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
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:
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 nate@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:
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).
On Sat, Jul 14, 2012 at 8:54 PM, christopher fletez-brant < cafletezbrant@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 nate@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:
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 cafletezbrant@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 nate@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:
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 nate@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 <
cafletezbrant@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 nate@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:
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 nate@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 cafletezbrant@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 nate@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:
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christopher fletez-brant -
Nate Coraor