Mercurial > repos > fabio > btman
view create.py @ 17:f02c2c58a6f9 draft
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author | fabio |
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date | Fri, 18 Jan 2019 10:12:40 -0500 |
parents | ba9d0fc8657f |
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#!/usr/bin/env python # https://github.com/ross/requests-futures # http://docs.python-requests.org/en/master/user/quickstart/#more-complicated-post-requests import sys, os, uuid, optparse, requests, json, time #from requests_futures.sessions import FuturesSession #### NN14 #### SERVICE_URL = "http://nn14.galaxyproject.org:8080/"; #service_url = "http://127.0.0.1:8082/"; CREATE_URL = SERVICE_URL+"tree/create"; STATUS_URL = SERVICE_URL+"status/<query_id>"; ############## # query delay in seconds QUERY_DELAY = 30; ############## __version__ = "1.0.0"; ERR_EXIT_CODE = 1; OK_EXIT_CODE = 0; def raiseException( exitcode, message, errorfilepath ): with open(errorfilepath, 'w') as out: out.write(message); sys.exit(exitcode); def create_request( options, args, data ): outfilepath = options.outfile; cluster_id_2_query_id = { }; for cluster_id in data: payload = { }; payload["accessions"] = data[cluster_id]; # add additional parameters to the payload payload["qualitycontrol"] = int(options.qualitycontrol); payload["qualitythreshold"] = float(options.qualitythreshold); payload["klen"] = int(options.klen); payload["minabundance"] = int(options.minabundance); # set the content type to application/json headers = {'Content-type': 'application/json'}; # create a session session = requests.Session(); # make a synchronous post request to the create route req = session.post(CREATE_URL, headers=headers, json=payload); resp_code = req.status_code; #print(str(req.content)+"\n\n"); if resp_code == requests.codes.ok: resp_content = str(req.content); # convert out to json json_content = json.loads(resp_content); # retrieve query id query_id = json_content['query_id']; cluster_id_2_query_id[cluster_id] = query_id; else: with open(outfilepath, 'a+') as outfile: outfile.write( "An error has occurred while submitting data to the /tree/create endpoint for the cluster " + cluster_id + "\n\n" ); build_flags = [ ] while len(build_flags) < len(cluster_id_2_query_id): for idx, cluster_id in enumerate( cluster_id_2_query_id ): if cluster_id not in build_flags: query_id = cluster_id_2_query_id[ cluster_id ]; # create a new session session = requests.Session(); # make a synchronous get request to the status route status_query_url = STATUS_URL.replace("<query_id>", query_id); status_req = session.get(status_query_url); status_resp_content = str(status_req.content); #print(status_resp_content+"\n\n"); # convert out to json json_status_content = json.loads(status_resp_content); # take a look at the state # state attribute is always available if json_status_content['state'] == 'SUCCESS': build_flags.append( cluster_id ); built_tree_id = json_status_content['results']['tree_id']; with open(outfilepath, 'a+') as outfile: outfile.write( "Query ID: " + str(query_id) + "\n" + "Query status: " + str(json_status_content['state']) + "\n" + "Cluster ID: " + cluster_id + "\n" + "Sequence Bloom Tree ID: " + built_tree_id + "\n\n" ); elif json_status_content['state'] in ['FAILURE', 'REVOKED']: build_flags.append( cluster_id ); with open(outfilepath, 'a+') as outfile: outfile.write( "Query ID: " + str(query_id) + "\n" + "Query status: " + str(json_status_content['state']) + "\n" + "Cluster ID: " + cluster_id + "\n\n" ); if len(build_flags) < len(cluster_id_2_query_id): time.sleep(QUERY_DELAY); # in seconds return sys.exit(OK_EXIT_CODE); def create( options, args ): multiple_data = {}; experiment_list_file_path = options.explist; with open(experiment_list_file_path) as explist: for line in explist: if line.strip() != "": line_split = line.strip().split("\t"); # split on tab if len(line_split) == 2: # 0:accession , 1:cluster_id , otherwise skip line accession = line_split[0]; cluster_id = line_split[1]; if cluster_id in multiple_data: multiple_data[cluster_id].append( accession ); else: multiple_data[cluster_id] = [ accession ]; if len(multiple_data) > 0: return create_request( options, args, multiple_data ); else: return raiseException( ERR_EXIT_CODE, "An error has occurred. Please be sure that your input file is valid.", options.outfile ); def __main__(): # Parse the command line options usage = "Usage: create.py --explist experiment_list --qualitycontrol quality_control --qualitythreshold quality_threshold --klen kmer_len --minabundance min_abundance --outfile output_file_path"; parser = optparse.OptionParser(usage = usage); parser.add_option("-v", "--version", action="store_true", dest="version", default=False, help="display version and exit") parser.add_option("-l", "--explist", type="string", action="store", dest="explist", help="tabular file with a list of SRA accessions and their cluster label"); parser.add_option("-q", "--qualitycontrol", type="int", default=0 action="store", dest="qualitycontrol", help="flag to enable or disable the experiment quality control"); parser.add_option("-t", "--qualitythreshold", type="float", default=0.0 action="store", dest="qualitythreshold", help="quality threshold, if quality control is enabled only"); parser.add_option("-k", "--klen", type="int", default=21, action="store", dest="klen", help="k-mer length"); parser.add_option("-m", "--minabundance", type="int", default=2, action="store", dest="minabundance", help="minimum abundance"); parser.add_option("-o", "--outfile", type="string", default="outfile_txt", action="store", dest="outfile", help="output file path"); (options, args) = parser.parse_args(); if options.version: print __version__; else: return create( options, args ); if __name__ == "__main__": __main__()