aboutsummaryrefslogtreecommitdiff
path: root/bh20simplewebuploader
diff options
context:
space:
mode:
authorPjotr Prins2020-07-19 12:49:43 +0100
committerPjotr Prins2020-07-19 12:49:43 +0100
commitd41ecc84e61048449538fbaabc1a777d95f42618 (patch)
tree187faf9cbe7a9edd8cf8d85c564d22757fda4efc /bh20simplewebuploader
parent20cbfb593e89b07d68e6c16106a24e79cea61329 (diff)
downloadbh20-seq-resource-d41ecc84e61048449538fbaabc1a777d95f42618.tar.gz
bh20-seq-resource-d41ecc84e61048449538fbaabc1a777d95f42618.tar.lz
bh20-seq-resource-d41ecc84e61048449538fbaabc1a777d95f42618.zip
EBI form filling
Diffstat (limited to 'bh20simplewebuploader')
-rw-r--r--bh20simplewebuploader/main.py7
-rw-r--r--bh20simplewebuploader/static/main.js2
-rw-r--r--bh20simplewebuploader/templates/ebi-sample.xml43
3 files changed, 18 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>
-