From 3239e6899a6866bf3e4c409c07d4d21be3c7801d Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 10 Apr 2024 17:40:58 -0500
Subject: [PATCH] Mitigate CSP warnings (#282)

---
 .../resources/views/fastaHelper.html          | 57 -------------------
 .../resources/views/fastaHelper.view.xml      |  6 --
 .../resources/external/minimalSession.json    |  2 +-
 .../src/org/labkey/jbrowse/JBrowseModule.java |  2 +-
 4 files changed, 2 insertions(+), 65 deletions(-)
 delete mode 100644 SequenceAnalysis/resources/views/fastaHelper.html
 delete mode 100644 SequenceAnalysis/resources/views/fastaHelper.view.xml

diff --git a/SequenceAnalysis/resources/views/fastaHelper.html b/SequenceAnalysis/resources/views/fastaHelper.html
deleted file mode 100644
index 6ee501edb..000000000
--- a/SequenceAnalysis/resources/views/fastaHelper.html
+++ /dev/null
@@ -1,57 +0,0 @@
-<script type="text/javascript" nonce="<%=scriptNonce%>">
-
-function whitelist(){
-    var names = document.getElementById('whitelistNames').value;
-    names = Ext4.String.trim(names);
-    names = names.split(/\r?\n/);
-    for (var i=0;i<names.length;i++){
-        names[i] = Ext4.String.trim(names[i]);
-    }
-
-    var fasta = document.getElementById('whitelistFasta').value;
-    fasta = Ext4.String.trim(fasta);
-    fasta = fasta.split('>');
-
-    var asCsv = document.getElementById('whitelistCheckBox').checked;
-
-    var toKeep = [];
-    Ext4.Array.forEach(fasta, function(seq){
-        var lines = seq.split(/\r?\n/);
-        var label = lines.shift();
-        label = Ext4.String.trim(label);
-        if (names.indexOf(label) > -1){
-            lines = lines.join('');
-            lines = lines.replace(/[\s]+/g, '');
-            if (asCsv){
-                toKeep.push(label + '\t' + lines);
-            }
-            else {
-                toKeep.push('>' + label + '\n' + lines);
-            }
-        }
-    }, this);
-
-    document.getElementById('whitelistTarget').value = toKeep.join('\n');
-}
-
-LABKEY.Utils.onReady(function(){
-    document.getElementById('whitelistButton')['onclick'] = whitelist;
-});
-</script>
-
-This page contains several basic utilities to process FASTA files.  See the instructions above each item for more information.
-
-<p/>
-<h3>1) Subset FASTA Based on List</h3>
-To use, simply cut/paste the FASTA contents into the box on the left.  Paste a list of allowable sequence names into the middle box, and hit the arrow to process.  Results will appear on the right.
-<p></p>
-<input type="checkbox" id="whitelistCheckBox"><label>Ouput As Table</label>
-<p></p>
-<table>
-    <tr>
-        <td>FASTA Contents:<span></span><br><textarea rows="10" cols="30" id="whitelistFasta"></textarea></td>
-        <td>Allowable Names:<span></span><br><textarea rows="10" cols="30" id="whitelistNames"></textarea></td>
-        <td><button id="whitelistButton">--></button></td>
-        <td>Matching Entries:<span></span><br><textarea rows="10" cols="30" id="whitelistTarget"></textarea></td>
-    </tr>
-</table>
\ No newline at end of file
diff --git a/SequenceAnalysis/resources/views/fastaHelper.view.xml b/SequenceAnalysis/resources/views/fastaHelper.view.xml
deleted file mode 100644
index 79de8cc90..000000000
--- a/SequenceAnalysis/resources/views/fastaHelper.view.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<view xmlns="http://labkey.org/data/xml/view" title="FASTA Helpers">
-    <dependencies>
-        <dependency path="laboratory.context"/>
-        <dependency path="SequenceAnalysis/sequenceAnalysis"/>
-    </dependencies>
-</view>
\ No newline at end of file
diff --git a/jbrowse/resources/external/minimalSession.json b/jbrowse/resources/external/minimalSession.json
index fe9ddea7e..c19f79578 100644
--- a/jbrowse/resources/external/minimalSession.json
+++ b/jbrowse/resources/external/minimalSession.json
@@ -66,7 +66,7 @@
       }
     },
     {
-      "type": "DemoTrack",
+      "type": "VariantTrack",
       "trackId": "clinvar_ncbi_hg38_2",
       "name": "ClinVar variants (NCBI)-2",
       "assemblyNames": ["hg38"],
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseModule.java b/jbrowse/src/org/labkey/jbrowse/JBrowseModule.java
index a05f1be6a..318b1fb42 100644
--- a/jbrowse/src/org/labkey/jbrowse/JBrowseModule.java
+++ b/jbrowse/src/org/labkey/jbrowse/JBrowseModule.java
@@ -113,7 +113,7 @@ public void doStartupAfterSpringConfig(ModuleContext moduleContext)
         JBrowseService.get().registerGroupsProvider(new JBrowseLuceneSearch.TestJBrowseGroupProvider());
 
         // These are all part of the JBrowse demo data:
-        ContentSecurityPolicyFilter.registerAllowedConnectionSource(this.getClass().getName(), "https://jbrowse.org", "https://s3.amazonaws.com", "https://ftp.ncbi.nlm.nih.gov/pub/clinvar");
+        ContentSecurityPolicyFilter.registerAllowedConnectionSource(this.getClass().getName(), "https://jbrowse.org", "https://s3.amazonaws.com", "https://ftp.ncbi.nlm.nih.gov");
     }
 
     public static void registerPipelineSteps()