Merge pull request I-TECH-UW#1 from mozzy11/main

add cql module
mozzy11 · Aug 12, 2024 · dc47881 · dc47881
2 parents f98e6f6 + 7680123
commit dc47881
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Showing 12 changed files with 307 additions and 9 deletions.
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -2,7 +2,7 @@ name: Build and Validate Configuration
 
 on:
   pull_request:
-    branches: [main]
+    branches: [none]
 
 jobs:
   build:

diff --git a/.github/workflows/e2e-on-release.yml b/.github/workflows/e2e-on-release.yml
@@ -2,7 +2,7 @@ name: Run E2E Tests on Release PRs
 
 on:
   pull_request:
-    branches: [main]
+    branches: [none]
 
 jobs:
   build:

diff --git a/.github/workflows/e2e-tests-on-commit.yml b/.github/workflows/e2e-tests-on-commit.yml
@@ -2,9 +2,9 @@ name: Run E2E Tests on PRs and Commits
 
 on:
   push:
-    branches: [main]
+    branches: [none]
   pull_request:
-    branches: [main]
+    branches: [none]
 
 jobs:
   build:

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -0,0 +1,55 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Publish Docker Images
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+env:
+  REGISTRY: docker.io
+  IMAGE_NAME: ${{ vars.DOCKERHUB_USERNAME }}/openmrs-distro-who-hiv-dak
+
+jobs:
+  build-and-push-image-backend-dev:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+
+        # Add support for more platforms with QEMU (optional)
+        # https://github.com/docker/setup-qemu-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE_NAME}}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/dak/content/libraries/Library-HIVDTTestLogic.json b/dak/content/libraries/Library-HIVDTTestLogic.json
@@ -0,0 +1,65 @@
+{
+    "resourceType" : "Library",
+    "id" : "HIVDTTestLogic",
+    "meta" : {
+      "profile" : ["http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablelibrary",
+      "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablelibrary",
+      "http://hl7.org/fhir/uv/cql/StructureDefinition/cql-library",
+      "http://hl7.org/fhir/uv/cql/StructureDefinition/cql-module"]
+    },
+    "text" : {
+      "status" : "generated",
+      "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Library HIVDTTestLogic</b></p><a name=\"HIVDTTestLogic\"> </a><a name=\"hcHIVDTTestLogic\"> </a><a name=\"HIVDTTestLogic-en-US\"> </a><h2>Parameters</h2><table class=\"grid\"><tr><td>True condition</td><td>out</td><td>0</td><td>1</td><td>boolean</td></tr><tr><td>False condition</td><td>out</td><td>0</td><td>1</td><td>boolean</td></tr><tr><td>Output text</td><td>out</td><td>0</td><td>1</td><td>string</td></tr></table><h2>Contents</h2><p><code>text/cql</code></p><pre><code class=\"language-sql\">define &quot;True condition&quot;:\n  true\n\ndefine &quot;False condition&quot;:\n  false\n\ndefine &quot;Output text&quot;:\n  'Spam! Spam! Spam! Spam! Lovely spam! Wonderful spam! Spam spa-a-a-a-a-am spam spa-a-a-a-a-am spam! Lovely spam! Lovely spam! Lovely spam! Lovely spam! Spam spam spam spam!'\n</code></pre><p><code>Content not shown - (</code><code>application/elm+xml</code>, size = 2Kb )</p></div>"
+    },
+    "extension" : [{
+      "url" : "http://hl7.org/fhir/StructureDefinition/cqf-knowledgeCapability",
+      "valueCode" : "computable"
+    }],
+    "url" : "http://smart.who.int/HIV/Library/HIVDTTestLogic",
+    "version" : "0.2.0",
+    "name" : "HIVDTTestLogic",
+    "title" : "HIV.DT Test Logic",
+    "status" : "draft",
+    "experimental" : true,
+    "type" : {
+      "coding" : [{
+        "system" : "http://terminology.hl7.org/CodeSystem/library-type",
+        "code" : "logic-library"
+      }]
+    },
+    "date" : "2024-08-08T06:57:34+00:00",
+    "publisher" : "WHO",
+    "contact" : [{
+      "name" : "WHO",
+      "telecom" : [{
+        "system" : "url",
+        "value" : "http://who.int"
+      }]
+    }],
+    "description" : "HIV.DT Test Logic",
+    "parameter" : [{
+      "name" : "True condition",
+      "use" : "out",
+      "min" : 0,
+      "max" : "1",
+      "type" : "boolean"
+    },
+    {
+      "name" : "False condition",
+      "use" : "out",
+      "min" : 0,
+      "max" : "1",
+      "type" : "boolean"
+    },
+    {
+      "name" : "Output text",
+      "use" : "out",
+      "min" : 0,
+      "max" : "1",
+      "type" : "string"
+    }],
+    "content" : [{
+      "contentType" : "text/cql",
+      "data" : "ZGVmaW5lICJUcnVlIGNvbmRpdGlvbiI6CiAgdHJ1ZQoKZGVmaW5lICJGYWxzZSBjb25kaXRpb24iOgogIGZhbHNlCgpkZWZpbmUgIk91dHB1dCB0ZXh0IjoKICAnU3BhbSEgU3BhbSEgU3BhbSEgU3BhbSEgTG92ZWx5IHNwYW0hIFdvbmRlcmZ1bCBzcGFtISBTcGFtIHNwYS1hLWEtYS1hLWFtIHNwYW0gc3BhLWEtYS1hLWEtYW0gc3BhbSEgTG92ZWx5IHNwYW0hIExvdmVseSBzcGFtISBMb3ZlbHkgc3BhbSEgTG92ZWx5IHNwYW0hIFNwYW0gc3BhbSBzcGFtIHNwYW0hJwo="
+    }]
+  }
diff --git a/dak/content/plandefinitions/PlanDefinition-HIVTestLogicDT.json b/dak/content/plandefinitions/PlanDefinition-HIVTestLogicDT.json
@@ -0,0 +1,109 @@
+{
+    "resourceType": "PlanDefinition",
+    "id": "HIVTestLogicDT",
+    "meta": {
+      "profile": [
+        "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-recommendationdefinition",
+        "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareableplandefinition",
+        "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishableplandefinition"
+      ]
+    },
+    "text": {
+      "status": "generated",
+      "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: PlanDefinition HIVTestLogicDT</b></p><a name=\"HIVTestLogicDT\"> </a><a name=\"hcHIVTestLogicDT\"> </a><a name=\"HIVTestLogicDT-en-US\"> </a><p><b>url</b>: <a href=\"PlanDefinition-HIVTestLogicDT.html\">PlanDefinition HIV.DT Test Logic Process</a></p><p><b>version</b>: 0.2.0</p><p><b>name</b>: HIVTestLogicDT</p><p><b>title</b>: HIV.DT Test Logic Process</p><p><b>type</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/plan-definition-type eca-rule}\">ECA Rule</span></p><p><b>status</b>: Draft</p><p><b>experimental</b>: true</p><p><b>date</b>: 2024-08-08 06:57:34+0000</p><p><b>publisher</b>: WHO</p><p><b>contact</b>: WHO: <a href=\"http://who.int\">http://who.int</a></p><p><b>description</b>: </p><div><p>Test Logic Process</p>\n</div><h3>RelatedArtifacts</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Type</b></td><td><b>Citation</b></td></tr><tr><td style=\"display: none\">*</td><td>Citation</td><td><div><p>Consolidated Guidelines on HIV Testing Services (2019)</p>\n</div></td></tr></table><p><b>library</b>: <a href=\"Library-HIVDTTestLogic.html\">HIV.DT Test Logic</a></p><blockquote><p><b>action</b></p><p><b>textEquivalent</b>: Spammy action</p><blockquote><p><b>condition</b></p><p><b>kind</b>: Applicability</p><h3>Expressions</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Language</b></td><td><b>Expression</b></td></tr><tr><td style=\"display: none\">*</td><td>text/cql-identifier</td><td>True condition</td></tr></table></blockquote><blockquote><p><b>dynamicValue</b></p><p><b>path</b>: description</p><h3>Expressions</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Language</b></td><td><b>Expression</b></td></tr><tr><td style=\"display: none\">*</td><td>text/cql-identifier</td><td>Output text</td></tr></table></blockquote></blockquote><blockquote><p><b>action</b></p><p><b>textEquivalent</b>: Non-spammy action</p><blockquote><p><b>condition</b></p><p><b>kind</b>: Applicability</p><h3>Expressions</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Language</b></td><td><b>Expression</b></td></tr><tr><td style=\"display: none\">*</td><td>text/cql-identifier</td><td>False condition</td></tr></table></blockquote><blockquote><p><b>dynamicValue</b></p><p><b>path</b>: description</p><h3>Expressions</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Language</b></td><td><b>Expression</b></td></tr><tr><td style=\"display: none\">*</td><td>text/cql-identifier</td><td>Output text</td></tr></table></blockquote></blockquote></div>"
+    },
+    "extension": [
+      {
+        "url": "http://hl7.org/fhir/StructureDefinition/cqf-knowledgeCapability",
+        "valueCode": "computable"
+      }
+    ],
+    "url": "http://smart.who.int/hiv/PlanDefinition/HIVB2DT",
+    "version": "0.2.0",
+    "name": "HIVTestLogicDT",
+    "title": "HIV.DT Test Logic Process",
+    "type": {
+      "coding": [
+        {
+          "system": "http://terminology.hl7.org/CodeSystem/plan-definition-type",
+          "code": "eca-rule"
+        }
+      ]
+    },
+    "status": "draft",
+    "experimental": true,
+    "date": "2024-08-08T06:57:34+00:00",
+    "publisher": "WHO",
+    "contact": [
+      {
+        "name": "WHO",
+        "telecom": [
+          {
+            "system": "url",
+            "value": "http://who.int"
+          }
+        ]
+      }
+    ],
+    "description": "Test Logic Process",
+    "relatedArtifact": [
+      {
+        "type": "citation",
+        "citation": "Consolidated Guidelines on HIV Testing Services (2019)"
+      }
+    ],
+    "library": [
+      "http://smart.who.int/HIV/Library/HIVDTTestLogic"
+    ],
+    "action": [
+      {
+        "title": "Test Action Gruop",
+        "action": [
+          {
+            "title": "Spammy action",
+            "textEquivalent": "Spammy action",
+            "condition": [
+              {
+                "kind": "applicability",
+                "expression": {
+                  "language": "text/cql-identifier",
+                  "expression": "True condition"
+                }
+              }
+            ],
+            "dynamicValue": [
+              {
+                "path": "description",
+                "expression": {
+                  "language": "text/cql-identifier",
+                  "expression": "Output text"
+                }
+              }
+            ]
+          },
+          {
+            "title": "Non-spammy action",
+            "textEquivalent": "Non-spammy action",
+            "condition": [
+              {
+                "kind": "applicability",
+                "expression": {
+                  "language": "text/cql-identifier",
+                  "expression": "True condition"
+                }
+              }
+            ],
+            "dynamicValue": [
+              {
+                "path": "description",
+                "expression": {
+                  "language": "text/cql-identifier",
+                  "expression": "Output text"
+                }
+              }
+            ]
+          }
+        ]
+      }
+    ]
+  }
diff --git a/dak/terminology/ValueSet-HIV.A.DE5.json b/dak/terminology/ValueSet-HIV.A.DE5.json
@@ -0,0 +1,52 @@
+{
+    "resourceType": "ValueSet",
+    "id": "HIV.A.DE5",
+    "meta": {
+      "profile": [
+        "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablevalueset",
+        "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablevalueset",
+        "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-computablevalueset"
+      ]
+    },
+    "text": {
+      "status": "extensions",
+      "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: ValueSet HIV.A.DE5</b></p><a name=\"HIV.A.DE5\"> </a><a name=\"hcHIV.A.DE5\"> </a><a name=\"HIV.A.DE5-en-US\"> </a><ul><li>Include these codes as defined in <a href=\"CodeSystem-HIVConcepts.html\"><code>http://smart.who.int/hiv/CodeSystem/HIVConcepts</code></a><table class=\"none\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td><a href=\"CodeSystem-HIVConcepts.html#HIVConcepts-HIV.46A.46DE6\">HIV.A.DE6</a></td><td>Community</td><td>Referred by the community level services</td></tr><tr><td><a href=\"CodeSystem-HIVConcepts.html#HIVConcepts-HIV.46A.46DE7\">HIV.A.DE7</a></td><td>Facility</td><td>Referred by the health facility</td></tr></table></li></ul></div>"
+    },
+    "url": "http://smart.who.int/hiv/ValueSet/HIV.A.DE5",
+    "version": "0.2.0",
+    "name": "HIVADE5",
+    "title": "Referred by ValueSet",
+    "status": "active",
+    "experimental": true,
+    "date": "2024-08-02T14:11:44+00:00",
+    "publisher": "WHO",
+    "contact": [
+      {
+        "name": "WHO",
+        "telecom": [
+          {
+            "system": "url",
+            "value": "http://who.int"
+          }
+        ]
+      }
+    ],
+    "description": "Value set of how the client was referred",
+    "compose": {
+      "include": [
+        {
+          "system": "http://smart.who.int/hiv/CodeSystem/HIVConcepts",
+          "concept": [
+            {
+              "code": "HIV.A.DE6",
+              "display": "Community"
+            },
+            {
+              "code": "HIV.A.DE7",
+              "display": "Facility"
+            }
+          ]
+        }
+      ]
+    }
+  }
diff --git a/distro/configuration/globalproperties/globalproperties-core_demo.xml b/distro/configuration/globalproperties/globalproperties-core_demo.xml
@@ -2,7 +2,7 @@
     <globalProperties>
         <globalProperty>
             <property>referencedemodata.createDemoPatientsOnNextStartup</property>
-            <value>50</value>
+            <value>1</value>
         </globalProperty>
     </globalProperties>
 

diff --git a/distro/distro.properties b/distro/distro.properties
@@ -28,4 +28,5 @@ omod.ordertemplates=${ordertemplates.version}
 omod.patientflags=${patientflags.version}
 omod.o3forms=${o3forms.version}
 omod.authentication=${authentication.version}
+omod.cql=${cql.version}
 
diff --git a/distro/pom.xml b/distro/pom.xml
@@ -47,8 +47,9 @@
     <htmlwidgets.version>1.11.0</htmlwidgets.version>
     <serialization-xstream.version>0.2.16</serialization-xstream.version>
     <ordertemplates.version>1.0.2</ordertemplates.version>
-    <patientflags.version>3.0.7</patientflags.version>
+    <patientflags.version>3.0.8-cql-SNAPSHOT</patientflags.version>
     <o3forms.version>2.3.0-SNAPSHOT</o3forms.version>
+     <cql.version>1.0.0-SNAPSHOT</cql.version>
   </properties>
 
   <dependencies>
@@ -199,6 +200,12 @@
       <version>${o3forms.version}</version>
       <scope>provided</scope>
     </dependency>
+    <dependency>
+      <groupId>org.openmrs.module</groupId>
+      <artifactId>cql-omod</artifactId>
+      <version>${cql.version}</version>
+      <scope>provided</scope>
+    </dependency>
   </dependencies>
 
   <build>

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -2,7 +2,8 @@ version: "3.7"
 
 services:
   gateway:
-    image: openmrs/openmrs-reference-application-3-gateway:${TAG:-qa}
+    image: openmrs/openmrs-reference-application-3-gateway:dev3
+    container_name: gateway
     restart: "unless-stopped"
     depends_on:
       - frontend
@@ -11,7 +12,8 @@ services:
       - "80:80"
 
   frontend:
-    image: openmrs/openmrs-reference-application-3-frontend:${TAG:-qa}
+    image: openmrs/openmrs-reference-application-3-frontend:dev3
+    container_name: frontend
     restart: "unless-stopped"
     environment:
       SPA_PATH: /openmrs/spa
@@ -25,7 +27,8 @@ services:
       - backend
 
   backend:
-    image: openmrs/openmrs-reference-application-3-backend:${TAG:-qa}
+    image: itechuw/openmrs-distro-who-hiv-dak:main
+    container_name: backend
     restart: "unless-stopped"
     depends_on:
       - db
@@ -41,6 +44,7 @@ services:
       test: ["CMD", "curl", "-f", "http://localhost:8080/openmrs"]
       timeout: 5s
     volumes:
+      - ./dak/:/openmrs/dak/
       - openmrs-data:/openmrs/data
 
   # MariaDB
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,7 @@ name: Build and Validate Configuration @@
     on:
       pull_request:
-        branches: [main]
+        branches: [none]
     jobs:
       build:
@@ Expand Down @@