aboutsummaryrefslogtreecommitdiff
path: root/bh20simplewebuploader
diff options
context:
space:
mode:
authorPjotr Prins2021-01-05 10:42:16 +0000
committerPjotr Prins2021-01-05 10:42:16 +0000
commitb26133cdaff3bba64c4fc294510b16d57030d071 (patch)
tree46816a066e528e7ba824817ae830b42692b7438a /bh20simplewebuploader
parent9d75ce088e6388bf23ae077fd06b2a3f51be1bda (diff)
downloadbh20-seq-resource-b26133cdaff3bba64c4fc294510b16d57030d071.tar.gz
bh20-seq-resource-b26133cdaff3bba64c4fc294510b16d57030d071.tar.lz
bh20-seq-resource-b26133cdaff3bba64c4fc294510b16d57030d071.zip
api: more cleanup
Diffstat (limited to 'bh20simplewebuploader')
-rw-r--r--bh20simplewebuploader/api.py122
-rw-r--r--bh20simplewebuploader/main.py3
2 files changed, 61 insertions, 64 deletions
diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py
index 11c74f2..761ad03 100644
--- a/bh20simplewebuploader/api.py
+++ b/bh20simplewebuploader/api.py
@@ -3,6 +3,7 @@
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
@@ -12,14 +13,16 @@ ARVADOS="https://collections.lugli.arvadosapi.com/c="
# Helper functions
-def fetch_sample_metadata(id):
- query = """
+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" ;
@@ -27,15 +30,49 @@ def fetch_sample_metadata(id):
evs:C25164 ?date .
?seq pubseq:technology ?tech ;
pubseq:sample ?sample .
- ?tech efo:EFO_0002699 ?mapper ;
- obo:OBI_0600047 ?sequencer .
+ 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)
- return r.json()['results']['bindings']
+ 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
@@ -52,74 +89,33 @@ notably: permalink, original metadata record and the fasta
data.
curl http://localhost:5067/api/sample/MT533203.1.json
-[
- {
- "collection": "http://covid19.genenetwork.org/resource/lugli-4zz18-uovend31hdwa5ks",
- "date": "2020-04-27",
- "fasta": "https://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/sequence.fasta",
- "id": "MT533203.1",
- "info": "http://identifiers.org/insdc/MT533203.1#sequence",
- "mapper": "minimap v. 2.17",
- "metadata": "https://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/metadata.yaml",
- "permalink": "http://covid19.genenetwork.org/resource/MT533203.1",
- "sequencer": "http://www.ebi.ac.uk/efo/EFO_0008632",
- "specimen": "http://purl.obolibrary.org/obo/NCIT_C155831"
- }
-]
-
+{
+ "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"
+}
"""
- # metadata = file.name(seq)+"/metadata.yaml"
- meta = fetch_sample_metadata(id)
- print(meta)
- # http://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/metadata.yaml
- return jsonify([{
- 'id': x['id']['value'],
- 'collection': x['seq']['value'],
- 'permalink': PUBSEQ+'/resource/'+x['id']['value'],
- 'fasta': ARVADOS+os.path.basename(x['seq']['value'])+'/sequence.fasta',
- 'metadata': ARVADOS+os.path.basename(x['seq']['value'])+'/metadata.yaml',
- 'date': x['date']['value'],
- 'info': x['info']['value'],
- 'specimen': x['specimen']['value'],
- 'sequencer': x['sequencer']['value'],
- 'mapper': x['mapper']['value'],
- } for x in meta])
+
+ return jsonify([fetch_one_record(id)])
@app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
def ebi_sample(id):
- meta = fetch_sample_metadata(id)[0]
+ 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'
+ 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"
- 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(sparqlURL, 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])
+ if s == "": s = "MT326090.1"
+ return jsonify([fetch_one_record(s)])
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index b620946..b4b72d2 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -34,6 +34,7 @@ if not os.path.isfile('bh20sequploader/main.py'):
print("WARNING: run FLASK from the root of the source repository!", file=sys.stderr)
app = Flask(__name__, static_url_path='/static', static_folder='static')
+app.config['JSON_SORT_KEYS'] = False
# Limit file upload size. We shouldn't be working with anything over 1 MB; these are small genomes.
# We will enforce the limit ourselves and set a higher safety limit here.
@@ -252,7 +253,7 @@ FORM_ITEMS = load_schema_generate_form()
def get_feed_items(name, start=0, stop=9):
redis_client = redis.Redis(host=os.environ.get('HOST', 'localhost'),
port=os.environ.get('PORT', 6379),
- db=os.environ.get('REDIS_DB', 0))
+ db=os.environ.get('REDIS_DB', 0))
feed_items = []
try:
for el in redis_client.zrevrange(name, start, stop):