[med-svn] r21704 - in trunk/packages/gmod/chado/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2016-04-12 15:52:06 +0000 (Tue, 12 Apr 2016)
New Revision: 21704

Modified:
   trunk/packages/gmod/chado/trunk/debian/changelog
   trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage
   trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch
   trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder
Log:
new upstream release 1.31

Modified: trunk/packages/gmod/chado/trunk/debian/changelog
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/changelog	2016-04-12 15:38:21 UTC (rev 21703)
+++ trunk/packages/gmod/chado/trunk/debian/changelog	2016-04-12 15:52:06 UTC (rev 21704)
@@ -1,3 +1,9 @@
+libchado-perl (1.31-1) unstable; urgency=medium
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou at debian.org>  Tue, 12 Apr 2016 17:45:45 +0200
+
 libchado-perl (1.23-5) unstable; urgency=medium
 
   * Enhanced patch from Niko Tyni really

Modified: trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage	2016-04-12 15:38:21 UTC (rev 21703)
+++ trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage	2016-04-12 15:52:06 UTC (rev 21704)
@@ -22,7 +22,7 @@
  
  =item Arguments
  
-@@ -3470,7 +3470,7 @@
+@@ -3476,7 +3476,7 @@
  --   short identifier that can help people find an analysis they
  --   want. for instance "tRNAscan", "cDNA", "FlyPep", "SwissProt"
  --   it should not be assumed to be unique. for instance, there may

Modified: trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch	2016-04-12 15:38:21 UTC (rev 21703)
+++ trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch	2016-04-12 15:52:06 UTC (rev 21704)
@@ -5,7 +5,7 @@
 Last-Updated: 19/03/2012
 --- a/INSTALL.Chado
 +++ b/INSTALL.Chado
-@@ -360,17 +360,17 @@
+@@ -367,17 +367,17 @@
  the Sequence Ontology (SO) is absolutely required for proper
  functioning of the database.  The commands to load an ontology are:
  
@@ -26,23 +26,3 @@
  file format.
  
  It is a good idea at this point to make a back up of the database,
---- a/lib/Bio/Chado/Builder.pm
-+++ b/lib/Bio/Chado/Builder.pm
-@@ -350,7 +350,7 @@
-       }
- 
-       # loading chadoxml
--      my $stag_string = "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
-+      my $stag_string = "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
-       $stag_string .= " --user $db_user " if $db_user;
-       $stag_string .= " --password '$db_pass' " if $db_pass;
-       $sys_call = join( ' ',
-@@ -387,7 +387,7 @@
- 
- 
-         $sys_call = join( ' ',
--          "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'",
-+          "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'",
-           catfile( $conf->{'path'}{'data'}, $deffile->{'local'}.'xml')
-         );
- 

Modified: trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder	2016-04-12 15:38:21 UTC (rev 21703)
+++ trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder	2016-04-12 15:52:06 UTC (rev 21704)
@@ -5,7 +5,7 @@
 update path for binaries to match gmod chado installation
 --- a/lib/Bio/Chado/Builder.pm
 +++ b/lib/Bio/Chado/Builder.pm
-@@ -96,12 +96,12 @@
+@@ -97,12 +97,12 @@
        my $result = `bin/gmod_add_organism.pl --name_only --common_name $db_org`;
        unless ($result) {
            print "Adding $db_org to the database...\n";
@@ -20,7 +20,7 @@
  
  }
  
-@@ -133,7 +133,7 @@
+@@ -134,7 +134,7 @@
  
    if (looks_like_number($version) and $version < $schema_version) {
      print "Attempting schema update.\n";