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author | Pjotr Prins | 2020-07-21 11:05:00 +0100 |
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committer | Pjotr Prins | 2020-07-21 11:05:00 +0100 |
commit | dceac420dffa3aa74ef49a50d9be01e450e9d339 (patch) | |
tree | 1d9e1d4f02c1b1b086494c6659d2fff06c77547e /bh20simplewebuploader | |
parent | 56b5c444fd10cc569c4c0d7b76d034799ce679f9 (diff) | |
download | bh20-seq-resource-dceac420dffa3aa74ef49a50d9be01e450e9d339.tar.gz bh20-seq-resource-dceac420dffa3aa74ef49a50d9be01e450e9d339.tar.lz bh20-seq-resource-dceac420dffa3aa74ef49a50d9be01e450e9d339.zip |
Add sequencer JSON/XML output
Diffstat (limited to 'bh20simplewebuploader')
-rw-r--r-- | bh20simplewebuploader/api.py | 40 | ||||
-rw-r--r-- | bh20simplewebuploader/templates/ebi-sample.xml | 4 |
2 files changed, 41 insertions, 3 deletions
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> |