Hi Vipin, How long should your test take to run? That (admittedly unclear) error is indicating that the job didn't finish before the test suite gave up trying to check the outputs. --nate Vipin TS wrote:
Hi Greg & Nate,
Thanks for your comments. I had changed the port and tried to run the test again, but it fails in an AssertionError ******************************** mGenePredict ( mgenepredict ) > Test-1 ... FAIL
====================================================================== FAIL: mGenePredict ( mgenepredict ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 114, in test_tool self.do_it() File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 54, in do_it self.verify_dataset_correctness( file ) File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 323, in verify_dataset_correctness if wait: self.wait() #wait for job to finish File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 617, in wait self.assertNotEqual(count, maxiter) AssertionError: 20 == 20
-------------------- >> begin captured stdout << --------------------- galaxy.tools.actions.upload INFO 2009-10-23 10:15:59,551 tool upload1 created job id 1 galaxy.tools.actions.upload INFO 2009-10-23 10:15:59,897 job id 1 ended ok, file size: 390.6 Kb Uploaded file: tair9_chr4_10000.fas , ftype: fasta , extra: {'ftype': 'fasta', 'value': 'tair9_chr4_10000.fas'}
form 'tool_form' contains the following controls ( note the values ) control 0: <HiddenControl(tool_id=mgenepredict) (readonly)> control 1: <HiddenControl(tool_state=800254e3010000306361383263373039613935626566386164663739383835643632653966356537376437656533393a37623232363836393733373436663732373935663736373335663730373236353734373236313639366536353634323233613230323237623563323237333666373537323633363535633232336132303563323237303732363537343732363136393665363536343563323232633230356332323666373236373631366536393733366435633232336132303563323236353663363536373631366537333563323232633230356332323566356636333735373237323635366537343566363336313733363535663566356332323361323033303764323232633230323235663566373036313637363535663566323233613230333032633230323236383639373337343666373237393566373637333566363936653734363537323665363136633232336132303232376235633232373336663735373236333635356332323361323035633232363836393733373436663732373935633232326332303563323236363631373337343631356636393665373037353734356332323361323033313263323035633232356635663633373537323732363536653734356636333631373336353566356635633232336132 30333037643232376471002e) (readonly)> control 2: <SubmitControl(runtool_btn=Execute) (readonly)> control 3: <SelectControl(history_vs_internal|source=[*history, internal])> base.twilltestcase DEBUG 2009-10-23 10:15:59,975 In submit_form, continuing, but caught exception: 'history_vs_internal|source' control 4: <SelectControl(history_vs_internal|fasta_input=[*1])> control 5: <SelectControl(history_vs_pretrained|source=[*pretrained, history])> control 6: <SelectControl(history_vs_pretrained|organism=[*elegans, arabidopsis])> control 7: <SubmitControl(runtool_btn=Execute) (readonly)> page_inputs (0) {'history_vs_pretrained|source': ['pretrained'], 'history_vs_pretrained|organism': ['arabidopsis']} galaxy.jobs DEBUG 2009-10-23 10:16:05,321 dispatching job 2 to local runner galaxy.jobs DEBUG 2009-10-23 10:16:05,502 job 2 dispatched galaxy.jobs.runners.local DEBUG 2009-10-23 10:16:05,770 executing: ~/bin/octave_start_script.sh "setup_mgene; galaxy_mgene_predict( '/tmp/tmpTpQQ6I/database/files/000/dataset_1.dat', '/tmp/tmpTpQQ6I/database/files/000/dataset_1_files', '', 'mgene:arabidopsis', '/tmp/tmpTpQQ6I/database/files/000/dataset_3.dat', '/tmp/tmpTpQQ6I/database/files/000/dataset_3_files', -1);">> /tmp/tmpTpQQ6I/database/files/000/dataset_2.dat ; ~/bin/cleanup_output.sh /tmp/tmpTpQQ6I/database/files/000/dataset_2.dat
--------------------- >> end captured stdout << ---------------------- ---------------------------------------------------------------------- Ran 1 test in 227.029s ********************************
Many thanks in advance, Vipin T S
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