On 18 April 2014 14:59, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Thu, Apr 17, 2014 at 10:39 PM, Saket Choudhary <sake...@gmail.com> wrote:
>> John pointed out that the error its the upload of the test file itself
>> which is failing. I can  locate the input files
>> in test-data/
>>
>> https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
>>
>> Any clues as to where exactly am I going wrong?
>
> Very strange. Adding "ls test-data" to the TravisCI list worked,
> and showed the input file condel_input.tabular was present:
> https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff194404cae05
> https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt
> https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
>
> How about replacing that with "ls -l test-data/condel_input.tabular"
> to verify the ownership and permissions (although if that was
> the upload problem, Galaxy could give a clearer error).
>

Thanks, tried it: https://travis-ci.org/saketkc/galaxy_tools/jobs/23270454#L530

This happens irrespective of using ftype. and the plce where ERROR
occurs is this:

galaxy.jobs.runners.local DEBUG 2014-04-17 21:25:53,808 execution
finished: GALAXY_SLOTS="1"; export GALAXY_SLOTS; python
/home/travis/build/saketkc/galaxy_tools/galaxy-central-master/tools/data_source/upload.py
/home/travis/build/saketkc/galaxy_tools/galaxy-central-master
/tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpvroRLA
/tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpv9tzOU
1:/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/dataset_1_files:/tmp/tmpNenHnc/tmp83XrmN/database/files/000/dataset_1.dat
galaxy.datatypes.metadata INFO 2014-04-17 21:25:55,902
/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_in_HistoryDatasetAssociation_1_bVl30h,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_kwds_HistoryDatasetAssociation_1_jiQBR3,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_out_HistoryDatasetAssociation_1_aoG7yJ,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_results_HistoryDatasetAssociation_1_JM1wqM,,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_override_HistoryDatasetAssociation_1_ZUFWdn
galaxy.jobs.runners DEBUG 2014-04-17 21:25:55,903 executing external
set_meta script for job 1:
/home/travis/build/saketkc/galaxy_tools/galaxy-central-master/set_metadata.sh
/tmp/tmpNenHnc/tmp83XrmN/database/files
/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1 .
/tmp/tmpNenHnc/functional_tests_wsgi.ini
/tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpvroRLA
/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/galaxy.json
/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_in_HistoryDatasetAssociation_1_bVl30h,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_kwds_HistoryDatasetAssociation_1_jiQBR3,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_out_HistoryDatasetAssociation_1_aoG7yJ,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_results_HistoryDatasetAssociation_1_JM1wqM,,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_override_HistoryDatasetAssociation_1_ZUFWdn
galaxy.jobs.runners DEBUG 2014-04-17 21:25:57,620 execution of
external set_meta for job 1 finished
galaxy.jobs DEBUG 2014-04-17 21:25:57,727 setting dataset state to ERROR



so my dataset state is set to ERROR, essentially upload failed. But
why, is what it doesn't tell me.

> Likely unrelated, but I don't think I have bothered to set the ftype
> when uploading tabular files / using them as test inputs. Did you
> ever try this without the ftype?
>
> Peter

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