Re: [galaxy-dev] Tool test question
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_00 (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
Re: [galaxy-dev] Tool test question
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_00 (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 @@ -chr104522044 4522438 -chr105650896 5651310 -chr105772258 5772663 -chr109135867 9136467 -chr109946900 9947273 -chr101079368910794313 -chr101579002315790478 -chr101604843516049028 -chr101762015517620367 -chr102171840421719020 -chr102296716922967533 -chr102299938322999802 -chr102451184524512748 -chr102477363624774006 -chr102597594325976389 -chr102662003226620396 -chr102690799226908408 -chr102830983328310034 -chr103090840730909220 -chr103118477631185151 -chr103119171731192170 -chr103165109831651551 -chr103242250232422880 -chr103331645333316817 -chr103435370034354168 -chr103457061234571026 -chr103485317834853542 -chr10
Re: [galaxy-dev] Tool test question
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 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_00 (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 @@ -chr104522044 4522438 -chr105650896 5651310 -chr105772258 5772663 -chr109135867 9136467 -chr109946900 9947273 -chr101079368910794313 -chr10
Re: [galaxy-dev] Tool test question
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_00 (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:
Re: [galaxy-dev] Tool test question
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/ ___ 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/
[galaxy-dev] Tool test question
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? 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/
