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
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
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> >
> >  http://lists.bx.psu.edu/
>
>
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