def tree_build():
opts = {}
# Hardcoded options, potentially expose
opts["data_file"] = "data.nex"
opts["seq_type"] = "dna"
opts["fields"] = ["uuid"]
opts["sort"] = ["uuid"]
opts["rq"] = request.args.get("rq")
opts["limit"] = request.args.get("limit", 10)
# Generate a uuid job id
opts["job_id"] = str(uuid.uuid4())
idb = idigbio.json()
results = idb.search_records(rq=opts["rq"], limit=opts["limit"],
fields=opts["fields"], sort=opts["sort"])
idb_uuids = []
for rec in results["items"]:
idb_uuids.append(rec["indexTerms"]["uuid"])
db = Database()
opts["raw_seqs"] = {}
for seq in db.sess.query(Sequence).filter(Sequence.idb_uuid.in_(idb_uuids)).filter(Sequence.can_use == True):
# The "-" char messes up MrBayes even in the taxon name string field.
# Change that here and it will percolate through the output without
# affecting the data sources on the front end.
opts["raw_seqs"][seq.idb_uuid.replace("-", "_")] = seq.seq
pipeline.delay(opts)
return jsonify({"job_id": opts["job_id"], "raw_seqs": opts["raw_seqs"], "rq": opts["rq"]})
def tree_build():
opts = {}
# Hardcoded options, potentially expose
opts["data_file"] = "data.nex"
opts["seq_type"] = "dna"
opts["fields"] = ["uuid"]
opts["sort"] = ["uuid"]
opts["rq"] = request.args.get("rq")
opts["limit"] = request.args.get("limit", 10)
# Generate a uuid job id
opts["job_id"] = str(uuid.uuid4())
idb = idigbio.json()
results = idb.search_records(rq=opts["rq"],
limit=opts["limit"],
fields=opts["fields"],
sort=opts["sort"])
idb_uuids = []
for rec in results["items"]:
idb_uuids.append(rec["indexTerms"]["uuid"])
db = Database()
opts["raw_seqs"] = {}
for seq in db.sess.query(Sequence).filter(
Sequence.idb_uuid.in_(idb_uuids)).filter(Sequence.can_use == True):
# The "-" char messes up MrBayes even in the taxon name string field.
# Change that here and it will percolate through the output without
# affecting the data sources on the front end.
opts["raw_seqs"][seq.idb_uuid.replace("-", "_")] = seq.seq
pipeline.delay(opts)
return jsonify({
"job_id": opts["job_id"],
"raw_seqs": opts["raw_seqs"],
"rq": opts["rq"]
})
idb = idigbio.json()
rq_ = {"genus": "acer"}
limit_ = 10
fields_ = ["uuid"]
sort_ = ["uuid"]
results = idb.search_records(rq=rq_, limit=limit_, fields=fields_, sort=sort_)
#print len(results["items"])
#print results["items"][0]["indexTerms"]["genus"]
#exit(0)
idb_uuids = []
for rec in results["items"]:
idb_uuids.append(rec["indexTerms"]["uuid"])
print idb_uuids
db = Database()
opts["raw_seqs"] = {}
for seq in db.sess.query(Sequence).filter(Sequence.idb_uuid.in_(idb_uuids)):
# The "-" char messes up MrBayes even in the taxon name string field.
# Change that here and it will percolate through the output without
# affecting the data sources on the front end.
opts["raw_seqs"][seq.idb_uuid.replace("-", "_")] = seq.seq
opts["seq_type"] = "dna"
print opts
#msa.delay(opts)
#build.delay(opts)
pipeline.delay(opts)
fields_ = ["uuid"]
sort_ = ["uuid"]
results = idb.search_records(rq=rq_, limit=limit_, fields=fields_, sort=sort_)
#print len(results["items"])
#print results["items"][0]["indexTerms"]["genus"]
#exit(0)
idb_uuids = []
for rec in results["items"]:
idb_uuids.append(rec["indexTerms"]["uuid"])
print idb_uuids
db = Database()
opts["raw_seqs"] = {}
for seq in db.sess.query(Sequence).filter(Sequence.idb_uuid.in_(idb_uuids)):
# The "-" char messes up MrBayes even in the taxon name string field.
# Change that here and it will percolate through the output without
# affecting the data sources on the front end.
opts["raw_seqs"][seq.idb_uuid.replace("-", "_")] = seq.seq
opts["seq_type"] = "dna"
print opts
#msa.delay(opts)
#build.delay(opts)
pipeline.delay(opts)
