Configuration of galaxy, metada values are missing
Hello community, I'm new to Galaxy and are currently trying to install a new instance on a debian system. So far I installed postgres and created a user and a database for galaxy. In the universe_wsgi.ini file I did the recommended changes and set this entry: database_connection = postgres:///galaxydb?host=/var/run/postgresql for the connection to postgres. For test purposes I uploaded the test file from http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt. After uploading the file I get a warning that "required metadata values are missing". Auto-detect doesn't help. Since it all works fine with sqlite, I assume an incorrect configuration of the postgres user and|or a missing or false entries in pg_hba.conf or universe_wsgi.ini. Thanks in advance for any suggestions Christian
Christian Dreischer wrote:
Hello community,
I'm new to Galaxy and are currently trying to install a new instance on a debian system. So far I installed postgres and created a user and a database for galaxy. In the universe_wsgi.ini file I did the recommended changes and set this entry: database_connection = postgres:///galaxydb?host=/var/run/postgresql for the connection to postgres. For test purposes I uploaded the test file from http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt. After uploading the file I get a warning that "required metadata values are missing". Auto-detect doesn't help. Since it all works fine with sqlite, I assume an incorrect configuration of the postgres user and|or a missing or false entries in pg_hba.conf or universe_wsgi.ini.
Hi Christian, Are there any messages related to metadata in the Galaxy server output (paster.log or console output)? --nate
Thanks in advance for any suggestions Christian _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Nate Coraor wrote:
Christian Dreischer wrote:
Hello community,
I'm new to Galaxy and are currently trying to install a new instance on a debian system. So far I installed postgres and created a user and a database for galaxy. In the universe_wsgi.ini file I did the recommended changes and set this entry: database_connection = postgres:///galaxydb?host=/var/run/postgresql for the connection to postgres. For test purposes I uploaded the test file from http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt. After uploading the file I get a warning that "required metadata values are missing". Auto-detect doesn't help. Since it all works fine with sqlite, I assume an incorrect configuration of the postgres user and|or a missing or false entries in pg_hba.conf or universe_wsgi.ini.
Hi Christian,
Are there any messages related to metadata in the Galaxy server output (paster.log or console output)?
--nate
Thanks in advance for any suggestions Christian _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Nate,
these are the entries concerning metadata in the paster.log: set_metadata.sh ./database/files ./database/tmp /extern1_512gb/cdreischer/galaxy-dist datatypes_conf.xml None database/tmp/metadata_in_HistoryDatasetAssociation_4_7q40pL,database/tmp/metadata_kwds_HistoryDatasetAssociation_4_sQy7Sw,database/tmp/metadata_out_HistoryDatasetAssociation_4_4PrDHi,database/tmp/metadata_results_HistoryDatasetAssociation_4_HhKfrH,,database/tmp/metadata_override_HistoryDatasetAssociation_4_l9bvY5 galaxy.jobs.runners.local DEBUG 2011-02-16 16:19:56,486 execution finished: /extern1_512gb/cdreischer/galaxy-dist/set_metadata.sh ./database/files ./database/tmp /extern1_512gb/cdreischer/galaxy-dist datatypes_conf.xml None database/tmp/metadata_in_HistoryDatasetAssociation_4_7q40pL,database/tmp/metadata_kwds_HistoryDatasetAssociation_4_sQy7Sw,database/tmp/metadata_out_HistoryDatasetAssociation_4_4PrDHi,database/tmp/metadata_results_HistoryDatasetAssociation_4_HhKfrH,,database/tmp/metadata_override_HistoryDatasetAssociation_4_l9bvY5 galaxy.datatypes.metadata DEBUG 2011-02-16 16:19:56,931 loading metadata from file for: HistoryDatasetAssociation 4 galaxy.jobs DEBUG 2011-02-16 16:19:57,019 job 8 ended galaxy.datatypes.metadata DEBUG 2011-02-16 16:19:57,020 Cleaning up external metadata files I also set "set_metadata_externally" and "retry_metadata_internally" to True, unfortunately without any change. -Christian
Christian, This is an issue with postgres9 and our JSONType custom datatype. I have a ticket open that you can follow if you'd like to be notified of the resolution. Here's the link: https://bitbucket.org/galaxy/galaxy-central/issue/434/error-listing-and-runn... -Dannon On Feb 16, 2011, at 10:54 AM, Christian Dreischer wrote:
Nate Coraor wrote:
Christian Dreischer wrote:
Hello community,
I'm new to Galaxy and are currently trying to install a new instance on a debian system. So far I installed postgres and created a user and a database for galaxy. In the universe_wsgi.ini file I did the recommended changes and set this entry: database_connection = postgres:///galaxydb?host=/var/run/postgresql for the connection to postgres. For test purposes I uploaded the test file from http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt. After uploading the file I get a warning that "required metadata values are missing". Auto-detect doesn't help. Since it all works fine with sqlite, I assume an incorrect configuration of the postgres user and|or a missing or false entries in pg_hba.conf or universe_wsgi.ini.
Hi Christian,
Are there any messages related to metadata in the Galaxy server output (paster.log or console output)?
--nate
Thanks in advance for any suggestions Christian _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Nate,
these are the entries concerning metadata in the paster.log:
set_metadata.sh ./database/files ./database/tmp /extern1_512gb/cdreischer/galaxy-dist datatypes_conf.xml None database/tmp/metadata_in_HistoryDatasetAssociation_4_7q40pL,database/tmp/metadata_kwds_HistoryDatasetAssociation_4_sQy7Sw,database/tmp/metadata_out_HistoryDatasetAssociation_4_4PrDHi,database/tmp/metadata_results_HistoryDatasetAssociation_4_HhKfrH,,database/tmp/metadata_override_HistoryDatasetAssociation_4_l9bvY5 galaxy.jobs.runners.local DEBUG 2011-02-16 16:19:56,486 execution finished: /extern1_512gb/cdreischer/galaxy-dist/set_metadata.sh ./database/files ./database/tmp /extern1_512gb/cdreischer/galaxy-dist datatypes_conf.xml None database/tmp/metadata_in_HistoryDatasetAssociation_4_7q40pL,database/tmp/metadata_kwds_HistoryDatasetAssociation_4_sQy7Sw,database/tmp/metadata_out_HistoryDatasetAssociation_4_4PrDHi,database/tmp/metadata_results_HistoryDatasetAssociation_4_HhKfrH,,database/tmp/metadata_override_HistoryDatasetAssociation_4_l9bvY5 galaxy.datatypes.metadata DEBUG 2011-02-16 16:19:56,931 loading metadata from file for: HistoryDatasetAssociation 4 galaxy.jobs DEBUG 2011-02-16 16:19:57,019 job 8 ended galaxy.datatypes.metadata DEBUG 2011-02-16 16:19:57,020 Cleaning up external metadata files
I also set "set_metadata_externally" and "retry_metadata_internally" to True, unfortunately without any change.
-Christian _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Dannon, two days of going crazy have an end. It works, tanks! -Christian Dannon Baker wrote:
Christian,
This is an issue with postgres9 and our JSONType custom datatype. I have a ticket open that you can follow if you'd like to be notified of the resolution. Here's the link: https://bitbucket.org/galaxy/galaxy-central/issue/434/error-listing-and-runn...
-Dannon
On Feb 16, 2011, at 10:54 AM, Christian Dreischer wrote:
Nate Coraor wrote:
Christian Dreischer wrote:
Hello community,
I'm new to Galaxy and are currently trying to install a new instance on a debian system. So far I installed postgres and created a user and a database for galaxy. In the universe_wsgi.ini file I did the recommended changes and set this entry: database_connection = postgres:///galaxydb?host=/var/run/postgresql for the connection to postgres. For test purposes I uploaded the test file from http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt. After uploading the file I get a warning that "required metadata values are missing". Auto-detect doesn't help. Since it all works fine with sqlite, I assume an incorrect configuration of the postgres user and|or a missing or false entries in pg_hba.conf or universe_wsgi.ini.
Hi Christian,
Are there any messages related to metadata in the Galaxy server output (paster.log or console output)?
--nate
Thanks in advance for any suggestions Christian _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Nate,
these are the entries concerning metadata in the paster.log:
set_metadata.sh ./database/files ./database/tmp /extern1_512gb/cdreischer/galaxy-dist datatypes_conf.xml None database/tmp/metadata_in_HistoryDatasetAssociation_4_7q40pL,database/tmp/metadata_kwds_HistoryDatasetAssociation_4_sQy7Sw,database/tmp/metadata_out_HistoryDatasetAssociation_4_4PrDHi,database/tmp/metadata_results_HistoryDatasetAssociation_4_HhKfrH,,database/tmp/metadata_override_HistoryDatasetAssociation_4_l9bvY5 galaxy.jobs.runners.local DEBUG 2011-02-16 16:19:56,486 execution finished: /extern1_512gb/cdreischer/galaxy-dist/set_metadata.sh ./database/files ./database/tmp /extern1_512gb/cdreischer/galaxy-dist datatypes_conf.xml None database/tmp/metadata_in_HistoryDatasetAssociation_4_7q40pL,database/tmp/metadata_kwds_HistoryDatasetAssociation_4_sQy7Sw,database/tmp/metadata_out_HistoryDatasetAssociation_4_4PrDHi,database/tmp/metadata_results_HistoryDatasetAssociation_4_HhKfrH,,database/tmp/metadata_override_HistoryDatasetAssociation_4_l9bvY5 galaxy.datatypes.metadata DEBUG 2011-02-16 16:19:56,931 loading metadata from file for: HistoryDatasetAssociation 4 galaxy.jobs DEBUG 2011-02-16 16:19:57,019 job 8 ended galaxy.datatypes.metadata DEBUG 2011-02-16 16:19:57,020 Cleaning up external metadata files
I also set "set_metadata_externally" and "retry_metadata_internally" to True, unfortunately without any change.
-Christian _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Christian Dreischer -
Dannon Baker -
Nate Coraor