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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