patch for new version of NCBI Seqviewer

cas-bioinf · Aug 29, 2019 · 32a9317 · 32a9317
1 parent 795444a
commit 32a9317
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Showing 7 changed files with 9 additions and 10 deletions.
diff --git a/rna_blast_analyze/BR_core/output/base.html b/rna_blast_analyze/BR_core/output/base.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta charset="UTF-8">
-    <title>RNA BLAST Analyze</title>
+    <title>rboAnalyzer</title>
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
 {% include 'style.css' %}
 {% include 'script.js' %}

diff --git a/rna_blast_analyze/BR_core/output/htmloutput.py b/rna_blast_analyze/BR_core/output/htmloutput.py
@@ -110,7 +110,7 @@ def _prepare_body(data):
         lx = len(data.query.seq)
 
         seqview = [
-            '?embeded=true',
+            'embedded=true',
             '&noviewheader=true',
             '&id={}'.format(onehit.source.annotations['blast'][0]),
             '&appname=rboAnalyzer',

diff --git a/rna_blast_analyze/BR_core/output/onehit.html b/rna_blast_analyze/BR_core/output/onehit.html
@@ -132,11 +132,12 @@ <h3 class="onehit_heading" style="background:{{data.h_color}};">
             {% endif %}
 
         {% if show_gene_browser %}
-            <div id="sv{{data.intid}}" data-sv_params="{{data.seqviewurl}}" class="sv">
+            <div id="sv{{data.intid}}" data-sv_params="{{ data.seqviewurl | safe }}" class="sv">
                 <button class= "seqviewbtn" onclick="viewRegion(this)" title="View selected Regions">Load Sequence viewer</button>
             </div>
+        {% else %}
+            <a class="small_font" target="_blank" rel="noopener noreferrer" href="{{ data.seqviewlink }}">link to genome</a>
         {% endif %}
-            <a class="small_font" target="_blank" rel="noopener noreferrer" href="{{data.seqviewlink}}">link to genome</a>
         {% if len(data.msgs) != 0 %}
             <div class="warnmsgs">
                 <p class="warn small_font">

diff --git a/rna_blast_analyze/BR_core/output/script.js b/rna_blast_analyze/BR_core/output/script.js
@@ -160,7 +160,7 @@ function viewRegion(button) {
   var svapp = SeqView.App.findAppByDivId(parent.id);
   if (!svapp)
     svapp = new SeqView.App(parent.id);
-  svapp.load(parent.dataset.sv_params);
+  svapp.reload(parent.dataset.sv_params);
 }
 
 function viewRegionCallback(button) {
@@ -210,6 +210,4 @@ function viewAllRegions() {
     viewRegionCallback(rem_sv_btns[i]);
   }
 }
-
-console.log("script loaded correctly");
 </script>
diff --git a/rna_blast_analyze/VERSION b/rna_blast_analyze/VERSION
@@ -1 +1 @@
-0.1.0
+0.1.1
diff --git a/test_func/test_data/RF00001_reference_missing_hit.html.md5 b/test_func/test_data/RF00001_reference_missing_hit.html.md5
@@ -1 +1 @@
-6006734df44d7ce997ec341c4f21070a
+c9ea04bf0a115e466cb603b19c414050
diff --git a/test_func/test_data/RF00001_reference_output.html.md5 b/test_func/test_data/RF00001_reference_output.html.md5
@@ -1 +1 @@
-13cb678adfab51b4fa9880985014b5e0
+cf7bd96127e4a0e0481956a0bb2afe8c