Merge branch 'master' into share_url_edits

igvteam · Jul 12, 2024 · fe9f249 · fe9f249
2 parents c96966e + de80176
commit fe9f249
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Showing 7 changed files with 170 additions and 31 deletions.
diff --git a/index.html b/index.html
@@ -275,13 +275,11 @@
                             Load URL ...
                         </button>
 
-                        <!-- Session List -->
-                        <div id="igv-session-list-divider" class="dropdown-divider"></div>
-
                         <div class="dropdown-divider"></div>
 
                         <!-- Save local session file -->
                         <button class="dropdown-item" type="button" data-toggle="modal"
+                                id="save-session-button"
                                 data-target="#igv-app-session-save-modal">
                             Save ...
                         </button>

diff --git a/js/app.js b/js/app.js
@@ -27,8 +27,17 @@ import * as GooglePicker from '../node_modules/google-utils/src/googleFilePicker
 import makeDraggable from "./widgets/utils/draggable.js"
 import AlertSingleton from "./widgets/alertSingleton.js"
 import {createSessionWidgets} from "./widgets/sessionWidgets.js"
-import {updateTrackMenusWithTrackConfigurations, createTrackWidgetsWithTrackRegistry, getPathsWithTrackRegistryFile} from "./widgets/trackWidgets.js"
-import {dropboxDropdownItem, dropboxButtonImageBase64, googleDriveButtonImageBase64, googleDriveDropdownItem} from "./widgets/markupFactory.js"
+import {
+    updateTrackMenusWithTrackConfigurations,
+    createTrackWidgetsWithTrackRegistry,
+    getPathsWithTrackRegistryFile
+} from "./widgets/trackWidgets.js"
+import {
+    dropboxDropdownItem,
+    dropboxButtonImageBase64,
+    googleDriveButtonImageBase64,
+    googleDriveDropdownItem
+} from "./widgets/markupFactory.js"
 import GenomeFileLoad from "./widgets/genomeFileLoad.js"
 import FileLoadManager from "./widgets/fileLoadManager.js"
 import FileLoadWidget from "./widgets/fileLoadWidget.js"
@@ -294,7 +303,7 @@ async function initializationHelper(browser, container, options) {
         sessionSaver)
 
     if (options.sessionRegistryFile) {
-        await createSessionMenu('igv-session-list-divider', options.sessionRegistryFile, sessionLoader)
+        await createSessionMenu('save-session-button', options.sessionRegistryFile, sessionLoader)
     } else {
         document.querySelector('#igv-session-list-divider').style.display = 'none'
     }
@@ -393,7 +402,9 @@ function createSampleInfoMenu(igvMain,
                 {
                     success: dbFiles => {
 
-                        const configList = dbFiles.map(({link}) => { return {url: link} })
+                        const configList = dbFiles.map(({link}) => {
+                            return {url: link}
+                        })
 
                         sampleInfoFileLoadHandler(configList[0])
                     },
@@ -480,7 +491,7 @@ function createSampleInfoMenu(igvMain,
 
     Utils.configureModal(fileLoadWidget, urlModal, async fileLoadWidget => {
         const paths = fileLoadWidget.retrievePaths()
-        await sampleInfoFileLoadHandler({url:paths[0]})
+        await sampleInfoFileLoadHandler({url: paths[0]})
         return true
     })
 
@@ -555,33 +566,61 @@ async function createSessionMenu(sessionListDivider, sessionRegistryFile, sessio
     if (sessionJSON) {
 
         const sessions = sessionJSON['sessions']
-
+        
         for (let {name, url} of sessions.reverse()) {
 
             const referenceNode = document.getElementById(sessionListDivider)
 
-            const button_id = `${id_prefix}_${guid()}`
-            const html = `<button id="${button_id}" class="dropdown-item" type="button">${name}</button>`
-            const fragment = document.createRange().createContextualFragment(html)
+            if (url) {
+                const button_id = `${id_prefix}_${guid()}`
+                const html = `<button id="${button_id}" class="dropdown-item" type="button">${name}</button>`
+                const fragment = document.createRange().createContextualFragment(html)
 
-            referenceNode.after(fragment.firstChild)
+                referenceNode.after(fragment.firstChild)
 
-            const button = document.getElementById(button_id)
-            button.addEventListener('click', () => {
+                const button = document.getElementById(button_id)
+                button.addEventListener('click', () => {
 
-                const config = {}
-                const key = true === isFile(url) ? 'file' : 'url'
-                config[key] = url
+                    const config = {}
+                    const key = true === isFile(url) ? 'file' : 'url'
+                    config[key] = url
 
-                sessionLoader(config)
+                    sessionLoader(config)
 
-            })
+                })
+            } else {
+                const html = `<h6 class="dropdown-header">${name}</h6>`
+                const el = fromHTML(html)
+                referenceNode.after(el)
+                referenceNode.after(fromHTML('<div class="dropdown-divider"/>'))
+            }
         }
 
     }
 
 }
 
+/**
+ * @param {String} HTML representing a single element.
+ * @param {Boolean} flag representing whether or not to trim input whitespace, defaults to true.
+ * @return {Element | HTMLCollection | null}
+ */
+function fromHTML(html, trim = true) {
+    // Process the HTML string.
+    html = trim ? html.trim() : html
+    if (!html) return null
+
+    // Then set up a new template element.
+    const template = document.createElement('template')
+    template.innerHTML = html
+    const result = template.content.children
+
+    // Then return either an HTMLElement or HTMLCollection,
+    // based on whether the input HTML had one or more roots.
+    if (result.length === 1) return result[0]
+    return result
+}
+
 function createAppBookmarkHandler($bookmark_button) {
 
     $bookmark_button.on('click', (e) => {

diff --git a/package.json b/package.json
@@ -20,7 +20,7 @@
     "fs-extra": "^8.1.0",
     "igv": "github:igvteam/igv.js#master",
     "data-modal": "github:igvteam/data-modal#v1.5.0",
-    "igv-utils": "github:igvteam/igv-utils#v1.5.4",
+    "igv-utils": "github:igvteam/igv-utils#v1.5.8",
     "google-utils": "github:igvteam/google-utils#v1.0.2",
     "rollup": "^2.28.1",
     "rollup-plugin-copy": "^3.3.0",

diff --git a/resources/sessions/1kg-variants-session.json b/resources/sessions/1kg-variants-session.json
@@ -0,0 +1,25 @@
+{
+  "genome":  "hg38",
+  "locus": "chr22:36,655,100-36,656,016",
+  "sampleinfo": [
+    {
+      "url": "https://igv-genepattern-org.s3.amazonaws.com/demo/integrated_call_samples_v3.20130502.ALL.panel"
+    }
+  ],
+  "tracks": [
+    {
+      "url": "https://igv-genepattern-org.s3.amazonaws.com/demo/ALL.apol1.sample.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz",
+      "name": "1KG Variants",
+      "format": "vcf",
+      "type": "variant",
+      "height": 700,
+      "sort": {
+        "option": "ATTRIBUTE",
+        "attribute": "pop",
+        "direction": "ASC"
+      },
+      "order": 1,
+      "displayMode": "SQUISHED"
+    }
+  ]
+}
diff --git a/resources/sessions/6mA_pacbio.json b/resources/sessions/6mA_pacbio.json
@@ -0,0 +1,38 @@
+{
+  "genome": "hg38",
+  "locus": "chr11:119094729-119094804",
+  "tracks": [
+    {
+      "type": "alignment",
+      "format": "bam",
+      "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
+      "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
+      "height": 300,
+      "name": "Base modifications",
+      "colorBy": "basemod",
+      "groupBy": "strand"
+    },
+    {
+      "type": "alignment",
+      "format": "bam",
+      "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
+      "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
+      "height": 300,
+      "name": "Base modifications - 2 Color",
+      "colorBy": "basemod2",
+      "groupBy": "strand",
+      "baseModificationThreshold": 0
+    },
+    {
+      "type": "alignment",
+      "format": "bam",
+      "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
+      "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
+      "height": 300,
+      "name": "5mC modifications - 2 Color",
+      "colorBy": "basemod2:m",
+      "groupBy": "strand",
+      "baseModificationThreshold": 0
+    }
+  ]
+}
diff --git a/resources/sessions/gbm-copynumber.json b/resources/sessions/gbm-copynumber.json
@@ -0,0 +1,25 @@
+{
+  "genome": "hg38",
+  "locus": "chr7:52,338,217-57,756,711",
+  "sampleinfo": [
+    {
+      "url": "https://igv-genepattern-org.s3.amazonaws.com/demo/GBM-sampletable-samplemapping-colors.txt"
+    }
+  ],
+  "tracks": [
+    {
+      "url": "https://igv-genepattern-org.s3.amazonaws.com/demo/GBMCopyNumber.seg.gz",
+      "name": "GBM Copy Number",
+      "order": 1,
+      "format": "seg",
+      "type": "seg",
+      "height": 400,
+      "displayMode": "SQUISHED",
+      "sort": {
+        "option": "ATTRIBUTE",
+        "attribute": "Subtype",
+        "direction": "ASC"
+      }
+    }
+  ]
+}
diff --git a/resources/sessions/sessionRegistry.json b/resources/sessions/sessionRegistry.json
@@ -1,5 +1,29 @@
 {
 "sessions": [
+  {
+    "name": "Examples - Sample Information"
+  },
+  {
+    "name": "Segmented Copy Number",
+    "description": "Segmented copy number for TCGA GBM data",
+    "url": "resources/sessions/gbm-copynumber.json"
+  },
+  {
+    "name": "1KG Variants",
+    "description": "1000 genomes variants",
+    "url": "resources/sessions/1kg-variants-session.json"
+  },
+  {
+    "name": "Examples - Base Modifications"
+  },
+  {
+    "name": "5mC and 6mA Modifications",
+    "description": "5mC and 6mA Modifications",
+    "url": "resources/sessions/6mA_pacbio.json"
+  },
+  {
+    "name": "Examples - Circular View"
+  },
   {
     "name": "SKBR3 - Illumina (Schatz)",
     "description": "SKBR3 - Illumina (Schatz)",
@@ -9,16 +33,6 @@
     "name": "SKBR3 - Pacbio (Schatz)",
     "description": "SKBR3 - Pacbio (Schatz)",
     "url": "resources/sessions/SKBR3-pacbio-session.json"
-  },
-  {
-    "name": "SKBR3 - Sniffles and Delly VCF (Schatz)",
-    "description": "SKBR3 - Sniffles and Delly VCF (Schatz)",
-    "url": "resources/sessions/SKBR3-vcf-session.json"
-  },
-  {
-    "name": "ChIA-Pet - Wei lab GSM3553630",
-    "description": "ChIA-Pet - Wei lab GSM3553630",
-    "url": "resources/sessions/ChIA-Pet-GSM3553630.json"
   }
 ]
 }