# HG changeset patch
# User fabio
# Date 1517432316 18000
# Node ID 97dd57f81d775b9052c0b1d1ef54ff7713edec2c
# Parent  5e2877685afcbc8a777ce7c807bba0b1a7f17de9
Uploaded 20180131

diff -r 5e2877685afc -r 97dd57f81d77 ._.shed.yml
Binary file ._.shed.yml has changed
diff -r 5e2877685afc -r 97dd57f81d77 ._example.tsv
Binary file ._example.tsv has changed
diff -r 5e2877685afc -r 97dd57f81d77 ._query.py
Binary file ._query.py has changed
diff -r 5e2877685afc -r 97dd57f81d77 ._query.xml
Binary file ._query.xml has changed
diff -r 5e2877685afc -r 97dd57f81d77 query.py
--- a/query.py	Wed Jan 31 11:29:01 2018 -0500
+++ b/query.py	Wed Jan 31 15:58:36 2018 -0500
@@ -12,6 +12,9 @@
 query_url = service_url+"tree/0/query";
 status_url = service_url+"status/<task_id>";
 ##############
+# query delay in seconds
+query_delay = 30;
+##############
 
 def query_request( options, args, payload ):
     # add additional parameters to the payload
@@ -27,7 +30,7 @@
     # make a synchronous post request to the query route
     req = session.post(query_url, headers=headers, json=payload);
     resp_code = req.status_code;
-    #print(str(req.content)+"\n\n");
+    print(str(req.content)+"\n\n");
     if resp_code == requests.codes.ok:
         resp_content = str(req.content);
         # convert out to json
@@ -45,7 +48,7 @@
             status_query_url = status_url.replace("<task_id>", task_id);
             status_req = session.get(status_query_url);
             status_resp_content = str(status_req.content);
-            #print(status_resp_content+"\n\n");
+            print(status_resp_content+"\n\n");
             # convert out to json
             json_status_content = json.loads(status_resp_content);
             # take a look at the state
@@ -56,7 +59,7 @@
             elif json_status_content['state'] in ['FAILURE', 'REVOKED']:
                 return "Task status: "+str(json_status_content['state']);
             else:
-                time.sleep(60); # in seconds
+                time.sleep(query_delay); # in seconds
         
         # get output dir (collection) path
         output_dir_path = options.outputdir;
@@ -102,7 +105,7 @@
                                 return "Error: the id '"+seq_id+"' is duplicated";
                             multiple_data[seq_id] = seq_text;
         if len(multiple_data) > 0:
-            return async_request( options, args,  multiple_data );
+            return query_request( options, args,  multiple_data );
             #return echo( options, args );
         else:
             return "An error has occurred. Please be sure that your input files are valid.";
@@ -126,7 +129,7 @@
                                 return "Error: the id '"+seq_id+"' is duplicated";
                             multiple_data[seq_id] = seq_text;
                 if len(multiple_data) > 0:
-                    return async_request( options, args, multiple_data );
+                    return query_request( options, args, multiple_data );
                     #return echo( options, args );
                 else:
                     return "An error has occurred. Please be sure that your input files are valid.";
@@ -164,7 +167,7 @@
     #--exact 0
     #--sequences 'id0__tc__CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC'
     #--outputdir 'collection_content'
-    #sequences = 'id0__tc__CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC';
+    #sequences = 'NM_001169378.2__tc__atttcggatgctttggagggaggaactctagtgctgcattgattggggcgtgtgttaatgatattcccagttcgcatggcgagcatcgattcctggtacgtatgtgggccccttgactcccacttatcgcacttgtcgttcgcaatttgcatgaattccgcttcgtctgaaacgcacttgcgccagacttctccggctggtctgatctggtctgtgatccggtctggtggggcgccagttgcgtttcgagctcatcaccagtcactccgcagtcgcattctgccagaggtctccgatcaagagcgcttctccattcgagattcaaacgcagcgcggtctgacgccgccacatcgagtgaaatccatatcgatggccacattcacacaggacgagatcgacttcctgcgcagccatggcaacgagctgtgtgccaagacctggctgggattgtgggatccgaagcgggctgtgcaccagcaggagcagcgcgaactgatgatggacaagtatgagcggaagcgatactacctggagccggccagtcctcttaagtcgctggccaatgcggtcaacctgaagtcgtctgctccggcgacgaaccacactcagaatggccaccaaaatgggtatgccagcatccatttgacgcctcctgctgcccagcggacctcggccaatggattgcagaaggtggccaactcgtcgagtaactcttctggaaagacctcatcctcgatcagtaggccacactataatcaccagaacaacagccaaaacaacaatcacgatgcctttggcctgggtggcggattgagcagcctgaacagcgccggttccacatccactggagctctttccgacaccagcagttgtgctagcaatggcttcggtgcggactgcgactttgtggctgactttggctcggccaacattttcgacgccacatcggcgcgttccacaggatcgccggcggtgtcgtccgtgtcctcagtgggttccagcaatggctacgccaaggtgcagcccatccgggcagctcatctccagcagcaacagcagttgcagcagcagctgcatcagcagcagctcctcaatggcaatggtcatcagggcactgagaactttgccgacttcgatcacgctcccatctacaatgcagtggctccaccgacttttaacgattggatcagcgactggagcaggcggggcttccacgatcccttcgacgattgcgatgactcgccaccaggtgcccgccctccagcacctgcgccagctcctgctcaagttcccgcagtatcatcaccattgccaaccgtccgagaagaaccagagcttgcgtggaatttttgggaggacgagatgcgaatagaggcgcaggaaaaggagtcccaaactaaacagccggagttgggctactccttttcgattagtactactacgcccctttccccttcgaatcccttcctgccctaccttgtcagtgaggagcagcatcgaaatcatccagagaagccctccttttcgtattcgttgttcagctccatatcaaatagttcgcaagaagatcaggcggatgatcatgagatgaatgttttaaatgccaatttccatgatttctttacgtggagtgctcccttgcagaacggccatacgaccagtccgcccaagggcggaaatgcagcgatggcgcccagtgaggatcgatatgccgctcttaaggatctcgacgagcagctgcgagaactgaaggccagcgaaagcgccacagagacgcccacgcccaccagtggcaatgttcaggccacagatgcctttggtggagccctcaacaacaatccaaatcccttcaagggccagcaacagcagcagctcagcagccatgtggtgaatccattccagcagcagcaacagcagcagcaccagcagaatctctatggccagttgacgctcataccaaatgcctacggcagcagttcccagcagcagatggggcaccatctcctccagcagcagcagcagcaacagcagagcttcttcaacttcaacaacaacgggttcgccatctcgcagggtctgcccaacggctgcggcttcggcagcatgcaacccgctcctgtgatggccaacaatccctttgcagccagcggcgccatgaacaccaacaatccattcttatgagactcaacccgggagaatccgcctcgcgccacctggcagaggcgctgagccagcgaacaaagagcagacgcggaggaaccgaaccgaaattagtccattttactaacaatagcgttaatctatgtatacataatgcacgccggagagcactctttgtgtacatagcccaaatatgtacacccgaaaggctccacgctgacgctagtcctcgcggatggcggaggcggactggggcgttgatatattcttttacatggtaactctactctaacgtttacggatacggatatttgtatttgccgtttgccctagaactctatacttgtactaagcgcccatgaacacttcatccactaacatagctactaatcctcatcctagtggaggatgcagttggtccagacactctgttatttgttttatccatcctcgtacttgtctttgtcccatttagcactttcgttgcggataagaactttgtcagttattgattgtgtggccttaataagattataaaactaaatattataacgtacgactatacatatacggatacagatacagattcagacacagttagtacagatacagatatacatatacgcttttgtacctaatgaattgcttcttgtttccattgctaatcatctgcttttcgtgtgctaattttatacactagtacgtgcgatatcggccgtgcagatagattgctcagctcgcgagtcaagcctcttttggttgcacccacggcagacatttgtacatatactgtctgattgtaagcctcgtgtaatacctccattaacaccactcccccaccacccatccatcgaaccccgaatccatgactcaattcactgctcacatgtccatgcccatgccttaacgtgtcaaacattatcgaagccttaaagttatttaaaactacgaaatttcaataaaaacaaataagaacgctatc';
     #print(sequences);
     #(options, args) = parser.parse_args(['-x', 'rrr', '-t', 0.5, '-s', sequences, '-o', 'collection_content']);