Uploading binary files to a library
Hi, not sure if this is a bug or a problem with our local install. I am having trouble uploading binary files to a library. The error given is "Unable to finish job, tool error", the full traceback is below. I have added a few extra binary datatypes to the binary.py file but this seems to be affecting all binary types. I have been able to upload these files in the past so I think the problem has been caused by a recent update. Thanks in advance for your help Shaun Webb galaxy.jobs.runners.local ERROR 2010-01-21 15:05:23,968 Job wrapper finish method failed Traceback (most recent call last): File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122, in run_job job_wrapper.finish( stdout, stderr ) File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 558, in finish dataset.set_peek() File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 537, in set_peek return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/datatypes/binary.py", line 38, in set_peek export_url = "/history_add_to?" + urlencode( {'history_id':dataset.history_id,'ext':'ab1','name':'ab1 sequence','info':'Sequence file','dbkey':dataset.dbkey} ) AttributeError: 'LibraryDatasetDatasetAssociation' object has no attribute 'history_id' 129.215.15.86 - - [21/Jan/2010:15:05:24 +0100] "POST /library_common/library_item_updates HTTP/1.1" 200 - "http://bifx3.bio.ed.ac.uk:8083/library_common/browse_library?cntrller=library_admin&id=2234cb1fd1df4331&created_ldda_ids=68" "Mozilla/5.0 (X11; U; Linux x86_64; en-GB; rv:1.9.0.17) Gecko/2010010604 Ubuntu/8.04 (hardy) Firefox/3.0.17" -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
On 1/21/10 4:13 PM, "SHAUN WEBB" <swebb1@staffmail.ed.ac.uk> wrote:
Hi, not sure if this is a bug or a problem with our local install. I am having trouble uploading binary files to a library. The error given is "Unable to finish job, tool error", the full traceback is below. I have added a few extra binary datatypes to the binary.py file but this seems to be affecting all binary types. I have been able to upload these files in the past so I think the problem has been caused by a recent update.
Hi We had a similar very bizarre problem: The uploads only worked, if the files were owned by the user 'galaxy'. As soon as they were owned by a different user (even if they were readable by the everybody) it didn't work. We don't have an explanation. It might just be a local curiosity, but give it a try. Hans
Thanks in advance for your help Shaun Webb
galaxy.jobs.runners.local ERROR 2010-01-21 15:05:23,968 Job wrapper finish method failed Traceback (most recent call last): File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122, in run_job job_wrapper.finish( stdout, stderr ) File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 558, in finish dataset.set_peek() File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 537, in set_peek return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/datatypes/binary.py", line 38, in set_peek export_url = "/history_add_to?" + urlencode( {'history_id':dataset.history_id,'ext':'ab1','name':'ab1 sequence','info':'Sequence file','dbkey':dataset.dbkey} ) AttributeError: 'LibraryDatasetDatasetAssociation' object has no attribute 'history_id' 129.215.15.86 - - [21/Jan/2010:15:05:24 +0100] "POST /library_common/library_item_updates HTTP/1.1" 200 - "http://bifx3.bio.ed.ac.uk:8083/library_common/browse_library?cntrller=librar... _admin&id=2234cb1fd1df4331&created_ldda_ids=68" "Mozilla/5.0 (X11; U; Linux x86_64; en-GB; rv:1.9.0.17) Gecko/2010010604 Ubuntu/8.04 (hardy) Firefox/3.0.17"
Hello Shaun, Thanks for pointing this out. The fix for this is in change set 3296:30cd8d9f8ac9 which is now available in the distribution. On Jan 21, 2010, at 10:13 AM, SHAUN WEBB wrote:
Hi, not sure if this is a bug or a problem with our local install. I am having trouble uploading binary files to a library. The error given is "Unable to finish job, tool error", the full traceback is below. I have added a few extra binary datatypes to the binary.py file but this seems to be affecting all binary types. I have been able to upload these files in the past so I think the problem has been caused by a recent update.
Thanks in advance for your help Shaun Webb
galaxy.jobs.runners.local ERROR 2010-01-21 15:05:23,968 Job wrapper finish method failed Traceback (most recent call last): File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/jobs/runners/ local.py", line 122, in run_job job_wrapper.finish( stdout, stderr ) File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 558, in finish dataset.set_peek() File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 537, in set_peek return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) File "/home/swebb/galaxy/galaxy_dist/lib/galaxy/datatypes/ binary.py", line 38, in set_peek export_url = "/history_add_to?" + urlencode ( {'history_id':dataset.history_id,'ext':'ab1','name':'ab1 sequence','info':'Sequence file','dbkey':dataset.dbkey} ) AttributeError: 'LibraryDatasetDatasetAssociation' object has no attribute 'history_id' 129.215.15.86 - - [21/Jan/2010:15:05:24 +0100] "POST /library_common/ library_item_updates HTTP/1.1" 200 - "http://bifx3.bio.ed.ac.uk:8083/library_common/browse_library?cntrller=library_admin&id=2234cb1fd1df4331&created_ldda_ids=68 " "Mozilla/5.0 (X11; U; Linux x86_64; en-GB; rv:1.9.0.17) Gecko/ 2010010604 Ubuntu/8.04 (hardy) Firefox/3.0.17"
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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participants (3)
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Greg Von Kuster -
Hotz, Hans-Rudolf -
SHAUN WEBB