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# Public API for PubSeq
import os
import requests
import sys
import types
from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
from bh20simplewebuploader.main import app, sparqlURL
PUBSEQ="http://covid19.genenetwork.org"
ARVADOS="https://collections.lugli.arvadosapi.com/c="
# Helper functions
def fetch_sample(id, query=None):
default_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/>
PREFIX evs: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
select distinct ?id ?seq ?date ?info ?specimen ?sequencer ?mapper
{
?sample sio:SIO_000115 "%s" ;
sio:SIO_000115 ?id ;
evs:C25164 ?date .
?seq pubseq:technology ?tech ;
pubseq:sample ?sample .
optional { ?tech efo:EFO_0002699 ?mapper } .
optional { ?tech obo:OBI_0600047 ?sequencer . }
optional { ?sample edam:data_2091 ?info } .
optional { ?sample obo:OBI_0001479 ?specimen } .
} limit 5
""" % id
if not query: query = default_query
print(query)
payload = {'query': query, 'format': 'json'}
r = requests.get(sparqlURL, params=payload)
res = r.json()
print(res)
return res['results']['bindings'],res['head']['vars']
def fetch_one_sample(id, query=None):
"""Get the top sample and return a SimpleNamespace"""
result,varlist = fetch_sample(id,query)
h = {}
row = result[0]
for key in varlist:
if key in row:
h[key] = row[key]['value']
print(h)
h['arv_id'] = os.path.basename(h['seq'])
return types.SimpleNamespace(**h)
def fetch_one_record(id):
m = fetch_one_sample(id)
arv_id = m.arv_id
rec = { "id": id,
'arv_id': arv_id,
"permalink": PUBSEQ+'/resource/'+id,
"collection": m.seq,
'collection_date': m.date,
'fasta': ARVADOS+arv_id+'/sequence.fasta',
'metadata': ARVADOS+arv_id+'/metadata.yaml',
}
h = m.__dict__ # for optional items
if 'mapper' in h: rec['mapper'] = m.mapper
if 'sequencer' in h: rec['sequencer']= m.sequencer
return rec
# 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):
"""
API sample should return a record pointing to other resources,
notably: permalink, original metadata record and the fasta
data.
curl http://localhost:5067/api/sample/MT533203.1.json
{
"id": "MT533203.1",
"permalink": "http://covid19.genenetwork.org/resource/MT533203.1",
"collection": "http://covid19.genenetwork.org/resource/lugli-4zz18-uovend31hdwa5ks",
"collection_date": "2020-04-27",
"fasta": "https://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/sequence.fasta",
"metadata": "https://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/metadata.yaml",
"mapper": "minimap v. 2.17",
"sequencer": "http://www.ebi.ac.uk/efo/EFO_0008632"
}
"""
return jsonify([fetch_one_record(id)])
@app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
def ebi_sample(id):
meta,varlist = fetch_sample(id)[0]
page = render_template('ebi-sample.xml',sampleid=id,sequencer=meta['sequencer']['value'],date=meta['date']['value'],specimen=meta['specimen']['value'])
return page
@app.route('/api/search', methods=['GET'])
def search():
"""
Execute a 'global search'. Currently just duplicates fetch one
sample. Should be more flexible FIXME.
"""
s = request.args.get('s')
if s == "": s = "MT326090.1"
return jsonify([fetch_one_record(s)])
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