Website updates, including reference sequence documentation

grunwaldlab · Jul 19, 2024 · 7c4e289 · 7c4e289
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commit 7c4e289
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diff --git a/data/.~lock.mycobacerium_5.csv# b/data/.~lock.mycobacerium_5.csv#
@@ -0,0 +1 @@
+,buchananr,pop-os,19.07.2024 16:04,file:///home/buchananr/.config/libreoffice/4;
diff --git a/data/mycobacerium_5.csv b/data/mycobacerium_5.csv
@@ -0,0 +1,6 @@
+ref_group_ids,ref_path,Ref_primary_usage,Ref_contextual_Usage
+abscessus,test/data/refs/mycobacterium_abscessus_reference1.fna,required,
+leprae,test/data/refs/mycobacterium_leprae_reference1.fna,required,
+leprae,test/data/refs/mycobacterium_leprae_reference2.fna,,optional
+leprae,test/data/refs/mycobacterium_leprae_reference3.fna,,optional
+leprae,test/data/refs/mycobacterium_leprae_reference4.fna,,optional
diff --git a/data/mycobacterium_1.csv b/data/mycobacterium_1.csv
@@ -0,0 +1,7 @@
+sample_id,ncbi accession
+mycobacterium_abscessus1,ERR7253671
+mycobacterium_abscessus2,ERR7253669
+mycobacterium_abscessus3,ERR7253671
+mycobacterium_leperae1,SRR6241707
+mycobacterium_leperae2,SRR6241708
+mycobacterium_leperae3,SRR6241709
diff --git a/data/mycobacterium_2.csv b/data/mycobacterium_2.csv
@@ -0,0 +1,7 @@
+sample_id,ncbi accession,ref_ncbi_accession,ref_primary_usage
+mycobacterium_abscessus1,ERR7253671,GCF_001632805.1,required
+mycobacterium_abscessus2,ERR7253669,GCF_001632805.1,required
+mycobacterium_abscessus3,ERR7253671,GCF_001632805.1,required
+mycobacterium_leprae1,SRR6241707,GCF_003253775.1,required
+mycobacterium_leprae2,SRR6241708,GCF_003253775.1,required
+mycobacterium_leprae3,SRR6241709,GCF_003253775.1,required
diff --git a/data/mycobacterium_3.csv b/data/mycobacterium_3.csv
@@ -0,0 +1,7 @@
+sample_id,ncbi accession,ref_ncbi_accession,ref_contextual_usage
+mycobacterium_abscessus1,ERR7253671,GCF_001632805.1,required
+mycobacterium_abscessus2,ERR7253669,GCF_001632805.1,required
+mycobacterium_abscessus3,ERR7253671,GCF_001632805.1,required
+mycobacterium_leprae1,SRR6241707,,
+mycobacterium_leprae2,SRR6241708,,
+mycobacterium_leprae3,SRR6241709,,
diff --git a/data/mycobacterium_4.csv b/data/mycobacterium_4.csv
@@ -0,0 +1,7 @@
+sample_id,ncbi accession,ref_ncbi_query,ref_ncbi_query_max
+mycobacterium_abscessus1,ERR7253671,,
+mycobacterium_abscessus2,ERR7253669,,
+mycobacterium_abscessus3,ERR7253671,,
+mycobacterium_leprae1,SRR6241707,mycobacterium leprae,100
+mycobacterium_leprae2,SRR6241708,mycobacterium leprae,100
+mycobacterium_leprae3,SRR6241709,mycobacterium leprae,100
diff --git a/data/mycobacterium_5.csv b/data/mycobacterium_5.csv
@@ -0,0 +1,6 @@
+ref_group_ids,ref_path,Ref primary usage,Ref contextual Usage
+abscessus,test/data/refs/mycobacterium_abscessus_reference1.fna,required,
+leprae,test/data/refs/mycobacterium_leprae_reference1.fna,required,
+leprae,test/data/refs/mycobacterium_leprae_reference2.fna,,optional
+leprae,test/data/refs/mycobacterium_leprae_reference3.fna,,optional
+leprae,test/data/refs/mycobacterium_leprae_reference4.fna,,optional
diff --git a/data/mycobacterium_6.csv b/data/mycobacterium_6.csv
@@ -0,0 +1,7 @@
+sample_id,ncbi accession,ref_group_ids
+mycobacterium_abscessus1,ERR7253671,abscessus
+mycobacterium_abscessus2,ERR7253669,abscessus
+mycobacterium_abscessus3,ERR7253671,abscessus
+mycobacterium_leprae1,SRR6241707,leprae
+mycobacterium_leprae2,SRR6241708,leprae
+mycobacterium_leprae3,SRR6241709,leprae
diff --git a/docs/documentation.html b/docs/documentation.html
diff --git a/docs/examplereports.html b/docs/examplereports.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.3.433">
+<meta name="generator" content="quarto-1.4.553">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -45,7 +45,13 @@
   "collapse-after": 3,
   "panel-placement": "start",
   "type": "textbox",
-  "limit": 20,
+  "limit": 50,
+  "keyboard-shortcut": [
+    "f",
+    "/",
+    "s"
+  ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -54,6 +60,7 @@
     "search-more-match-text": "more match in this document",
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
+    "search-text-placeholder": "",
     "search-detached-cancel-button-title": "Cancel",
     "search-submit-button-title": "Submit",
     "search-label": "Search"
@@ -71,12 +78,12 @@
   <header id="quarto-header" class="headroom fixed-top">
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./examplereports.html">Example Reports</a></li></ol></nav>
-      <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
-      </a>
+        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./examplereports.html">Example Reports</a></li></ol></nav>
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        </a>
       <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
         <i class="bi bi-search"></i>
       </button>
@@ -86,7 +93,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation docked overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation docked overflow-auto">
     <div class="pt-lg-2 mt-2 text-left sidebar-header">
     <div class="sidebar-title mb-0 py-0">
       <a href="./">Pathogen Surveillance Documentation</a> 
@@ -138,7 +145,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active">
@@ -168,8 +175,10 @@ <h1 class="title">Example Reports</h1>
   </div>
 
 
+
 </header>
 
+
 <section id="example-1---xanthomonas" class="level2">
 <h2 class="anchored" data-anchor-id="example-1---xanthomonas">Example 1 - xanthomonas</h2>
 <p><a href="https://grunwaldlab.github.io/pathogensurveillance_documentation/xanthomonas" target="_blank">example 1 report</a></p>
@@ -179,7 +188,7 @@ <h2 class="anchored" data-anchor-id="example-1---xanthomonas">Example 1 - xantho
 </section>
 <section id="example-2---mycobacterium" class="level2">
 <h2 class="anchored" data-anchor-id="example-2---mycobacterium">Example 2 - mycobacterium</h2>
-<p><a href="https://grunwaldlab.github.io/pathogensurveillance_documentation/mycobateroides_small" target="_blank">example 2 report</a></p>
+<p><a href="https://grunwaldlab.github.io/pathogensurveillance_documentation/mycobacteroides_small" target="_blank">example 2 report</a></p>
 <blockquote class="blockquote">
 <p>Bryant, Josephine M., et al.&nbsp;“Population-level genomics identifies the emergence and global spread of a human transmissible multidrug-resistant nontuberculous mycobacterium.” Science (New York, NY) 354.6313 (2016): 751.</p>
 </blockquote>
@@ -267,10 +276,27 @@ <h2 class="anchored" data-anchor-id="example-2---mycobacterium">Example 2 - myco
     // clear code selection
     e.clearSelection();
   });
-  function tippyHover(el, contentFn) {
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+    var mailtoRegex = new RegExp(/^mailto:/);
+      var filterRegex = new RegExp('/' + window.location.host + '/');
+    var isInternal = (href) => {
+        return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
+    }
+    // Inspect non-navigation links and adorn them if external
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+    for (var i=0; i<links.length; i++) {
+      const link = links[i];
+      if (!isInternal(link.href)) {
+        // undo the damage that might have been done by quarto-nav.js in the case of
+        // links that we want to consider external
+        if (link.dataset.originalHref !== undefined) {
+          link.href = link.dataset.originalHref;
+        }
+      }
+    }
+  function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
-      content: contentFn,
       maxWidth: 500,
       delay: 100,
       arrow: false,
@@ -280,8 +306,17 @@ <h2 class="anchored" data-anchor-id="example-2---mycobacterium">Example 2 - myco
       interactive: true,
       interactiveBorder: 10,
       theme: 'quarto',
-      placement: 'bottom-start'
+      placement: 'bottom-start',
     };
+    if (contentFn) {
+      config.content = contentFn;
+    }
+    if (onTriggerFn) {
+      config.onTrigger = onTriggerFn;
+    }
+    if (onUntriggerFn) {
+      config.onUntrigger = onUntriggerFn;
+    }
     window.tippy(el, config); 
   }
   const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
@@ -293,7 +328,130 @@ <h2 class="anchored" data-anchor-id="example-2---mycobacterium">Example 2 - myco
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
+      if (note) {
+        return note.innerHTML;
+      } else {
+        return "";
+      }
+    });
+  }
+  const xrefs = window.document.querySelectorAll('a.quarto-xref');
+  const processXRef = (id, note) => {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    if (id === null || id.startsWith('sec-')) {
+      // Special case sections, only their first couple elements
+      const container = document.createElement("div");
+      if (note.children && note.children.length > 2) {
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
+        }
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(container);
+        }
+        return container.innerHTML
+      } else {
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(note);
+        }
+        return note.innerHTML;
+      }
+    } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      if (window.Quarto?.typesetMath) {
+        window.Quarto.typesetMath(note);
+      }
+      // TODO in 1.5, we should make sure this works without a callout special case
+      if (note.classList.contains("callout")) {
+        return note.outerHTML;
+      } else {
+        return note.innerHTML;
+      }
+    }
+  }
+  for (var i=0; i<xrefs.length; i++) {
+    const xref = xrefs[i];
+    tippyHover(xref, undefined, function(instance) {
+      instance.disable();
+      let url = xref.getAttribute('href');
+      let hash = undefined; 
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
+        }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
+      }
+    }, function(instance) {
     });
   }
       let selectedAnnoteEl;
@@ -337,6 +495,7 @@ <h2 class="anchored" data-anchor-id="example-2---mycobacterium">Example 2 - myco
             }
             div.style.top = top - 2 + "px";
             div.style.height = height + 4 + "px";
+            div.style.left = 0;
             let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
             if (gutterDiv === null) {
               gutterDiv = window.document.createElement("div");
@@ -362,6 +521,32 @@ <h2 class="anchored" data-anchor-id="example-2---mycobacterium">Example 2 - myco
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -425,4 +610,5 @@ <h2 class="anchored" data-anchor-id="example-2---mycobacterium">Example 2 - myco
 
 
 
+
 </body></html>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		,buchananr,pop-os,19.07.2024 16:04,file:///home/buchananr/.config/libreoffice/4;