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The PomBase community curation tool
https://curation.pombase.org
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session admin: bug: internal error 109/ various #329

Closed pombase-admin closed 9 years ago

pombase-admin commented 12 years ago

This was definately caused by having the session open in 2 windows

happened when selecting phenotype term curs/45dd89cc4951b51a/annotation/edit/12/phenotype#c=FYPO%3A0001214&s=sensitito+potas

Gene: spt7 Questions? Contact curators ... Internal error DBIx::Class::ResultSet::delete(): DBI Exception: DBD::SQLite::st execute failed: database is locked [for Statement "DELETE FROM cursprop WHERE ( ( ( curs = ? AND type = ? ) AND curs = ? ) )"] at lib/PomCur/Track/StatusStorage.pm line 109 There has been an internal error. The problem has been logged and will be investigated.

Original comment by: ValWood

pombase-admin commented 11 years ago

I still don't know how this could happen except when the ontology update runs at stupid o'clock. I'll keep thinking.

Original comment by: kimrutherford

pombase-admin commented 11 years ago

transferring from https://sourceforge.net/tracker/?func=detail&aid=3561245&group\_id=65526&atid=2525791

I have never seen this before I was adding the MF GO:0016887 to curs e73b6293989d19a9 and got: Internal error DBIx::Class::ResultSet::delete(): DBI Exception: DBD::SQLite::st execute failed: database is locked [for Statement "DELETE FROM cursprop WHERE ( ( ( curs = ? AND type = ? ) AND curs = ? ) )"] at lib/PomCur/Track/StatusStorage.pm line 109

Original comment by: ValWood

pombase-admin commented 11 years ago

Same error here: transferred from https://sourceforge.net/tracker/index.php?func=detail&aid=3564994&group\_id=65526&atid=2525791

I tried to edit a phenotype annotation to add a condition, and it all seemed to go fine until I hit 'add', and got this:

Internal error DBIx::Class::ResultSet::delete(): DBI Exception: DBD::SQLite::st execute failed: database is locked [for Statement "DELETE FROM cursprop WHERE ( ( ( curs = ? AND type = ? ) AND curs = ? ) )"] at lib/PomCur/Track/StatusStorage.pm line 109 Error There has been an internal error. The problem has been logged and will be investigated.

It's http://curation.pombase.org/pombe/curs/982304b134332abd/annotation/process\_alleles/18

Original comment by: ValWood

pombase-admin commented 11 years ago

Original comment by: ValWood

pombase-admin commented 11 years ago

Original comment by: ValWood

pombase-admin commented 11 years ago

I think I've fixed this. Has anyone seen a problem like this recently?

Original comment by: kimrutherford

pombase-admin commented 11 years ago

Original comment by: ValWood

pombase-admin commented 11 years ago

No will open new if we do val

Original comment by: ValWood

pombase-admin commented 10 years ago

I've just fixed a bug that was occasionally causing "database is locked" when running the tests on the server, but not on my laptop. It took a while to track down.

http://en.wikipedia.org/wiki/Heisenbug

I was seeing the bug in the tests but I think it could have happened in the live site too. I'm fairly sure it's fixed now. As usual, let me know if you spot any problems.

Original comment by: kimrutherford