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gmod-schema-cmts
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From: <sco...@us...> - 2009-12-03 15:48:48
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Revision: 22313
http://gmod.svn.sourceforge.net/gmod/?rev=22313&view=rev
Author: scottcain
Date: 2009-12-03 15:48:37 +0000 (Thu, 03 Dec 2009)
Log Message:
-----------
adding to the changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2009-12-03 11:50:10 UTC (rev 22312)
+++ schema/trunk/chado/Changes 2009-12-03 15:48:37 UTC (rev 22313)
@@ -36,6 +36,9 @@
a database that has been affected by this bug, see http://.... for a fix.
* Added a __DIE__ signal handler to gmod_bulk_load_gff3.pl so that the
databsae will be cleaned up in most cases before the loader croaks.
+* Fixed gmod_bulk_load_gff3.pl so that when loading dna sequence from the
+fasta section it won't accidentally add sequence to a feature that has
+the same uniquename but different organism_id to the actual target.
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From: <sco...@us...> - 2009-12-09 17:29:34
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Revision: 22344
http://gmod.svn.sourceforge.net/gmod/?rev=22344&view=rev
Author: scottcain
Date: 2009-12-09 17:29:20 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Updating Changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2009-12-09 03:34:42 UTC (rev 22343)
+++ schema/trunk/chado/Changes 2009-12-09 17:29:20 UTC (rev 22344)
@@ -39,6 +39,11 @@
* Fixed gmod_bulk_load_gff3.pl so that when loading dna sequence from the
fasta section it won't accidentally add sequence to a feature that has
the same uniquename but different organism_id to the actual target.
+* Adding a update_sequences method for use by gmod_bulk_load_gff3.pl
+that will check the next value available to the database sequences
+that generate primary keys and update them when necessary. This
+can happen when another database load adds data to chado but does
+not update the sequence.
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From: <sco...@us...> - 2009-12-10 03:12:55
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Revision: 22354
http://gmod.svn.sourceforge.net/gmod/?rev=22354&view=rev
Author: scottcain
Date: 2009-12-10 03:12:39 +0000 (Thu, 10 Dec 2009)
Log Message:
-----------
adding the tmp dir info to the changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2009-12-09 22:18:45 UTC (rev 22353)
+++ schema/trunk/chado/Changes 2009-12-10 03:12:39 UTC (rev 22354)
@@ -44,6 +44,9 @@
that generate primary keys and update them when necessary. This
can happen when another database load adds data to chado but does
not update the sequence.
+* Adding the ability to specify that gmod_bulk_load_gff3.pl use the
+system tmp directory rather than using the current working directory
+for writing the temporary load files.
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From: <sco...@us...> - 2010-01-27 20:16:37
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Revision: 22629
http://gmod.svn.sourceforge.net/gmod/?rev=22629&view=rev
Author: scottcain
Date: 2010-01-27 20:16:27 +0000 (Wed, 27 Jan 2010)
Log Message:
-----------
updating changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-01-27 15:05:39 UTC (rev 22628)
+++ schema/trunk/chado/Changes 2010-01-27 20:16:27 UTC (rev 22629)
@@ -49,6 +49,9 @@
for writing the temporary load files.
* Added a --fastafile option to gmod_bulk_load_gff3.pl to use when
loading fasta files.
+* Removed the cause of the error messages at the end of ontology loading:
+it was a patch to correct for bad behavior that DBIx::DBStag which was
+fixed some time ago.
Below this line are changes up until a few years ago and are included
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From: <sco...@us...> - 2010-05-18 19:16:22
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Revision: 23232
http://gmod.svn.sourceforge.net/gmod/?rev=23232&view=rev
Author: scottcain
Date: 2010-05-18 19:15:29 +0000 (Tue, 18 May 2010)
Log Message:
-----------
minor change to Changes
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-05-18 19:02:40 UTC (rev 23231)
+++ schema/trunk/chado/Changes 2010-05-18 19:15:29 UTC (rev 23232)
@@ -32,8 +32,7 @@
die gracefully.
* Fixed gmod_bulk_load_gff3.pl so that featureloc.srcfeature_id will
not be sometimes set incorrectly when there are multiple organisms
-with chromosomes (or other srcfeatures) with the same name. If you have
-a database that has been affected by this bug, see http://.... for a fix.
+with chromosomes (or other srcfeatures) with the same name.
* Added a __DIE__ signal handler to gmod_bulk_load_gff3.pl so that the
databsae will be cleaned up in most cases before the loader croaks.
* Fixed gmod_bulk_load_gff3.pl so that when loading dna sequence from the
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From: <sco...@us...> - 2010-05-25 15:11:51
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Revision: 23273
http://gmod.svn.sourceforge.net/gmod/?rev=23273&view=rev
Author: scottcain
Date: 2010-05-25 15:11:41 +0000 (Tue, 25 May 2010)
Log Message:
-----------
adding to Changes
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-05-25 15:01:39 UTC (rev 23272)
+++ schema/trunk/chado/Changes 2010-05-25 15:11:41 UTC (rev 23273)
@@ -1,5 +1,10 @@
-Version 1.01
+Version 1.11 Tue May 25 11:10:47 EDT 2010
+* fixed an issue with accessing the primary_id of
+Bio::Annotation::DBLink objects (Naama)
+
+Version 1.1
+
* Fixes to gmod_gff3_preprocessor.pl so that file splitting will work
as expected.
* Minor fix to Bio::GMOD::DB::Adaptor (used by gmod_bulk_load_gff3.pl)
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From: <nm...@us...> - 2010-06-29 18:51:35
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Revision: 23495
http://gmod.svn.sourceforge.net/gmod/?rev=23495&view=rev
Author: nm249
Date: 2010-06-29 18:51:17 +0000 (Tue, 29 Jun 2010)
Log Message:
-----------
added info about recent changes to cxgn-based gmod loading scripts
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-06-29 18:34:13 UTC (rev 23494)
+++ schema/trunk/chado/Changes 2010-06-29 18:51:17 UTC (rev 23495)
@@ -1,3 +1,9 @@
+Version 1.12 2010-06-29
+* Fixes issue with dependencies on CXGN-specific code. Now all
+db connection parameters for cxgn - contributed scripts should be passed
+in a gmod_config file, or in command line options as listed in the POD.
+
+
Version 1.11 Tue May 25 11:10:47 EDT 2010
* fixed an issue with accessing the primary_id of
Bio::Annotation::DBLink objects (Naama)
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From: <sco...@us...> - 2010-06-29 18:53:29
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Revision: 23497
http://gmod.svn.sourceforge.net/gmod/?rev=23497&view=rev
Author: scottcain
Date: 2010-06-29 18:53:15 +0000 (Tue, 29 Jun 2010)
Log Message:
-----------
updated changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-06-29 18:51:27 UTC (rev 23496)
+++ schema/trunk/chado/Changes 2010-06-29 18:53:15 UTC (rev 23497)
@@ -1,12 +1,12 @@
-Version 1.12 2010-06-29
-* Fixes issue with dependencies on CXGN-specific code. Now all
-db connection parameters for cxgn - contributed scripts should be passed
-in a gmod_config file, or in command line options as listed in the POD.
-
-
Version 1.11 Tue May 25 11:10:47 EDT 2010
* fixed an issue with accessing the primary_id of
Bio::Annotation::DBLink objects (Naama)
+* Fixes issue with dependencies on CXGN-specific code. Now all
+db connection parameters for cxgn - contributed scripts should be passed
+in a gmod_config file, or in command line options as listed in the POD.
+* Made gmod_materialized_view_tool.pl able to accept all configuration
+parameters on the command line (this is to make it work with automatic
+MV creation for full text searching) (Scott).
Version 1.1
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From: <sco...@us...> - 2010-08-11 19:47:14
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Revision: 23660
http://gmod.svn.sourceforge.net/gmod/?rev=23660&view=rev
Author: scottcain
Date: 2010-08-11 19:47:07 +0000 (Wed, 11 Aug 2010)
Log Message:
-----------
updatinge changes for bulk loader fix
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-08-11 19:45:54 UTC (rev 23659)
+++ schema/trunk/chado/Changes 2010-08-11 19:47:07 UTC (rev 23660)
@@ -2,6 +2,8 @@
* Added some error checking to gmod_fasta2gff3.pl (Rob)
* Updated Bio::Chado::Builder to detect recent versions of go-perl. They
no longer have .pl at the end of the go2fmt script name (Rob)
+* The GFF3 bulk loader will now ignore ##sequence-region directives;
+previously, their presence caused the loader to fail (Scott)
Version 1.11 Tue May 25 11:10:47 EDT 2010
* fixed an issue with accessing the primary_id of
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From: <sco...@us...> - 2010-09-23 15:25:24
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Revision: 23843
http://gmod.svn.sourceforge.net/gmod/?rev=23843&view=rev
Author: scottcain
Date: 2010-09-23 15:25:15 +0000 (Thu, 23 Sep 2010)
Log Message:
-----------
adding to changes file for a Naama commit
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-09-23 15:20:23 UTC (rev 23842)
+++ schema/trunk/chado/Changes 2010-09-23 15:25:15 UTC (rev 23843)
@@ -4,6 +4,10 @@
no longer have .pl at the end of the go2fmt script name (Rob)
* The GFF3 bulk loader will now ignore ##sequence-region directives;
previously, their presence caused the loader to fail (Scott)
+* added a check for the nodes file downloaded from NCBI. There have been
+cases of missing nodes/parents. Code dies if parent is missing. User
+must check the nodes file. This needs further investigation with NCBI
+taxonomy. (Naama)
Version 1.11 Tue May 25 11:10:47 EDT 2010
* fixed an issue with accessing the primary_id of
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From: <sco...@us...> - 2010-10-13 16:03:12
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Revision: 23964
http://gmod.svn.sourceforge.net/gmod/?rev=23964&view=rev
Author: scottcain
Date: 2010-10-13 16:03:04 +0000 (Wed, 13 Oct 2010)
Log Message:
-----------
updating Chagnes file for gff-bridge fixes
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-10-13 16:01:00 UTC (rev 23963)
+++ schema/trunk/chado/Changes 2010-10-13 16:03:04 UTC (rev 23964)
@@ -8,6 +8,8 @@
cases of missing nodes/parents. Code dies if parent is missing. User
must check the nodes file. This needs further investigation with NCBI
taxonomy. (Naama)
+* Fix the code in the gff-bridge in the sequence module so that GFF dumping
+from GBrowse will work correctly (Scott)
Version 1.11 Tue May 25 11:10:47 EDT 2010
* fixed an issue with accessing the primary_id of
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From: <sco...@us...> - 2010-11-10 15:52:39
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Revision: 24115
http://gmod.svn.sourceforge.net/gmod/?rev=24115&view=rev
Author: scottcain
Date: 2010-11-10 15:46:50 +0000 (Wed, 10 Nov 2010)
Log Message:
-----------
updating the changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2010-11-10 15:43:27 UTC (rev 24114)
+++ schema/trunk/chado/Changes 2010-11-10 15:46:50 UTC (rev 24115)
@@ -10,6 +10,10 @@
taxonomy. (Naama)
* Fix the code in the gff-bridge in the sequence module so that GFF dumping
from GBrowse will work correctly (Scott)
+* Added a cvprop table to capture things like obo file version from
+a loaded cv. (Scott)
+* Removed the "DB:" prefix from all of the names of databases that go
+into the db table. (Scott)
Version 1.11 Tue May 25 11:10:47 EDT 2010
* fixed an issue with accessing the primary_id of
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From: <sco...@us...> - 2011-08-31 23:40:10
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Revision: 25170
http://gmod.svn.sourceforge.net/gmod/?rev=25170&view=rev
Author: scottcain
Date: 2011-08-31 23:40:02 +0000 (Wed, 31 Aug 2011)
Log Message:
-----------
added to the changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2011-08-31 23:38:06 UTC (rev 25169)
+++ schema/trunk/chado/Changes 2011-08-31 23:40:02 UTC (rev 25170)
@@ -17,6 +17,10 @@
* Removed the dependency on Log::Log4perl (it was overkill for what it
was being used for) (Scott)
* Bumped the version to 1.2 because of the new schema module. (Scott)
+* Added gmod_chado_properties.pl to examine the chadoprop table and return
+values on the command line (like the schema version) (Scott)
+* Added gmod_update_chado.pl to update the schema automatically, and added
+a make target (make update) to make updating easier. (Scott)
Version 1.11 Tue May 25 11:10:47 EDT 2010
* fixed an issue with accessing the primary_id of
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From: <sco...@us...> - 2011-10-20 14:53:58
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Revision: 25227
http://gmod.svn.sourceforge.net/gmod/?rev=25227&view=rev
Author: scottcain
Date: 2011-10-20 14:53:51 +0000 (Thu, 20 Oct 2011)
Log Message:
-----------
updating Changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2011-10-20 14:52:33 UTC (rev 25226)
+++ schema/trunk/chado/Changes 2011-10-20 14:53:51 UTC (rev 25227)
@@ -1,3 +1,7 @@
+Version 1.21 Thu Oct 20 10:52:55 EDT 2011
+* Added rudimentary support for non-public schemas in Postgres, though it's
+only good for Tripal at the moment.
+
Version 1.2 Tue Aug 10 13:59:05 EDT 2010
* Added some error checking to gmod_fasta2gff3.pl (Rob)
* Updated Bio::Chado::Builder to detect recent versions of go-perl. They
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From: <sco...@us...> - 2011-11-15 20:38:45
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Revision: 25244
http://gmod.svn.sourceforge.net/gmod/?rev=25244&view=rev
Author: scottcain
Date: 2011-11-15 20:38:32 +0000 (Tue, 15 Nov 2011)
Log Message:
-----------
adding to changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2011-11-15 20:23:05 UTC (rev 25243)
+++ schema/trunk/chado/Changes 2011-11-15 20:38:32 UTC (rev 25244)
@@ -3,6 +3,8 @@
only good for Tripal at the moment.
* Fixed database initialization step "make prepdb" so that the version of the
schema gets set in the chadoprop table.
+* Fixed bug in gmod_chado_properties.pl that caused it to crash when updating the
+schema version.
Version 1.2 Tue Aug 10 13:59:05 EDT 2010
* Added some error checking to gmod_fasta2gff3.pl (Rob)
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From: <sco...@us...> - 2011-11-16 18:53:10
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Revision: 25246
http://gmod.svn.sourceforge.net/gmod/?rev=25246&view=rev
Author: scottcain
Date: 2011-11-16 18:52:59 +0000 (Wed, 16 Nov 2011)
Log Message:
-----------
formatting fix
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2011-11-15 21:19:32 UTC (rev 25245)
+++ schema/trunk/chado/Changes 2011-11-16 18:52:59 UTC (rev 25246)
@@ -3,8 +3,8 @@
only good for Tripal at the moment.
* Fixed database initialization step "make prepdb" so that the version of the
schema gets set in the chadoprop table.
-* Fixed bug in gmod_chado_properties.pl that caused it to crash when updating the
-schema version.
+* Fixed bug in gmod_chado_properties.pl that caused it to crash when updating
+the schema version.
Version 1.2 Tue Aug 10 13:59:05 EDT 2010
* Added some error checking to gmod_fasta2gff3.pl (Rob)
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From: <sco...@us...> - 2011-11-17 17:49:07
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Revision: 25249
http://gmod.svn.sourceforge.net/gmod/?rev=25249&view=rev
Author: scottcain
Date: 2011-11-17 17:48:58 +0000 (Thu, 17 Nov 2011)
Log Message:
-----------
version bump
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2011-11-17 17:47:56 UTC (rev 25248)
+++ schema/trunk/chado/Changes 2011-11-17 17:48:58 UTC (rev 25249)
@@ -1,3 +1,7 @@
+Version 1.11 Thu Nov 17 12:48:10 EST 2011
+* Created a script to automatically create the schemas dirs for a release and
+add them to the manifest.
+
Version 1.21 Thu Oct 20 10:52:55 EDT 2011
* Added rudimentary support for non-public schemas in Postgres, though it's
only good for Tripal at the moment.
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From: <sco...@us...> - 2012-03-13 18:41:55
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Revision: 25260
http://gmod.svn.sourceforge.net/gmod/?rev=25260&view=rev
Author: scottcain
Date: 2012-03-13 18:41:31 +0000 (Tue, 13 Mar 2012)
Log Message:
-----------
updating changes
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2012-03-13 18:26:05 UTC (rev 25259)
+++ schema/trunk/chado/Changes 2012-03-13 18:41:31 UTC (rev 25260)
@@ -3,6 +3,8 @@
Bio::DB::Das::Chado it would be happy.
* Changed all perl script #! lines to use /usr/bin/env perl instead of the
mishmash that was being used in various scripts.
+* Fixed the GFF3 preprocessor so that if an insert into the sorting table fails,
+the script will die to avoid losing GFF lines in the resulting file.
Version 1.22 Thu Nov 17 12:48:10 EST 2011
* Created a script to automatically create the schemas dirs for a release and
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From: <sco...@us...> - 2013-03-04 22:28:06
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Revision: 25286
http://gmod.svn.sourceforge.net/gmod/?rev=25286&view=rev
Author: scottcain
Date: 2013-03-04 22:27:55 +0000 (Mon, 04 Mar 2013)
Log Message:
-----------
updating the changes file
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2013-03-04 22:09:03 UTC (rev 25285)
+++ schema/trunk/chado/Changes 2013-03-04 22:27:55 UTC (rev 25286)
@@ -1,3 +1,7 @@
+Version 1.24 Mon Mar 4 17:18:47 EST 2013
+* Patched gmod_bulk_load_gff3.pl (provided by Alexie P) to fix the
+"orgainism from data" option.
+
Version 1.23 Thu Dec 1 14:45:22 EST 2011
* Added $VERSION to Bio::GMOD::DB::Config so that when installing
Bio::DB::Das::Chado it would be happy.
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From: <sco...@us...> - 2013-05-29 17:04:57
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Revision: 25288
http://gmod.svn.sourceforge.net/gmod/?rev=25288&view=rev
Author: scottcain
Date: 2013-05-29 17:04:46 +0000 (Wed, 29 May 2013)
Log Message:
-----------
added note about taxonomy loader fix
Modified Paths:
--------------
schema/trunk/chado/Changes
Modified: schema/trunk/chado/Changes
===================================================================
--- schema/trunk/chado/Changes 2013-05-29 16:35:23 UTC (rev 25287)
+++ schema/trunk/chado/Changes 2013-05-29 17:04:46 UTC (rev 25288)
@@ -1,4 +1,5 @@
Version 1.24 Mon Mar 4 17:18:47 EST 2013
+* 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.
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