EBI form filling

4 files changed, 19 insertions, 34 deletions

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index d524efe..b40db6f 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -937,6 +937,7 @@ def getSEQbyLocationAndSpecimenSource():
     result = r.json()['results']['bindings']
     return str(result)
 
-@app.route('/api/ebi-sample.xml', methods=['GET'])
-def ebi_sample():
-    return render_template('ebi-sample.xml')
+@app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
+def ebi_sample(id):
+    page = render_template('ebi-sample.xml',**locals())
+    return page
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index deda6ec..a12311e 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -24,7 +24,7 @@ function toDIVTable(rows) {
             html += '<div class="rTableRow">';
             html += cell('<a href="'+info+'">'+id+'</a>');
             html += cell('<a href="'+seq+'">FASTA</a>');
-            html += cell('<a href="/api/ebi-sample.xml?id='+id+'">EBI/ENA export XML</a>');
+            html += cell('<a href="/api/ebi/sample-'+id+'.xml">EBI/ENA export XML</a>');
             html += '</div>';
         });
         html += '</div>';
diff --git a/bh20simplewebuploader/templates/ebi-sample.xml b/bh20simplewebuploader/templates/ebi-sample.xml
index 694c471..441e29e 100644
--- a/bh20simplewebuploader/templates/ebi-sample.xml
+++ b/bh20simplewebuploader/templates/ebi-sample.xml
@@ -1,62 +1,46 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <SAMPLE_SET>
-  <SAMPLE alias="PubSeqSam0001" center_name="PubSeq01">
-    <TITLE>human gastric microbiota, mucosal</TITLE>
+  <SAMPLE alias="{{ id }}" center_name="COVID-19 PubSeq">
+    <TITLE>COVID-19 PubSeq Sample</TITLE>
     <SAMPLE_NAME>
-      <TAXON_ID>1284369</TAXON_ID>
-      <SCIENTIFIC_NAME>stomach metagenome</SCIENTIFIC_NAME>
-      <COMMON_NAME></COMMON_NAME>
+      <TAXON_ID>2697049</TAXON_ID>
+      <SCIENTIFIC_NAME>Severe acute respiratory syndrome coronavirus 2</SCIENTIFIC_NAME>
+      <COMMON_NAME>SARS-CoV-2</COMMON_NAME>
     </SAMPLE_NAME>
     <SAMPLE_ATTRIBUTES>
       <SAMPLE_ATTRIBUTE>
         <TAG>investigation type</TAG>
-        <VALUE>mimarks-survey</VALUE>
+        <VALUE>{{ investigation_type }}</VALUE>
       </SAMPLE_ATTRIBUTE>
       <SAMPLE_ATTRIBUTE>
         <TAG>sequencing method</TAG>
-        <VALUE>pyrosequencing</VALUE>
+        <VALUE>{{ sequence_method }}</VALUE>
       </SAMPLE_ATTRIBUTE>
       <SAMPLE_ATTRIBUTE>
         <TAG>collection date</TAG>
-        <VALUE>2010</VALUE>
-      </SAMPLE_ATTRIBUTE>
-      <SAMPLE_ATTRIBUTE>
-        <TAG>host body site</TAG>
-        <VALUE>Mucosa of stomach</VALUE>
-      </SAMPLE_ATTRIBUTE>
-      <SAMPLE_ATTRIBUTE>
-        <TAG>human-associated environmental package</TAG>
-        <VALUE>human-associated</VALUE>
+        <VALUE>{{ time }}</VALUE>
       </SAMPLE_ATTRIBUTE>
       <SAMPLE_ATTRIBUTE>
         <TAG>geographic location (latitude)</TAG>
-        <VALUE>1.81</VALUE>
+        <VALUE>{{ latidude }}</VALUE>
      <UNITS>DD</UNITS>
       </SAMPLE_ATTRIBUTE>
       <SAMPLE_ATTRIBUTE>
         <TAG>geographic location (longitude)</TAG>
-        <VALUE>-78.76</VALUE>
+        <VALUE>{{ longitude }}</VALUE>
      <UNITS>DD</UNITS>
       </SAMPLE_ATTRIBUTE>
       <SAMPLE_ATTRIBUTE>
      <TAG>geographic location (country and/or sea)</TAG>
-     <VALUE>Colombia</VALUE>
+     <VALUE>{{ country }}</VALUE>
       </SAMPLE_ATTRIBUTE>
       <SAMPLE_ATTRIBUTE>
         <TAG>geographic location (region and locality)</TAG>
-        <VALUE>Tumaco</VALUE>
-      </SAMPLE_ATTRIBUTE>
-      <SAMPLE_ATTRIBUTE>
-        <TAG>environment (biome)</TAG>
-        <VALUE>coast</VALUE>
-      </SAMPLE_ATTRIBUTE>
-      <SAMPLE_ATTRIBUTE>
-        <TAG>environment (feature)</TAG>
-        <VALUE>human-associated habitat</VALUE>
+        <VALUE>{{ locality }}</VALUE>
       </SAMPLE_ATTRIBUTE>
       <SAMPLE_ATTRIBUTE>
         <TAG>environment (material)</TAG>
-        <VALUE>gastric biopsy</VALUE>
+        <VALUE>{{ material }}</VALUE>
       </SAMPLE_ATTRIBUTE>
       <SAMPLE_ATTRIBUTE>
         <TAG>ENA-CHECKLIST</TAG>
@@ -65,4 +49,3 @@
     </SAMPLE_ATTRIBUTES>
   </SAMPLE>
 </SAMPLE_SET>
-
diff --git a/doc/blog/using-covid-19-pubseq-part6.org b/doc/blog/using-covid-19-pubseq-part6.org
index 6ee68bb..664170b 100644
--- a/doc/blog/using-covid-19-pubseq-part6.org
+++ b/doc/blog/using-covid-19-pubseq-part6.org
@@ -111,6 +111,7 @@ need the =--insecure= switch to circumvent certificate checking.
 
 * Define the EBI sample
 
+EBI's sample form for virus is defined [[https://www.ebi.ac.uk/ena/browser/view/ERC000033][here]].
 
 /work in progress (WIP)/