From kawas at dev.open-bio.org Mon Jun 7 15:34:51 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jun 2010 15:34:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006071934.o57JYpq8010487@dev.open-bio.org>
kawas
Mon Jun 7 15:34:50 EDT 2010
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv10452/xmls
Modified Files:
deployBuild.xml
Log Message:
updated the match attribute in -find-services
moby-live/Java/xmls deployBuild.xml,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2009/02/03 08:59:20 1.10
+++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2010/06/07 19:34:50 1.11
@@ -221,7 +221,9 @@
-
+
+
+
@@ -266,10 +268,10 @@
- -
+ -
No list of service names found.
===============================
@@ -282,7 +284,8 @@
way (implementation class is not needed), or simpler by creating
a property 'services.list' containing a comma-delimited list of
names of services to be undeployed.
-
+
+
From kawas at dev.open-bio.org Tue Jun 8 09:48:58 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 8 Jun 2010 09:48:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006081348.o58DmwTb024193@dev.open-bio.org>
kawas
Tue Jun 8 09:48:58 EDT 2010
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv24158
Modified Files:
deployBuild.xml
Log Message:
fixed typo that Elise pointed out on line 347
moby-live/Java/xmls deployBuild.xml,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2010/06/07 19:34:50 1.11
+++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2010/06/08 13:48:58 1.12
@@ -344,7 +344,7 @@
-
+
From gordonp at dev.open-bio.org Tue Jun 15 18:20:52 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Tue, 15 Jun 2010 18:20:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006152220.o5FMKqJs022087@dev.open-bio.org>
gordonp
Tue Jun 15 18:20:52 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv22051/src/main/ca/ucalgary/seahawk/gui
Modified Files:
FilterSearchWidget.java
Log Message:
Catch bad regex syntax, paint search field red
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java 2010/05/04 16:15:47 1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java 2010/06/15 22:20:51 1.7
@@ -2,6 +2,7 @@
import ca.ucalgary.seahawk.util.*;
+import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.*;
import java.net.URL;
@@ -224,8 +225,15 @@
"Delay less than 100ms on search input due to interrupt",
e);
}
- pane.applyFilter(true);
- sem.release();
+
+ try{
+ sf.setBackground(Color.WHITE);
+ pane.applyFilter(true);
+ }catch(Exception e){
+ sf.setBackground(Color.RED);
+ }finally{
+ sem.release();
+ }
}
}
}.start();
From kawas at dev.open-bio.org Thu Jun 24 14:23:17 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:23:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241823.o5OINH6K004101@dev.open-bio.org>
kawas
Thu Jun 24 14:23:16 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv4066/lib/MOBY/Client
Modified Files:
OntologyServer.pm
Log Message:
fix: dont ping to get biomoby default UNLESS one is NOT defined!
moby-live/Perl/MOBY-Server/lib/MOBY/Client OntologyServer.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm 2008/09/02 13:11:40 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm 2010/06/24 18:23:16 1.3
@@ -127,8 +127,12 @@
$self->{$attrname} = $self->_default_for( $attrname );
}
}
- my ($ontologyserver) = _getOntologyServer(); # get default from moby central
+ # get ontology server if not defined in ENV
+ do {
+ my ($ontologyserver) = _getOntologyServer(); # get default from moby central
$self->host($ontologyserver) if $ontologyserver;
+ } unless $ENV{MOBY_ONTOLOGYSERVER};
+ # use the ENV version if it exists
$self->host($ENV{MOBY_ONTOLOGYSERVER}) if ($ENV{MOBY_ONTOLOGYSERVER}); # override with user preference if set in their environment
return undef unless $self->host;
return $self;
From kawas at dev.open-bio.org Thu Jun 24 14:23:47 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:23:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241823.o5OINlZx004141@dev.open-bio.org>
kawas
Thu Jun 24 14:23:47 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv4106
Modified Files:
Changes
Log Message:
updated to reflect recent changes.
moby-live/Perl/MOBY-Server Changes,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2010/05/03 18:36:27 1.32
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2010/06/24 18:23:47 1.33
@@ -1,5 +1,8 @@
Revision history for Perl extension MOBY.
+1.14
+ - fix: dont make an un-necessary network call when instantiating
+ a MOBY::Client::OntologyServer object.
1.13
- fix: no longer allow colons to be used in names for terms in
registerX methods.
From kawas at dev.open-bio.org Thu Jun 24 14:24:05 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:24:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241824.o5OIO5gd004181@dev.open-bio.org>
kawas
Thu Jun 24 14:24:05 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv4146
Modified Files:
Makefile.PL
Log Message:
updated version for cpan release
moby-live/Perl/MOBY-Server Makefile.PL,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2010/05/03 18:36:27 1.22
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2010/06/24 18:24:05 1.23
@@ -3,7 +3,7 @@
# Define metadata
name 'MOBY';
- version '1.13';
+ version '1.14';
license 'perl';
abstract
'This distribution is for communicating with or creating your own MOBY Central registry';
From kawas at dev.open-bio.org Thu Jun 24 14:25:29 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:25:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241825.o5OIPTPd004241@dev.open-bio.org>
kawas
Thu Jun 24 14:25:29 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv4206
Modified Files:
Changes
Log Message:
updated to reflect recent changes.
moby-live/Perl/MOBY-Client Changes,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/09/01 20:13:51 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2010/06/24 18:25:29 1.11
@@ -1,5 +1,8 @@
Revision history for MOBY-Client
+1.06
+ * fix: dont make an un-necessary network call when instantiating
+ a MOBY::Client::OntologyServer object.
1.05
* Updated the Makefile.PL to handle some missing dependencies.
* Updated CommonSubs to remove all hard coded entries for the
From kawas at dev.open-bio.org Thu Jun 24 14:25:39 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:25:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241825.o5OIPdPu004281@dev.open-bio.org>
kawas
Thu Jun 24 14:25:39 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv4246
Modified Files:
Makefile.PL
Log Message:
updated version for cpan release
moby-live/Perl/MOBY-Client Makefile.PL,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/09/01 20:13:51 1.14
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2010/06/24 18:25:39 1.15
@@ -4,7 +4,7 @@
# all_from 'lib/MOBY/Client/Central.pm';
author 'Mark Wilkinson ';
-version '1.05';
+version '1.06';
license 'perl';
abstract 'This distribution is for communicating with a MOBY Central registry';
From kawas at dev.open-bio.org Mon Jun 7 19:34:51 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jun 2010 15:34:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006071934.o57JYpq8010487@dev.open-bio.org>
kawas
Mon Jun 7 15:34:50 EDT 2010
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv10452/xmls
Modified Files:
deployBuild.xml
Log Message:
updated the match attribute in -find-services
moby-live/Java/xmls deployBuild.xml,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2009/02/03 08:59:20 1.10
+++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2010/06/07 19:34:50 1.11
@@ -221,7 +221,9 @@
-
+
+
+
@@ -266,10 +268,10 @@
- -
+ -
No list of service names found.
===============================
@@ -282,7 +284,8 @@
way (implementation class is not needed), or simpler by creating
a property 'services.list' containing a comma-delimited list of
names of services to be undeployed.
-
+
+
From kawas at dev.open-bio.org Tue Jun 8 13:48:58 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 8 Jun 2010 09:48:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006081348.o58DmwTb024193@dev.open-bio.org>
kawas
Tue Jun 8 09:48:58 EDT 2010
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv24158
Modified Files:
deployBuild.xml
Log Message:
fixed typo that Elise pointed out on line 347
moby-live/Java/xmls deployBuild.xml,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2010/06/07 19:34:50 1.11
+++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2010/06/08 13:48:58 1.12
@@ -344,7 +344,7 @@
-
+
From gordonp at dev.open-bio.org Tue Jun 15 22:20:52 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Tue, 15 Jun 2010 18:20:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006152220.o5FMKqJs022087@dev.open-bio.org>
gordonp
Tue Jun 15 18:20:52 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv22051/src/main/ca/ucalgary/seahawk/gui
Modified Files:
FilterSearchWidget.java
Log Message:
Catch bad regex syntax, paint search field red
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java 2010/05/04 16:15:47 1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java 2010/06/15 22:20:51 1.7
@@ -2,6 +2,7 @@
import ca.ucalgary.seahawk.util.*;
+import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.*;
import java.net.URL;
@@ -224,8 +225,15 @@
"Delay less than 100ms on search input due to interrupt",
e);
}
- pane.applyFilter(true);
- sem.release();
+
+ try{
+ sf.setBackground(Color.WHITE);
+ pane.applyFilter(true);
+ }catch(Exception e){
+ sf.setBackground(Color.RED);
+ }finally{
+ sem.release();
+ }
}
}
}.start();
From kawas at dev.open-bio.org Thu Jun 24 18:23:17 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:23:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241823.o5OINH6K004101@dev.open-bio.org>
kawas
Thu Jun 24 14:23:16 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv4066/lib/MOBY/Client
Modified Files:
OntologyServer.pm
Log Message:
fix: dont ping to get biomoby default UNLESS one is NOT defined!
moby-live/Perl/MOBY-Server/lib/MOBY/Client OntologyServer.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm 2008/09/02 13:11:40 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm 2010/06/24 18:23:16 1.3
@@ -127,8 +127,12 @@
$self->{$attrname} = $self->_default_for( $attrname );
}
}
- my ($ontologyserver) = _getOntologyServer(); # get default from moby central
+ # get ontology server if not defined in ENV
+ do {
+ my ($ontologyserver) = _getOntologyServer(); # get default from moby central
$self->host($ontologyserver) if $ontologyserver;
+ } unless $ENV{MOBY_ONTOLOGYSERVER};
+ # use the ENV version if it exists
$self->host($ENV{MOBY_ONTOLOGYSERVER}) if ($ENV{MOBY_ONTOLOGYSERVER}); # override with user preference if set in their environment
return undef unless $self->host;
return $self;
From kawas at dev.open-bio.org Thu Jun 24 18:23:47 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:23:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241823.o5OINlZx004141@dev.open-bio.org>
kawas
Thu Jun 24 14:23:47 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv4106
Modified Files:
Changes
Log Message:
updated to reflect recent changes.
moby-live/Perl/MOBY-Server Changes,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2010/05/03 18:36:27 1.32
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2010/06/24 18:23:47 1.33
@@ -1,5 +1,8 @@
Revision history for Perl extension MOBY.
+1.14
+ - fix: dont make an un-necessary network call when instantiating
+ a MOBY::Client::OntologyServer object.
1.13
- fix: no longer allow colons to be used in names for terms in
registerX methods.
From kawas at dev.open-bio.org Thu Jun 24 18:24:05 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:24:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241824.o5OIO5gd004181@dev.open-bio.org>
kawas
Thu Jun 24 14:24:05 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv4146
Modified Files:
Makefile.PL
Log Message:
updated version for cpan release
moby-live/Perl/MOBY-Server Makefile.PL,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2010/05/03 18:36:27 1.22
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2010/06/24 18:24:05 1.23
@@ -3,7 +3,7 @@
# Define metadata
name 'MOBY';
- version '1.13';
+ version '1.14';
license 'perl';
abstract
'This distribution is for communicating with or creating your own MOBY Central registry';
From kawas at dev.open-bio.org Thu Jun 24 18:25:29 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:25:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241825.o5OIPTPd004241@dev.open-bio.org>
kawas
Thu Jun 24 14:25:29 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv4206
Modified Files:
Changes
Log Message:
updated to reflect recent changes.
moby-live/Perl/MOBY-Client Changes,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/09/01 20:13:51 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2010/06/24 18:25:29 1.11
@@ -1,5 +1,8 @@
Revision history for MOBY-Client
+1.06
+ * fix: dont make an un-necessary network call when instantiating
+ a MOBY::Client::OntologyServer object.
1.05
* Updated the Makefile.PL to handle some missing dependencies.
* Updated CommonSubs to remove all hard coded entries for the
From kawas at dev.open-bio.org Thu Jun 24 18:25:39 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 24 Jun 2010 14:25:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201006241825.o5OIPdPu004281@dev.open-bio.org>
kawas
Thu Jun 24 14:25:39 EDT 2010
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv4246
Modified Files:
Makefile.PL
Log Message:
updated version for cpan release
moby-live/Perl/MOBY-Client Makefile.PL,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/09/01 20:13:51 1.14
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2010/06/24 18:25:39 1.15
@@ -4,7 +4,7 @@
# all_from 'lib/MOBY/Client/Central.pm';
author 'Mark Wilkinson ';
-version '1.05';
+version '1.06';
license 'perl';
abstract 'This distribution is for communicating with a MOBY Central registry';