
-                || column.getColumnType().equals(ColumnType.HYPERLINK_ARRAY)) {
-              var resource = Values.iri(value.stringValue());
-              builder.add(resource, RDFS.LABEL, Values.literal(value.stringValue()));
-            }
-          }
+        // Adds file metadata.
+        if (column.isFile()) {
+          IRI fileSubject = (IRI) value;
+          builder.add(fileSubject, RDF.TYPE, IRI_FILE);
+          builder.add(
+              fileSubject,
+              DCTERMS.TITLE,
+              Values.literal(row.getString(column.getName() + "_filename")));
+          builder.add(
+              fileSubject,
+              DCTERMS.FORMAT,
+              Values.iri(
+                  "http://www.iana.org/assignments/media-types/"
+                      + row.getString(column.getName() + "_mimetype")));
         }
       }
     }
@@ -603,15 +594,28 @@ private String getLabelForRow(final Row row, final TableMetadata metadata) {
 
   private List<Row> getRows(Table table, final String rowId) {
     Query query = table.query();
+
+    List<SelectColumn> selectColumns = new ArrayList<>();
+    for (Column c : table.getMetadata().getColumns()) {
+      if (c.isFile()) {
+        selectColumns.add(s(c.getName(), s("id"), s("filename"), s("mimetype")));
+      } else if (c.isReference()) {
+        c.getReferences().forEach(i -> selectColumns.add(s(i.getName())));
+      } else {
+        selectColumns.add(s(c.getName()));
+      }
+    }
+    SelectColumn[] selectArray = selectColumns.toArray(SelectColumn[]::new);
+
     if (rowId != null) {
       // first find from root table
       PrimaryKey key = PrimaryKey.makePrimaryKeyFromEncodedKey(rowId);
-      List<Row> oneRow = query.where(key.getFilter()).retrieveRows();
+      List<Row> oneRow = query.select(selectArray).where(key.getFilter()).retrieveRows();
       // if subclass
       if (oneRow.size() == 1 && oneRow.get(0).getString(MG_TABLECLASS) != null) {
         Row row = oneRow.get(0);
         table = getSubclassTableForRowBasedOnMgTableclass(table, row);
-        return table.query().where(key.getFilter()).retrieveRows();
+        return table.query().select(selectArray).where(key.getFilter()).retrieveRows();
       }
       return oneRow;
     } else {
@@ -619,10 +623,14 @@ private List<Row> getRows(Table table, final String rowId) {
         var tableName = table.getSchema().getName() + "." + table.getName();
         query.where(f("mg_tableclass", EQUALS, tableName));
       }
-      return query.retrieveRows();
+      return query.select(selectArray).retrieveRows();
     }
   }
 
+  private IRI getIriForRow(final Row row, final Table table) {
+    return getIriForRow(row, table.getMetadata());
+  }
+
   private IRI getIriForRow(final Row row, final TableMetadata metadata) {
     final String rootTableName =
         UrlEscapers.urlPathSegmentEscaper().escape(metadata.getRootTable().getIdentifier());
@@ -643,106 +651,4 @@ private IRI getIriForRow(final Row row, final TableMetadata metadata) {
     PrimaryKey key = new PrimaryKey(keyParts);
     return Values.iri(ns, rootTableName + "?" + key.getEncodedValue());
   }
-
-  private List<IRI> getIriValue(final Row row, final Column column) {
-    final TableMetadata target = column.getRefTable();
-    final String rootTableName =
-        UrlEscapers.urlPathSegmentEscaper().escape(target.getRootTable().getIdentifier());
-    final Namespace ns = getSchemaNamespace(target.getRootTable().getSchema());
-
-    final Set<IRI> iris = new HashSet<>();
-    final Map<Integer, Map<String, String>> items = new HashMap<>();
-    for (final Reference reference : column.getReferences()) {
-      final String localColumn = reference.getName();
-      final String targetColumn = reference.getRefTo();
-      if (column.isArray()) {
-        final String[] values = row.getStringArray(localColumn);
-        if (values != null) {
-          for (int i = 0; i < values.length; i++) {
-            var keyValuePairs = items.getOrDefault(i, new LinkedHashMap<>());
-            keyValuePairs.put(targetColumn, values[i]);
-            items.put(i, keyValuePairs);
-          }
-        }
-      } else {
-        final String value = row.getString(localColumn);
-        if (value != null) {
-          var keyValuePairs = items.getOrDefault(0, new LinkedHashMap<>());
-          keyValuePairs.put(targetColumn, value);
-          items.put(0, keyValuePairs);
-        }
-      }
-    }
-
-    for (final var item : items.values()) {
-      PrimaryKey key = new PrimaryKey(item);
-      iris.add(Values.iri(ns, rootTableName + "?" + key.getEncodedValue()));
-    }
-    return List.copyOf(iris);
-  }
-
-  private List<Value> formatValue(final Row row, final Column column) {
-    final List<Value> values = new ArrayList<>();
-    final ColumnType columnType = column.getColumnType();
-    if (columnType.isReference()) {
-      values.addAll(getIriValue(row, column));
-    } else if (columnType.equals(ColumnType.FILE)) {
-      if (row.getString(column.getName() + "_id") != null) {
-        final String schemaPath =
-            UrlEscapers.urlPathSegmentEscaper().escape(column.getSchemaName());
-        final String tablePath = UrlEscapers.urlPathSegmentEscaper().escape(column.getTableName());
-        final String columnPath = UrlEscapers.urlPathSegmentEscaper().escape(column.getName());
-        values.add(Values.iri(schemaPath + "/api/file/" + tablePath + "/" + columnPath + "/"));
-      }
-    } else {
-      values.addAll(getLiteralValues(row, column));
-    }
-    return values;
-  }
-
-  private List<Value> getLiteralValues(final Row row, final Column column) {
-    CoreDatatype.XSD xsdType = columnTypeToXSD(column.getColumnType());
-    if (row.getString(column.getName()) == null) {
-      return List.of();
-    }
-    return switch (xsdType) {
-      case BOOLEAN ->
-          Arrays.stream(row.getBooleanArray(column.getName()))
-              .map(value -> (Value) literal(value))
-              .toList();
-      case DATE ->
-          Arrays.stream(row.getDateArray(column.getName()))
-              .map(value -> (Value) literal(value.toString(), xsdType))
-              .toList();
-      case DATETIME ->
-          Arrays.stream(row.getDateTimeArray(column.getName()))
-              .map(value -> (Value) literal(dateTimeFormatter.format(value), xsdType))
-              .toList();
-      case DECIMAL ->
-          Arrays.stream(row.getDecimalArray(column.getName()))
-              .map(value -> (Value) literal(value))
-              .toList();
-      case STRING ->
-          Arrays.stream(row.getStringArray(column.getName()))
-              .map(value -> (Value) literal(value))
-              .toList();
-      case ANYURI ->
-          Arrays.stream(row.getStringArray(column.getName()))
-              .map(value -> (Value) encodedIRI(value))
-              .toList();
-      case INT ->
-          Arrays.stream(row.getIntegerArray(column.getName()))
-              .map(value -> (Value) literal(value))
-              .toList();
-      case LONG ->
-          Arrays.stream(row.getLongArray(column.getName()))
-              .map(value -> (Value) literal(value))
-              .toList();
-      case DURATION ->
-          Arrays.stream(row.getPeriodArray(column.getName()))
-              .map(value -> (Value) literal(value))
-              .toList();
-      default -> throw new MolgenisException("XSD type formatting not supported for: " + xsdType);
-    };
-  }
 }
diff --git a/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapperTest.java b/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapperTest.java
new file mode 100644
index 0000000000..bc71a1d7d7
--- /dev/null
+++ b/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapperTest.java
@@ -0,0 +1,428 @@
+package org.molgenis.emx2.rdf;
+
+import static org.molgenis.emx2.Column.column;
+import static org.molgenis.emx2.Row.row;
+import static org.molgenis.emx2.TableMetadata.table;
+
+import java.io.File;
+import java.util.*;
+import java.util.stream.Collectors;
+import org.eclipse.rdf4j.model.Value;
+import org.eclipse.rdf4j.model.base.CoreDatatype;
+import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
+import org.eclipse.rdf4j.model.util.Values;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.molgenis.emx2.*;
+import org.molgenis.emx2.sql.TestDatabaseFactory;
+
+/**
+ * When a new {@link ColumnType} is added and/or {@link #validateAllColumnTypesCovered()} fails, be
+ * sure to add thew new {@link ColumnType} to all tests!!!
+ */
+class ColumnTypeRdfMapperTest {
+  static final String TEST_SCHEMA = "AllColumnTypes";
+  static final String TEST_TABLE = "TestTable";
+  static final String REF_TABLE = "TestRefTable";
+  static final String REFBACK_TABLE = "TestRefBackTable";
+  static final String ONT_TABLE = "TestOntology";
+  static final ClassLoader classLoader = ColumnTypeRdfMapperTest.class.getClassLoader();
+  static final SimpleValueFactory factory = SimpleValueFactory.getInstance();
+  static final String baseUrl = "http://localhost:8080/";
+  static final String rdfApiUrlPrefix = baseUrl + TEST_SCHEMA + "/api/rdf/";
+  static final String fileApiUrlPrefix = baseUrl + TEST_SCHEMA + "/api/file/";
+  static final ColumnTypeRdfMapper mapper = new ColumnTypeRdfMapper(baseUrl);
+  static final File TEST_FILE =
+      new File(classLoader.getResource("testfiles/molgenis.png").getFile());
+
+  static Database database;
+  static Schema allColumnTypes;
+  static Row firstRow;
+
+  @BeforeAll
+  public static void setup() {
+    // Initialize schema.
+    database = TestDatabaseFactory.getTestDatabase();
+    allColumnTypes = database.dropCreateSchema(TEST_SCHEMA);
+
+    // Generates a column for each ColumnType.
+    // Filters out REFBACK so that it can be added as last step when all REFs are generated.
+    Column[] columns =
+        Arrays.stream(ColumnType.values())
+            .map((value) -> column(value.name(), value))
+            .filter((column -> !column.getColumnType().equals(ColumnType.REFBACK)))
+            .toArray(Column[]::new);
+
+    // Defines column-specific settings.
+    for (Column column : columns) {
+      switch (column.getColumnType()) {
+        case STRING -> column.setPkey();
+        case REF, REF_ARRAY -> column.setRefTable(REF_TABLE);
+        case ONTOLOGY, ONTOLOGY_ARRAY -> column.setRefTable(ONT_TABLE);
+      }
+    }
+
+    // Creates tables.
+    allColumnTypes.create(
+        // Ontology table
+        table(ONT_TABLE).setTableType(TableType.ONTOLOGIES),
+        // Table to ref towards
+        table(REF_TABLE, column("id", ColumnType.STRING).setPkey()),
+        // Table to test on
+        table(TEST_TABLE, columns),
+        // Table to get refbacks from
+        table(
+            REFBACK_TABLE,
+            column("id", ColumnType.STRING).setPkey(),
+            column("ref", ColumnType.REF).setRefTable(TEST_TABLE)));
+
+    // Adds REFBACK.
+    allColumnTypes
+        .getTable(TEST_TABLE)
+        .getMetadata()
+        .add(
+            column(ColumnType.REFBACK.name(), ColumnType.REFBACK)
+                .setRefTable(REFBACK_TABLE)
+                .setRefBack("ref"));
+
+    // Inserts table data
+    allColumnTypes
+        .getTable(ONT_TABLE)
+        .insert(
+            row("name", "aa", "ontologyTermURI", "http://example.com/aa"),
+            row("name", "bb", "ontologyTermURI", "http://example.com/bb"),
+            row("name", "cc", "ontologyTermURI", "http://example.com/cc"));
+
+    allColumnTypes.getTable(REF_TABLE).insert(row("id", "1"), row("id", "2"), row("id", "3"));
+
+    allColumnTypes
+        .getTable(TEST_TABLE)
+        .insert(
+            row(
+                // SIMPLE
+                ColumnType.BOOL.name(),
+                "true",
+                ColumnType.BOOL_ARRAY.name(),
+                "true,false",
+                ColumnType.UUID.name(),
+                "e8af409e-86f7-11ef-85b2-6b76fd707d70",
+                ColumnType.UUID_ARRAY.name(),
+                "e8af409e-86f7-11ef-85b2-6b76fd707d70,14bfb4ca-86f8-11ef-8cc0-378b59fe72e8",
+                ColumnType.FILE.name(),
+                TEST_FILE,
+                // STRING
+                ColumnType.STRING.name(),
+                "lonelyString",
+                ColumnType.STRING_ARRAY.name(),
+                "string1,string2",
+                ColumnType.TEXT.name(),
+                "lonelyText",
+                ColumnType.TEXT_ARRAY.name(),
+                "text1,text2",
+                ColumnType.INT.name(),
+                "0",
+                ColumnType.INT_ARRAY.name(),
+                "1,2",
+                ColumnType.LONG.name(),
+                "3",
+                ColumnType.LONG_ARRAY.name(),
+                "4,5",
+                ColumnType.DECIMAL.name(),
+                "0.5",
+                ColumnType.DECIMAL_ARRAY.name(),
+                "1.5,2.5",
+                ColumnType.DATE.name(),
+                "2000-01-01",
+                ColumnType.DATE_ARRAY.name(),
+                "2001-01-01,2002-01-01",
+                ColumnType.DATETIME.name(),
+                "3000-01-01T12:30:00",
+                ColumnType.DATETIME_ARRAY.name(),
+                "3001-01-01T12:30:00,3002-01-01T12:30:00",
+                ColumnType.PERIOD.name(),
+                "P1D",
+                ColumnType.PERIOD_ARRAY.name(),
+                "P1M,P1Y",
+                // COMPOSITE
+                ColumnType.JSONB.name(),
+                "{\"a\":1,\"b\":2}",
+                ColumnType.JSONB_ARRAY.name(), // TODO: Remove if deprecated.
+                "{\"c\":3},{\"d\":4,\"e\":5}",
+                // RELATIONSHIP
+                ColumnType.REF.name(),
+                "1",
+                ColumnType.REF_ARRAY.name(),
+                "2,3",
+                // -- no manual entry: ColumnType.REFBACK
+                // LAYOUT and other constants
+                ColumnType.HEADING.name(),
+                "heading",
+                // format flavors that extend a baseType
+                // -- no manual entry: ColumnType.AUTO_ID
+                ColumnType.ONTOLOGY.name(),
+                "aa",
+                ColumnType.ONTOLOGY_ARRAY.name(),
+                "bb,cc",
+                ColumnType.EMAIL.name(),
+                "aap@example.com",
+                ColumnType.EMAIL_ARRAY.name(),
+                "noot@example.com,mies@example.com",
+                ColumnType.HYPERLINK.name(),
+                "https://molgenis.org",
+                ColumnType.HYPERLINK_ARRAY.name(),
+                "https://molgenis.org, https://github.com/molgenis"));
+
+    allColumnTypes.getTable(REFBACK_TABLE).insert(row("id", "1", "ref", "lonelyString"));
+
+    // Use query to explicitly retrieve all rows as the following would exclude REFBACK values:
+    // allColumnTypes.getTable(TEST_TABLE).retrieveRows()
+    SelectColumn[] selectColumns =
+        Arrays.stream(ColumnType.values())
+            .map(i -> new SelectColumn(i.name()))
+            .toArray(SelectColumn[]::new);
+
+    // Describe first row for easy access.
+    firstRow =
+        allColumnTypes.getTable(TEST_TABLE).query().select(selectColumns).retrieveRows().get(0);
+  }
+
+  @AfterAll
+  public static void tearDown() {
+    database = TestDatabaseFactory.getTestDatabase();
+    database.dropSchema(allColumnTypes.getName());
+  }
+
+  private Set<Value> retrieveValues(String columnName) {
+    return mapper.retrieveValues(
+        firstRow, allColumnTypes.getTable(TEST_TABLE).getMetadata().getColumn(columnName));
+  }
+
+  private Value retrieveFirstValue(String columnName) {
+    return retrieveValues(columnName).stream().findFirst().get();
+  }
+
+  /**
+   * If {@link ColumnTypeRdfMapper} misses any mappings for {@link ColumnType}, this test will fail.
+   * Should prevent new types being added without implementing the API support as well.
+   */
+  @Test
+  void validateAllColumnTypesCovered() {
+    Set<ColumnType> columnTypes = Arrays.stream(ColumnType.values()).collect(Collectors.toSet());
+    Set<ColumnType> columnMappings = ColumnTypeRdfMapper.getMapperKeys();
+
+    Assertions.assertEquals(columnTypes, columnMappings);
+  }
+
+  /**
+   * Validates if {@link org.eclipse.rdf4j.model.Value} is of expected type. Only validates the
+   * non-array {@link ColumnType}{@code s} (as array-versions should be of identical type).
+   */
+  @Test
+  void validateValueTypes() {
+    Row row = allColumnTypes.getTable(TEST_TABLE).retrieveRows().get(0);
+
+    Assertions.assertAll(
+        // SIMPLE
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.BOOL.name()).isLiteral()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.UUID.name()).isIRI()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.FILE.name()).isIRI()),
+        // STRING
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.STRING.name()).isLiteral()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.TEXT.name()).isLiteral()),
+
+        // NUMERIC
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.INT.name()).isLiteral()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.LONG.name()).isLiteral()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.DECIMAL.name()).isLiteral()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.DATE.name()).isLiteral()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.DATETIME.name()).isLiteral()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.PERIOD.name()).isLiteral()),
+
+        // COMPOSITE
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.JSONB.name()).isLiteral()),
+
+        // RELATIONSHIP
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.REF.name()).isIRI()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.REFBACK.name()).isIRI()),
+
+        // LAYOUT and other constants
+        // ColumnType.HEADING.name() -> no Value should be present to validate on
+
+        // format flavors that extend a baseType
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.AUTO_ID.name()).isLiteral()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.ONTOLOGY.name()).isIRI()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.EMAIL.name()).isIRI()),
+        () -> Assertions.assertTrue(retrieveFirstValue(ColumnType.HYPERLINK.name()).isIRI()));
+  }
+
+  @Test
+  void validateValuesRetrieval() {
+    Assertions.assertAll(
+        // SIMPLE
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal(true)), retrieveValues(ColumnType.BOOL.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal(true), Values.literal(false)),
+                retrieveValues(ColumnType.BOOL_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.iri("urn:uuid:e8af409e-86f7-11ef-85b2-6b76fd707d70")),
+                retrieveValues(ColumnType.UUID.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.iri("urn:uuid:e8af409e-86f7-11ef-85b2-6b76fd707d70"),
+                    Values.iri("urn:uuid:14bfb4ca-86f8-11ef-8cc0-378b59fe72e8")),
+                retrieveValues(ColumnType.UUID_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.iri(
+                        fileApiUrlPrefix
+                            + TEST_TABLE
+                            + "/"
+                            + ColumnType.FILE.name()
+                            + "/"
+                            // Not sure how to retrieve more directly as changes everytime
+                            + firstRow.getString(ColumnType.FILE.name()))),
+                retrieveValues(ColumnType.FILE.name())),
+        // STRING
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal("lonelyString", CoreDatatype.XSD.STRING)),
+                retrieveValues(ColumnType.STRING.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.literal("string1", CoreDatatype.XSD.STRING),
+                    Values.literal("string2", CoreDatatype.XSD.STRING)),
+                retrieveValues(ColumnType.STRING_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal("lonelyText", CoreDatatype.XSD.STRING)),
+                retrieveValues(ColumnType.TEXT.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.literal("text1", CoreDatatype.XSD.STRING),
+                    Values.literal("text2", CoreDatatype.XSD.STRING)),
+                retrieveValues(ColumnType.TEXT_ARRAY.name())),
+        // NUMERIC
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal(0)), retrieveValues(ColumnType.INT.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal(1), Values.literal(2)),
+                retrieveValues(ColumnType.INT_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal(3L)), retrieveValues(ColumnType.LONG.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal(4L), Values.literal(5L)),
+                retrieveValues(ColumnType.LONG_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal(0.5D)), retrieveValues(ColumnType.DECIMAL.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal(1.5D), Values.literal(2.5D)),
+                retrieveValues(ColumnType.DECIMAL_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal("2000-01-01", CoreDatatype.XSD.DATE)),
+                retrieveValues(ColumnType.DATE.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.literal("2001-01-01", CoreDatatype.XSD.DATE),
+                    Values.literal("2002-01-01", CoreDatatype.XSD.DATE)),
+                retrieveValues(ColumnType.DATE_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal("3000-01-01T12:30:00", CoreDatatype.XSD.DATETIME)),
+                retrieveValues(ColumnType.DATETIME.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.literal("3001-01-01T12:30:00", CoreDatatype.XSD.DATETIME),
+                    Values.literal("3002-01-01T12:30:00", CoreDatatype.XSD.DATETIME)),
+                retrieveValues(ColumnType.DATETIME_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal("P1D", CoreDatatype.XSD.DURATION)),
+                retrieveValues(ColumnType.PERIOD.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.literal("P1M", CoreDatatype.XSD.DURATION),
+                    Values.literal("P1Y", CoreDatatype.XSD.DURATION)),
+                retrieveValues(ColumnType.PERIOD_ARRAY.name())),
+
+        // COMPOSITE
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.literal("{\"a\":1,\"b\":2}", CoreDatatype.XSD.STRING)),
+                retrieveValues(ColumnType.JSONB.name())),
+        // TODO: Remove if deprecated.
+        () -> Assertions.assertEquals(Set.of(), retrieveValues(ColumnType.JSONB_ARRAY.name())),
+        // RELATIONSHIP
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.iri(rdfApiUrlPrefix + REF_TABLE + "?id=1")),
+                retrieveValues(ColumnType.REF.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.iri(rdfApiUrlPrefix + REF_TABLE + "?id=2"),
+                    Values.iri(rdfApiUrlPrefix + REF_TABLE + "?id=3")),
+                retrieveValues(ColumnType.REF_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.iri(rdfApiUrlPrefix + REFBACK_TABLE + "?id=1")),
+                retrieveValues(ColumnType.REFBACK.name())),
+        // LAYOUT and other constants -> should return empty sets as they should be excluded
+        () -> Assertions.assertEquals(Set.of(), retrieveValues(ColumnType.HEADING.name())),
+        // format flavors that extend a baseType
+        () -> // AUTO_ID is unique so full equality check not possible
+        Assertions.assertTrue(
+                retrieveValues(ColumnType.AUTO_ID.name()).stream()
+                    .findFirst()
+                    .get()
+                    .stringValue()
+                    .matches("[0-9a-zA-Z]+")),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.iri(rdfApiUrlPrefix + ONT_TABLE + "?name=aa")),
+                retrieveValues(ColumnType.ONTOLOGY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.iri(rdfApiUrlPrefix + ONT_TABLE + "?name=bb"),
+                    Values.iri(rdfApiUrlPrefix + ONT_TABLE + "?name=cc")),
+                retrieveValues(ColumnType.ONTOLOGY_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.iri("mailto:aap@example.com")),
+                retrieveValues(ColumnType.EMAIL.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.iri("mailto:noot@example.com"), Values.iri("mailto:mies@example.com")),
+                retrieveValues(ColumnType.EMAIL_ARRAY.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(Values.iri("https://molgenis.org")),
+                retrieveValues(ColumnType.HYPERLINK.name())),
+        () ->
+            Assertions.assertEquals(
+                Set.of(
+                    Values.iri("https://molgenis.org"), Values.iri("https://github.com/molgenis")),
+                retrieveValues(ColumnType.HYPERLINK_ARRAY.name())));
+  }
+}
diff --git a/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/RDFTest.java b/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/RDFTest.java
index 51a19fddd5..dec3ecf5ea 100644
--- a/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/RDFTest.java
+++ b/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/RDFTest.java
@@ -7,6 +7,7 @@
 import static org.molgenis.emx2.datamodels.DataModels.Regular.PET_STORE;
 
 import java.io.ByteArrayOutputStream;
+import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.StringReader;
@@ -24,6 +25,7 @@
 import org.eclipse.rdf4j.model.impl.SimpleNamespace;
 import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
 import org.eclipse.rdf4j.model.util.Values;
+import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
 import org.eclipse.rdf4j.model.vocabulary.OWL;
 import org.eclipse.rdf4j.model.vocabulary.RDF;
 import org.eclipse.rdf4j.model.vocabulary.RDFS;
@@ -49,6 +51,8 @@ public class RDFTest {
   /** Advanced setting field for adding custom RDF to the API. */
   private static final String SETTING_CUSTOM_RDF = "custom_rdf";
 
+  static final ClassLoader classLoader = ColumnTypeRdfMapperTest.class.getClassLoader();
+
   static Database database;
   static List<Schema> petStoreSchemas;
   static final String RDF_API_LOCATION = "/api/rdf";
@@ -58,6 +62,8 @@ public class RDFTest {
   static Schema ontologyTest;
   static Schema tableInherTest;
   static Schema tableInherExtTest;
+  static Schema fileTest;
+  static Schema refBackTest;
 
   final Set<Namespace> DEFAULT_NAMESPACES =
       new HashSet<>() {
@@ -225,6 +231,43 @@ public static void setup() {
     tableInherExtTest
         .getTable("ExternalUnrelated")
         .insert(row("id", "a", "externalUnrelatedColumn", "unrelated data"));
+
+    // Test FILE
+    fileTest = database.dropCreateSchema("fileTest");
+    fileTest.create(
+        table(
+            "myFiles",
+            column("id").setType(ColumnType.STRING).setPkey(),
+            column("file").setType(ColumnType.FILE)));
+
+    fileTest
+        .getTable("myFiles")
+        .insert(
+            row(
+                "id",
+                "1",
+                "file",
+                new File(classLoader.getResource("testfiles/molgenis.png").getFile())));
+
+    // Refback test (petstore refback uses auto id)
+    refBackTest = database.dropCreateSchema("refBackTest");
+    refBackTest.create(
+        table(
+            "tableRef",
+            column("id").setType(ColumnType.STRING).setPkey(),
+            column("link").setType(ColumnType.REF).setRefTable("tableRefBack")),
+        table("tableRefBack", column("id").setType(ColumnType.STRING).setPkey()));
+    refBackTest
+        .getTable("tableRefBack")
+        .getMetadata()
+        .add(
+            column("backlink")
+                .setType(ColumnType.REFBACK)
+                .setRefTable("tableRef")
+                .setRefBack("link"));
+
+    refBackTest.getTable("tableRefBack").insert(row("id", "a"));
+    refBackTest.getTable("tableRef").insert(row("id", "1", "link", "a"));
   }
 
   @AfterAll
@@ -236,6 +279,8 @@ public static void tearDown() {
     database.dropSchema(ontologyTest.getName());
     database.dropSchema(tableInherExtTest.getName());
     database.dropSchema(tableInherTest.getName());
+    database.dropSchema(fileTest.getName());
+    database.dropSchema(refBackTest.getName());
   }
 
   @Test
@@ -1158,6 +1203,49 @@ void testCustomOrEmptyRdf() throws IOException {
     validateNamespaces(handler, "RdfcustomOrEmpty", expectedNamespaces, customRdf1, customRdf2);
   }
 
+  @Test
+  void testFileMetadataTriples() throws IOException {
+    var handler = new InMemoryRDFHandler() {};
+    getAndParseRDF(Selection.of(fileTest), handler);
+
+    Set<Value> files =
+        handler
+            .resources
+            .get(Values.iri("http://localhost:8080/fileTest/api/rdf/MyFiles?id=1"))
+            .get(Values.iri("http://localhost:8080/fileTest/api/rdf/MyFiles/column/file"));
+
+    IRI fileIRI = (IRI) files.stream().findFirst().get();
+
+    Set<Value> fileNames = handler.resources.get(fileIRI).get(DCTERMS.TITLE);
+    Set<Value> fileFormats = handler.resources.get(fileIRI).get(DCTERMS.FORMAT);
+
+    assertAll(
+        () -> assertEquals(1, files.size()),
+        () -> assertEquals(1, fileNames.size()),
+        () -> assertEquals(Values.literal("molgenis.png"), fileNames.stream().findFirst().get()),
+        () -> assertEquals(1, fileFormats.size()),
+        () ->
+            assertEquals(
+                Values.iri("http://www.iana.org/assignments/media-types/image/png"),
+                fileFormats.stream().findFirst().get()));
+  }
+
+  @Test
+  void refBackInRdf() throws IOException {
+    var handler = new InMemoryRDFHandler() {};
+    getAndParseRDF(Selection.of(refBackTest), handler);
+
+    Set<Value> refBacks =
+        handler
+            .resources
+            .get(Values.iri("http://localhost:8080/refBackTest/api/rdf/TableRefBack?id=a"))
+            .get(
+                Values.iri(
+                    "http://localhost:8080/refBackTest/api/rdf/TableRefBack/column/backlink"));
+    assertEquals(
+        Set.of(Values.iri("http://localhost:8080/refBackTest/api/rdf/TableRef?id=1")), refBacks);
+  }
+
   /**
    * Helper test method to compare namespaces of 2 schemas.
    *
diff --git a/backend/molgenis-emx2-rdf/src/test/resources/testfiles/molgenis.png b/backend/molgenis-emx2-rdf/src/test/resources/testfiles/molgenis.png
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zxu-%^_18fIgkK9#*Zay0ehlEj5!%vu+cd6QSW7rsIyVSEo8Fju^MqfOJx9~^|1?Gs
z0)2f=7th6?P5m-dD*nmO#etVd!X@SW0#WBZ5dO_%Ex<wfi$H9OP*7$>eO7a_BxNSG
zpmtntSNP4<blsT0e46&i@h_3&odZk>cRscc`h$l5dGR$h81`owslc#x6q-hY!)yW<
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z2Pzq1bi$a9Oj1hW4oIHALDb_nw9vlNSo|a+<Lb_AV}nD6nGHbZf4HMd1dEg~oTkpk
z<pX)eA+_c9)RZ-|-Hzt%(TD|ulhGji&{y{_#bI|=k)#ER|3@&GMG9b##!C&0QjkRO
z$Y%;Sh@&LKXGN>1wbs||!v~tUoRDIjoZ_$&$uAjA+5er?8yWz}gcRg@HIEQU;$rIh
z)qv9UeWtd#LqXt#t7M}>%2~z;A(4}eNb(N_a=EeU<pcD<gyov&5}`Ud|4)C~{Yd<6
zl^d%l5REbuSN6{&laMg8mj+98CnJUqv7$1Hd~DcJVL4-GYbRn+Bod}IKg?PF&tCqI
pvj58QzvB51%l;sTt}5sbb5rLHjeA)ZHw^G6@k&;t_@(aq{{b^l<yim#

literal 0
HcmV?d00001


From e9a3fcf1e4b29b81a803229707bdaa563e7598df Mon Sep 17 00:00:00 2001
From: Hessel Haagsma <h.haagsma@umcg.nl>
Date: Fri, 22 Nov 2024 13:13:19 +0100
Subject: [PATCH 25/46] Add combined networks to biobanks (#4512)

* Fix CSV formatting

* Add combined_network attribute

* Typos

* Clarify description

* Add combined_network to demo data
---
 data/biobank-directory/demo/Biobanks.csv |  6 +++---
 data/biobank-directory/molgenis.csv      | 17 +++++++++--------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/data/biobank-directory/demo/Biobanks.csv b/data/biobank-directory/demo/Biobanks.csv
index f38139fb35..a071cad459 100644
--- a/data/biobank-directory/demo/Biobanks.csv
+++ b/data/biobank-directory/demo/Biobanks.csv
@@ -1,3 +1,3 @@
-id,pid,name,acronym,description,url,location,country,latitude,longitude,head,contact,juridical_person,network,also_known,services,collaboration_commercial,collaboration_non_for_profit,national_node,withdrawn
-bbmri-eric:ID:DE_biobank1,pid_biobank1,Biobank1,bb1,The description of biobank1,,Berlin,DE,,,bbmri-eric:contactID:DE_head_bb1,bbmri-eric:contactID:contact_bb1,A university,bbmri-eric:networkID:DE_network1,bbmri-eric:akiID:DE_00001,"bbmri-eric:serviceID:DE_1234",true,false,DE,false
-bbmri-eric:ID:NL_biobank2,pid_biobank2,Biobank2,bb2,The description of biobank2,,Amsterdam,NL,,,bbmri-eric:contactID:NL_person1,bbmri-eric:contactID:NL_person1,An institute,bbmri-eric:networkID:EU_network,bbmri-eric:akiID:NL_00001,"bbmri-eric:serviceID:NL_541",false,true,NL,false
\ No newline at end of file
+id,pid,name,acronym,description,url,location,country,latitude,longitude,head,contact,juridical_person,network,combined_network,also_known,services,collaboration_commercial,collaboration_non_for_profit,national_node,withdrawn
+bbmri-eric:ID:DE_biobank1,pid_biobank1,Biobank1,bb1,The description of biobank1,,Berlin,DE,,,bbmri-eric:contactID:DE_head_bb1,bbmri-eric:contactID:contact_bb1,A university,bbmri-eric:networkID:DE_network1,bbmri-eric:networkID:DE_network1,bbmri-eric:akiID:DE_00001,"bbmri-eric:serviceID:DE_1234",true,false,DE,false
+bbmri-eric:ID:NL_biobank2,pid_biobank2,Biobank2,bb2,The description of biobank2,,Amsterdam,NL,,,bbmri-eric:contactID:NL_person1,bbmri-eric:contactID:NL_person1,An institute,bbmri-eric:networkID:EU_network,bbmri-eric:networkID:EU_network,bbmri-eric:akiID:NL_00001,"bbmri-eric:serviceID:NL_541",false,true,NL,false
\ No newline at end of file
diff --git a/data/biobank-directory/molgenis.csv b/data/biobank-directory/molgenis.csv
index 06fd642416..e59a97c34e 100644
--- a/data/biobank-directory/molgenis.csv
+++ b/data/biobank-directory/molgenis.csv
@@ -28,7 +28,8 @@ Biobanks,,longitude,Longitude,string,,false,,"Longitude of the biobank in the WG
 Biobanks,,head,Head of the Biobank,ref,,false,,Person in charge of the biobank.,,Persons,,${email},,,,,
 Biobanks,,contact,Contact Person,ref,,true,,Contact person of the biobank.,,Persons,,${email},,,,,
 Biobanks,,juridical_person,Juridical Person,string,,true,,Juristic person of a biobank according to MIABIS 2.0 - MIABIS-2.0-05.,,,,,,,,,
-Biobanks,,network,Networks,ref_array,,false,,"Reference to a biobank network ID, to which the biobank belongs; this attribute can also be used for biobank network, where it refers to the superior biobank network.",,Networks,,${name},,,,,
+Biobanks,,network,Networks,ref_array,,false,,"Reference to a biobank network ID, to which the biobank belongs.",,Networks,,${name},,,,,
+Biobanks,,combined_network,Combined Network,ref_array,,false,,"Reference to one or more network IDs, to which the biobank belongs directly or indirectly (i.e., either the biobank is explicitly marked as part of the network or its network is).",,Networks,,${name},,,,,
 Biobanks,,also_known,Also Known In,ref_array,,false,,The biobank also exists in …,,AlsoKnownIn,,${name_system},,,,,
 Biobanks,,collections,Collections,refback,,false,,Collections belonging to the biobank.,,Collections,biobank,${name},,,,,
 Biobanks,,services,Services,ref_array,,false,,Capabilities and services that the biobank organisation can offer to a researcher.,,Services,,${name},,,,,
@@ -75,8 +76,8 @@ Collections,,belongs_to,Belongs to,heading,,false,,The collection belongs to ...
 Collections,,parent_collection,Parent Collection,ref,,false,,"Reference to a collection ID, refers to the superior collection.",,Collections,,${name},,,,,
 Collections,,sub_collections,Sub Collections,refback,,false,,"Reference to a collection ID, refers to one or more sub-collections.",,Collections,parent_collection,${name},,,,,
 Collections,,biobank,Biobank,ref,,true,,"Reference to a biobank ID, to which the collection belongs.",,Biobanks,,${name},,,,,
-Collections,,biobank_label,Biobank Label,string,,true,,"Name of the biobank, to which the collection belongs to.",,,,,,,,,
-Collections,,network,Network,ref_array,,false,,"Reference to a network ID, to which the collection belongs to.",,Networks,,${name},,,,,
+Collections,,biobank_label,Biobank Label,string,,true,,"Name of the biobank, to which the collection belongs.",,,,,,,,,
+Collections,,network,Network,ref_array,,false,,"Reference to a network ID, to which the collection belongs.",,Networks,,${name},,,,,
 Collections,,combined_network,Combined Network,ref_array,,false,,"Reference to one or more network IDs, to which the collection belongs directly or indirectly (i.e., either the collection is explicitly marked as part of the network or its biobank is).",,Networks,,${name},,,,,
 Collections,,also_known,Also Known In,ref_array,,false,,The collection also exists in …,,AlsoKnownIn,,${name_system},,,,,
 Collections,,studies,Studies,ref_array,,false,,A link to studies during which the collection was generated,,Studies,,${title},,,,,
@@ -171,23 +172,23 @@ QualityInfoServices,,assessmentLevel,Assessment Level,ontology,,true,,,Directory
 QualityInfoServices,,certificationNumber,Certification Number,string,,false,,,,,,,,,,,
 QualityInfoServices,,certificationReport,Certification Report,hyperlink,,false,,,,,,,,,,,
 QualityInfoServices,,certificationImageLink,Certification Image,hyperlink,,false,,,,,,,,,,,
-Services,,,,,,,,Biobank Capabilities and Services
-Services,,id,ID,string,1,true,,"Unique ID of the service, prefixed with bbmri-eric:serviceID:"
+Services,,,,,,,,Biobank Capabilities and Services,,,,,,,,,
+Services,,id,ID,string,1,true,,"Unique ID of the service, prefixed with bbmri-eric:serviceID:",,,,,,,,,
 Services,,name,Service Name,string,2,true,,Name of the service (preferably in English).,,,,,,,,,
-Services,,serviceTypes,Service Types,ref_array,,true,,Related service types,DirectoryOntologies,ServiceTypes,,${label}
+Services,,serviceTypes,Service Types,ref_array,,true,,Related service types,DirectoryOntologies,ServiceTypes,,${label},,,,,
 Services,,acronym,Acronym,string,,false,,Short name in use for the service. If applicable.,,,,,,,,,
 Services,,description,Description,string,,true,,Full description of the service (in English),,,,,,,,,
 Services,,descriptionUrl,Description URL,hyperlink,,false,,URL address of the service description if available.,,,,,,,,,
 Services,,device,Device,string,,false,,Name of the device(s) if the service is provided with the use of them.,,,,,,,,,
 Services,,deviceSystem,Device System,string,,false,,Name of a software system or platform if important for the device characteristics.,,,,,,,,,
-Services,,tRL,Technology Readiness Level ,ontology,,false,,Technology Readiness Level - a concept for self-assessment of the service maturity,DirectoryOntologies,TRLs,,${label},,,,,
+Services,,tRL,Technology Readiness Level,ontology,,false,,Technology Readiness Level - a concept for self-assessment of the service maturity,DirectoryOntologies,TRLs,,${label},,,,,
 Services,,accessDescription,Access Description,string,,true,,Description of the access policy of the service.,,,,,,,,,
 Services,,accessDescriptionUrl,Access Description URL,hyperlink,,false,,URL of the service access policy if available..,,,,,,,,,
 Services,,unitOfAccess,Unit of Access,string,,false,,Information about a standard unit used in calculations of costs of service provision.,,,,,,,,,
 Services,,accessDescription,Access Description,string,,true,,Description of the access policy of the service,,,,,,,,,
 Services,,unitCost,Unit Cost,string,,false,,Cost per unit.,,,,,,,,,
 Services,,qualityStandards,Quality Standards,refback,,false,true,The standards and/or technical specifications that the service is certified or accredited for.,,QualityInfoServices,service,${qualityStandard.label},,,,,
-Services,,contactInformation,Contact Information,ref,,false,,Contact information for the contact person or responsible person of the service ,,Persons,
+Services,,contactInformation,Contact Information,ref,,false,,Contact information for the contact person or responsible person of the service,,Persons,,,,,,,
 Services,,national_node,National Node,ref,,true,,The study originates from this national node.,,NationalNodes,,${description},,,,,
 Studies,,,,,,,,Table with information about the studies in which context the collection was generated,,,,,,,,,
 Studies,,id,ID,string,1,true,,"Unique ID of the study, prefixed with bbmri-eric:studyID:<id_of_the_study>",,,,,,,,,

From ba25da872eb54474ffe3855725cf1252274a6a96 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 26 Nov 2024 10:27:40 +0000
Subject: [PATCH 26/46] feat: added display for input data

---
 .../pages/input/Listbox.story.vue                   | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index f9314fc5e3..f1103c8d53 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -80,7 +80,7 @@
       <InputString id="listbox-placeholder" v-model="listboxPlaceholder" />
     </div>
   </form>
-  <div class="mb-2 bg-white rounded p-6">
+  <div class="mb-6 bg-white rounded p-6">
     <h3 class="text-heading-lg mb-2">Listbox example</h3>
     <InputLabel
       id="listbox-input-label"
@@ -105,6 +105,17 @@
       >
     </output>
   </div>
+  <div class="mb-2 bg-white rounded p-6">
+    <h3 class="text-heading-lg mb-2">Input data structure</h3>
+    <p>Based on the selection above, the input data is shown below.</p>
+    <output
+      class="block w-full mt-6 bg-gray-100 py-3 px-2 pl-6 h-60 overflow-y-scroll shadow-inner"
+    >
+      <pre class="indent-[-5em]">
+        {{ listboxData }}
+      </pre>
+    </output>
+  </div>
 </template>
 
 <script lang="ts" setup>

From f2d32213680a3f76ea9037e8c217621ace542cfb Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 26 Nov 2024 10:28:50 +0000
Subject: [PATCH 27/46] fix: consolidated functions; implemented other minor
 changes from review

---
 .../components/input/Listbox.vue              | 63 ++++++++-----------
 1 file changed, 27 insertions(+), 36 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index 8262fe064f..d8a0db74a1 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -8,7 +8,7 @@
       aria-haspopup="listbox"
       :aria-controls="`listbox-${id}-options`"
       :aria-required="required"
-      :aria-expanded="listboxIsExpanded"
+      :aria-expanded="isExpanded"
       :aria-labelledby="labelId"
       class="flex justify-start items-center h-10 w-full text-left pl-10 border bg-input rounded-search-input text-button-input-toggle focus:ring-blue-300"
       :class="{
@@ -31,12 +31,12 @@
       :id="`listbox-${id}-options`"
       role="listbox"
       ref="listbox-ul"
-      :aria-expanded="listboxIsExpanded"
+      :aria-expanded="isExpanded"
       class="absolute b-0 w-full overflow-y-scroll z-10 bg-listbox"
       :class="{
-        hidden: !listboxIsExpanded,
-        'h-44': listboxIsExpanded && listboxOptions.length > 5,
-        'shadow-inner': listboxIsExpanded,
+        hidden: !isExpanded,
+        'h-44': isExpanded && listboxOptions.length > 5,
+        'shadow-inner': isExpanded,
       }"
       @keydown.prevent="onListboxKeyDown"
     >
@@ -101,7 +101,7 @@ const props = withDefaults(
 const sourceDataType = ref<string>("");
 const sourceData = ref<IListboxOption[]>();
 const focusCounter = ref<number>(0);
-const listboxIsExpanded = ref<boolean>(false);
+const isExpanded = ref<boolean>(false);
 const modelValue = defineModel<IListboxOption | IListboxValueArray>();
 const ulElemRef = useTemplateRef<HTMLUListElement>("listbox-ul");
 const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listbox-li");
@@ -113,22 +113,32 @@ function counterIsInRange(value: number) {
   return value <= listboxOptions.value.length - 1 && value >= 0;
 }
 
-function isIListboxOption(
-  data: IListboxOption[] | IListboxValueArray[]
-): boolean {
-  const testDataValue: IListboxOption | IListboxValueArray = data[0];
-  return (
-    typeof testDataValue === "object" && Object.hasOwn(testDataValue, "value")
-  );
-}
+const listboxOptions = computed<IInternalListboxOption[]>(() => {
+  const testDataValue: IListboxOption | IListboxValueArray = props.options[0];
+  if (
+    typeof testDataValue === "object" &&
+    Object.hasOwn(testDataValue, "value")
+  ) {
+    sourceDataType.value = "ListboxOptions";
+    sourceData.value = props.options as IListboxOption[];
+  } else {
+    sourceDataType.value = "ListboxValueArray";
+    const inputData = props.options as IListboxValueArray[];
+    const processedData = inputData.map(
+      (value: IListboxValueArray): IListboxOption => {
+        return { value: value };
+      }
+    );
+    sourceData.value = processedData as IListboxOption[];
+  }
 
-function prepareIListboxOptions(): IInternalListboxOption[] {
   const defaultOption: IListboxOption = {
     value: null,
     label: props.placeholder,
   };
   const inputData = sourceData.value as IListboxOption[];
   const data: IListboxOption[] = [defaultOption, ...inputData];
+
   return data.map((option: IListboxOption, index: number) => {
     return {
       ...option,
@@ -136,25 +146,6 @@ function prepareIListboxOptions(): IInternalListboxOption[] {
       elemId: `listbox-${props.id}-options-${index}`,
     };
   });
-}
-
-function asIListboxOption(data: IListboxValueArray[]): IListboxOption[] {
-  return data.map((value: IListboxValueArray): IListboxOption => {
-    return { value: value };
-  });
-}
-
-const listboxOptions = computed<IInternalListboxOption[]>(() => {
-  if (isIListboxOption(props.options)) {
-    sourceDataType.value = "ListboxOptions";
-    sourceData.value = props.options as IListboxOption[];
-  } else {
-    sourceDataType.value = "ListboxValueArray";
-    const inputData = props.options as IListboxValueArray[];
-    const processedData = asIListboxOption(inputData);
-    sourceData.value = processedData as IListboxOption[];
-  }
-  return prepareIListboxOptions();
 });
 
 function updateCounter(value: number) {
@@ -235,8 +226,8 @@ function focusListboxButton() {
 }
 
 function openCloseListbox() {
-  listboxIsExpanded.value = !listboxIsExpanded.value;
-  if (listboxIsExpanded.value) {
+  isExpanded.value = !isExpanded.value;
+  if (isExpanded.value) {
     ulElemRef.value?.setAttribute("tabindex", "0");
     if (modelValue.value) {
       updateCounter(startingCounter.value);

From 99ee1da7a2bbe2e2e801e6e519cbe9b0d1cfac7a Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Thu, 5 Dec 2024 11:13:07 +0000
Subject: [PATCH 28/46] fix: minor revisions from review

---
 .../components/input/Listbox.vue              | 54 +++++++++++--------
 .../pages/input/Listbox.story.vue             | 13 ++---
 apps/tailwind-components/types/listbox.ts     |  4 +-
 3 files changed, 42 insertions(+), 29 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index d8a0db74a1..edbd68670e 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -19,7 +19,7 @@
       @keydown.prevent="onListboxButtonKeyDown"
     >
       <span class="w-full">
-        {{ listboxDisplayText }}
+        {{ displayText }}
       </span>
       <div class="w-[60px] flex flex-col">
         <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
@@ -47,10 +47,11 @@
         role="option"
         class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
         :class="{
-          '!bg-listbox-selected !text-listbox-selected':
-            option.value === (modelValue as IListboxOption)?.value || option.value === modelValue,
+          '!bg-listbox-selected !text-listbox-selected': isSelected(
+            option.value
+          ),
         }"
-        :aria-selected="option.value === (modelValue as IListboxOption)?.value || option.value === modelValue"
+        :aria-selected="isSelected(option.value)"
         @click="onListboxOptionClick(option)"
         @blur="blurListOption(option)"
         @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
@@ -58,7 +59,7 @@
         <BaseIcon
           name="Check"
           class="fill-listbox-selected"
-          :class="option.value === (modelValue as IListboxOption)?.value || option.value === modelValue ? 'visible' : 'invisible'"
+          :class="isSelected(option.value) ? 'visible' : 'invisible'"
           :width="18"
         />
         <span v-if="option.label">
@@ -73,9 +74,9 @@
 </template>
 
 <script lang="ts" setup>
-import { ref, useTemplateRef, nextTick } from "vue";
+import { ref, useTemplateRef, nextTick, watch } from "vue";
 import type {
-  IListboxValueArray,
+  IListboxValue,
   IListboxOption,
   IInternalListboxOption,
 } from "../../types/listbox";
@@ -84,7 +85,7 @@ const props = withDefaults(
   defineProps<{
     id: string;
     labelId: string;
-    options: IListboxOption[] | IListboxValueArray[];
+    options: IListboxOption[] | IListboxValue[];
     required?: boolean;
     hasError?: boolean;
     placeholder?: string;
@@ -102,11 +103,11 @@ const sourceDataType = ref<string>("");
 const sourceData = ref<IListboxOption[]>();
 const focusCounter = ref<number>(0);
 const isExpanded = ref<boolean>(false);
-const modelValue = defineModel<IListboxOption | IListboxValueArray>();
+const modelValue = defineModel<IListboxOption | IListboxValue>();
 const ulElemRef = useTemplateRef<HTMLUListElement>("listbox-ul");
 const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listbox-li");
 const btnElemRef = useTemplateRef<HTMLButtonElement>("listbox-button");
-const listboxDisplayText = ref<string>(props.placeholder);
+const displayText = ref<string>(props.placeholder);
 const startingCounter = ref<number>(0);
 
 function counterIsInRange(value: number) {
@@ -114,18 +115,18 @@ function counterIsInRange(value: number) {
 }
 
 const listboxOptions = computed<IInternalListboxOption[]>(() => {
-  const testDataValue: IListboxOption | IListboxValueArray = props.options[0];
+  const testDataValue: IListboxOption | IListboxValue = props.options[0];
   if (
     typeof testDataValue === "object" &&
-    Object.hasOwn(testDataValue, "value")
+    Object.hasOwn(testDataValue as IListboxOption, "value")
   ) {
     sourceDataType.value = "ListboxOptions";
     sourceData.value = props.options as IListboxOption[];
   } else {
     sourceDataType.value = "ListboxValueArray";
-    const inputData = props.options as IListboxValueArray[];
+    const inputData = props.options as IListboxValue[];
     const processedData = inputData.map(
-      (value: IListboxValueArray): IListboxOption => {
+      (value: IListboxValue): IListboxOption => {
         return { value: value };
       }
     );
@@ -180,11 +181,11 @@ function blurListOption(option: IInternalListboxOption) {
   });
 }
 
-function updateListboxDisplayText(text: string | undefined | null): string {
-  if (typeof text === "undefined") {
+function updateDisplayText(text: string | undefined | null): string {
+  if (typeof text === "undefined" || text === null) {
     return props.placeholder;
   }
-  return text as string;
+  return text;
 }
 
 function updateModelValue(selection: IInternalListboxOption) {
@@ -196,19 +197,23 @@ function updateModelValue(selection: IInternalListboxOption) {
     const selectedOption: IListboxOption = { value: selection.value };
     if (Object.hasOwn(selection, "label")) {
       selectedOption.label = selection.label;
-      listboxDisplayText.value = updateListboxDisplayText(selectedOption.label);
+      displayText.value = updateDisplayText(selectedOption.label);
     } else {
-      listboxDisplayText.value = updateListboxDisplayText(selectedOption.value);
+      displayText.value = updateDisplayText(selectedOption.value as string);
     }
 
     modelValue.value = selectedOption;
   } else {
-    modelValue.value = selection.value as IListboxValueArray;
-    listboxDisplayText.value = selection.value as string;
+    modelValue.value = selection.value as IListboxValue;
+    displayText.value = updateDisplayText(selection.value as string);
   }
   openCloseListbox();
 }
 
+function isSelected(value: IListboxValue): boolean {
+  return value === modelValue.value || value === modelValue.value;
+}
+
 function focusPreviousOption(by: number = 1) {
   const newCounterValue = focusCounter.value - by;
   updateCounter(newCounterValue);
@@ -342,4 +347,11 @@ function onListboxOptionKeyDown(
       break;
   }
 }
+
+watch(
+  () => props.placeholder,
+  () => {
+    displayText.value = props.placeholder;
+  }
+);
 </script>
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index f1103c8d53..4c04952af5 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -21,7 +21,7 @@
     </p>
     <ul class="pl-6 mb-4 list-disc">
       <li>
-        <code>IListboxValueArray</code>: an array of values (as strings, or
+        <code>IListboxValue</code>: an array of values (as strings, or
         string[]). For now, this component only supports string arrays.
       </li>
       <li>
@@ -80,12 +80,14 @@
       <InputString id="listbox-placeholder" v-model="listboxPlaceholder" />
     </div>
   </form>
-  <div class="mb-6 bg-white rounded p-6">
+  <div class="mb-6 bg-white rounded px-6 py-8">
     <h3 class="text-heading-lg mb-2">Listbox example</h3>
     <InputLabel
       id="listbox-input-label"
       for="listbox-input"
       class="block mb-3 pl-0"
+      :disabled="listboxState === 'disabled'"
+      :has-error="listboxState === 'error'"
     >
       <span>Select a group assignment</span>
     </InputLabel>
@@ -120,9 +122,8 @@
 
 <script lang="ts" setup>
 import { ref, computed } from "vue";
-import type { IListboxValueArray, IListboxOption } from "../../types/listbox";
+import type { IListboxValue, IListboxOption } from "../../types/listbox";
 
-// as ListboxOption
 const letters: string[] = [...Array(26).keys()].map((num) =>
   String.fromCharCode(num + 65)
 );
@@ -136,9 +137,9 @@ const listboxSelection = ref();
 const listboxPlaceholder = ref<string>("Select an option");
 const listboxDataType = ref<string>("string");
 
-const listboxData = computed<IListboxOption[] | IListboxValueArray[]>(() => {
+const listboxData = computed<IListboxOption[] | IListboxValue[]>(() => {
   if (listboxDataType.value === "string") {
-    return letters as IListboxValueArray[];
+    return letters as IListboxValue[];
   } else {
     return lettersWithLabels as IListboxOption[];
   }
diff --git a/apps/tailwind-components/types/listbox.ts b/apps/tailwind-components/types/listbox.ts
index df0f5fcfe1..9c9ee4e8d8 100644
--- a/apps/tailwind-components/types/listbox.ts
+++ b/apps/tailwind-components/types/listbox.ts
@@ -1,8 +1,8 @@
 
-export type IListboxValueArray = string;
+export type IListboxValue = string | number | boolean | undefined | null;
 
 export interface IListboxOption {
-  value: string | undefined | null;
+  value: IListboxValue;
   label?: string;
 }
 

From d4f8aee5ccffd2dae0a2acb14d84ce84bca6884d Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Thu, 5 Dec 2024 15:11:59 +0000
Subject: [PATCH 29/46] feat: added events; added auto selection on load;
 updated story; minor ts fixes

---
 .../components/input/Listbox.vue              | 36 ++++++++++++++++---
 apps/tailwind-components/pages/Form.story.vue | 32 +++++++++++------
 .../pages/input/Listbox.story.vue             |  2 +-
 3 files changed, 54 insertions(+), 16 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index edbd68670e..40bc4348f4 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -74,7 +74,7 @@
 </template>
 
 <script lang="ts" setup>
-import { ref, useTemplateRef, nextTick, watch } from "vue";
+import { ref, useTemplateRef, nextTick, watch, onMounted } from "vue";
 import type {
   IListboxValue,
   IListboxOption,
@@ -99,6 +99,10 @@ const props = withDefaults(
   }
 );
 
+const emit = defineEmits<{
+  (e: "change", value: IListboxOption | IListboxValue): void;
+}>();
+
 const sourceDataType = ref<string>("");
 const sourceData = ref<IListboxOption[]>();
 const focusCounter = ref<number>(0);
@@ -188,7 +192,10 @@ function updateDisplayText(text: string | undefined | null): string {
   return text;
 }
 
-function updateModelValue(selection: IInternalListboxOption) {
+function updateModelValue(
+  selection: IInternalListboxOption,
+  enableToggling: boolean = false
+) {
   btnElemRef.value?.setAttribute("aria-activedescendant", selection.elemId);
   focusCounter.value = selection.index;
   startingCounter.value = selection.index;
@@ -207,11 +214,16 @@ function updateModelValue(selection: IInternalListboxOption) {
     modelValue.value = selection.value as IListboxValue;
     displayText.value = updateDisplayText(selection.value as string);
   }
-  openCloseListbox();
+
+  emit("change", modelValue.value);
+
+  if (enableToggling) {
+    openCloseListbox();
+  }
 }
 
 function isSelected(value: IListboxValue): boolean {
-  return value === modelValue.value || value === modelValue.value;
+  return value === (modelValue.value as IInternalListboxOption).value;
 }
 
 function focusPreviousOption(by: number = 1) {
@@ -348,6 +360,22 @@ function onListboxOptionKeyDown(
   }
 }
 
+onMounted(() => {
+  if (modelValue.value && listboxOptions.value) {
+    const initalValue: IInternalListboxOption[] = listboxOptions.value.filter(
+      (row: IInternalListboxOption) => {
+        return (
+          row.value === (modelValue.value as IListboxOption).value ||
+          row.value === (modelValue.value as IListboxValue)
+        );
+      }
+    );
+    if (initalValue) {
+      updateModelValue(initalValue[0], false);
+    }
+  }
+});
+
 watch(
   () => props.placeholder,
   () => {
diff --git a/apps/tailwind-components/pages/Form.story.vue b/apps/tailwind-components/pages/Form.story.vue
index ad5d786fbe..1f025d0df0 100644
--- a/apps/tailwind-components/pages/Form.story.vue
+++ b/apps/tailwind-components/pages/Form.story.vue
@@ -5,15 +5,21 @@ import type {
   ISchemaMetaData,
   ITableMetaData,
 } from "../../metadata-utils/src/types";
+import type { IListboxOption } from "../types/listbox";
 
-const sampleType = ref("simple");
+const exampleForms: IListboxOption[] = [
+  { value: "simple", label: "Simple form example" },
+  { value: "complex", label: "Complex form example" },
+];
+
+const formType = ref<IListboxOption>(exampleForms[0]);
 
 // just assuming that the table is there for the demo
 const schemaId = computed(() =>
-  sampleType.value === "simple" ? "pet store" : "catalogue-demo"
+  formType.value.value === "simple" ? "pet store" : "catalogue-demo"
 );
 const tableId = computed(() =>
-  sampleType.value === "simple" ? "Pet" : "Resources"
+  formType.value.value === "simple" ? "Pet" : "Resources"
 );
 
 const {
@@ -30,6 +36,7 @@ const tableMeta = computed(
 );
 
 function refetch() {
+  console.log("refetching...");
   refetchMetadata();
 }
 
@@ -42,14 +49,17 @@ const formFields = ref<InstanceType<typeof FormFields>>();
   <div>Demo controles:</div>
 
   <div class="p-4 border-2 mb-2">
-    <select
-      @change="refetch()"
-      v-model="sampleType"
-      class="border-1 border-black"
-    >
-      <option value="simple">Simple form example</option>
-      <option value="complex">Complex form example</option>
-    </select>
+    <InputLabel for="form-example" id="form-example-title">
+      Select a form to display
+    </InputLabel>
+    <InputListbox
+      id="form-example"
+      label-id="form-example-title"
+      @change="refetch"
+      v-model="formType"
+      :options="exampleForms"
+      placeholder="Select a form type"
+    />
 
     <div>schema id = {{ schemaId }}</div>
     <div>table id = {{ tableId }}</div>
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index 4c04952af5..d420d55d6f 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -133,7 +133,7 @@ const lettersWithLabels: IListboxOption[] = letters.map((letter: string) => {
 });
 
 const listboxState = ref<string>("");
-const listboxSelection = ref();
+const listboxSelection = ref("");
 const listboxPlaceholder = ref<string>("Select an option");
 const listboxDataType = ref<string>("string");
 

From 623c311e19ca8a2eb248addcd6809108cd02c2d2 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Fri, 6 Dec 2024 09:12:41 +0000
Subject: [PATCH 30/46] fix: added check for modelValue type

---
 apps/tailwind-components/components/input/Listbox.vue | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index 40bc4348f4..adf8e4bf73 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -194,7 +194,7 @@ function updateDisplayText(text: string | undefined | null): string {
 
 function updateModelValue(
   selection: IInternalListboxOption,
-  enableToggling: boolean = false
+  enableToggling: boolean = true
 ) {
   btnElemRef.value?.setAttribute("aria-activedescendant", selection.elemId);
   focusCounter.value = selection.index;
@@ -223,7 +223,10 @@ function updateModelValue(
 }
 
 function isSelected(value: IListboxValue): boolean {
-  return value === (modelValue.value as IInternalListboxOption).value;
+  return (
+    value === (modelValue.value as IInternalListboxOption).value ||
+    value === (modelValue.value as IListboxValue)
+  );
 }
 
 function focusPreviousOption(by: number = 1) {

From 660cf3a50cebc89cbc6beb2d489035436437f187 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 10 Dec 2024 13:30:27 +0100
Subject: [PATCH 31/46] feat: initial form connection

---
 .../components/form/Field.vue                 | 14 +++++++++++++
 .../components/form/FieldInput.vue            | 20 +++++++++++++++++--
 2 files changed, 32 insertions(+), 2 deletions(-)

diff --git a/apps/tailwind-components/components/form/Field.vue b/apps/tailwind-components/components/form/Field.vue
index e6926a7bee..609f1a6620 100644
--- a/apps/tailwind-components/components/form/Field.vue
+++ b/apps/tailwind-components/components/form/Field.vue
@@ -35,6 +35,18 @@ function validate(value: columnValue) {
 
   formFieldInput.value.validate(value);
 }
+
+const refData = ref();
+
+onMounted(async () => {
+  if (["ONTOLOGY", "ONTOLOGY_ARRAY"].includes(props.column.columnType)) {
+    const response = await fetchTableData(
+      props.column.refSchemaId as string,
+      props.column.refTableId as string
+    );
+    refData.value = response.rows.map((row) => row.name);
+  }
+});
 </script>
 
 <template>
@@ -49,11 +61,13 @@ function validate(value: columnValue) {
       {{ column.description }}
     </div>
     <div>
+      {{ column }}
       <FormFieldInput
         :type="column.columnType"
         :id="column.id"
         :label="column.label"
         :data="data"
+        :options="refData ? refData : null"
         :required="!!column.required"
         :aria-invalid="hasError"
         :aria-desribedBy="`${column.id}-input-error`"
diff --git a/apps/tailwind-components/components/form/FieldInput.vue b/apps/tailwind-components/components/form/FieldInput.vue
index b15b55b1b6..de7df07e7b 100644
--- a/apps/tailwind-components/components/form/FieldInput.vue
+++ b/apps/tailwind-components/components/form/FieldInput.vue
@@ -3,6 +3,7 @@ import type {
   InputString,
   InputTextArea,
   InputPlaceHolder,
+  InputListbox,
 } from "#build/components";
 import type {
   columnId,
@@ -10,6 +11,8 @@ import type {
   CellValueType,
 } from "../../../metadata-utils/src/types";
 
+import type { IListboxValue } from "~/types/listbox";
+
 type inputComponent =
   | InstanceType<typeof InputString>
   | InstanceType<typeof InputTextArea>
@@ -21,6 +24,7 @@ defineProps<{
   label: string;
   required: boolean;
   data: columnValue;
+  options?: IListboxValue[];
 }>();
 
 defineEmits(["focus", "error", "update:modelValue"]);
@@ -47,7 +51,7 @@ function validate(value: columnValue) {
     :id="id"
     :label="label"
     :required="required"
-    :value="data as string"
+    :value="(data as string)"
     @focus="$emit('focus')"
     @update:modelValue="$emit('update:modelValue', $event)"
     @error="$emit('error', $event)"
@@ -58,10 +62,22 @@ function validate(value: columnValue) {
     :id="id"
     :label="label"
     :required="required"
-    :value="data as string"
+    :value="(data as string)"
     @focus="$emit('focus')"
     @update:modelValue="$emit('update:modelValue', $event)"
     @error="$emit('error', $event)"
   ></LazyInputTextArea>
+  <template
+    v-else-if="['ONTOLOGY', 'ONTOLOGY_ARRAY'].includes(type) && options"
+  >
+    <LazyInputListbox
+      ref="input"
+      :id="id"
+      :label-id="id"
+      :required="required"
+      :options="options"
+      :placeholder="`Select a ${id}`"
+    />
+  </template>
   <LazyInputPlaceHolder v-else ref="input" :type="type" />
 </template>

From 2617d037695a9c13829abc2c892fcb7f740ec480 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 11 Dec 2024 11:30:37 +0100
Subject: [PATCH 32/46] feat: added FormField properties and methods; fixed:
 null value handling, minor ts revisions

---
 .../components/input/Listbox.vue              | 50 ++++++++++++++-----
 .../pages/input/Listbox.story.vue             |  4 +-
 2 files changed, 39 insertions(+), 15 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index adf8e4bf73..05f31e6b16 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -32,7 +32,7 @@
       role="listbox"
       ref="listbox-ul"
       :aria-expanded="isExpanded"
-      class="absolute b-0 w-full overflow-y-scroll z-10 bg-listbox"
+      class="absolute b-0 w-full overflow-y-scroll z-10"
       :class="{
         hidden: !isExpanded,
         'h-44': isExpanded && listboxOptions.length > 5,
@@ -45,7 +45,7 @@
         ref="listbox-li"
         :id="option.elemId"
         role="option"
-        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
+        class="flex justify-start items-center gap-3 pl-3 py-1 bg-listbox text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
         :class="{
           '!bg-listbox-selected !text-listbox-selected': isSelected(
             option.value
@@ -75,6 +75,10 @@
 
 <script lang="ts" setup>
 import { ref, useTemplateRef, nextTick, watch, onMounted } from "vue";
+import type {
+  columnValue,
+  IFieldError,
+} from "../../../metadata-utils/src/types";
 import type {
   IListboxValue,
   IListboxOption,
@@ -86,6 +90,7 @@ const props = withDefaults(
     id: string;
     labelId: string;
     options: IListboxOption[] | IListboxValue[];
+    value?: IListboxOption | IListboxValue;
     required?: boolean;
     hasError?: boolean;
     placeholder?: string;
@@ -100,14 +105,21 @@ const props = withDefaults(
 );
 
 const emit = defineEmits<{
-  (e: "change", value: IListboxOption | IListboxValue): void;
+  (e: "update:modelValue", value: IListboxOption | IListboxValue | null): void;
+  (e: "error", value: IFieldError[] | null): void;
+  (e: "blur", value: null): void;
+  (e: "focus", value: null): void;
 }>();
 
+defineExpose({
+  validate,
+});
+
 const sourceDataType = ref<string>("");
 const sourceData = ref<IListboxOption[]>();
 const focusCounter = ref<number>(0);
 const isExpanded = ref<boolean>(false);
-const modelValue = defineModel<IListboxOption | IListboxValue>();
+const modelValue = defineModel<IListboxOption | IListboxValue | null>();
 const ulElemRef = useTemplateRef<HTMLUListElement>("listbox-ul");
 const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listbox-li");
 const btnElemRef = useTemplateRef<HTMLButtonElement>("listbox-button");
@@ -127,7 +139,7 @@ const listboxOptions = computed<IInternalListboxOption[]>(() => {
     sourceDataType.value = "ListboxOptions";
     sourceData.value = props.options as IListboxOption[];
   } else {
-    sourceDataType.value = "ListboxValueArray";
+    sourceDataType.value = "ListboxValue";
     const inputData = props.options as IListboxValue[];
     const processedData = inputData.map(
       (value: IListboxValue): IListboxOption => {
@@ -215,7 +227,7 @@ function updateModelValue(
     displayText.value = updateDisplayText(selection.value as string);
   }
 
-  emit("change", modelValue.value);
+  emit("update:modelValue", modelValue.value);
 
   if (enableToggling) {
     openCloseListbox();
@@ -223,10 +235,14 @@ function updateModelValue(
 }
 
 function isSelected(value: IListboxValue): boolean {
-  return (
-    value === (modelValue.value as IInternalListboxOption).value ||
-    value === (modelValue.value as IListboxValue)
-  );
+  if (modelValue.value) {
+    return (
+      value === (modelValue.value as IInternalListboxOption).value ||
+      value === (modelValue.value as IListboxValue)
+    );
+  } else {
+    return value === null;
+  }
 }
 
 function focusPreviousOption(by: number = 1) {
@@ -363,13 +379,21 @@ function onListboxOptionKeyDown(
   }
 }
 
+function validate(value: columnValue) {
+  if (props.required && value === "") {
+    emit("error", [{ message: `${props.id} required to complete the form` }]);
+  } else {
+    emit("error", null);
+  }
+}
+
 onMounted(() => {
-  if (modelValue.value && listboxOptions.value) {
+  if (props.value && listboxOptions.value) {
     const initalValue: IInternalListboxOption[] = listboxOptions.value.filter(
       (row: IInternalListboxOption) => {
         return (
-          row.value === (modelValue.value as IListboxOption).value ||
-          row.value === (modelValue.value as IListboxValue)
+          row.value === (props.value as IListboxOption).value ||
+          row.value === (props.value as IListboxValue)
         );
       }
     );
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index d420d55d6f..1ed01117d1 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -95,10 +95,10 @@
       id="listbox-input"
       labelId="listbox-input-label"
       :options="listboxData"
-      v-model="listboxSelection"
       :hasError="listboxState === 'error'"
       :disabled="listboxState === 'disabled'"
       :placeholder="listboxPlaceholder"
+      @update:model-value="(value) => (listboxSelection = value)"
     />
     <output class="block w-full mt-6 bg-gray-100 py-3 px-2 pl-6">
       <code
@@ -133,7 +133,7 @@ const lettersWithLabels: IListboxOption[] = letters.map((letter: string) => {
 });
 
 const listboxState = ref<string>("");
-const listboxSelection = ref("");
+const listboxSelection = ref<IListboxValue | IListboxOption>("");
 const listboxPlaceholder = ref<string>("Select an option");
 const listboxDataType = ref<string>("string");
 

From 9a60d03b69d3fc331910055264ce79bd5f4f650e Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 11 Dec 2024 11:32:54 +0100
Subject: [PATCH 33/46] feat: added listbox as field input; improved links
 between text elements and their inputs

---
 .../components/form/Field.vue                 | 24 +++++++++++++------
 .../components/form/FieldInput.vue            | 23 +++++++++---------
 2 files changed, 29 insertions(+), 18 deletions(-)

diff --git a/apps/tailwind-components/components/form/Field.vue b/apps/tailwind-components/components/form/Field.vue
index 609f1a6620..3f4e2792d4 100644
--- a/apps/tailwind-components/components/form/Field.vue
+++ b/apps/tailwind-components/components/form/Field.vue
@@ -52,16 +52,22 @@ onMounted(async () => {
 <template>
   <div class="flex flex-col gap-1">
     <div>
-      <label :for="column.id" class="capitalize text-title font-bold">{{
-        column.label
-      }}</label>
+      <label
+        :id="`${column.id}-label`"
+        :for="column.id"
+        class="capitalize text-title font-bold"
+        >{{ column.label }}</label
+      >
       <span class="text-disabled ml-3" v-show="column.required">Required</span>
     </div>
-    <div class="text-title" v-if="column.description">
+    <span
+      :id="`${column.id}-description`"
+      class="text-title"
+      v-if="column.description"
+    >
       {{ column.description }}
-    </div>
+    </span>
     <div>
-      {{ column }}
       <FormFieldInput
         :type="column.columnType"
         :id="column.id"
@@ -70,7 +76,11 @@ onMounted(async () => {
         :options="refData ? refData : null"
         :required="!!column.required"
         :aria-invalid="hasError"
-        :aria-desribedBy="`${column.id}-input-error`"
+        :aria-desribedBy="
+          column.description
+            ? `${column.id}-description ${column.id}-input-error`
+            : `${column.id}-input-error`
+        "
         @focus="touched = true"
         @input="pristine = false"
         @update:modelValue="$emit('update:modelValue', $event)"
diff --git a/apps/tailwind-components/components/form/FieldInput.vue b/apps/tailwind-components/components/form/FieldInput.vue
index de7df07e7b..b4032ca1fc 100644
--- a/apps/tailwind-components/components/form/FieldInput.vue
+++ b/apps/tailwind-components/components/form/FieldInput.vue
@@ -67,17 +67,18 @@ function validate(value: columnValue) {
     @update:modelValue="$emit('update:modelValue', $event)"
     @error="$emit('error', $event)"
   ></LazyInputTextArea>
-  <template
+  <LazyInputListbox
     v-else-if="['ONTOLOGY', 'ONTOLOGY_ARRAY'].includes(type) && options"
-  >
-    <LazyInputListbox
-      ref="input"
-      :id="id"
-      :label-id="id"
-      :required="required"
-      :options="options"
-      :placeholder="`Select a ${id}`"
-    />
-  </template>
+    ref="input"
+    :id="id"
+    :label-id="`${id}-label`"
+    :required="required"
+    :options="options"
+    :placeholder="`Select a ${id}`"
+    :value="(data as string)"
+    @focus="$emit('focus')"
+    @update:modelValue="$emit('update:modelValue', $event)"
+    @error="$emit('error', $event)"
+  />
   <LazyInputPlaceHolder v-else ref="input" :type="type" />
 </template>

From f669076ec7d3a0804a640bdac3cead887e476f49 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 11 Dec 2024 12:07:18 +0100
Subject: [PATCH 34/46] minor revisions post review

---
 .../components/form/FieldInput.vue            |  3 +-
 .../components/input/Listbox.vue              | 46 +++++++++----------
 apps/tailwind-components/pages/Form.story.vue |  1 -
 3 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/apps/tailwind-components/components/form/FieldInput.vue b/apps/tailwind-components/components/form/FieldInput.vue
index b4032ca1fc..ddb4edb067 100644
--- a/apps/tailwind-components/components/form/FieldInput.vue
+++ b/apps/tailwind-components/components/form/FieldInput.vue
@@ -16,7 +16,8 @@ import type { IListboxValue } from "~/types/listbox";
 type inputComponent =
   | InstanceType<typeof InputString>
   | InstanceType<typeof InputTextArea>
-  | InstanceType<typeof InputPlaceHolder>;
+  | InstanceType<typeof InputPlaceHolder>
+  | InstanceType<typeof InputListbox>;
 
 defineProps<{
   type: CellValueType;
diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index 05f31e6b16..c3e0e04747 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -126,6 +126,29 @@ const btnElemRef = useTemplateRef<HTMLButtonElement>("listbox-button");
 const displayText = ref<string>(props.placeholder);
 const startingCounter = ref<number>(0);
 
+onMounted(() => {
+  if (props.value && listboxOptions.value) {
+    const initalValue: IInternalListboxOption[] = listboxOptions.value.filter(
+      (row: IInternalListboxOption) => {
+        return (
+          row.value === (props.value as IListboxOption).value ||
+          row.value === (props.value as IListboxValue)
+        );
+      }
+    );
+    if (initalValue) {
+      updateModelValue(initalValue[0], false);
+    }
+  }
+});
+
+watch(
+  () => props.placeholder,
+  () => {
+    displayText.value = props.placeholder;
+  }
+);
+
 function counterIsInRange(value: number) {
   return value <= listboxOptions.value.length - 1 && value >= 0;
 }
@@ -386,27 +409,4 @@ function validate(value: columnValue) {
     emit("error", null);
   }
 }
-
-onMounted(() => {
-  if (props.value && listboxOptions.value) {
-    const initalValue: IInternalListboxOption[] = listboxOptions.value.filter(
-      (row: IInternalListboxOption) => {
-        return (
-          row.value === (props.value as IListboxOption).value ||
-          row.value === (props.value as IListboxValue)
-        );
-      }
-    );
-    if (initalValue) {
-      updateModelValue(initalValue[0], false);
-    }
-  }
-});
-
-watch(
-  () => props.placeholder,
-  () => {
-    displayText.value = props.placeholder;
-  }
-);
 </script>
diff --git a/apps/tailwind-components/pages/Form.story.vue b/apps/tailwind-components/pages/Form.story.vue
index 1f025d0df0..4c40d67378 100644
--- a/apps/tailwind-components/pages/Form.story.vue
+++ b/apps/tailwind-components/pages/Form.story.vue
@@ -36,7 +36,6 @@ const tableMeta = computed(
 );
 
 function refetch() {
-  console.log("refetching...");
   refetchMetadata();
 }
 

From 8d0aedf1e7c1cc140bad717343ce14caef7df4ca Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 11 Dec 2024 12:23:43 +0100
Subject: [PATCH 35/46] fix: adjusted error typing

---
 apps/tailwind-components/components/input/Listbox.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index c3e0e04747..6d77a23751 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -106,7 +106,7 @@ const props = withDefaults(
 
 const emit = defineEmits<{
   (e: "update:modelValue", value: IListboxOption | IListboxValue | null): void;
-  (e: "error", value: IFieldError[] | null): void;
+  (e: "error", value: IFieldError[]): void;
   (e: "blur", value: null): void;
   (e: "focus", value: null): void;
 }>();
@@ -406,7 +406,7 @@ function validate(value: columnValue) {
   if (props.required && value === "") {
     emit("error", [{ message: `${props.id} required to complete the form` }]);
   } else {
-    emit("error", null);
+    emit("error", []);
   }
 }
 </script>

From 65f262e39815c9f32cd5ae8d9f1d58bee69d1075 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 11 Dec 2024 13:08:36 +0100
Subject: [PATCH 36/46] fix: selected form properly updates display; expanded
 listbox display conditions

---
 apps/tailwind-components/components/form/FieldInput.vue | 5 ++++-
 apps/tailwind-components/pages/Form.story.vue           | 8 ++++----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/apps/tailwind-components/components/form/FieldInput.vue b/apps/tailwind-components/components/form/FieldInput.vue
index ddb4edb067..e751b7b16e 100644
--- a/apps/tailwind-components/components/form/FieldInput.vue
+++ b/apps/tailwind-components/components/form/FieldInput.vue
@@ -69,7 +69,10 @@ function validate(value: columnValue) {
     @error="$emit('error', $event)"
   ></LazyInputTextArea>
   <LazyInputListbox
-    v-else-if="['ONTOLOGY', 'ONTOLOGY_ARRAY'].includes(type) && options"
+    v-else-if="
+      ['ONTOLOGY', 'ONTOLOGY_ARRAY', 'REF', 'REF_ARRAY'].includes(type) &&
+      options
+    "
     ref="input"
     :id="id"
     :label-id="`${id}-label`"
diff --git a/apps/tailwind-components/pages/Form.story.vue b/apps/tailwind-components/pages/Form.story.vue
index 4c40d67378..e845715be4 100644
--- a/apps/tailwind-components/pages/Form.story.vue
+++ b/apps/tailwind-components/pages/Form.story.vue
@@ -5,7 +5,7 @@ import type {
   ISchemaMetaData,
   ITableMetaData,
 } from "../../metadata-utils/src/types";
-import type { IListboxOption } from "../types/listbox";
+import type { IListboxOption, IListboxValue } from "../types/listbox";
 
 const exampleForms: IListboxOption[] = [
   { value: "simple", label: "Simple form example" },
@@ -35,7 +35,8 @@ const tableMeta = computed(
     ) as ITableMetaData
 );
 
-function refetch() {
+function refetch(value: IListboxOption) {
+  formType.value = value;
   refetchMetadata();
 }
 
@@ -54,8 +55,7 @@ const formFields = ref<InstanceType<typeof FormFields>>();
     <InputListbox
       id="form-example"
       label-id="form-example-title"
-      @change="refetch"
-      v-model="formType"
+      @update:modelValue="(value) => refetch(value as IListboxOption)"
       :options="exampleForms"
       placeholder="Select a form type"
     />

From f2a9ee2849743e17aa06dc3cfaef0c4747356ffc Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 11 Dec 2024 14:20:09 +0100
Subject: [PATCH 37/46] fix: adjusted test as the placeholder option is the
 default

---
 e2e/tests/tailwind-components/input/listbox.spec.ts | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/e2e/tests/tailwind-components/input/listbox.spec.ts b/e2e/tests/tailwind-components/input/listbox.spec.ts
index 843bde5d88..b781b744e1 100644
--- a/e2e/tests/tailwind-components/input/listbox.spec.ts
+++ b/e2e/tests/tailwind-components/input/listbox.spec.ts
@@ -65,7 +65,11 @@ test(
     combobox.click();
     await expect(combobox).toHaveAttribute("aria-expanded", "true");
     for (const option of await page.getByRole("option").all()) { 
-      await expect(option).toHaveAttribute("aria-selected", "false");
+      if (await option.innerText() === "Select an option") {
+        await expect(option).toHaveAttribute("aria-selected", "true");
+      } else {
+        await expect(option).toHaveAttribute("aria-selected", "false");
+      }
     }
   }
 )

From 542525879b26bfbb6202aead55b3dcb6fbc7a14c Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Thu, 12 Dec 2024 13:03:53 +0100
Subject: [PATCH 38/46] fix: adjusted component events

---
 .../components/input/Listbox.vue              | 29 +++++++------------
 1 file changed, 11 insertions(+), 18 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index 6d77a23751..535087226e 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -10,13 +10,13 @@
       :aria-required="required"
       :aria-expanded="isExpanded"
       :aria-labelledby="labelId"
-      class="flex justify-start items-center h-10 w-full text-left pl-10 border bg-input rounded-search-input text-button-input-toggle focus:ring-blue-300"
+      class="flex justify-start items-center h-10 w-full text-left pl-11 border bg-input rounded-search-input text-button-input-toggle focus:ring-blue-300"
       :class="{
         'border-disabled text-disabled bg-disabled': disabled,
         'border-invalid text-invalid': hasError,
       }"
       @click.prevent="openCloseListbox"
-      @keydown.prevent="onListboxButtonKeyDown"
+      @keydown="onListboxButtonKeyDown"
     >
       <span class="w-full">
         {{ displayText }}
@@ -32,7 +32,7 @@
       role="listbox"
       ref="listbox-ul"
       :aria-expanded="isExpanded"
-      class="absolute b-0 w-full overflow-y-scroll z-10"
+      class="absolute b-0 w-full overflow-y-scroll z-10 bg-listbox border"
       :class="{
         hidden: !isExpanded,
         'h-44': isExpanded && listboxOptions.length > 5,
@@ -45,11 +45,9 @@
         ref="listbox-li"
         :id="option.elemId"
         role="option"
-        class="flex justify-start items-center gap-3 pl-3 py-1 bg-listbox text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox"
+        class="flex justify-start items-center gap-3 pl-3 py-1 text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox focus:ring-blue-300"
         :class="{
-          '!bg-listbox-selected !text-listbox-selected': isSelected(
-            option.value
-          ),
+          '!border-2 !border-blue-300': isSelected(option.value),
         }"
         :aria-selected="isSelected(option.value)"
         @click="onListboxOptionClick(option)"
@@ -58,7 +56,7 @@
       >
         <BaseIcon
           name="Check"
-          class="fill-listbox-selected"
+          class="text-listbox"
           :class="isSelected(option.value) ? 'visible' : 'invisible'"
           :width="18"
         />
@@ -296,6 +294,7 @@ function openCloseListbox() {
     focusListOption();
   } else {
     ulElemRef.value?.setAttribute("tabindex", "-1");
+    focusListboxButton();
   }
 }
 
@@ -362,11 +361,6 @@ function onListboxKeyDown(event: KeyboardEvent) {
   }
 }
 
-function onListboxOptionClick(option: IInternalListboxOption) {
-  updateModelValue(option);
-  focusListboxButton();
-}
-
 function onListboxOptionKeyDown(
   event: KeyboardEvent,
   option: IInternalListboxOption
@@ -375,33 +369,32 @@ function onListboxOptionKeyDown(
   switch (key) {
     case "Enter":
       updateModelValue(option);
-      focusListboxButton();
       break;
 
     case "Spacebar":
       updateModelValue(option);
-      focusListboxButton();
       break;
 
     // spacebar (for older browser support)
     case " ":
       updateModelValue(option);
-      focusListboxButton();
       break;
 
     case "Tab":
       updateModelValue(option);
-      focusListboxButton();
       break;
 
     case "Escape":
       blurListOption(option);
       openCloseListbox();
-      focusListboxButton();
       break;
   }
 }
 
+function onListboxOptionClick(option: IInternalListboxOption) {
+  updateModelValue(option);
+}
+
 function validate(value: columnValue) {
   if (props.required && value === "") {
     emit("error", [{ message: `${props.id} required to complete the form` }]);

From fa01c1a51a86a778f0298cda59919dcd0f61c04d Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Mon, 20 Jan 2025 14:57:22 +0100
Subject: [PATCH 39/46] feat: isolated elements into components

---
 .../components/input/Listbox.vue              | 79 +++++++++----------
 .../components/input/listbox/List.vue         | 32 ++++++++
 .../components/input/listbox/ListItem.vue     | 38 +++++++++
 .../components/input/listbox/Toggle.vue       | 44 +++++++++++
 apps/tailwind-components/types/listbox.ts     | 11 +++
 apps/tailwind-components/utils/listbox.ts     | 16 ++++
 6 files changed, 179 insertions(+), 41 deletions(-)
 create mode 100644 apps/tailwind-components/components/input/listbox/List.vue
 create mode 100644 apps/tailwind-components/components/input/listbox/ListItem.vue
 create mode 100644 apps/tailwind-components/components/input/listbox/Toggle.vue
 create mode 100644 apps/tailwind-components/utils/listbox.ts

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index f68d1b27a1..303cd41a21 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,46 +1,39 @@
 <template>
   <div class="w-full relative">
-    <button
+    <inputListboxToggle
       :id="id"
       ref="listbox-button"
-      role="combobox"
-      :disabled="disabled"
-      aria-haspopup="listbox"
       :aria-controls="`listbox-${id}-options`"
-      :aria-required="required"
-      :aria-expanded="isExpanded"
+      :required="required"
+      :isExpanded="isExpanded"
+      :disabled="disabled"
       :aria-labelledby="labelId"
-      class="flex justify-start items-center h-10 w-full text-left pl-11 border bg-input rounded-search-input text-button-input-toggle focus:ring-blue-300"
-      :class="{
-        'border-disabled text-disabled bg-disabled': disabled,
-        'border-invalid text-invalid': hasError,
-      }"
       @click.prevent="openCloseListbox"
       @keydown="onListboxButtonKeyDown"
     >
       <span class="w-full">
         {{ displayText }}
       </span>
-      <div class="w-[60px] flex flex-col">
-        <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
-        <BaseIcon :width="18" name="caret-down" class="mx-auto -my-1" />
-      </div>
-    </button>
+    </inputListboxToggle>
 
-    <ul
-      :id="`listbox-${id}-options`"
-      role="listbox"
+    <inputListboxList
       ref="listbox-ul"
-      :aria-expanded="isExpanded"
-      class="absolute b-0 w-full overflow-y-scroll z-10 bg-listbox border"
-      :class="{
-        hidden: !isExpanded,
-        'h-44': isExpanded && listboxOptions.length > 5,
-        'shadow-inner': isExpanded,
-      }"
+      :id="`listbox-${id}-options`"
+      :isExpanded="isExpanded"
+      :hasFixedHeight="listboxOptions.length > 5"
       @keydown.prevent="onListboxKeyDown"
     >
-      <li
+      <InputListboxListItem
+        v-for="option in listboxOptions"
+        ref="listbox-li"
+        :id="option.elemId"
+        :isSelected="isSelected(option.value)"
+        :label="option.label || (option.value as string)"
+        @click="onListboxOptionClick(option)"
+        @blur="blurListOption(option)"
+        @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
+      />
+      <!-- <li
         v-for="option in listboxOptions"
         ref="listbox-li"
         :id="option.elemId"
@@ -70,8 +63,9 @@
         <span v-else>
           {{ option.value }}
         </span>
-      </li>
-    </ul>
+      </li> -->
+    </inputListboxList>
+    <!-- </ul> -->
   </div>
 </template>
 
@@ -85,6 +79,9 @@ import type {
   IListboxValue,
   IListboxOption,
   IInternalListboxOption,
+  IListboxUlRef,
+  IListboxButtonef,
+  IListboxLiRef,
 } from "../../types/listbox";
 
 const props = withDefaults(
@@ -122,9 +119,9 @@ const sourceData = ref<IListboxOption[]>();
 const focusCounter = ref<number>(0);
 const isExpanded = ref<boolean>(false);
 const modelValue = defineModel<IListboxOption | IListboxValue | null>();
-const ulElemRef = useTemplateRef<HTMLUListElement>("listbox-ul");
-const olElemRefs = useTemplateRef<HTMLOptionElement[]>("listbox-li");
-const btnElemRef = useTemplateRef<HTMLButtonElement>("listbox-button");
+const ulElemRef = useTemplateRef<IListboxUlRef>("listbox-ul");
+const liElemRefs = useTemplateRef<IListboxLiRef[]>("listbox-li");
+const btnElemRef = useTemplateRef<IListboxButtonef>("listbox-button");
 const displayText = ref<string>(props.placeholder);
 const startingCounter = ref<number>(0);
 
@@ -204,8 +201,8 @@ function updateCounter(value: number) {
 
 function focusListOption() {
   nextTick(() => {
-    if (olElemRefs.value) {
-      const targetElem = olElemRefs.value[focusCounter.value];
+    if (liElemRefs.value) {
+      const targetElem = liElemRefs.value[focusCounter.value].li;
       targetElem.setAttribute("tabindex", "0");
       targetElem.focus();
     }
@@ -214,8 +211,8 @@ function focusListOption() {
 
 function blurListOption(option: IInternalListboxOption) {
   nextTick(() => {
-    if (olElemRefs.value) {
-      const targetElem = olElemRefs.value[option.index];
+    if (liElemRefs.value) {
+      const targetElem = liElemRefs.value[option.index].li;
       targetElem.setAttribute("tabindex", "-1");
       targetElem.blur();
     }
@@ -233,7 +230,7 @@ function updateModelValue(
   selection: IInternalListboxOption,
   enableToggling: boolean = true
 ) {
-  btnElemRef.value?.setAttribute("aria-activedescendant", selection.elemId);
+  btnElemRef.value!.button.setAttribute("aria-activedescendant", selection.elemId);
   focusCounter.value = selection.index;
   startingCounter.value = selection.index;
 
@@ -248,7 +245,7 @@ function updateModelValue(
 
     modelValue.value = selectedOption;
   } else {
-    modelValue.value = selection.value as IListboxValue;
+    modelValue.value = (selection.value as IListboxValue);
     displayText.value = updateDisplayText(selection.value as string);
   }
 
@@ -283,13 +280,13 @@ function focusNextOption(by: number = 1) {
 }
 
 function focusListboxButton() {
-  btnElemRef.value?.focus();
+  btnElemRef.value?.button.focus();
 }
 
 function openCloseListbox() {
   isExpanded.value = !isExpanded.value;
   if (isExpanded.value) {
-    ulElemRef.value?.setAttribute("tabindex", "0");
+    ulElemRef.value?.ul.setAttribute("tabindex", "0");
     if (modelValue.value) {
       updateCounter(startingCounter.value);
     } else {
@@ -297,7 +294,7 @@ function openCloseListbox() {
     }
     focusListOption();
   } else {
-    ulElemRef.value?.setAttribute("tabindex", "-1");
+    ulElemRef.value?.ul.setAttribute("tabindex", "-1");
     focusListboxButton();
   }
 }
diff --git a/apps/tailwind-components/components/input/listbox/List.vue b/apps/tailwind-components/components/input/listbox/List.vue
new file mode 100644
index 0000000000..0a7d552f0f
--- /dev/null
+++ b/apps/tailwind-components/components/input/listbox/List.vue
@@ -0,0 +1,32 @@
+<template>
+  <ul
+    role="listbox"
+    ref="ul"
+    :aria-expanded="isExpanded"
+    class="absolute b-0 w-full overflow-y-scroll z-10 bg-listbox border"
+    :class="{
+      'hidden': !isExpanded,
+      'h-44': isExpanded && hasFixedHeight,
+      'shadow-inner': isExpanded,
+    }"
+  >
+    <slot></slot>
+  </ul>
+</template>
+  
+<script lang="ts" setup>
+withDefaults(
+  defineProps<{
+    isExpanded: boolean;
+    hasFixedHeight: boolean;
+  }>(), {
+    isExpanded: false,
+    hasFixedHeight: false,
+  }
+)
+
+const ul = useTemplateRef<HTMLUListElement>("ul");
+defineExpose({
+  ul
+});
+</script>
\ No newline at end of file
diff --git a/apps/tailwind-components/components/input/listbox/ListItem.vue b/apps/tailwind-components/components/input/listbox/ListItem.vue
new file mode 100644
index 0000000000..d4e34e18ce
--- /dev/null
+++ b/apps/tailwind-components/components/input/listbox/ListItem.vue
@@ -0,0 +1,38 @@
+<template>
+  <li
+    ref="li"
+    role="option"
+    class="flex justify-start items-center gap-3 pl-3 py-1 bg-listbox text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox focus:ring-blue-300"
+    :class="{
+      '!bg-listbox-selected !text-listbox-selected': isSelected,
+    }"
+    :aria-selected="isSelected"
+  >
+    <BaseIcon
+      name="Check"
+      class="fill-listbox-selected invisible"
+      :class="{
+        '!visible': isSelected,
+      }"
+      :width="18"
+    />
+    <span>{{ label }}</span>
+  </li>
+</template>
+
+<script lang="ts" setup>
+withDefaults(
+  defineProps<{
+    isSelected: boolean;
+    label: string | number | boolean;
+  }>(),
+  {
+    isSelected: false,
+  }
+);
+
+const li = useTemplateRef<HTMLLIElement>("li");
+defineExpose({
+  li
+});
+</script>
\ No newline at end of file
diff --git a/apps/tailwind-components/components/input/listbox/Toggle.vue b/apps/tailwind-components/components/input/listbox/Toggle.vue
new file mode 100644
index 0000000000..b93f3af905
--- /dev/null
+++ b/apps/tailwind-components/components/input/listbox/Toggle.vue
@@ -0,0 +1,44 @@
+<template>
+  <button
+    role="combobox"
+    ref="button"
+    aria-haspopup="listbox"
+    :aria-required="required"
+    :aria-expanded="isExpanded"
+    class="flex justify-start items-center h-10 w-full text-left pl-11 border bg-input rounded-search-input text-button-input-toggle focus:ring-blue-300"
+    :class="{
+      'border-disabled text-disabled bg-disabled': disabled,
+      'border-invalid text-invalid': hasError,
+    }"
+    >
+    <slot></slot>
+    <div class="w-[60px] flex flex-col">
+      <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
+      <BaseIcon :width="18" name="caret-down" class="mx-auto -my-1" />
+    </div>
+  </button>
+</template>
+
+<script lang="ts" setup>
+
+withDefaults(
+  defineProps<{
+    isExpanded: boolean;
+    required?: boolean;  
+    disabled?: boolean;
+    hasError?: boolean;
+  }>(),
+  {
+    isExpanded: false,
+    required: false,
+    disabled: false,
+    hasError: false,
+  }
+)
+
+const button = useTemplateRef<HTMLButtonElement>("button");
+defineExpose({
+  button
+});
+
+</script>
diff --git a/apps/tailwind-components/types/listbox.ts b/apps/tailwind-components/types/listbox.ts
index 9c9ee4e8d8..fc674ec692 100644
--- a/apps/tailwind-components/types/listbox.ts
+++ b/apps/tailwind-components/types/listbox.ts
@@ -10,3 +10,14 @@ export interface IInternalListboxOption extends IListboxOption {
   index: number;
   elemId: string;
 }
+
+export interface IListboxUlRef {
+  ul: HTMLUListElement;
+}
+
+export interface IListboxButtonef {
+  button: HTMLButtonElement;
+}
+export interface IListboxLiRef {
+  li: HTMLLIElement;
+}
\ No newline at end of file
diff --git a/apps/tailwind-components/utils/listbox.ts b/apps/tailwind-components/utils/listbox.ts
new file mode 100644
index 0000000000..d4c7bf677b
--- /dev/null
+++ b/apps/tailwind-components/utils/listbox.ts
@@ -0,0 +1,16 @@
+
+interface IPrepListboxData {
+  data: object[];
+  valueKey: string;
+  labelKey?: string;
+}
+
+export function prepareListboxData({data, valueKey, labelKey}: IPrepListboxData) {
+  const testValue = data[0];
+  
+  if (typeof testValue === "object") {
+    
+  } else {
+    
+  } 
+}
\ No newline at end of file

From a5b4742228364c51bc1233f6178c169df5790795 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 22 Jan 2025 08:54:00 +0100
Subject: [PATCH 40/46] created child listbox components

---
 .../components/input/Listbox.vue              | 52 ++++---------------
 .../components/input/listbox/List.vue         | 13 ++---
 .../components/input/listbox/ListItem.vue     |  4 +-
 .../components/input/listbox/Toggle.vue       | 10 ++--
 4 files changed, 23 insertions(+), 56 deletions(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index 303cd41a21..80a3ad2bd5 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,6 +1,6 @@
 <template>
   <div class="w-full relative">
-    <inputListboxToggle
+    <InputListboxToggle
       :id="id"
       ref="listbox-button"
       :aria-controls="`listbox-${id}-options`"
@@ -14,9 +14,8 @@
       <span class="w-full">
         {{ displayText }}
       </span>
-    </inputListboxToggle>
-
-    <inputListboxList
+    </InputListboxToggle>
+    <InputListboxList
       ref="listbox-ul"
       :id="`listbox-${id}-options`"
       :isExpanded="isExpanded"
@@ -33,39 +32,7 @@
         @blur="blurListOption(option)"
         @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
       />
-      <!-- <li
-        v-for="option in listboxOptions"
-        ref="listbox-li"
-        :id="option.elemId"
-        role="option"
-        class="flex justify-start items-center gap-3 pl-3 py-1 bg-listbox text-listbox border-t-[1px] border-t-listbox-option hover:cursor-pointer hover:bg-listbox-hover hover:text-listbox focus:bg-listbox-hover focus:text-listbox focus:ring-blue-300"
-        :class="{
-          '!bg-listbox-selected !text-listbox-selected': isSelected(
-            option.value
-          ),
-        }"
-        :aria-selected="isSelected(option.value)"
-        @click="onListboxOptionClick(option)"
-        @blur="blurListOption(option)"
-        @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
-      >
-        <BaseIcon
-          name="Check"
-          class="fill-listbox-selected invisible"
-          :class="{
-            '!visible': isSelected(option.value),
-          }"
-          :width="18"
-        />
-        <span v-if="option.label">
-          {{ option.label }}
-        </span>
-        <span v-else>
-          {{ option.value }}
-        </span>
-      </li> -->
-    </inputListboxList>
-    <!-- </ul> -->
+    </InputListboxList>
   </div>
 </template>
 
@@ -143,9 +110,7 @@ onMounted(() => {
 
 watch(
   () => props.placeholder,
-  () => {
-    displayText.value = props.placeholder;
-  }
+  () => (displayText.value = props.placeholder)
 );
 
 function counterIsInRange(value: number) {
@@ -230,7 +195,10 @@ function updateModelValue(
   selection: IInternalListboxOption,
   enableToggling: boolean = true
 ) {
-  btnElemRef.value!.button.setAttribute("aria-activedescendant", selection.elemId);
+  btnElemRef.value!.button.setAttribute(
+    "aria-activedescendant",
+    selection.elemId
+  );
   focusCounter.value = selection.index;
   startingCounter.value = selection.index;
 
@@ -245,7 +213,7 @@ function updateModelValue(
 
     modelValue.value = selectedOption;
   } else {
-    modelValue.value = (selection.value as IListboxValue);
+    modelValue.value = selection.value as IListboxValue;
     displayText.value = updateDisplayText(selection.value as string);
   }
 
diff --git a/apps/tailwind-components/components/input/listbox/List.vue b/apps/tailwind-components/components/input/listbox/List.vue
index 0a7d552f0f..780cf058b3 100644
--- a/apps/tailwind-components/components/input/listbox/List.vue
+++ b/apps/tailwind-components/components/input/listbox/List.vue
@@ -5,7 +5,7 @@
     :aria-expanded="isExpanded"
     class="absolute b-0 w-full overflow-y-scroll z-10 bg-listbox border"
     :class="{
-      'hidden': !isExpanded,
+      hidden: !isExpanded,
       'h-44': isExpanded && hasFixedHeight,
       'shadow-inner': isExpanded,
     }"
@@ -13,20 +13,21 @@
     <slot></slot>
   </ul>
 </template>
-  
+
 <script lang="ts" setup>
 withDefaults(
   defineProps<{
     isExpanded: boolean;
     hasFixedHeight: boolean;
-  }>(), {
+  }>(),
+  {
     isExpanded: false,
     hasFixedHeight: false,
   }
-)
+);
 
 const ul = useTemplateRef<HTMLUListElement>("ul");
 defineExpose({
-  ul
+  ul,
 });
-</script>
\ No newline at end of file
+</script>
diff --git a/apps/tailwind-components/components/input/listbox/ListItem.vue b/apps/tailwind-components/components/input/listbox/ListItem.vue
index d4e34e18ce..dc67261d01 100644
--- a/apps/tailwind-components/components/input/listbox/ListItem.vue
+++ b/apps/tailwind-components/components/input/listbox/ListItem.vue
@@ -33,6 +33,6 @@ withDefaults(
 
 const li = useTemplateRef<HTMLLIElement>("li");
 defineExpose({
-  li
+  li,
 });
-</script>
\ No newline at end of file
+</script>
diff --git a/apps/tailwind-components/components/input/listbox/Toggle.vue b/apps/tailwind-components/components/input/listbox/Toggle.vue
index b93f3af905..5ef70d45ec 100644
--- a/apps/tailwind-components/components/input/listbox/Toggle.vue
+++ b/apps/tailwind-components/components/input/listbox/Toggle.vue
@@ -10,7 +10,7 @@
       'border-disabled text-disabled bg-disabled': disabled,
       'border-invalid text-invalid': hasError,
     }"
-    >
+  >
     <slot></slot>
     <div class="w-[60px] flex flex-col">
       <BaseIcon :width="18" name="caret-up" class="mx-auto -my-1" />
@@ -20,11 +20,10 @@
 </template>
 
 <script lang="ts" setup>
-
 withDefaults(
   defineProps<{
     isExpanded: boolean;
-    required?: boolean;  
+    required?: boolean;
     disabled?: boolean;
     hasError?: boolean;
   }>(),
@@ -34,11 +33,10 @@ withDefaults(
     disabled: false,
     hasError: false,
   }
-)
+);
 
 const button = useTemplateRef<HTMLButtonElement>("button");
 defineExpose({
-  button
+  button,
 });
-
 </script>

From 18a7678fd5596a9e257f6178043aa4b9cb1ca8a0 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 22 Jan 2025 09:46:45 +0100
Subject: [PATCH 41/46] merged listbox v2 branch; changed typing

---
 apps/metadata-utils/src/types.ts              |  8 +++
 .../input/{Listbox.vue => listbox/index.vue}  | 56 +++++++++----------
 .../pages/input/Listbox.story.vue             | 14 ++---
 apps/tailwind-components/types/listbox.ts     |  9 +--
 4 files changed, 44 insertions(+), 43 deletions(-)
 rename apps/tailwind-components/components/input/{Listbox.vue => listbox/index.vue} (84%)

diff --git a/apps/metadata-utils/src/types.ts b/apps/metadata-utils/src/types.ts
index c31dd39a4f..9abcc65b1c 100644
--- a/apps/metadata-utils/src/types.ts
+++ b/apps/metadata-utils/src/types.ts
@@ -97,3 +97,11 @@ export type columnValue = string | number | boolean | columnValueObject;
 interface columnValueObject {
   [x: string]: columnValue;
 }
+
+
+export type IInputValue = string | number | boolean;
+
+export type IInputValueLabel = {
+  value: IInputValue | IInputValue[];
+  label?: string;
+}
\ No newline at end of file
diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/listbox/index.vue
similarity index 84%
rename from apps/tailwind-components/components/input/Listbox.vue
rename to apps/tailwind-components/components/input/listbox/index.vue
index 80a3ad2bd5..d5b085827e 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/listbox/index.vue
@@ -26,7 +26,7 @@
         v-for="option in listboxOptions"
         ref="listbox-li"
         :id="option.elemId"
-        :isSelected="isSelected(option.value)"
+        :isSelected="isSelected(option.value as IInputValue)"
         :label="option.label || (option.value as string)"
         @click="onListboxOptionClick(option)"
         @blur="blurListOption(option)"
@@ -41,22 +41,22 @@ import { ref, useTemplateRef, nextTick, watch, onMounted } from "vue";
 import type {
   columnValue,
   IFieldError,
-} from "../../../metadata-utils/src/types";
+  IInputValue,
+  IInputValueLabel,
+} from "../../../../metadata-utils/src/types";
 import type {
-  IListboxValue,
-  IListboxOption,
   IInternalListboxOption,
   IListboxUlRef,
   IListboxButtonef,
   IListboxLiRef,
-} from "../../types/listbox";
+} from "../../../types/listbox";
 
 const props = withDefaults(
   defineProps<{
     id: string;
     labelId: string;
-    options: IListboxOption[] | IListboxValue[];
-    value?: IListboxOption | IListboxValue;
+    options: IInputValue[] | IInputValueLabel[];
+    value?: IInputValue | IInputValueLabel;
     required?: boolean;
     hasError?: boolean;
     placeholder?: string;
@@ -71,7 +71,7 @@ const props = withDefaults(
 );
 
 const emit = defineEmits<{
-  (e: "update:modelValue", value: IListboxOption | IListboxValue | null): void;
+  (e: "update:modelValue", value: IInputValue | IInputValueLabel): void;
   (e: "error", value: IFieldError[]): void;
   (e: "blur", value: null): void;
   (e: "focus", value: null): void;
@@ -82,10 +82,10 @@ defineExpose({
 });
 
 const sourceDataType = ref<string>("");
-const sourceData = ref<IListboxOption[]>();
+const sourceData = ref<IInputValueLabel[]>();
 const focusCounter = ref<number>(0);
 const isExpanded = ref<boolean>(false);
-const modelValue = defineModel<IListboxOption | IListboxValue | null>();
+const modelValue = defineModel<IInputValue | IInputValueLabel | null>();
 const ulElemRef = useTemplateRef<IListboxUlRef>("listbox-ul");
 const liElemRefs = useTemplateRef<IListboxLiRef[]>("listbox-li");
 const btnElemRef = useTemplateRef<IListboxButtonef>("listbox-button");
@@ -97,8 +97,8 @@ onMounted(() => {
     const initalValue: IInternalListboxOption[] = listboxOptions.value.filter(
       (row: IInternalListboxOption) => {
         return (
-          row.value === (props.value as IListboxOption).value ||
-          row.value === (props.value as IListboxValue)
+          row.value === (props.value as IInputValueLabel).value ||
+          row.value === (props.value as IInputValue)
         );
       }
     );
@@ -118,32 +118,32 @@ function counterIsInRange(value: number) {
 }
 
 const listboxOptions = computed<IInternalListboxOption[]>(() => {
-  const testDataValue: IListboxOption | IListboxValue = props.options[0];
+  const testDataValue: IInputValue | IInputValueLabel = props.options[0];
   if (
     typeof testDataValue === "object" &&
-    Object.hasOwn(testDataValue as IListboxOption, "value")
+    Object.hasOwn(testDataValue as IInputValueLabel, "value")
   ) {
     sourceDataType.value = "ListboxOptions";
-    sourceData.value = props.options as IListboxOption[];
+    sourceData.value = props.options as IInputValueLabel[];
   } else {
     sourceDataType.value = "ListboxValue";
-    const inputData = props.options as IListboxValue[];
+    const inputData = props.options as IInputValue[];
     const processedData = inputData.map(
-      (value: IListboxValue): IListboxOption => {
+      (value: IInputValue): IInputValueLabel => {
         return { value: value };
       }
     );
-    sourceData.value = processedData as IListboxOption[];
+    sourceData.value = processedData as IInputValueLabel[];
   }
 
-  const defaultOption: IListboxOption = {
-    value: null,
+  const defaultOption: IInputValueLabel = {
+    value: "",
     label: props.placeholder,
   };
-  const inputData = sourceData.value as IListboxOption[];
-  const data: IListboxOption[] = [defaultOption, ...inputData];
+  const inputData = sourceData.value as IInputValueLabel[];
+  const data: IInputValueLabel[] = [defaultOption, ...inputData];
 
-  return data.map((option: IListboxOption, index: number) => {
+  return data.map((option: IInputValueLabel, index: number) => {
     return {
       ...option,
       index: index,
@@ -203,7 +203,7 @@ function updateModelValue(
   startingCounter.value = selection.index;
 
   if (sourceDataType.value === "ListboxOptions") {
-    const selectedOption: IListboxOption = { value: selection.value };
+    const selectedOption: IInputValueLabel = { value: selection.value };
     if (Object.hasOwn(selection, "label")) {
       selectedOption.label = selection.label;
       displayText.value = updateDisplayText(selectedOption.label);
@@ -213,7 +213,7 @@ function updateModelValue(
 
     modelValue.value = selectedOption;
   } else {
-    modelValue.value = selection.value as IListboxValue;
+    modelValue.value = selection.value as IInputValue;
     displayText.value = updateDisplayText(selection.value as string);
   }
 
@@ -224,11 +224,11 @@ function updateModelValue(
   }
 }
 
-function isSelected(value: IListboxValue): boolean {
+function isSelected(value: IInputValue): boolean {
   if (modelValue.value) {
     return (
-      value === (modelValue.value as IInternalListboxOption).value ||
-      value === (modelValue.value as IListboxValue)
+      value === (modelValue.value as IInputValueLabel).value ||
+      value === (modelValue.value as IInputValue)
     );
   } else {
     return value === null;
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index c48804a508..759cc5f63e 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -122,28 +122,26 @@
 
 <script lang="ts" setup>
 import { ref, computed } from "vue";
-import type { IListboxValue, IListboxOption } from "../../types/listbox";
-
-const modelValue = defineModel<IListboxValue | IListboxOption | null>();
+import type { IInputValue, IInputValueLabel } from "../../../metadata-utils/src/types";
 
+const modelValue = defineModel<IInputValue | IInputValueLabel>();
 const letters: string[] = [...Array(26).keys()].map((num) =>
   String.fromCharCode(num + 65)
 );
 
-const lettersWithLabels: IListboxOption[] = letters.map((letter: string) => {
+const lettersWithLabels: IInputValueLabel[] = letters.map((letter: string) => {
   return { value: letter, label: `Group ${letter}` };
 });
 
 const listboxState = ref<string>("");
 const listboxPlaceholder = ref<string>("Select an option");
 const listboxDataType = ref<string>("string");
-const hasStartingValue = ref<boolean>(false);
 
-const listboxData = computed<IListboxOption[] | IListboxValue[]>(() => {
+const listboxData = computed<IInputValue[] | IInputValueLabel[]>(() => {
   if (listboxDataType.value === "string") {
-    return letters as IListboxValue[];
+    return letters as IInputValue[];
   } else {
-    return lettersWithLabels as IListboxOption[];
+    return lettersWithLabels as IInputValueLabel[];
   }
 });
 </script>
diff --git a/apps/tailwind-components/types/listbox.ts b/apps/tailwind-components/types/listbox.ts
index fc674ec692..8cadf0e9dc 100644
--- a/apps/tailwind-components/types/listbox.ts
+++ b/apps/tailwind-components/types/listbox.ts
@@ -1,12 +1,7 @@
 
-export type IListboxValue = string | number | boolean | undefined | null;
+import type { IInputValueLabel } from "../../metadata-utils/src/types"; 
 
-export interface IListboxOption {
-  value: IListboxValue;
-  label?: string;
-}
-
-export interface IInternalListboxOption extends IListboxOption {
+export interface IInternalListboxOption extends IInputValueLabel {
   index: number;
   elemId: string;
 }

From ea406b80084b0861953cc60627cb6908dc672046 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 22 Jan 2025 10:20:12 +0100
Subject: [PATCH 42/46] removed file

---
 apps/tailwind-components/utils/listbox.ts | 16 ----------------
 1 file changed, 16 deletions(-)
 delete mode 100644 apps/tailwind-components/utils/listbox.ts

diff --git a/apps/tailwind-components/utils/listbox.ts b/apps/tailwind-components/utils/listbox.ts
deleted file mode 100644
index d4c7bf677b..0000000000
--- a/apps/tailwind-components/utils/listbox.ts
+++ /dev/null
@@ -1,16 +0,0 @@
-
-interface IPrepListboxData {
-  data: object[];
-  valueKey: string;
-  labelKey?: string;
-}
-
-export function prepareListboxData({data, valueKey, labelKey}: IPrepListboxData) {
-  const testValue = data[0];
-  
-  if (typeof testValue === "object") {
-    
-  } else {
-    
-  } 
-}
\ No newline at end of file

From d45100bc8c0d79c03f7e4fc234683b773097652f Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 22 Jan 2025 13:41:42 +0100
Subject: [PATCH 43/46] feat: improved ref handling; simplified typing;

---
 .../components/form/FieldInput.vue            |  5 ++-
 .../components/input/listbox/List.vue         |  1 +
 .../components/input/listbox/Toggle.vue       | 12 +++++--
 .../components/input/listbox/index.vue        | 31 ++++++++-----------
 apps/tailwind-components/pages/Form.story.vue | 24 +++++++-------
 .../pages/input/Listbox.story.vue             |  5 ++-
 apps/tailwind-components/types/listbox.ts     |  7 -----
 7 files changed, 42 insertions(+), 43 deletions(-)

diff --git a/apps/tailwind-components/components/form/FieldInput.vue b/apps/tailwind-components/components/form/FieldInput.vue
index e751b7b16e..e513007fa9 100644
--- a/apps/tailwind-components/components/form/FieldInput.vue
+++ b/apps/tailwind-components/components/form/FieldInput.vue
@@ -9,10 +9,9 @@ import type {
   columnId,
   columnValue,
   CellValueType,
+  IInputValueLabel,
 } from "../../../metadata-utils/src/types";
 
-import type { IListboxValue } from "~/types/listbox";
-
 type inputComponent =
   | InstanceType<typeof InputString>
   | InstanceType<typeof InputTextArea>
@@ -25,7 +24,7 @@ defineProps<{
   label: string;
   required: boolean;
   data: columnValue;
-  options?: IListboxValue[];
+  options?: IInputValueLabel[];
 }>();
 
 defineEmits(["focus", "error", "update:modelValue"]);
diff --git a/apps/tailwind-components/components/input/listbox/List.vue b/apps/tailwind-components/components/input/listbox/List.vue
index 780cf058b3..a7f28414d9 100644
--- a/apps/tailwind-components/components/input/listbox/List.vue
+++ b/apps/tailwind-components/components/input/listbox/List.vue
@@ -9,6 +9,7 @@
       'h-44': isExpanded && hasFixedHeight,
       'shadow-inner': isExpanded,
     }"
+    :tabindex="isExpanded ? 1 : 0"
   >
     <slot></slot>
   </ul>
diff --git a/apps/tailwind-components/components/input/listbox/Toggle.vue b/apps/tailwind-components/components/input/listbox/Toggle.vue
index 5ef70d45ec..7e3229930e 100644
--- a/apps/tailwind-components/components/input/listbox/Toggle.vue
+++ b/apps/tailwind-components/components/input/listbox/Toggle.vue
@@ -5,11 +5,13 @@
     aria-haspopup="listbox"
     :aria-required="required"
     :aria-expanded="isExpanded"
+    :aria-activedescendant="selectedElementId"
     class="flex justify-start items-center h-10 w-full text-left pl-11 border bg-input rounded-search-input text-button-input-toggle focus:ring-blue-300"
     :class="{
       'border-disabled text-disabled bg-disabled': disabled,
       'border-invalid text-invalid': hasError,
     }"
+    @click="onClick()"
   >
     <slot></slot>
     <div class="w-[60px] flex flex-col">
@@ -22,21 +24,27 @@
 <script lang="ts" setup>
 withDefaults(
   defineProps<{
-    isExpanded: boolean;
     required?: boolean;
     disabled?: boolean;
     hasError?: boolean;
+    selectedElementId?: string;
   }>(),
   {
-    isExpanded: false,
     required: false,
     disabled: false,
     hasError: false,
   }
 );
 
+const isExpanded = ref<boolean>(false);
+
+function onClick() {
+  isExpanded.value = !isExpanded.value;
+}
+
 const button = useTemplateRef<HTMLButtonElement>("button");
 defineExpose({
   button,
+  expanded: isExpanded,
 });
 </script>
diff --git a/apps/tailwind-components/components/input/listbox/index.vue b/apps/tailwind-components/components/input/listbox/index.vue
index d5b085827e..0f4bd267cb 100644
--- a/apps/tailwind-components/components/input/listbox/index.vue
+++ b/apps/tailwind-components/components/input/listbox/index.vue
@@ -2,13 +2,12 @@
   <div class="w-full relative">
     <InputListboxToggle
       :id="id"
-      ref="listbox-button"
+      ref="btnElemRef"
       :aria-controls="`listbox-${id}-options`"
       :required="required"
-      :isExpanded="isExpanded"
       :disabled="disabled"
       :aria-labelledby="labelId"
-      @click.prevent="openCloseListbox"
+      :selected-element-id="selectedElementId"
       @keydown="onListboxButtonKeyDown"
     >
       <span class="w-full">
@@ -16,7 +15,6 @@
       </span>
     </InputListboxToggle>
     <InputListboxList
-      ref="listbox-ul"
       :id="`listbox-${id}-options`"
       :isExpanded="isExpanded"
       :hasFixedHeight="listboxOptions.length > 5"
@@ -46,11 +44,11 @@ import type {
 } from "../../../../metadata-utils/src/types";
 import type {
   IInternalListboxOption,
-  IListboxUlRef,
-  IListboxButtonef,
   IListboxLiRef,
 } from "../../../types/listbox";
 
+import { InputListboxToggle } from "#components";
+
 const props = withDefaults(
   defineProps<{
     id: string;
@@ -84,13 +82,16 @@ defineExpose({
 const sourceDataType = ref<string>("");
 const sourceData = ref<IInputValueLabel[]>();
 const focusCounter = ref<number>(0);
-const isExpanded = ref<boolean>(false);
 const modelValue = defineModel<IInputValue | IInputValueLabel | null>();
-const ulElemRef = useTemplateRef<IListboxUlRef>("listbox-ul");
 const liElemRefs = useTemplateRef<IListboxLiRef[]>("listbox-li");
-const btnElemRef = useTemplateRef<IListboxButtonef>("listbox-button");
+const btnElemRef = ref<InstanceType<typeof InputListboxToggle>>();
 const displayText = ref<string>(props.placeholder);
 const startingCounter = ref<number>(0);
+const selectedElementId = ref<string>("");
+
+const isExpanded = computed<boolean>(() => {
+  return btnElemRef.value?.expanded as boolean;
+});
 
 onMounted(() => {
   if (props.value && listboxOptions.value) {
@@ -195,10 +196,6 @@ function updateModelValue(
   selection: IInternalListboxOption,
   enableToggling: boolean = true
 ) {
-  btnElemRef.value!.button.setAttribute(
-    "aria-activedescendant",
-    selection.elemId
-  );
   focusCounter.value = selection.index;
   startingCounter.value = selection.index;
 
@@ -216,7 +213,7 @@ function updateModelValue(
     modelValue.value = selection.value as IInputValue;
     displayText.value = updateDisplayText(selection.value as string);
   }
-
+  selectedElementId.value = selection.elemId;
   emit("update:modelValue", modelValue.value);
 
   if (enableToggling) {
@@ -248,13 +245,12 @@ function focusNextOption(by: number = 1) {
 }
 
 function focusListboxButton() {
-  btnElemRef.value?.button.focus();
+  btnElemRef.value?.button?.focus();
 }
 
 function openCloseListbox() {
-  isExpanded.value = !isExpanded.value;
+  btnElemRef.value!.expanded = !btnElemRef.value!.expanded;
   if (isExpanded.value) {
-    ulElemRef.value?.ul.setAttribute("tabindex", "0");
     if (modelValue.value) {
       updateCounter(startingCounter.value);
     } else {
@@ -262,7 +258,6 @@ function openCloseListbox() {
     }
     focusListOption();
   } else {
-    ulElemRef.value?.ul.setAttribute("tabindex", "-1");
     focusListboxButton();
   }
 }
diff --git a/apps/tailwind-components/pages/Form.story.vue b/apps/tailwind-components/pages/Form.story.vue
index d32ba4b2f8..79d8bc6ee1 100644
--- a/apps/tailwind-components/pages/Form.story.vue
+++ b/apps/tailwind-components/pages/Form.story.vue
@@ -5,15 +5,15 @@ import type {
   IFieldError,
   ISchemaMetaData,
   ITableMetaData,
+  IInputValueLabel,
 } from "../../metadata-utils/src/types";
-import type { IListboxOption, IListboxValue } from "../types/listbox";
 
-const exampleForms: IListboxOption[] = [
+const exampleForms: IInputValueLabel[] = [
   { value: "simple", label: "Simple form example" },
   { value: "complex", label: "Complex form example" },
 ];
 
-const formType = ref<IListboxOption>(exampleForms[0]);
+const formType = ref<IInputValueLabel>(exampleForms[0]);
 
 // just assuming that the table is there for the demo
 const schemaId = computed(() =>
@@ -36,7 +36,7 @@ const tableMeta = computed(
     ) as ITableMetaData
 );
 
-function refetch(value: IListboxOption) {
+function refetch(value: IInputValueLabel) {
   formType.value = value;
   refetchMetadata();
 }
@@ -75,14 +75,14 @@ function onErrors(newErrors: Record<string, IFieldError[]>) {
       <div>Demo controls, settings and status:</div>
 
       <div class="p-4 border-2 mb-2">
-        <select
-          @change="refetch()"
-          v-model="sampleType"
-          class="border-1 border-black"
-        >
-          <option value="simple">Simple form example</option>
-          <option value="complex">Complex form example</option>
-        </select>
+        <InputLabel for="form-example"> Select a form to display </InputLabel>
+        <InputListbox
+          id="form-example"
+          label-id="form-example-title"
+          :options="exampleForms"
+          :value="formType"
+          @update:model-value="(value) => refetch(value as IInputValueLabel)"
+        />
 
         <div>schema id = {{ schemaId }}</div>
         <div>table id = {{ tableId }}</div>
diff --git a/apps/tailwind-components/pages/input/Listbox.story.vue b/apps/tailwind-components/pages/input/Listbox.story.vue
index 759cc5f63e..72c5391219 100644
--- a/apps/tailwind-components/pages/input/Listbox.story.vue
+++ b/apps/tailwind-components/pages/input/Listbox.story.vue
@@ -122,7 +122,10 @@
 
 <script lang="ts" setup>
 import { ref, computed } from "vue";
-import type { IInputValue, IInputValueLabel } from "../../../metadata-utils/src/types";
+import type {
+  IInputValue,
+  IInputValueLabel,
+} from "../../../metadata-utils/src/types";
 
 const modelValue = defineModel<IInputValue | IInputValueLabel>();
 const letters: string[] = [...Array(26).keys()].map((num) =>
diff --git a/apps/tailwind-components/types/listbox.ts b/apps/tailwind-components/types/listbox.ts
index 8cadf0e9dc..d7d02e26b3 100644
--- a/apps/tailwind-components/types/listbox.ts
+++ b/apps/tailwind-components/types/listbox.ts
@@ -6,13 +6,6 @@ export interface IInternalListboxOption extends IInputValueLabel {
   elemId: string;
 }
 
-export interface IListboxUlRef {
-  ul: HTMLUListElement;
-}
-
-export interface IListboxButtonef {
-  button: HTMLButtonElement;
-}
 export interface IListboxLiRef {
   li: HTMLLIElement;
 }
\ No newline at end of file

From 90ec1032b6c53ca403945226a0c7f323ac3b02a0 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Wed, 22 Jan 2025 16:17:01 +0100
Subject: [PATCH 44/46] ran formatter

---
 apps/metadata-utils/src/types.ts | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/apps/metadata-utils/src/types.ts b/apps/metadata-utils/src/types.ts
index 9abcc65b1c..45c0d2061f 100644
--- a/apps/metadata-utils/src/types.ts
+++ b/apps/metadata-utils/src/types.ts
@@ -98,10 +98,9 @@ interface columnValueObject {
   [x: string]: columnValue;
 }
 
-
 export type IInputValue = string | number | boolean;
 
 export type IInputValueLabel = {
   value: IInputValue | IInputValue[];
   label?: string;
-}
\ No newline at end of file
+};

From f4107a5a1cf005f8eecfd5568d13cf0fe7aeb653 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Mon, 27 Jan 2025 15:47:41 +0100
Subject: [PATCH 45/46] minor revisions to typing; fixed e2e tests

---
 apps/metadata-utils/src/types.ts              |   2 +-
 .../components/form/FieldInput.vue            |  20 +-
 .../input/{listbox/index.vue => Listbox.vue}  |  12 +-
 apps/yarn.lock                                |   1 +
 .../tailwind-components/input/listbox.spec.ts | 246 +++++++++++++-----
 5 files changed, 189 insertions(+), 92 deletions(-)
 rename apps/tailwind-components/components/input/{listbox/index.vue => Listbox.vue} (96%)

diff --git a/apps/metadata-utils/src/types.ts b/apps/metadata-utils/src/types.ts
index 94001057a9..3c1e5567ec 100644
--- a/apps/metadata-utils/src/types.ts
+++ b/apps/metadata-utils/src/types.ts
@@ -108,6 +108,6 @@ interface columnValueObject {
 export type IInputValue = string | number | boolean;
 
 export type IInputValueLabel = {
-  value: IInputValue | IInputValue[];
+  value: IInputValue | IInputValue[] | null;
   label?: string;
 };
diff --git a/apps/tailwind-components/components/form/FieldInput.vue b/apps/tailwind-components/components/form/FieldInput.vue
index e513007fa9..fb8fb3350f 100644
--- a/apps/tailwind-components/components/form/FieldInput.vue
+++ b/apps/tailwind-components/components/form/FieldInput.vue
@@ -3,7 +3,6 @@ import type {
   InputString,
   InputTextArea,
   InputPlaceHolder,
-  InputListbox,
 } from "#build/components";
 import type {
   columnId,
@@ -15,8 +14,7 @@ import type {
 type inputComponent =
   | InstanceType<typeof InputString>
   | InstanceType<typeof InputTextArea>
-  | InstanceType<typeof InputPlaceHolder>
-  | InstanceType<typeof InputListbox>;
+  | InstanceType<typeof InputPlaceHolder>;
 
 defineProps<{
   type: CellValueType;
@@ -67,21 +65,5 @@ function validate(value: columnValue) {
     @update:modelValue="$emit('update:modelValue', $event)"
     @error="$emit('error', $event)"
   ></LazyInputTextArea>
-  <LazyInputListbox
-    v-else-if="
-      ['ONTOLOGY', 'ONTOLOGY_ARRAY', 'REF', 'REF_ARRAY'].includes(type) &&
-      options
-    "
-    ref="input"
-    :id="id"
-    :label-id="`${id}-label`"
-    :required="required"
-    :options="options"
-    :placeholder="`Select a ${id}`"
-    :value="(data as string)"
-    @focus="$emit('focus')"
-    @update:modelValue="$emit('update:modelValue', $event)"
-    @error="$emit('error', $event)"
-  />
   <LazyInputPlaceHolder v-else ref="input" :type="type" />
 </template>
diff --git a/apps/tailwind-components/components/input/listbox/index.vue b/apps/tailwind-components/components/input/Listbox.vue
similarity index 96%
rename from apps/tailwind-components/components/input/listbox/index.vue
rename to apps/tailwind-components/components/input/Listbox.vue
index 0f4bd267cb..fffba94db3 100644
--- a/apps/tailwind-components/components/input/listbox/index.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,4 +1,5 @@
 <template>
+  model: {{ modelValue }}
   <div class="w-full relative">
     <InputListboxToggle
       :id="id"
@@ -24,8 +25,8 @@
         v-for="option in listboxOptions"
         ref="listbox-li"
         :id="option.elemId"
-        :isSelected="isSelected(option.value as IInputValue)"
-        :label="option.label || (option.value as string)"
+        :isSelected="option.value === '' || isSelected(option.value as IInputValue)"
+        :label="(option.label as string) || (option.value as string)"
         @click="onListboxOptionClick(option)"
         @blur="blurListOption(option)"
         @keydown="(event: KeyboardEvent) => onListboxOptionKeyDown(event, option)"
@@ -41,11 +42,11 @@ import type {
   IFieldError,
   IInputValue,
   IInputValueLabel,
-} from "../../../../metadata-utils/src/types";
+} from "../../../metadata-utils/src/types";
 import type {
   IInternalListboxOption,
   IListboxLiRef,
-} from "../../../types/listbox";
+} from "../../types/listbox";
 
 import { InputListboxToggle } from "#components";
 
@@ -138,7 +139,7 @@ const listboxOptions = computed<IInternalListboxOption[]>(() => {
   }
 
   const defaultOption: IInputValueLabel = {
-    value: "",
+    value: null,
     label: props.placeholder,
   };
   const inputData = sourceData.value as IInputValueLabel[];
@@ -186,6 +187,7 @@ function blurListOption(option: IInternalListboxOption) {
 }
 
 function updateDisplayText(text: string | undefined | null): string {
+  console.log(text);
   if (typeof text === "undefined" || text === null) {
     return props.placeholder;
   }
diff --git a/apps/yarn.lock b/apps/yarn.lock
index 0d98292f35..872b7cf21e 100644
--- a/apps/yarn.lock
+++ b/apps/yarn.lock
@@ -14248,6 +14248,7 @@ wordwrap@^1.0.0, wordwrap@~1.0.0:
   integrity sha512-gvVzJFlPycKc5dZN4yPkP8w7Dc37BtP1yczEneOb4uq34pXZcvrtRTmWV8W+Ume+XCxKgbjM+nevkyFPMybd4Q==
 
 "wrap-ansi-cjs@npm:wrap-ansi@^7.0.0", wrap-ansi@^7.0.0:
+  name wrap-ansi-cjs
   version "7.0.0"
   resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43"
   integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==
diff --git a/e2e/tests/tailwind-components/input/listbox.spec.ts b/e2e/tests/tailwind-components/input/listbox.spec.ts
index b781b744e1..3589c0f0fc 100644
--- a/e2e/tests/tailwind-components/input/listbox.spec.ts
+++ b/e2e/tests/tailwind-components/input/listbox.spec.ts
@@ -1,75 +1,187 @@
 import { test, expect } from "@playwright/test";
 
-test(
-  "Listbox: button has correct aria attributes @tw-components @tw-forms @tw-listbox",
-  async({ page }) => {
-    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
-    const combobox = await page.getByRole("combobox");
-    await expect(combobox).toHaveAttribute("aria-required");
-    await expect(combobox).toHaveAttribute("aria-expanded");
-    await expect(combobox).toHaveAttribute("aria-labelledby");
-    await expect(combobox).toHaveAttribute("role", "combobox");
-    await expect(combobox).toHaveAttribute("aria-haspopup", "listbox");
-  }
-);
 
-test(
-  "Listbox: combox is properly linked to the listbox @tw-components @tw-forms @tw-listbox",
-  async ({ page }) => {
-    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
-    const combobox = await page.getByRole("combobox");
-    const listbox = await page.getByRole("listbox");
-    await combobox.click();
-    
-    const comboxId = await combobox.getAttribute("aria-controls");
-    const listboxId = await listbox.getAttribute("id");
-    await expect(comboxId).toEqual(listboxId);   
-  }
-)
+test.describe("Listbox component", {
+  tag: "@tw-components @tw-forms @tw-listbox"
+}, () => {
+  
+  test(
+    "toggle has correct aria attributes",
+    async({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      await expect(combobox).toHaveAttribute("aria-required");
+      await expect(combobox).toHaveAttribute("aria-expanded");
+      await expect(combobox).toHaveAttribute("aria-labelledby");
+      await expect(combobox).toHaveAttribute("role", "combobox");
+      await expect(combobox).toHaveAttribute("aria-haspopup", "listbox");
+    }
+  );
+  
+  test(
+    "options list is properly linked to the listbox",
+    async ({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      const listbox = await page.getByRole("listbox");
+      await combobox.click();
+      
+      const comboxId = await combobox.getAttribute("aria-controls");
+      const listboxId = await listbox.getAttribute("id");
+      await expect(comboxId).toEqual(listboxId);   
+    }
+  )
+  
+  test(
+    "listbox is properly labelled",
+    async ({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      const comboxId = await combobox.getAttribute("aria-labelledby");
+      await page.locator(`label[for='${comboxId}']`);
+    }
+  )
+  
+  test(
+    "aria expand properties correctly update when opened",
+    async({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      await expect(combobox).toHaveAttribute("aria-expanded", "false");
+    }
+  );
+  
+  test(
+    "placeholder is always the first element in the list",
+    async ({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      await combobox.click();
+      const option = await page.getByRole("option").first();
+      await expect(option).toHaveText("Select an option");
+    }
+  );
+  
+  test(
+    "list items have the proper attributes",
+    async ({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      await combobox.click();
+      await expect(combobox).toHaveAttribute("aria-expanded", "true");
+      for (const option of await page.getByRole("option").all()) { 
+        if (await option.innerText() === "Select an option") {
+          await expect(option).toHaveAttribute("aria-selected", "true");
+        } else {
+          await expect(option).toHaveAttribute("aria-selected", "false");
+        }
+      }
+    }
+  );
+  
+  test(
+    "down key opens listbox",
+    {
+      tag: '@keyboard-events'
+    },
+    async ({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      const listbox = await page.getByRole("listbox");
+
+      await combobox.focus();
+      await page.keyboard.press("ArrowDown");
+      await expect(combobox).toHaveAttribute("aria-expanded", "true");
+      await expect(listbox).toHaveAttribute("aria-expanded", "true");
+    }
+  );
+  
+  test(
+    "enter key opens and closes listbox",
+    {
+      tag: '@keyboard-events'
+    },
+    async({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      const listbox = await page.getByRole("listbox");
 
-test(
-  "Listbox: listbox has is properly labelled @tw-components @tw-forms @tw-listbox",
-  async ({ page }) => {
-    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
-    const combobox = await page.getByRole("combobox");
-    const comboxId = await combobox.getAttribute("aria-labelledby");
-    await page.locator(`label[for='${comboxId}']`);
-  }
-)
+      await combobox.focus();
+      await page.keyboard.press("Enter");
+      await expect(combobox).toHaveAttribute("aria-expanded", "true");
+      await expect(listbox).toHaveAttribute("aria-expanded", "true");
+      
+      await page.keyboard.press("Enter");
+      await expect(combobox).toHaveAttribute("aria-expanded", "false");
+      await expect(listbox).toBeHidden();
+      
+    }
+  );
+  
+  test(
+    "space key opens and closes listbox",
+    {
+      tag: '@keyboard-events'
+    },
+    async({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
+      const listbox = await page.getByRole("listbox");
 
-test(
-  "Listbox: aria expand properties correctly update when expanded @tw-components @tw-forms @tw-listbox",
-  async({ page }) => {
-    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
-    const combobox = await page.getByRole("combobox");
-    await expect(combobox).toHaveAttribute("aria-expanded", "false");
-  }
-);
+      await combobox.focus();
+      await page.keyboard.press("Space");
+      await expect(combobox).toHaveAttribute("aria-expanded", "true");
+      await expect(listbox).toHaveAttribute("aria-expanded", "true");
+      
+      await page.keyboard.press("Space");
+      await expect(combobox).toHaveAttribute("aria-expanded", "false");
+      await expect(listbox).toBeHidden();
+      
+    }
+  );
+  
+  test(
+    "End and home buttons focuses the last and first options",
+    {
+      tag: '@keyboard-events'
+    },
+    async({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
 
-test(
-  "Listbox: placeholder is the first element in the list @tw-components @tw-forms @tw-listbox",
-  async ({ page }) => {
-    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
-    const combobox = await page.getByRole("combobox");
-    await combobox.click();
-    const option = await page.getByRole("option").first();
-    await expect(option).toHaveText("Select an option");
-  }
-)
+      await combobox.focus();
+      await page.keyboard.press("Enter");
+      await page.keyboard.press("End");
+      
+      const lastOption = await page.getByRole("option").last();
+      await expect(lastOption).toBeFocused();
+      
+      await page.keyboard.press("Home");
+      const firstOption = await page.getByRole("option").first();
+      await expect(firstOption).toBeFocused();
+    }
+  );
+  
+  test(
+    "When opened, arrow keys properly focus and select items",
+    {
+      tag: '@keyboard-events'
+    },
+    async({ page }) => {
+      await page.goto("/apps/tailwind-components/#/input/Listbox.story");
+      const combobox = await page.getByRole("combobox");
 
-test(
-  "Listbox: list items have the proper attributes @tw-components @tw-forms @tw-listbox",
-  async ({ page }) => {
-    await page.goto("/apps/tailwind-components/#/input/Listbox.story");
-    const combobox = await page.getByRole("combobox");
-    combobox.click();
-    await expect(combobox).toHaveAttribute("aria-expanded", "true");
-    for (const option of await page.getByRole("option").all()) { 
-      if (await option.innerText() === "Select an option") {
-        await expect(option).toHaveAttribute("aria-selected", "true");
-      } else {
-        await expect(option).toHaveAttribute("aria-selected", "false");
-      }
+      await combobox.focus();
+      await page.keyboard.press("Enter");
+      await page.keyboard.press("ArrowDown");
+      const secondOption = await page.getByRole("option").nth(1);
+      await expect(secondOption).toBeFocused();
     }
-  }
-)
+  )
+  
+})
+
+
+
+
+

From d4dea39fd36fa86c2437c714f7f68cfde2b204c6 Mon Sep 17 00:00:00 2001
From: dcruvolo <davidruvolo51@gmail.com>
Date: Tue, 28 Jan 2025 10:44:52 +0100
Subject: [PATCH 46/46] fix: removed remaining modelvalue test

---
 apps/tailwind-components/components/input/Listbox.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/apps/tailwind-components/components/input/Listbox.vue b/apps/tailwind-components/components/input/Listbox.vue
index fffba94db3..19faaabe6d 100644
--- a/apps/tailwind-components/components/input/Listbox.vue
+++ b/apps/tailwind-components/components/input/Listbox.vue
@@ -1,5 +1,4 @@
 <template>
-  model: {{ modelValue }}
   <div class="w-full relative">
     <InputListboxToggle
       :id="id"