--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create.py	Fri Jan 18 10:12:19 2019 -0500
@@ -0,0 +1,132 @@
+#!/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__()