On Jul 18, 2012, at 5:02 PM, christopher fletez-brant wrote:

> Hi Nate,
> 
> The test XML is:
> 
>    <tests>
>     <test>
>       <param name="input" value="nullseq_test.bed" ftype="bed" />
>       <param name="fold" value="1" />
>       <param name="gc_err" value="0.02" />
>       <param name="rpt_err" value="0'02" />
>       <param name="rseed" value="1" />
>       <param name="indices_path"  value="hg19" />
>       <output name="output" file="nullseq_output.bed" />
>     </test>
>   </tests>
> 
> And the XML for the problematic parameter, indices_path, is:
> 
>     <param name="indices_path" type="select" label="Available Datasets">
>       <options from_file="nullseq_indices.loc">
>         <column name="dbkey" index="0"/>
>         <column name="value" index="0"/>
>         <column name="name" index="1"/>
>         <column name="path" index="2"/>
>         <!--filter type="data_meta" ref="input" key="dbkey" column="0" /-->
>       </options>
>      </param>


Hi,

Sorry I didn't get back to you.  If you set your upload's dbkey to "hg19", e.g.:

      <param name="input" value="nullseq_test.bed" ftype="bed" dbkey="hg19" />

I believe it'll fix the issue.

--nate

> 
> Thanks for the reply!
> On Wed, Jul 18, 2012 at 3:55 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> 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
> > > ___________________________________________________________
> > > Please keep all replies on the list by using "reply all"
> > > in your mail client.  To manage your subscriptions to this
> > > and other Galaxy lists, please use the interface at:
> > >
> > >  http://lists.bx.psu.edu/
> >
> >
> >
> 
> 


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