Re: [galaxy-dev] Puzzling test failure with data_column parameter

On Tue, Nov 23, 2010 at 2:06 PM, Peter Cock <p.j.a.cock(a)googlemail.com&gt; wrote: Hello again, See http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003867.html for the original email and full log. The most interesting part of the logging was the caught exception (and the tool being tested was never run): cannot find value/label "blastp_four_human_vs_rhodopsin.tabular" in list control I don't recall if/how this was resolved, I've since deprecated this tool itself - replacing it with a more general version: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id However, I've just hit what seems to be a very similar issue while trying to add what should be a simple unit test to my sequence renaming script, seq_rename.py / seq_rename.py which is in the main Tool Shed here: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename Here's the current latest code (not yet pushed to the public Tool Shed), which is now on the test Tool Shed and on my bitbucket branch: http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://bitbucket.org/peterjc/galaxy-central/src/7750adf18b1fab953d7cccd0... Here's the test itself, <tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="1" /> <param name="new_column" value="2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> </tests> Now I am quite puzzled by what happens running the test, the full output is at the end of this email. Strangely the tool itself is never actually run, and instead Galaxy compares one of the input files to the expected output file and they don't match. As in my email from 2010, this is most interesting line in the output, just after the two input files are 'uploaded' to the current history: base.twilltestcase DEBUG 2013-04-22 18:20:18,061 In submit_form, continuing, but caught exception: cannot find value/label "four_human_proteins.rename.tabular" in list control It would appear that the tabular file has not been added to the potential valid datasets available to the $input_tabular parameter? This test should have been attempted on the Test Tool Shed last night, but there is nothing to show for it - something that has happened in other corner cases - I'll flag this on the other thread. Likely this is due to the exception within the test framework itself. Regards, Peter -- $ ./run_functional_tests.sh -id seq_rename ... functional_tests.py INFO 2013-04-22 18:20:02,192 Functional tests will be run against localhost:9176 nose.plugins.manager DEBUG 2013-04-22 18:20:02,212 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy nose.plugins.manager DEBUG 2013-04-22 18:20:02,222 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTestDiff nose.plugins.manager DEBUG 2013-04-22 18:20:02,224 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML Rename sequences ( seq_rename ) > Test-1 ... galaxy.web.framework DEBUG 2013-04-22 18:20:03,447 This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework DEBUG 2013-04-22 18:20:03,447 This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework DEBUG 2013-04-22 18:20:03,493 This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework DEBUG 2013-04-22 18:20:03,494 This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework DEBUG 2013-04-22 18:20:03,659 This request returned None from get_history(): http://localhost:9176/user/logout galaxy.web.framework DEBUG 2013-04-22 18:20:03,659 This request returned None from get_history(): http://localhost:9176/user/logout galaxy.web.framework DEBUG 2013-04-22 18:20:03,700 This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework DEBUG 2013-04-22 18:20:03,700 This request returned None from get_history(): http://localhost:9176/ galaxy.tools.actions.upload_common INFO 2013-04-22 18:20:06,350 tool upload1 created job id 1 galaxy.jobs DEBUG 2013-04-22 18:20:06,649 (1) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/1 galaxy.jobs.handler DEBUG 2013-04-22 18:20:06,713 (1) Dispatching to local runner galaxy.jobs DEBUG 2013-04-22 18:20:07,088 (1) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-04-22 18:20:07,195 (1) Job dispatched galaxy.jobs.runners.local DEBUG 2013-04-22 18:20:07,825 (1) executing: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpYyosAY/database/tmp/tmpIPAfMX /tmp/tmpYyosAY/database/tmp/tmpd7kJZZ 1:/mnt/galaxy/galaxy-central/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpYyosAY/database/files/000/dataset_1.dat galaxy.jobs DEBUG 2013-04-22 18:20:07,895 (1) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-04-22 18:20:09,254 execution finished: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpYyosAY/database/tmp/tmpIPAfMX /tmp/tmpYyosAY/database/tmp/tmpd7kJZZ 1:/mnt/galaxy/galaxy-central/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpYyosAY/database/files/000/dataset_1.dat galaxy.jobs DEBUG 2013-04-22 18:20:09,327 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-04-22 18:20:09,826 job 1 ended galaxy.tools.actions.upload_common INFO 2013-04-22 18:20:11,435 tool upload1 created job id 2 galaxy.jobs DEBUG 2013-04-22 18:20:11,774 (2) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/2 galaxy.jobs.handler DEBUG 2013-04-22 18:20:11,839 (2) Dispatching to local runner galaxy.jobs DEBUG 2013-04-22 18:20:12,221 (2) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-04-22 18:20:12,328 (2) Job dispatched galaxy.jobs.runners.local DEBUG 2013-04-22 18:20:12,893 (2) executing: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpYyosAY/database/tmp/tmpIPAfMX /tmp/tmpYyosAY/database/tmp/tmpeA1apX 2:/mnt/galaxy/galaxy-central/database/job_working_directory/000/2/dataset_2_files:/tmp/tmpYyosAY/database/files/000/dataset_2.dat galaxy.jobs DEBUG 2013-04-22 18:20:12,968 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-04-22 18:20:14,497 execution finished: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpYyosAY/database/tmp/tmpIPAfMX /tmp/tmpYyosAY/database/tmp/tmpeA1apX 2:/mnt/galaxy/galaxy-central/database/job_working_directory/000/2/dataset_2_files:/tmp/tmpYyosAY/database/files/000/dataset_2.dat galaxy.jobs DEBUG 2013-04-22 18:20:14,600 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-04-22 18:20:17,018 job 2 ended base.twilltestcase DEBUG 2013-04-22 18:20:18,061 In submit_form, continuing, but caught exception: cannot find value/label "four_human_proteins.rename.tabular" in list control base.twilltestcase INFO 2013-04-22 18:20:18,690 ## files diff on /mnt/galaxy/galaxy-central/test-data/four_human_proteins.rename.fasta and /tmp/tmpYyosAY/database/tmp/tmpAVYLNlfour_human_proteins.rename.fasta lines_diff=0, found diff = 13 ---------------------- >> begin tool stdout << ----------------------- ----------------------- >> end tool stdout << ------------------------ ---------------------- >> begin tool stderr << ----------------------- ----------------------- >> end tool stderr << ------------------------ FAIL ====================================================================== FAIL: Rename sequences ( seq_rename ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/mnt/galaxy/galaxy-central/test/base/twilltestcase.py", line 849, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 2 different than expected, difference (using diff): ( /mnt/galaxy/galaxy-central/test-data/four_human_proteins.rename.fasta v. /tmp/tmpYyosAY/database/tmp/tmpAVYLNlfour_human_proteins.rename.fasta ) --- local_file +++ history_data @@ -1,8 +1,5 @@ ->Q9BS26 Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 -MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL ->Q9NSY1 BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 -MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEGGFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQVSYFAFKFAKKDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDTIGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPEILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQQQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQYQQAFFQQQMLAQHQPSQQQASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSVADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEELLDREFDLLRSNRLEERASSDKNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKDQRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPENLGHRPLLMDSEDEEEEEKHSSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSAQLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTKAPFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFDEITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARRHKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLSWHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQSQQSQPVELDPFGAAPFPSKQ ->P06213 Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 -MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIGPLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEMEFEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSNPS ->P08100 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 -MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA +#FASTA ID +sp|Q9BS26|ERP44_HUMAN Q9BS26 +sp|Q9NSY1|BMP2K_HUMAN Q9NSY1 +sp|P06213|INSR_HUMAN P06213 +sp|P08100|OPSD_HUMAN P08100 -------------------- >> begin captured stdout << --------------------- Uploaded file: four_human_proteins.fasta , ftype: fasta , extra: {'ftype': 'fasta', 'value': 'four_human_proteins.fasta', 'children': []} Uploaded file: four_human_proteins.rename.tabular , ftype: tabular , extra: {'ftype': 'tabular', 'value': 'four_human_proteins.rename.tabular', 'children': []} form 'tool_form' contains the following controls ( note the values ) control 0: <HiddenControl(refresh=refresh) (readonly)> control 1: <HiddenControl(tool_id=seq_rename) (readonly)> control 2: <HiddenControl(tool_state=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) (readonly)> control 3: <SelectControl(input_file=[*1])> control 4: <SelectControl(input_tabular=[1, *2])> control 5: <SelectControl(old_column=[*1, 2])> control 6: <SelectControl(new_column=[*1, 2])> control 7: <SubmitControl(runtool_btn=Execute) (readonly)> page_inputs (0) {'new_column': ['2'], 'input_tabular': ['four_human_proteins.rename.tabular'], 'old_column': ['1'], 'input_file': ['four_human_proteins.fasta']} --------------------- >> end captured stdout << ---------------------- -------------------- >> begin captured logging << -------------------- galaxy.web.framework: DEBUG: This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework: DEBUG: This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework: DEBUG: This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework: DEBUG: This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework: DEBUG: This request returned None from get_history(): http://localhost:9176/user/logout galaxy.web.framework: DEBUG: This request returned None from get_history(): http://localhost:9176/user/logout galaxy.web.framework: DEBUG: This request returned None from get_history(): http://localhost:9176/ galaxy.web.framework: DEBUG: This request returned None from get_history(): http://localhost:9176/ galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 galaxy.jobs: DEBUG: (1) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/1 galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///) galaxy.jobs.handler: INFO: (1) Job dispatched galaxy.jobs.runners.local: DEBUG: (1) executing: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpYyosAY/database/tmp/tmpIPAfMX /tmp/tmpYyosAY/database/tmp/tmpd7kJZZ 1:/mnt/galaxy/galaxy-central/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpYyosAY/database/files/000/dataset_1.dat galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local: DEBUG: execution finished: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpYyosAY/database/tmp/tmpIPAfMX /tmp/tmpYyosAY/database/tmp/tmpd7kJZZ 1:/mnt/galaxy/galaxy-central/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpYyosAY/database/files/000/dataset_1.dat galaxy.jobs: DEBUG: Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs: DEBUG: job 1 ended galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2 galaxy.jobs: DEBUG: (2) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/2 galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) galaxy.jobs.handler: INFO: (2) Job dispatched galaxy.jobs.runners.local: DEBUG: (2) executing: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpYyosAY/database/tmp/tmpIPAfMX /tmp/tmpYyosAY/database/tmp/tmpeA1apX 2:/mnt/galaxy/galaxy-central/database/job_working_directory/000/2/dataset_2_files:/tmp/tmpYyosAY/database/files/000/dataset_2.dat galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local: DEBUG: execution finished: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpYyosAY/database/tmp/tmpIPAfMX /tmp/tmpYyosAY/database/tmp/tmpeA1apX 2:/mnt/galaxy/galaxy-central/database/job_working_directory/000/2/dataset_2_files:/tmp/tmpYyosAY/database/files/000/dataset_2.dat galaxy.jobs: DEBUG: Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs: DEBUG: job 2 ended base.twilltestcase: DEBUG: In submit_form, continuing, but caught exception: cannot find value/label "four_human_proteins.rename.tabular" in list control base.twilltestcase: INFO: ## files diff on /mnt/galaxy/galaxy-central/test-data/four_human_proteins.rename.fasta and /tmp/tmpYyosAY/database/tmp/tmpAVYLNlfour_human_proteins.rename.fasta lines_diff=0, found diff = 13 --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 1 test in 15.564s FAILED (failures=1)