[Gmod-schema-cmts] SF.net SVN: gmod:[25290] schema/trunk/chado

[<sco...@us...>]

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');
  
 

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