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)