On 18 April 2014 14:59, Peter Cock <[email protected]> wrote: > On Thu, Apr 17, 2014 at 10:39 PM, Saket Choudhary <[email protected]> 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 ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
