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

24 Apr 2013

On Tue, Nov 23, 2010 at 2:06 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
...
Hi all,
I'm working on a FASTA filter script, as per this email:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003819.html
Current code here:
http://bitbucket.org/peterjc/galaxy-central/src/c3ac6d7a02f7/
I've added a basic test, but it won't run (see output below). I think
the interesting bit of the error output is this exception: cannot find
value/label "blastp_four_human_vs_rhodopsin.tabular" in list control,
coming from function set_form_control_value in the twill.utils module.
This is something to do with the columns parameter, a multiselect
option referencing the columns in this tabular file. Removing the
validator makes no difference. However, if I change the columns
parameter to a plain text parameter, the test passes:
$ hg diff
diff -r c3ac6d7a02f7 tools/fasta_tools/fasta_filter_by_id.xml

--- a/tools/fasta_tools/fasta_filter_by_id.xml  Tue Nov 23 11:37:35 2010 +0000
+++ b/tools/fasta_tools/fasta_filter_by_id.xml  Tue Nov 23 14:03:31 2010 +0000
@@ -4,9 +4,7 @@
        <inputs>
                <param name="input_fasta" type="data" format="fasta" label="FASTA
file to filter on the identifiers"/>
                <param name="input_tabular" type="data" format="tabular"
label="Tabular file containing FASTA identifiers"/>
-               <param name="columns" type="data_column" data_ref="input_tabular"
multiple="True" numerical="False" label="Column(s) containing FASTA
identifiers" help="Multi-select list - hold the appropriate key while
clicking to select multiple columns">
-                       <validator type="no_options" message="Pick at least one column"/>
-               </param>
+               <param name="columns" type="text" label="Column(s) containing FASTA
identifiers" />
        </inputs>
        <outputs>
                <data name="output_pos" format="fasta" label="With matched ID" />
I've tried searching the provided wrappers for similar examples (column
multi-select from a tabular file). I found filters/uniq.xml (works but uses
a bed file rather than a simple tabular file) and stats/cor.xml (needs R
and rpy which I don't have installed yet) which have tests, and finally
plotting/bar_chart.xml which has no unit tests.
Would someone familiar with the internals of the Galaxy tests and
how they set tool parameters be able to try reproducing this for me?
The branch has all the unit test files required, and there are no new
dependencies needed.
Thank you,
Peter
--
Here is the output (on Linux - other tests tried pass):
$ ./run_functional_tests.sh -id fasta_filter_by_id
...
base.twilltestcase DEBUG 2010-11-23 13:59:53,747 In submit_form,
continuing, but caught exception: cannot find value/label
"blastp_four_human_vs_rhodopsin.tabular" in list control
...
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/7750adf18b1fab953d7cccd0216...

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=800255f5643331613637623836313633636133663739623531386230366564393538633934343264643230303a37623232356635663730363136373635356635663232336132303330326332303232366536353737356636333666366337353664366532323361323032323563323233313563323232323263323032323639366537303735373435663636363936633635323233613230323233313232326332303232366636633634356636333666366337353664366532323361323032323563323233313563323232323263323032323639366537303735373435663734363136323735366336313732323233613230323233323232376471002e)
(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)

    