i've also been getting metadata errors (below) for several weeks, but it works with the set_metadata_externally option (in the universe config file) set to False. for large files, it could take many minutes for your job server to check the metadata, and no new jobs will be run or completed jobs picked up during this delay, but at least it works reliably.

fyi, the time these errors appeared roughly coincided with when i moved the data files (database/) to a different disk than the galaxy code. i don't know for sure if that's the issue or not, but may be a clue; i will experiment when i get a chance.

galaxy.datatypes.metadata DEBUG 2011-11-28 12:39:01,129 setting metadata externally failed for Hist

oryDatasetAssociation 449: External set_meta() not called

galaxy.jobs DEBUG 2011-11-28 12:39:01,221 job 355 ended

galaxy.datatypes.metadata DEBUG 2011-11-28 12:39:01,357 Cleaning up external metadata files

galaxy.datatypes.metadata DEBUG 2011-11-28 12:39:01,496 Failed to cleanup MetadataTempFile temp fil

es from ../../../groupdirs/Galaxy/dev/database/tmp/metadata_out_HistoryDatasetAssociation_449_sB_cT

B: No JSON object could be decoded: line 1 column 0 (char 0)

On Wed, Nov 16, 2011 at 3:00 AM, Mattias de Hollander <m.dehollander@nioo.knaw.nl> wrote:

Hello,

I just noticed I get metadata errors in the paster.log file. Can someone tell me what they are and if they are related to above problem?

galaxy.jobs.runners.drmaa DEBUG 2011-11-16 11:55:28,037 (840/588) state change: job finished normally
galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,231 setting metadata externally failed for HistoryDatasetAssociation 1680: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1680_N7JVtq'
galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,325 setting metadata externally failed for HistoryDatasetAssociation 1679: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1679_oTzTG_'
galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,634 setting metadata externally failed for HistoryDatasetAssociation 1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1678_MgW15e'
galaxy.jobs DEBUG 2011-11-16 11:55:29,103 job 840 ended
galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,103 Cleaning up external metadata files
galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup MetadataTempFile temp files from ../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8'
galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup external metadata file (filename_in) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1678_MgW15e'
galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup external metadata file (filename_out) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8'
galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,153 Failed to cleanup external metadata file (filename_kwds) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_kwds_HistoryDatasetAssociation_1678_3SDMLo'

And of course, how to solve it :)

Any help is appreciated.

Mattias

-- 
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands

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