Menu
▾
▴
gmod-schema-cmts
|
From: <sco...@us...> - 2010-01-26 20:54:14
|
Revision: 22617
http://gmod.svn.sourceforge.net/gmod/?rev=22617&view=rev
Author: scottcain
Date: 2010-01-26 20:53:50 +0000 (Tue, 26 Jan 2010)
Log Message:
-----------
taking out the "fix" for DBIx::DBStag; it probably hasn't been necessary for a few years!
Modified Paths:
--------------
schema/trunk/chado/lib/Bio/Chado/Builder.pm
Modified: schema/trunk/chado/lib/Bio/Chado/Builder.pm
===================================================================
--- schema/trunk/chado/lib/Bio/Chado/Builder.pm 2010-01-26 20:51:47 UTC (rev 22616)
+++ schema/trunk/chado/lib/Bio/Chado/Builder.pm 2010-01-26 20:53:50 UTC (rev 22617)
@@ -360,16 +360,16 @@
}
#fix up DBIx::DBStag stomping on part_of and derives_from
- $m->log->debug("fix up DBIx::DBStag stomping on part_of and derives_from");
- my $dbh = DBI->connect("dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port",
- $db_user, $db_pass);
- $dbh->do("UPDATE cvterm SET
- cv_id = (SELECT cv_id FROM cv WHERE name='relationship')
- WHERE name='derives_from'");
- $dbh->do("UPDATE cvterm SET
- cv_id = (SELECT cv_id FROM cv WHERE name='relationship')
- WHERE name='part_of'");
- $dbh->disconnect;
+# $m->log->debug("fix up DBIx::DBStag stomping on part_of and derives_from");
+# my $dbh = DBI->connect("dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port",
+# $db_user, $db_pass);
+# $dbh->do("UPDATE cvterm SET
+# cv_id = (SELECT cv_id FROM cv WHERE name='relationship')
+# WHERE name='derives_from'");
+# $dbh->do("UPDATE cvterm SET
+# cv_id = (SELECT cv_id FROM cv WHERE name='relationship')
+# WHERE name='part_of'");
+# $dbh->disconnect;
$m->log->info("leaving ACTION_ontologies");
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rb...@us...> - 2010-08-10 17:54:32
|
Revision: 23650
http://gmod.svn.sourceforge.net/gmod/?rev=23650&view=rev
Author: rbuels
Date: 2010-08-10 17:54:24 +0000 (Tue, 10 Aug 2010)
Log Message:
-----------
update Bio::Chado::Builder to detect recent versions of go-perl. they no longer have .pl at the end of the go2fmt script name
Modified Paths:
--------------
schema/trunk/chado/lib/Bio/Chado/Builder.pm
Modified: schema/trunk/chado/lib/Bio/Chado/Builder.pm
===================================================================
--- schema/trunk/chado/lib/Bio/Chado/Builder.pm 2010-08-10 17:48:14 UTC (rev 23649)
+++ schema/trunk/chado/lib/Bio/Chado/Builder.pm 2010-08-10 17:54:24 UTC (rev 23650)
@@ -15,6 +15,9 @@
use LWP::Simple qw(mirror is_success status_message);
use Log::Log4perl;
use DBI;
+use IPC::Cmd ();
+my $go2fmt = IPC::Cmd::can_run('go2fmt') ? 'go2fmt' : 'go2fmt.pl'; #< detect new version of go2fmt
+
Log::Log4perl::init('load/etc/log.conf');
no warnings;
@@ -270,14 +273,16 @@
my $sys_call;
if ($file->{type} eq 'obo') {
$sys_call = join( ' ',
- 'go2fmt.pl -p obo_text -w xml',
+ $go2fmt,
+ '-p obo_text -w xml',
catfile( $conf->{'path'}{'data'}, $file->{'local'}),
'| go-apply-xslt oboxml_to_chadoxml - >',
catfile( $conf->{'path'}{'data'}, $file->{'local'}.'xml')
);
} elsif ($file->{type} eq 'ontology') {
$sys_call = join( ' ',
- 'go2fmt.pl -p go_ont -w xml',
+ $go2fmt,
+ '-p go_ont -w xml',
catfile( $conf->{'path'}{'data'}, $file->{'local'}),
'| go-apply-xslt oboxml_to_chadoxml - >',
catfile( $conf->{'path'}{'data'}, $file->{'local'}.'xml')
@@ -317,7 +322,8 @@
if ($deffile) {
$sys_call = join( ' ',
- 'go2fmt.pl -p go_def -w xml',
+ $go2fmt,
+ '-p go_def -w xml',
catfile( $conf->{'path'}{'data'}, $deffile->{'local'}),
'| go-apply-xslt oboxml_to_chadoxml - >',
catfile( $conf->{'path'}{'data'}, $deffile->{'local'}.'xml')
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sco...@us...> - 2011-08-31 23:38:16
|
Revision: 25169
http://gmod.svn.sourceforge.net/gmod/?rev=25169&view=rev
Author: scottcain
Date: 2011-08-31 23:38:06 +0000 (Wed, 31 Aug 2011)
Log Message:
-----------
with this, "make update" should work.
Modified Paths:
--------------
schema/trunk/chado/lib/Bio/Chado/Builder.pm
Modified: schema/trunk/chado/lib/Bio/Chado/Builder.pm
===================================================================
--- schema/trunk/chado/lib/Bio/Chado/Builder.pm 2011-08-31 23:17:45 UTC (rev 25168)
+++ schema/trunk/chado/lib/Bio/Chado/Builder.pm 2011-08-31 23:38:06 UTC (rev 25169)
@@ -130,6 +130,7 @@
if (looks_like_number($version) and $version < $schema_version) {
print "Attempting schema update.\n";
+ system("gmod_update_chado.pl --dbprofile $db_name");
}
elsif (looks_like_number($version) and $version >= $schema_version) {
print "No update necessary.\n";
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sco...@us...> - 2011-09-20 19:34:29
|
Revision: 25199
http://gmod.svn.sourceforge.net/gmod/?rev=25199&view=rev
Author: scottcain
Date: 2011-09-20 19:34:21 +0000 (Tue, 20 Sep 2011)
Log Message:
-----------
fixing the auto adding of organisms to not fire when "none" is specified
Modified Paths:
--------------
schema/trunk/chado/lib/Bio/Chado/Builder.pm
Modified: schema/trunk/chado/lib/Bio/Chado/Builder.pm
===================================================================
--- schema/trunk/chado/lib/Bio/Chado/Builder.pm 2011-09-20 19:20:39 UTC (rev 25198)
+++ schema/trunk/chado/lib/Bio/Chado/Builder.pm 2011-09-20 19:34:21 UTC (rev 25199)
@@ -92,7 +92,7 @@
my $db_org = $conf->{'database'}{'db_organism'};
- if ($db_org and ($db_org ne 'none')) {
+ if ($db_org and $db_org ne 'none' and ref $db_org ne 'HASH') {
my $result = `bin/gmod_add_organism.pl --name_only --common_name $db_org`;
unless ($result) {
print "Adding $db_org to the database...\n";
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sco...@us...> - 2012-03-14 02:34:12
|
Revision: 25261
http://gmod.svn.sourceforge.net/gmod/?rev=25261&view=rev
Author: scottcain
Date: 2012-03-14 02:33:59 +0000 (Wed, 14 Mar 2012)
Log Message:
-----------
quoting the password so special characters will be protected. Thanks to Hans Kraus for pointing it out.
Modified Paths:
--------------
schema/trunk/chado/lib/Bio/Chado/Builder.pm
Modified: schema/trunk/chado/lib/Bio/Chado/Builder.pm
===================================================================
--- schema/trunk/chado/lib/Bio/Chado/Builder.pm 2012-03-13 18:41:31 UTC (rev 25260)
+++ schema/trunk/chado/lib/Bio/Chado/Builder.pm 2012-03-14 02:33:59 UTC (rev 25261)
@@ -352,7 +352,7 @@
# loading chadoxml
my $stag_string = "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
$stag_string .= " --user $db_user " if $db_user;
- $stag_string .= " --password $db_pass " if $db_pass;
+ $stag_string .= " --password '$db_pass' " if $db_pass;
$sys_call = join( ' ',
$stag_string,
catfile( $conf->{'path'}{'data'}, $file->{'local'}.'xml')
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
Thanks for helping keep SourceForge clean.
X