On Jul 18, 2012, at 2:55 PM, christopher fletez-brant wrote:
> Hi, just wondering if anyone has any insight into this issue, as it is
> driving me crazy, especially given that the correct list control element is
> selected (hg19).
>From the output you sent, it doesn't look like your tool is actually running,
>just the upload. What does your test XML look like?
--nate
>
> On Sat, Jul 14, 2012 at 8:54 PM, christopher fletez-brant
> <cafletezbr...@gmail.com> wrote:
> Hi Nate,
>
> Thanks for the reply. Error messages are output at the bottom of the
> message. Setup is that the tool has a number of inputs, one of which is
> actually a directory containing reference files. We pass the directory by
> allowing users to select from a menu the genome whose information is held in
> that directory; this is done by means of a *.loc file, whose value in the
> tool config is 'indices_path' below. Run from the Galaxy server, this tool
> works perfectly. However, I think that perhaps it cannot find the directory
> for some reason? I just note that diff reports the values listed as missing,
> but no '+' values indicating what is in their place. Any advice would be
> appreciated.
>
> Thank you,
> Kipper
>
> alaxy.tools.actions.upload_common INFO 2012-07-14 20:39:41,302 tool upload1
> created job id 1
> galaxy.jobs.manager DEBUG 2012-07-14 20:39:47,663 (1) Job assigned to handler
> 'main'
> galaxy.jobs DEBUG 2012-07-14 20:39:52,828 (1) Working directory for job is:
> /home/fake/galaxy-dist/database/job_working_directory/000/1
> galaxy.jobs.handler DEBUG 2012-07-14 20:39:52,829 dispatching job 1 to local
> runner
> galaxy.jobs.handler INFO 2012-07-14 20:39:53,008 (1) Job dispatched
> galaxy.jobs.runners.local DEBUG 2012-07-14 20:39:53,255 executing: python
> /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist
> /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL
>
> 1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat
> galaxy.jobs.runners.local DEBUG 2012-07-14 20:39:54,480 execution finished:
> python /home/fake/galaxy-dist/tools/data_source/upload.py
> /home/fake/galaxy-dist /tmp/tmpeEp5KR/database/tmp/tmpfYngg0
> /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL
> 1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat
> galaxy.jobs DEBUG 2012-07-14 20:39:54,759 job 1 ended
> base.twilltestcase INFO 2012-07-14 20:39:55,782 ## files diff on
> /home/fake/galaxy-dist/test-data/nullseq_output.bed and
> /tmp/tmpeEp5KR/database/tmp/tmpuT588_nullseq_output.bed lines_diff=0, found
> diff = 200
> ---------------------- >> begin tool stdout << -----------------------
>
> ----------------------- >> end tool stdout << ------------------------
>
> ---------------------- >> begin tool stderr << -----------------------
>
> ----------------------- >> end tool stderr << ------------------------
>
> FAIL
>
> ======================================================================
> FAIL: test_tool_000000 (functional.test_toolbox.TestForTool_kmersvm_nullseq)
> Generate Null Sequence ( kmersvm_nullseq ) > Test-1
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/home/fake/galaxy-dist/test/functional/test_toolbox.py", line 171, in
> test_tool
> self.do_it( td, shed_tool_id=shed_tool_id )
> File "/home/fake/galaxy-dist/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 "/home/fake/galaxy-dist/test/base/twilltestcase.py", line 733, in
> verify_dataset_correctness
> raise AssertionError( errmsg )
> AssertionError: History item 1 different than expected, difference (using
> diff):
> --- local_file
> +++ history_data
> @@ -1,100 +1,100 @@
> -chr10 4522044 4522438
> -chr10 5650896 5651310
> -chr10 5772258 5772663
> -chr10 9135867 9136467
> -chr10 9946900 9947273
> -chr10 10793689 10794313
> -chr10 15790023 15790478
> -chr10 16048435 16049028
> -chr10 17620155 17620367
> -chr10 21718404 21719020
> -chr10 22967169 22967533
> -chr10 22999383 22999802
> -chr10 24511845 24512748
> -chr10 24773636 24774006
> -chr10 25975943 25976389
> -chr10 26620032 26620396
> -chr10 26907992 26908408
> -chr10 28309833 28310034
> -chr10 30908407 30909220
> -chr10 31184776 31185151
> -chr10 31191717 31192170
> -chr10 31651098 31651551
> -chr10 32422502 32422880
> -chr10 33316453 33316817
> -chr10 34353700 34354168
> -chr10 34570612 34571026
> -chr10 34853178 34853542
> -chr10 34857471 34857818
> -chr10 34994111 34994269
> -chr10 38557788 38558691
> -chr10 43296854 43297454
> -chr10 44159102 44159480
> -chr10 45208753 45209123
> -chr10 45246414 45246794
> -chr10 46861707 46862080
> -chr10 47021051 47021457
> -chr10 47716908 47717259
>
> -------------------- >> begin captured stdout << ---------------------
>
> Uploaded file: nullseq_test.bed , ftype: bed , extra: {'ftype': 'bed',
> 'value': 'nullseq_test.bed', 'children': []}
> excluded not declared in tool test, will not change default value.
>
> form 'tool_form' contains the following controls ( note the values )
> control 0: <HiddenControl(tool_id=kmersvm_nullseq) (readonly)>
> control 1:
> <HiddenControl(tool_state=80025461010000396439396665663230383837313531356332333061366366376365626135376535623937323433343a37623232356635663730363136373635356635663232336132303330326332303232373237303734356636353732373232323361323032323563323233303265333033323563323232323263323032323732373336353635363432323361323032323563323233313563323232323263323032323636366636633634323233613230323235633232333135633232323232633230323236393665363436393633363537333566373036313734363832323361323032323563323236643664333935633232323232633230323236353738363336633735363436353634323233613230323236653735366336633232326332303232363736333566363537323732323233613230323235633232333032653330333235633232323232633230323236393665373037353734323233613230323233313232376471002e)
> (readonly)>
> control 2: <TextControl(fold=1)>
> control 3: <TextControl(gc_err=0.02)>
> control 4: <TextControl(rpt_err=0.02)>
> control 5: <TextControl(rseed=1)>
> control 6: <SelectControl(input=[*1])>
> control 7: <SelectControl(excluded=[1, *None])>
> control 8: <SelectControl(indices_path=[*mm9, mm8, hg18, hg19])>
> control 9: <SubmitControl(runtool_btn=Execute) (readonly)>
> page_inputs (0) {'rpt_err': ["0'02"], 'rseed': ['1'], 'fold': ['1'],
> 'indices_path': ['hg19'], 'gc_err': ['0.02'], 'input': ['nullseq_test.bed']}
>
> --------------------- >> end captured stdout << ----------------------
> -------------------- >> begin captured logging << --------------------
> galaxy.web.framework: DEBUG: Error: this request returned None from
> get_history(): http://localhost:8368/
> galaxy.web.framework: DEBUG: Error: this request returned None from
> get_history(): http://localhost:8368/
> galaxy.web.framework: DEBUG: Error: this request returned None from
> get_history(): http://localhost:8368/user/logout
> galaxy.web.framework: DEBUG: Error: this request returned None from
> get_history(): http://localhost:8368/
> galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1
> galaxy.jobs.manager: DEBUG: (1) Job assigned to handler 'main'
> galaxy.jobs: DEBUG: (1) Working directory for job is:
> /home/fake/galaxy-dist/database/job_working_directory/000/1
> galaxy.jobs.handler: DEBUG: dispatching job 1 to local runner
> galaxy.jobs.handler: INFO: (1) Job dispatched
> galaxy.jobs.runners.local: DEBUG: executing: python
> /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist
> /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL
>
> 1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat
> galaxy.jobs.runners.local: DEBUG: execution finished: python
> /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist
> /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL
>
> 1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat
> galaxy.jobs: DEBUG: job 1 ended
> base.twilltestcase: INFO: ## files diff on
> /home/fake/galaxy-dist/test-data/nullseq_output.bed and
> /tmp/tmpeEp5KR/database/tmp/tmpuT588_nullseq_output.bed lines_diff=0, found
> diff = 200
> --------------------- >> end captured logging << ---------------------
>
> ----------------------------------------------------------------------
> Ran 1 test in 16.540s
>
> FAILED (failures=1)
>
>
> On Thu, Jul 12, 2012 at 4:20 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> On Jul 5, 2012, at 8:20 PM, christopher fletez-brant wrote:
>
> > Dear Dev List,
> >
> > I am currently writing tests for a tool I am developing and am coming up
> > short in understanding why it's failing. Using the test data, I can
> > generate output identical to the output provided for testing every time I
> > run the tool from my local Galaxy server. However, when I run the tool
> > test through run_functional_tests.sh, it always fails, and apparently fails
> > on every line.
> >
> > Because I consistently see the same output from the Galaxy server-based
> > tool, I'm sure I'm missing something simple and want to look at the
> > test-generated output. Is there a way I can set run_functional_tests to
> > print the generated tool output file in its entirety?
>
> Hi Kipper,
>
> It'd be helpful if you could provide the output of run_functional_tests.sh so
> we could see exactly what was failing.
>
> Thanks,
> --nate
>
> >
> > Thank you,
> > Kipper Fletez-Brant
> > ___________________________________________________________
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>
>
>
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