# HG changeset patch
# User fabio
# Date 1519410074 18000
# Node ID dd3c4fd6440271f337bf3ef90e1aaf9a2af22d53
# Parent  c1b3f351021937cfa07cb250853b2f1e3215aab2
Uploaded 20180223

diff -r c1b3f3510219 -r dd3c4fd64402 ._.shed.yml
Binary file ._.shed.yml has changed
diff -r c1b3f3510219 -r dd3c4fd64402 ._example.tsv
Binary file ._example.tsv has changed
diff -r c1b3f3510219 -r dd3c4fd64402 query.py
--- a/query.py	Thu Feb 01 17:28:33 2018 -0500
+++ b/query.py	Fri Feb 23 13:21:14 2018 -0500
@@ -10,7 +10,7 @@
 SERVICE_URL = "http://nn14.galaxyproject.org:8080/";
 #service_url = "http://127.0.0.1:8082/";
 QUERY_URL = SERVICE_URL+"tree/0/query";
-STATUS_URL = SERVICE_URL+"status/<task_id>";
+STATUS_URL = SERVICE_URL+"status/<query_id>";
 ##############
 # query delay in seconds
 QUERY_DELAY = 30;
@@ -48,16 +48,16 @@
         resp_content = str(req.content);
         # convert out to json
         json_content = json.loads(resp_content);
-        # retrieve task id
-        task_id = json_content['task_id'];
-        task_processed = False;
+        # retrieve query id
+        query_id = json_content['query_id'];
+        query_processed = False;
         # results json content
         json_status_content = None;
-        while task_processed is False:
+        while query_processed is False:
             # create a new session
             session = requests.Session();
             # make a synchronous get request to the status route
-            status_query_url = STATUS_URL.replace("<task_id>", task_id);
+            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");
@@ -66,10 +66,10 @@
             # take a look at the state
             # state attribute is always available
             if json_status_content['state'] == 'SUCCESS':
-                task_processed = True;
+                query_processed = True;
                 break;
             elif json_status_content['state'] in ['FAILURE', 'REVOKED']:
-                return raiseException( ERR_EXIT_CODE, "Task ID: "+str(task_id)+"\nTask status: "+str(json_status_content['state']), output_dir_path, str(options.errorfile) );
+                return raiseException( ERR_EXIT_CODE, "Query ID: "+str(query_id)+"\nQuery status: "+str(json_status_content['state']), output_dir_path, str(options.errorfile) );
             else:
                 time.sleep(QUERY_DELAY); # in seconds
         
diff -r c1b3f3510219 -r dd3c4fd64402 query.xml
--- a/query.xml	Thu Feb 01 17:28:33 2018 -0500
+++ b/query.xml	Fri Feb 23 13:21:14 2018 -0500
@@ -41,7 +41,7 @@
                 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="false" help="Insert a list of (ID, TRANSCRIPT) couples in a tab delimited format, one for each line. The content of this text box will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." />
             </when>
         </conditional>            
-        <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." />
+        <param name="sthreshold" size="3" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." />
     </inputs>
     <outputs>
         <collection name="output_collect" type="list" label="AllSome Sequence Bloom Tree Search Collection">