| Previous changeset 17:c1b3f3510219 (2018-02-01) Next changeset 19:604e373b3b45 (2018-02-23) |
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Commit message:
Uploaded 20180223 |
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modified:
query.py query.xml |
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added:
._.shed.yml ._example.tsv |
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| diff -r c1b3f3510219 -r dd3c4fd64402 ._.shed.yml |
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| Binary file ._.shed.yml has changed |
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| diff -r c1b3f3510219 -r dd3c4fd64402 ._example.tsv |
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| Binary file ._example.tsv has changed |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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"> |