From: <sco...@us...> - 2013-07-26 17:24:10
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Revision: 25290 http://sourceforge.net/p/gmod/svn/25290 Author: scottcain Date: 2013-07-26 17:23:56 +0000 (Fri, 26 Jul 2013) Log Message: ----------- added a warning message for the GFF bulk loader if part_of isn't found and a minor doc fix for UPGRADE.txt. Modified Paths: -------------- schema/trunk/chado/Changes schema/trunk/chado/UPGRADE.txt schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm Modified: schema/trunk/chado/Changes =================================================================== --- schema/trunk/chado/Changes 2013-07-16 17:49:23 UTC (rev 25289) +++ schema/trunk/chado/Changes 2013-07-26 17:23:56 UTC (rev 25290) @@ -1,4 +1,5 @@ Version 1.24 Mon Mar 4 17:18:47 EST 2013 +* Added a warning message for the GFF bulk loader if part_of isn't found. * Fixed ncbi_taxonomy loader to load entire NCBI taxonomy (Naama) * Patched gmod_bulk_load_gff3.pl (provided by Alexie P) to fix the "orgainism from data" option. Modified: schema/trunk/chado/UPGRADE.txt =================================================================== --- schema/trunk/chado/UPGRADE.txt 2013-07-16 17:49:23 UTC (rev 25289) +++ schema/trunk/chado/UPGRADE.txt 2013-07-26 17:23:56 UTC (rev 25290) @@ -16,7 +16,7 @@ perl Makefile.PL make - make install + sudo make install and then, rather than doing the next step (make load_schema) which would wipe out the current database, do Modified: schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm =================================================================== --- schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm 2013-07-16 17:49:23 UTC (rev 25289) +++ schema/trunk/chado/lib/Bio/GMOD/DB/Adapter.pm 2013-07-26 17:23:56 UTC (rev 25290) @@ -1506,6 +1506,9 @@ $sth->execute; ($part_of) = $sth->fetchrow_array(); + warn "\n\nWARNING:\nUnable to find a 'part_of' term in the relationship ontology;\nIt's absense indicates that there is something really wrong with the database.\nConsider stopping and checking the state of your cvterm table.\n\n\n"; + + $sth = $self->dbh->prepare( "select cvterm_id from cvterm where name = 'derives_from' and cv_id in ( SELECT cv_id FROM cv WHERE name='relationship' @@ -3432,6 +3435,7 @@ $tuniquename = $target_id; $name = $target_id; } +###FIXME: put my $tuniquename = $target_id.'_'.$self->nextfeature; in else here $self->print_f($self->nextfeature, $self->organism_id(), $name,$tuniquename , $type, '\N','\N'); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |