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# Public API for PubSeq
import os
import requests
import sys
from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
from bh20simplewebuploader.main import app, baseURL
@app.route('/api/version')
def version():
return jsonify({ 'service': 'PubSeq', 'version': 0.10 })
@app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
def ebi_sample(id):
page = render_template('ebi-sample.xml',**locals())
return page
@app.route('/api/search', methods=['GET'])
def search():
"""
Execute a 'global search'
"""
s = request.args.get('s')
if s == "":
s = "MT326090.1"
query = """
PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/>
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 edam:data_2091 ?info .
} limit 100
""" % s
payload = {'query': query, 'format': 'json'}
r = requests.get(baseURL, params=payload)
result = r.json()['results']['bindings']
# metadata = file.name(seq)+"/metadata.yaml"
print(result)
return jsonify([{
'id': x['id']['value'],
'fasta': x['seq']['value'],
'collection': os.path.dirname(x['seq']['value']),
'info': x['info']['value'],
} for x in result])
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