From 8daab3253b042a60fd1acc81469c410a04de5c6b Mon Sep 17 00:00:00 2001
From: Douglass Turner <douglass.turner@gmail.com>
Date: Wed, 4 Dec 2024 17:36:52 -0500
Subject: [PATCH] Bug Fixes (#306)

* Do not convert chromosome names to lower case

* Bug fix: change to html to allow presentation of Dropbox chooser from Juicebox panel

* css tweaks

* IGV and Juicebox panels: dropdown menu css tweaks

* CNDB bug fix: support loading from ensemble group list

* Ensemble Group List: now properly sorted
---
 index.html                            | 10 ++++++++--
 js/datasource/CNDBDatasource.js       |  4 ++--
 js/juicebox/juiceboxPanel.js          |  3 ++-
 js/juicebox/liveMapState.js           |  3 ++-
 js/panel.js                           |  1 -
 js/spacewalkFileLoadWidgetServices.js | 16 +++++++++++++++-
 js/utils/liveMapUtils.js              |  4 +++-
 styles/_igv_panel.scss                | 10 ++++++++++
 styles/_juicebox_panel.scss           | 16 ++++++++++++++++
 styles/app.css                        | 21 +++++++++++++++++++++
 styles/app.css.map                    |  2 +-
 11 files changed, 80 insertions(+), 10 deletions(-)

diff --git a/index.html b/index.html
index e7ea158b..825f717d 100644
--- a/index.html
+++ b/index.html
@@ -452,9 +452,15 @@
             <!-- Hi-C map file chooser -->
             <li id="hic-file-chooser-dropdown" class="list-group-item mx-auto py-1 ps-1">
               <div class="dropdown">
-                <button id="hic-contact-map-dropdown" class="btn btn-sm btn-outline-secondary dropdown-toggle" type="button" data-bs-toggle="dropdown">
+
+<!--                <button id="hic-contact-map-dropdown" class="dropdown-toggle btn btn-sm btn-outline-secondary" type="button" data-bs-toggle="dropdown">-->
+<!--                  Load Hi-C Map-->
+<!--                </button>-->
+
+                <a id="hic-contact-map-dropdown" class="dropdown-toggle" data-bs-toggle="dropdown">
                   Load Hi-C Map
-                </button>
+                </a>
+
                 <ul class="dropdown-menu">
 
                   <!-- ENCODE Maps -->
diff --git a/js/datasource/CNDBDatasource.js b/js/datasource/CNDBDatasource.js
index 0d263bb7..ab3617c0 100644
--- a/js/datasource/CNDBDatasource.js
+++ b/js/datasource/CNDBDatasource.js
@@ -24,7 +24,7 @@ class CNDBDatasource extends DataSourceBase {
 
         this.isPointCloud = await isPointCloud(hdf5, this.replicaKeys)
 
-        await this.updateWithReplicaKey(this.replicaKeys[ 0 ])
+        await this.updateWithEnsembleGroupKey(this.replicaKeys[ 0 ])
 
         hideGlobalSpinner()
 
@@ -43,7 +43,7 @@ class CNDBDatasource extends DataSourceBase {
         return { sample: 'Unspecified Sample', genomeAssembly }
     }
 
-    async updateWithReplicaKey(replicaKey) {
+    async updateWithEnsembleGroupKey(replicaKey) {
 
         this.currentReplicaKey = replicaKey
 
diff --git a/js/juicebox/juiceboxPanel.js b/js/juicebox/juiceboxPanel.js
index 26a57fe7..2172b7a8 100644
--- a/js/juicebox/juiceboxPanel.js
+++ b/js/juicebox/juiceboxPanel.js
@@ -298,7 +298,8 @@ function juiceboxMouseHandler({ xBP, yBP, startXBP, startYBP, endXBP, endYBP, in
 function isLiveMapSupported() {
 
     const { chr } = ensembleManager.locus
-    const chromosome = igvPanel.browser.genome.getChromosome(chr.toLowerCase())
+    // const chromosome = igvPanel.browser.genome.getChromosome(chr.toLowerCase())
+    const chromosome = igvPanel.browser.genome.getChromosome(chr)
     if (undefined === chromosome) {
         console.warn(`Live Maps are not available for chromosome ${ chr }. No associated genome found`)
         return false
diff --git a/js/juicebox/liveMapState.js b/js/juicebox/liveMapState.js
index 7f2055e1..1abf0c89 100644
--- a/js/juicebox/liveMapState.js
+++ b/js/juicebox/liveMapState.js
@@ -20,7 +20,8 @@ class LiveMapState extends hic.State {
        const [ xBin, yBin] = [ genomicStart / binSize, genomicStart / binSize ]
 
        // chromosome index
-       const chromosome = igvPanel.browser.genome.getChromosome(chr.toLowerCase())
+       // const chromosome = igvPanel.browser.genome.getChromosome(chr.toLowerCase())
+       const chromosome = igvPanel.browser.genome.getChromosome(chr)
        let { order } = chromosome
 
        super(1 + order, 1 + order, 0, xBin, yBin, width, height, pixelSize, 'NONE')
diff --git a/js/panel.js b/js/panel.js
index 383ad7e5..c4ccb518 100644
--- a/js/panel.js
+++ b/js/panel.js
@@ -1,4 +1,3 @@
-import igv from 'igv'
 import SpacewalkEventBus from './spacewalkEventBus.js'
 import { makeDraggable } from "./utils/draggable.js"
 
diff --git a/js/spacewalkFileLoadWidgetServices.js b/js/spacewalkFileLoadWidgetServices.js
index 2d189338..2c3dc053 100644
--- a/js/spacewalkFileLoadWidgetServices.js
+++ b/js/spacewalkFileLoadWidgetServices.js
@@ -173,7 +173,21 @@ function createAndConfigureEnsembleGroupSelectModal(parentElement, ensembleGroup
 
         selectElement.appendChild(createPlaceholderOptionElement())
 
-        for (const key of data ) {
+        // sort
+        const sorted = data.sort((a, b) => {
+            // Extract the first number after the initial string
+            const firstNumberA = parseInt(a.match(/^\D+(\d+)/)?.[1] || 0, 10);
+            const firstNumberB = parseInt(b.match(/^\D+(\d+)/)?.[1] || 0, 10);
+
+            // Extract the second number, whether it's foo23, foo_23, or foo_03
+            const secondNumberA = parseInt(a.match(/\D(\d+)$/)?.[1] || 0, 10);
+            const secondNumberB = parseInt(b.match(/\D(\d+)$/)?.[1] || 0, 10);
+
+            // Sort by the first number, then by the second number
+            return firstNumberA - firstNumberB || secondNumberA - secondNumberB;
+        });
+
+        for (const key of sorted ) {
             const html = `<option value=\"${ key }\">${ key }</option>`
             const fragment = document.createRange().createContextualFragment(html)
             selectElement.appendChild(fragment.firstChild)
diff --git a/js/utils/liveMapUtils.js b/js/utils/liveMapUtils.js
index 593afa9d..c23ac204 100644
--- a/js/utils/liveMapUtils.js
+++ b/js/utils/liveMapUtils.js
@@ -4,7 +4,9 @@ import SWBDatasource from "../datasource/SWBDatasource.js"
 async function enableLiveMaps() {
 
     const { chr } = ensembleManager.locus
-    const chromosome = igvPanel.browser.genome.getChromosome(chr.toLowerCase())
+
+    // let chromosome = igvPanel.browser.genome.getChromosome(chr.toLowerCase())
+    const chromosome = igvPanel.browser.genome.getChromosome(chr)
 
     if (chromosome) {
         if (ensembleManager.datasource instanceof SWBDatasource) {
diff --git a/styles/_igv_panel.scss b/styles/_igv_panel.scss
index dfd1e591..5cc660da 100644
--- a/styles/_igv_panel.scss
+++ b/styles/_igv_panel.scss
@@ -84,6 +84,16 @@ $spacewalk_igv_panel_heigth: 256px;
 
       a.dropdown-toggle {
         color: unset;
+        text-decoration-line: unset;
+        cursor: pointer;
+      }
+
+      a.dropdown-toggle:hover {
+        border-color: rgba(0, 0, 0, 0.3);
+        border-style: solid;
+        border-width: thin;
+        border-radius: 2px;
+        padding: 4px;
       }
     }
 
diff --git a/styles/_juicebox_panel.scss b/styles/_juicebox_panel.scss
index a6d175cf..7bfc0916 100644
--- a/styles/_juicebox_panel.scss
+++ b/styles/_juicebox_panel.scss
@@ -22,6 +22,22 @@
     .list-group {
       width: 100%;
       background-color: white;
+
+      #hic-contact-map-dropdown.dropdown-toggle {
+        color: unset;
+        text-decoration-line: unset;
+        cursor: pointer;
+      }
+
+      #hic-contact-map-dropdown.dropdown-toggle:hover {
+        border-color: rgba(0, 0, 0, 0.3);
+        border-style: solid;
+        border-width: thin;
+        border-radius: 2px;
+        padding: 4px;
+      }
+
+
       #hic-live-contact-frequency-map-threshold-widget.list-group-item {
         div.input-group {
           width: 200px;
diff --git a/styles/app.css b/styles/app.css
index ce602e13..19793d29 100644
--- a/styles/app.css
+++ b/styles/app.css
@@ -217,6 +217,18 @@ div.navbar-brand {
   width: 100%;
   background-color: white;
 }
+#spacewalk_juicebox_panel.card .card-header .list-group #hic-contact-map-dropdown.dropdown-toggle {
+  color: unset;
+  text-decoration-line: unset;
+  cursor: pointer;
+}
+#spacewalk_juicebox_panel.card .card-header .list-group #hic-contact-map-dropdown.dropdown-toggle:hover {
+  border-color: rgba(0, 0, 0, 0.3);
+  border-style: solid;
+  border-width: thin;
+  border-radius: 2px;
+  padding: 4px;
+}
 #spacewalk_juicebox_panel.card .card-header .list-group #hic-live-contact-frequency-map-threshold-widget.list-group-item div.input-group {
   width: 200px;
 }
@@ -284,6 +296,15 @@ div.navbar-brand {
 }
 #spacewalk_igv_panel.card #spacewalk_igv_container.card-body .spacewalk_card_drag_container a.dropdown-toggle {
   color: unset;
+  text-decoration-line: unset;
+  cursor: pointer;
+}
+#spacewalk_igv_panel.card #spacewalk_igv_container.card-body .spacewalk_card_drag_container a.dropdown-toggle:hover {
+  border-color: rgba(0, 0, 0, 0.3);
+  border-style: solid;
+  border-width: thin;
+  border-radius: 2px;
+  padding: 4px;
 }
 #spacewalk_igv_panel.card #spacewalk_igv_container.card-body #spacewalk_igv_root_container {
   overflow: scroll;
diff --git a/styles/app.css.map b/styles/app.css.map
index 2cef93c3..cfdfc281 100644
--- a/styles/app.css.map
+++ b/styles/app.css.map
@@ -1 +1 @@
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