diff options
Diffstat (limited to 'bh20simplewebuploader/api.py')
| -rw-r--r-- | bh20simplewebuploader/api.py | 37 |
1 files changed, 35 insertions, 2 deletions
diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py index 8bd1a22..29fa2b8 100644 --- a/bh20simplewebuploader/api.py +++ b/bh20simplewebuploader/api.py @@ -1,10 +1,11 @@ # Public API for PubSeq -import sys +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 +from bh20simplewebuploader.main import app, baseURL @app.route('/api/version') def version(): @@ -14,3 +15,35 @@ def version(): 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]) |