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-rw-r--r--bh20simplewebuploader/main.py10
-rw-r--r--bh20simplewebuploader/static/main.js5
-rw-r--r--bh20simplewebuploader/templates/ebi-sample.xml68
-rw-r--r--bh20simplewebuploader/templates/export.html2
4 files changed, 81 insertions, 4 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 673f913..d524efe 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -696,12 +696,13 @@ def search():
query = """
PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/>
- select distinct ?id ?seq
+ PREFIX edam: <http://edamontology.org/>
+ select distinct ?id ?seq ?info
{
?sample sio:SIO_000115 "%s" .
?sample sio:SIO_000115 ?id .
?seq pubseq:sample ?sample .
- ?sample ?p ?o .
+ ?sample edam:data_2091 ?info .
} limit 100
""" % s
payload = {'query': query, 'format': 'json'}
@@ -711,6 +712,7 @@ def search():
return jsonify([{
'id': x['id']['value'],
'seq': x['seq']['value'],
+ 'info': x['info']['value'],
} for x in result])
@app.route('/api/getAllaccessions', methods=['GET'])
@@ -934,3 +936,7 @@ def getSEQbyLocationAndSpecimenSource():
r = requests.get(baseURL, params=payload)
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')
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 208823a..deda6ec 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -18,10 +18,13 @@ function toDIVTable(rows) {
else {
html = '<div class="rTable">';
rows.forEach(row => {
+ id = row['id'];
seq = row['seq'];
+ info = row['info'];
html += '<div class="rTableRow">';
- html += cell(row['id']);
+ 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 += '</div>';
});
html += '</div>';
diff --git a/bh20simplewebuploader/templates/ebi-sample.xml b/bh20simplewebuploader/templates/ebi-sample.xml
new file mode 100644
index 0000000..694c471
--- /dev/null
+++ b/bh20simplewebuploader/templates/ebi-sample.xml
@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SAMPLE_SET>
+ <SAMPLE alias="PubSeqSam0001" center_name="PubSeq01">
+ <TITLE>human gastric microbiota, mucosal</TITLE>
+ <SAMPLE_NAME>
+ <TAXON_ID>1284369</TAXON_ID>
+ <SCIENTIFIC_NAME>stomach metagenome</SCIENTIFIC_NAME>
+ <COMMON_NAME></COMMON_NAME>
+ </SAMPLE_NAME>
+ <SAMPLE_ATTRIBUTES>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>investigation type</TAG>
+ <VALUE>mimarks-survey</VALUE>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>sequencing method</TAG>
+ <VALUE>pyrosequencing</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>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>geographic location (latitude)</TAG>
+ <VALUE>1.81</VALUE>
+ <UNITS>DD</UNITS>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>geographic location (longitude)</TAG>
+ <VALUE>-78.76</VALUE>
+ <UNITS>DD</UNITS>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>geographic location (country and/or sea)</TAG>
+ <VALUE>Colombia</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>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>environment (material)</TAG>
+ <VALUE>gastric biopsy</VALUE>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>ENA-CHECKLIST</TAG>
+ <VALUE>ERC000011</VALUE>
+ </SAMPLE_ATTRIBUTE>
+ </SAMPLE_ATTRIBUTES>
+ </SAMPLE>
+</SAMPLE_SET>
+
diff --git a/bh20simplewebuploader/templates/export.html b/bh20simplewebuploader/templates/export.html
index 1f0d9b7..aaceac9 100644
--- a/bh20simplewebuploader/templates/export.html
+++ b/bh20simplewebuploader/templates/export.html
@@ -31,7 +31,7 @@
</p>
<div class="search">
- <input id="search-input" type="search" placeholder="e.g. MT246484" required>
+ <input id="search-input" type="search" placeholder="e.g. MT326090.1" required>
<button class="button search-button" type="submit" onclick="searchGlobaltoDIVTable()">
<span class="icon ion-search">
<span class="sr-only">Search</span>