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UCLOrengoGroup / genome3d-openapi-client

Tool to interact with the Genome3D API
GNU General Public License v3.0
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Error while uploading the xml containing SUPERFAMILY domain annotation #6

Closed arunpandu closed 6 years ago

arunpandu commented 6 years ago

Tried to upload the xml file using the below command ./genome3d-api -o updateDomainPrediction -u V5QRX7 -r SUPERFAMILY --xmlfile=../tuberculosis/V5QRX7.xml

Resulted in the following output and error message

Tue Jul 24 08:29:41 2018 INFO | APP.OPENAPI_SPEC http://daily.genome3d.eu/api/openapi.json Tue Jul 24 08:29:41 2018 INFO | APP.MODE DAILY Tue Jul 24 08:29:41 2018 INFO | REQUEST.OPERATION updateDomainPrediction Tue Jul 24 08:29:41 2018 INFO | REQUEST.DATA {"uniprot_acc":"V5QRX7","xmlfile":[{"file":"../tuberculosis/V5QRX7.xml"}],"operation":"updateDomainPrediction","resource_id":"SUPERFAMILY"} Tue Jul 24 08:29:41 2018 INFO | REQUEST.URL http://daily.genome3d.eu/api/v1/uniprot/V5QRX7/domain_prediction/SUPERFAMILY [400] ERROR: Bad Request ({"message":"DBIx::Class::Storage::DBI::_dbh_execute(): DBI Exception: DBD::Pg::st execute failed: ERROR: permission denied for relation annotation [for Statement \"INSERT INTO annotation ( classification_node, confidence, domain_number, resource, ty...)

The input xml used is the same that was tried in issue 4 https://github.com/UCLOrengoGroup/genome3d-openapi-client/issues/4

sillitoe commented 6 years ago

Thanks - I can reproduce this error.

Worked after a server restart yesterday - I think this has to be how the "daily" database is being refreshed (which happens daily at midnight).

Sorting now

sillitoe commented 6 years ago

As suspected, this did come down to the way the "daily" sandbox was being created.

Looks like dropping/creating a schema disrupts permissions for existing database connections (which does kind of makes sense).

Workaround involved leaving the schema in place and just dropping tables/sequences.

Tested for "daily" and "head" (before and after running the daily backup script).

More detail here:

https://dba.stackexchange.com/questions/213085/permission-errors-on-insert-after-schema-drop-create-pg-9-0-23/213105#213105