From dceac420dffa3aa74ef49a50d9be01e450e9d339 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 21 Jul 2020 11:05:00 +0100
Subject: Add sequencer JSON/XML output
---
bh20simplewebuploader/api.py | 40 +++++++++++++++++++++++++-
bh20simplewebuploader/templates/ebi-sample.xml | 4 +--
2 files changed, 41 insertions(+), 3 deletions(-)
(limited to 'bh20simplewebuploader')
diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py
index 29fa2b8..ff82b72 100644
--- a/bh20simplewebuploader/api.py
+++ b/bh20simplewebuploader/api.py
@@ -7,13 +7,51 @@ import sys
from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
from bh20simplewebuploader.main import app, baseURL
+# Helper functions
+
+def fetch_sample_metadata(id):
+ query = """
+ PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+ PREFIX sio: <http://semanticscience.org/resource/>
+ PREFIX edam: <http://edamontology.org/>
+ PREFIX efo: <http://www.ebi.ac.uk/efo/>
+ select distinct ?id ?seq ?info ?sequencer
+ {
+ ?sample sio:SIO_000115 "%s" .
+ ?sample sio:SIO_000115 ?id .
+ ?seq pubseq:technology ?tech .
+ ?seq pubseq:sample ?sample .
+ ?sample edam:data_2091 ?info .
+ ?tech efo:EFO_0002699 ?sequencer .
+ } limit 5
+ """ % id
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(baseURL, params=payload)
+ return r.json()['results']['bindings']
+
+# Main API routes
+
@app.route('/api/version')
def version():
return jsonify({ 'service': 'PubSeq', 'version': 0.10 })
+@app.route('/api/sample/<id>.json')
+def sample(id):
+ # metadata = file.name(seq)+"/metadata.yaml"
+ meta = fetch_sample_metadata(id)
+ return jsonify([{
+ 'id': x['id']['value'],
+ 'fasta': x['seq']['value'],
+ 'collection': os.path.dirname(x['seq']['value']),
+ 'info': x['info']['value'],
+ 'sequencer': x['sequencer']['value'],
+ } for x in meta])
+
@app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
def ebi_sample(id):
- page = render_template('ebi-sample.xml',**locals())
+ meta = fetch_sample_metadata(id)[0]
+ print("HERE",meta,file=sys.stderr)
+ page = render_template('ebi-sample.xml',sampleid=id,sequencer=meta['sequencer']['value'])
return page
@app.route('/api/search', methods=['GET'])
diff --git a/bh20simplewebuploader/templates/ebi-sample.xml b/bh20simplewebuploader/templates/ebi-sample.xml
index 441e29e..0b6b39e 100644
--- a/bh20simplewebuploader/templates/ebi-sample.xml
+++ b/bh20simplewebuploader/templates/ebi-sample.xml
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<SAMPLE_SET>
- <SAMPLE alias="{{ id }}" center_name="COVID-19 PubSeq">
+ <SAMPLE alias="{{ sampleid }}" center_name="COVID-19 PubSeq">
<TITLE>COVID-19 PubSeq Sample</TITLE>
<SAMPLE_NAME>
<TAXON_ID>2697049</TAXON_ID>
@@ -14,7 +14,7 @@
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sequencing method</TAG>
- <VALUE>{{ sequence_method }}</VALUE>
+ <VALUE>{{ sequencer }}</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>collection date</TAG>
--
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