The service API, which
describes how to interact with a service provided under the MOBY
framework: it describes what messages you can send to a service,
how should they be structured,
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFdm008375@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/main/org/biomoby/shared/parser
Modified Files:
ServiceException.java
Log Message:
moby-live/Java/src/main/org/biomoby/shared/parser ServiceException.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java 2006/11/11 23:04:34 1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java 2007/05/21 00:56:15 1.12
@@ -405,7 +405,7 @@
/**************************************************************************
*
*************************************************************************/
- public Element toDOM() {
+ public Element toXML() {
Element elem = MobyPackage.getXMLElement (MobyTags.MOBYEXCEPTION);
MobyPackage.setXMLAttribute (elem, MobyTags.SEVERITY, getSeverityAsString());
if (refQueryID != null)
@@ -479,26 +479,26 @@
return ex;
}
- public String toXML(){
- StringBuffer xml = new StringBuffer(" \n");
-
- xml.append(""+code+"");
+// public String toXML(){
+// StringBuffer xml = new StringBuffer(" \n");
+
+// xml.append(""+code+"");
+
+// if(getMessage() != null){
+// xml.append(" "+getMessage()+"");
+// }
- if(getMessage() != null){
- xml.append(" "+getMessage()+"");
- }
-
- xml.append(" ");
+// xml.append(" ");
- return xml.toString();
- }
+// return xml.toString();
+// }
}
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFpm008321@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/main/org/biomoby/registry/meta
Modified Files:
RegistriesList.java
Log Message:
moby-live/Java/src/main/org/biomoby/registry/meta RegistriesList.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/RegistriesList.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/RegistriesList.java 2006/12/05 17:18:16 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/RegistriesList.java 2007/05/21 00:56:15 1.3
@@ -20,7 +20,8 @@
* Please edit this file if you want to have your BioMoby registry
* visible to others (for example, in BioMoby Dashboard).
*
- * Or, you can also replace this implementation by your own, with your own list of registries
+ * Or, you can also replace this implementation by your own, with your
+ * own list of registries.
*
* @author Martin Senger
* @version $Id$
@@ -53,6 +54,15 @@
"The MOBY registry at the International Rice Research Institute (IRRI) is intended mostly for Generation Challenge Program (GCP) developers. It allows the registration of experimental moby entities within GCP."),
new Registry
+ ("INAB",
+ "http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl",
+ "http://moby-dev.inab.org/MOBY/Central",
+ "INAB, Spain",
+ "",
+ true,
+ "The MOBY registry at the Instituto Nacional de Bioinform??tica, Spain."),
+
+ new Registry
("testing",
"http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl",
"http://bioinfo.icapture.ubc.ca/MOBY/Central",
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFZo008339@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/chooser
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/main/org/biomoby/service/dashboard/chooser
Modified Files:
DateTimeChooserEditor.java
Log Message:
moby-live/Java/src/main/org/biomoby/service/dashboard/chooser DateTimeChooserEditor.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/chooser/DateTimeChooserEditor.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/chooser/DateTimeChooserEditor.java 2006/02/08 17:24:13 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/chooser/DateTimeChooserEditor.java 2007/05/21 00:56:15 1.2
@@ -31,8 +31,8 @@
/**
* A cell editor that invokes {@link DateTimeChooser} to get a
* calendar GUI. The editor is supposed to be used for editing cells
- * in JTable, and it complies wiht the Biomoby specification for
- * dat-time formats.
+ * in JTable, and it complies with the Biomoby specification for
+ * date-time formats.
*
* @author Martin Senger
* @version $Id$
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFVC008271@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv8252/docs
Modified Files:
ChangeLog
Log Message:
moby-live/Java/docs ChangeLog,1.77,1.78
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.77
retrieving revision 1.78
diff -u -r1.77 -r1.78
--- /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/04/18 16:33:45 1.77
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/21 00:56:14 1.78
@@ -1,3 +1,11 @@
+2007-05-20 Martin Senger
+
+ * Fixed: the date format of MobyDateTime is now fully compliant
+ with the ISO8601.
+
+ * Fixed: method ServiceException.toXML() is back as it was
+ originally. Method ServiceException.toDOM() removed.
+
2007-04-18 Paul Gordon
* Added support for binary data file loading, and Web image display in Seahawk & ACDServlet
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFn9008357@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/main/org/biomoby/shared/datatypes
Modified Files:
MobyDateTime.java
Log Message:
moby-live/Java/src/main/org/biomoby/shared/datatypes MobyDateTime.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyDateTime.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyDateTime.java 2006/02/05 12:11:08 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyDateTime.java 2007/05/21 00:56:15 1.3
@@ -40,7 +40,7 @@
* A string defining (in symbols used in Java's SimpleDateFormat)
* a full Biomoby DateTime format complying with ISO 8601.
*/
- public static final String FULL_FORMAT = "yyyy-MM-dd'T'HH:mm:ss'Z'Z";
+ public static final String FULL_FORMAT = "yyyy-MM-dd'T'HH:mm:ssZ";
/**
* An array defining all allowed formats for Biomoby DateTime
@@ -57,7 +57,6 @@
"yyyy-MM-dd'T'HH:mm",
"yyyy-MM-dd'T'HH:mm:ss",
"yyyy-MM-dd'T'HH:mm:ss",
- "yyyy-MM-dd'T'HH:mm:ss'Z'",
FULL_FORMAT
};
@@ -91,25 +90,45 @@
* Additionally to the same method in the superclass, it checks
* for a correct format.
*
+ * It also allows values with the time zone in the format "+hhmm"
+ * and "-hhmm" (instead of correct ones "+hh:mm" and
+ * "-hh:mm"). Such values are the result of SimpleDateFormat
+ * constructor when fed with the {@link #FULL_FORMAT}.
+ *
* @param value to be stored; if it is null or an empty string it
- * creates a date/time of the current moment
+ * creates a date/time of the current moment
+ *
* @throws MobyException if the 'value' does not follow the ISO
* 8601 specification
*************************************************************************/
public void setValue (String value)
throws MobyException {
GregorianCalendar calendar;
- if ( value == null || "".equals (value.trim()) ) {
+ if (value == null) {
calendar = MobyDataDateTime.parseISO8601 (null);
} else {
- // validate
- try {
- calendar = MobyDataDateTime.parseISO8601 (value.trim());
- } catch (IllegalArgumentException e) {
- throw new MobyException (MSG_NOT_VALID_DATE (getName(), value.trim()));
+ String tValue = value.trim();
+ if ("".equals (tValue)) {
+ calendar = MobyDataDateTime.parseISO8601 (null);
+ } else {
+ // validate
+ try {
+ int len = tValue.length();
+ if (len > 5 &&
+ ( tValue.charAt (len - 5) == '+' ||
+ tValue.charAt (len - 5) == '-' )) {
+ tValue =
+ tValue.substring (0, len - 2) +
+ ':' +
+ tValue.substring (len - 2);
+ }
+ calendar = MobyDataDateTime.parseISO8601 (tValue);
+ } catch (IllegalArgumentException e) {
+ throw new MobyException (MSG_NOT_VALID_DATE (getName(), tValue));
+ }
}
}
- super.setValue (MobyDataDateTime.getString (calendar));
+ super.setValue (MobyDataDateTime.getString (calendar));
}
}
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFc8008303@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/Clients
Added Files:
TestDate.java
Log Message:
moby-live/Java/src/Clients TestDate.java,NONE,1.1
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFN8008289@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs/API
In directory dev.open-bio.org:/tmp/cvs-serv8252/docs/API
Modified Files:
.cvsignore.template
Log Message:
moby-live/Java/docs/API .cvsignore.template,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2005/05/19 20:27:02 1.4
+++ /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2007/05/21 00:56:15 1.5
@@ -5,4 +5,5 @@
class-use
org
embl
+ca
resources
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFdN008390@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/client
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/samples/org/jmoby/tutorial/client
Added Files:
TestCreateGCP_LocusCollection.java.txt
Removed Files:
TestCreateGCP_LocusCollection.java
Log Message:
moby-live/Java/src/samples/org/jmoby/tutorial/client TestCreateGCP_LocusCollection.java.txt,NONE,1.1 TestCreateGCP_LocusCollection.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/client/RCS/TestCreateGCP_LocusCollection.java,v: No such file or directory
From senger at dev.open-bio.org Sun May 20 20:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFfk008417@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/samples/org/jmoby/tutorial/service
Added Files:
TestServiceNotesImpl.java
Log Message:
moby-live/Java/src/samples/org/jmoby/tutorial/service TestServiceNotesImpl.java,NONE,1.1
From senger at dev.open-bio.org Sun May 20 20:56:46 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uk56008472@dev.open-bio.org>
senger
Sun May 20 20:56:46 EDT 2007
Update of /home/repository/moby/moby-live/Java/data
In directory dev.open-bio.org:/tmp/cvs-serv8457/data
Added Files:
TestServiceNotes-input.xml
Log Message:
moby-live/Java/data TestServiceNotes-input.xml,NONE,1.1
From mwilkinson at dev.open-bio.org Thu May 24 13:50:37 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 24 May 2007 13:50:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705241750.l4OHobdk021458@dev.open-bio.org>
mwilkinson
Thu May 24 13:50:36 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv21439/MOBY-S_API/Perl
Modified Files:
DiscoverService.html
Log Message:
fixed error in docs
moby-live/Docs/MOBY-S_API/Perl DiscoverService.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/DiscoverService.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/DiscoverService.html 2007/02/19 22:36:12 1.2
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/DiscoverService.html 2007/05/24 17:50:36 1.3
@@ -73,7 +73,7 @@
use MOBY::Client::Central;
my $m = MOBY::Client::Central->new;
-my ($serv_instances, $reg) = $findService->(
+my ($serv_instances, $reg) = $m->findService(
authURI => "mydomain.mycompany.org",
serviceName => "getGoTerm");
From mwilkinson at dev.open-bio.org Thu May 24 15:46:38 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 24 May 2007 15:46:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705241946.l4OJkcYu021627@dev.open-bio.org>
mwilkinson
Thu May 24 15:46:38 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv21608/MOBY-S_API/Perl
Modified Files:
ExecuteSyncService.html
Log Message:
fixed error in docs
moby-live/Docs/MOBY-S_API/Perl ExecuteSyncService.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/02/19 22:36:12 1.2
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/24 19:46:38 1.3
@@ -105,7 +105,7 @@
# we now have the WSDL description of the Service
# we use this to create a MOBY::Client::Service object
-my $SERV = MOBY::Client::Service->new(service => $SI);
+my $SERV = MOBY::Client::Service->new(service => $wsdl);
# the $SERV object knows everything it needs to know to interact with
# that Moby Service, so all we have to do it provide the correct data
From mwilkinson at dev.open-bio.org Thu May 24 15:56:48 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 24 May 2007 15:56:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705241956.l4OJumEY021668@dev.open-bio.org>
mwilkinson
Thu May 24 15:56:47 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv21649/MOBY-S_API/Perl
Modified Files:
ExecuteSyncService.html
Log Message:
fixed error in docs
moby-live/Docs/MOBY-S_API/Perl ExecuteSyncService.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/24 19:46:38 1.3
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/24 19:56:47 1.4
@@ -116,8 +116,8 @@
@single_invocation = ([$articleName, $inputdata1]);
@multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2])
-my $result1 = $SERV->execute(XMLInputList => \@single_invocation);
-my $result2 = $SERV->execute(XMLInputList => \@multiple_invocation);
+my $result1 = $SERV->execute(XMLinputlist => \@single_invocation);
+my $result2 = $SERV->execute(XMLinputlist => \@multiple_invocation);
# The content of $result is the raw XML of whatever the service provider
# gave us. There are a variety of ways to deal with this data, or you
From mwilkinson at dev.open-bio.org Fri May 25 09:22:56 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 25 May 2007 09:22:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705251322.l4PDMuWc023386@dev.open-bio.org>
mwilkinson
Fri May 25 09:22:56 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv23367/MOBY
Modified Files:
CommonSubs.pm
Log Message:
fixed documentation error
moby-live/Perl/MOBY CommonSubs.pm,1.96,1.97
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.96
retrieving revision 1.97
diff -u -r1.96 -r1.97
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2007/02/09 00:27:07 1.96
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2007/05/25 13:22:56 1.97
@@ -38,7 +38,7 @@
my $responses = serviceResponseParser($resp); # returns MOBY objects
foreach my $queryID(keys %$responses){
- $this_invocation = $inputs->{$queryID}; # this is the block with this queryID
+ $this_invocation = $responses->{$queryID}; # this is the block with this queryID
my $this_output = "";
if (my $data = $this_invocation->{'responseArticleName'}){
From mwilkinson at dev.open-bio.org Fri May 25 09:25:14 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 25 May 2007 09:25:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705251325.l4PDPEAR023426@dev.open-bio.org>
mwilkinson
Fri May 25 09:25:14 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv23407/MOBY-S_API/Perl
Modified Files:
ExecuteSyncService.html
Log Message:
fixed doc rendering of XML
moby-live/Docs/MOBY-S_API/Perl ExecuteSyncService.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/24 19:56:47 1.4
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/25 13:25:14 1.5
@@ -110,8 +110,8 @@
# that Moby Service, so all we have to do it provide the correct data
my $articleName =
-my $inputdata1 = "
The service API, which
describes how to interact with a service provided under the MOBY
framework: it describes what messages you can send to a service,
how should they be structured,
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFdm008375@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/main/org/biomoby/shared/parser
Modified Files:
ServiceException.java
Log Message:
moby-live/Java/src/main/org/biomoby/shared/parser ServiceException.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java 2006/11/11 23:04:34 1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java 2007/05/21 00:56:15 1.12
@@ -405,7 +405,7 @@
/**************************************************************************
*
*************************************************************************/
- public Element toDOM() {
+ public Element toXML() {
Element elem = MobyPackage.getXMLElement (MobyTags.MOBYEXCEPTION);
MobyPackage.setXMLAttribute (elem, MobyTags.SEVERITY, getSeverityAsString());
if (refQueryID != null)
@@ -479,26 +479,26 @@
return ex;
}
- public String toXML(){
- StringBuffer xml = new StringBuffer(" \n");
-
- xml.append(""+code+"");
+// public String toXML(){
+// StringBuffer xml = new StringBuffer(" \n");
+
+// xml.append(""+code+"");
+
+// if(getMessage() != null){
+// xml.append(" "+getMessage()+"");
+// }
- if(getMessage() != null){
- xml.append(" "+getMessage()+"");
- }
-
- xml.append(" ");
+// xml.append(" ");
- return xml.toString();
- }
+// return xml.toString();
+// }
}
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFpm008321@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/main/org/biomoby/registry/meta
Modified Files:
RegistriesList.java
Log Message:
moby-live/Java/src/main/org/biomoby/registry/meta RegistriesList.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/RegistriesList.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/RegistriesList.java 2006/12/05 17:18:16 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/RegistriesList.java 2007/05/21 00:56:15 1.3
@@ -20,7 +20,8 @@
* Please edit this file if you want to have your BioMoby registry
* visible to others (for example, in BioMoby Dashboard).
*
- * Or, you can also replace this implementation by your own, with your own list of registries
+ * Or, you can also replace this implementation by your own, with your
+ * own list of registries.
*
* @author Martin Senger
* @version $Id$
@@ -53,6 +54,15 @@
"The MOBY registry at the International Rice Research Institute (IRRI) is intended mostly for Generation Challenge Program (GCP) developers. It allows the registration of experimental moby entities within GCP."),
new Registry
+ ("INAB",
+ "http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl",
+ "http://moby-dev.inab.org/MOBY/Central",
+ "INAB, Spain",
+ "",
+ true,
+ "The MOBY registry at the Instituto Nacional de Bioinform??tica, Spain."),
+
+ new Registry
("testing",
"http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl",
"http://bioinfo.icapture.ubc.ca/MOBY/Central",
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFZo008339@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/chooser
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/main/org/biomoby/service/dashboard/chooser
Modified Files:
DateTimeChooserEditor.java
Log Message:
moby-live/Java/src/main/org/biomoby/service/dashboard/chooser DateTimeChooserEditor.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/chooser/DateTimeChooserEditor.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/chooser/DateTimeChooserEditor.java 2006/02/08 17:24:13 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/chooser/DateTimeChooserEditor.java 2007/05/21 00:56:15 1.2
@@ -31,8 +31,8 @@
/**
* A cell editor that invokes {@link DateTimeChooser} to get a
* calendar GUI. The editor is supposed to be used for editing cells
- * in JTable, and it complies wiht the Biomoby specification for
- * dat-time formats.
+ * in JTable, and it complies with the Biomoby specification for
+ * date-time formats.
*
* @author Martin Senger
* @version $Id$
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFVC008271@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv8252/docs
Modified Files:
ChangeLog
Log Message:
moby-live/Java/docs ChangeLog,1.77,1.78
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.77
retrieving revision 1.78
diff -u -r1.77 -r1.78
--- /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/04/18 16:33:45 1.77
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/21 00:56:14 1.78
@@ -1,3 +1,11 @@
+2007-05-20 Martin Senger
+
+ * Fixed: the date format of MobyDateTime is now fully compliant
+ with the ISO8601.
+
+ * Fixed: method ServiceException.toXML() is back as it was
+ originally. Method ServiceException.toDOM() removed.
+
2007-04-18 Paul Gordon
* Added support for binary data file loading, and Web image display in Seahawk & ACDServlet
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFn9008357@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/main/org/biomoby/shared/datatypes
Modified Files:
MobyDateTime.java
Log Message:
moby-live/Java/src/main/org/biomoby/shared/datatypes MobyDateTime.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyDateTime.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyDateTime.java 2006/02/05 12:11:08 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyDateTime.java 2007/05/21 00:56:15 1.3
@@ -40,7 +40,7 @@
* A string defining (in symbols used in Java's SimpleDateFormat)
* a full Biomoby DateTime format complying with ISO 8601.
*/
- public static final String FULL_FORMAT = "yyyy-MM-dd'T'HH:mm:ss'Z'Z";
+ public static final String FULL_FORMAT = "yyyy-MM-dd'T'HH:mm:ssZ";
/**
* An array defining all allowed formats for Biomoby DateTime
@@ -57,7 +57,6 @@
"yyyy-MM-dd'T'HH:mm",
"yyyy-MM-dd'T'HH:mm:ss",
"yyyy-MM-dd'T'HH:mm:ss",
- "yyyy-MM-dd'T'HH:mm:ss'Z'",
FULL_FORMAT
};
@@ -91,25 +90,45 @@
* Additionally to the same method in the superclass, it checks
* for a correct format.
*
+ * It also allows values with the time zone in the format "+hhmm"
+ * and "-hhmm" (instead of correct ones "+hh:mm" and
+ * "-hh:mm"). Such values are the result of SimpleDateFormat
+ * constructor when fed with the {@link #FULL_FORMAT}.
+ *
* @param value to be stored; if it is null or an empty string it
- * creates a date/time of the current moment
+ * creates a date/time of the current moment
+ *
* @throws MobyException if the 'value' does not follow the ISO
* 8601 specification
*************************************************************************/
public void setValue (String value)
throws MobyException {
GregorianCalendar calendar;
- if ( value == null || "".equals (value.trim()) ) {
+ if (value == null) {
calendar = MobyDataDateTime.parseISO8601 (null);
} else {
- // validate
- try {
- calendar = MobyDataDateTime.parseISO8601 (value.trim());
- } catch (IllegalArgumentException e) {
- throw new MobyException (MSG_NOT_VALID_DATE (getName(), value.trim()));
+ String tValue = value.trim();
+ if ("".equals (tValue)) {
+ calendar = MobyDataDateTime.parseISO8601 (null);
+ } else {
+ // validate
+ try {
+ int len = tValue.length();
+ if (len > 5 &&
+ ( tValue.charAt (len - 5) == '+' ||
+ tValue.charAt (len - 5) == '-' )) {
+ tValue =
+ tValue.substring (0, len - 2) +
+ ':' +
+ tValue.substring (len - 2);
+ }
+ calendar = MobyDataDateTime.parseISO8601 (tValue);
+ } catch (IllegalArgumentException e) {
+ throw new MobyException (MSG_NOT_VALID_DATE (getName(), tValue));
+ }
}
}
- super.setValue (MobyDataDateTime.getString (calendar));
+ super.setValue (MobyDataDateTime.getString (calendar));
}
}
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFc8008303@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/Clients
Added Files:
TestDate.java
Log Message:
moby-live/Java/src/Clients TestDate.java,NONE,1.1
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFN8008289@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs/API
In directory dev.open-bio.org:/tmp/cvs-serv8252/docs/API
Modified Files:
.cvsignore.template
Log Message:
moby-live/Java/docs/API .cvsignore.template,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2005/05/19 20:27:02 1.4
+++ /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2007/05/21 00:56:15 1.5
@@ -5,4 +5,5 @@
class-use
org
embl
+ca
resources
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFdN008390@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/client
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/samples/org/jmoby/tutorial/client
Added Files:
TestCreateGCP_LocusCollection.java.txt
Removed Files:
TestCreateGCP_LocusCollection.java
Log Message:
moby-live/Java/src/samples/org/jmoby/tutorial/client TestCreateGCP_LocusCollection.java.txt,NONE,1.1 TestCreateGCP_LocusCollection.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/client/RCS/TestCreateGCP_LocusCollection.java,v: No such file or directory
From senger at dev.open-bio.org Mon May 21 00:56:15 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uFfk008417@dev.open-bio.org>
senger
Sun May 20 20:56:15 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv8252/src/samples/org/jmoby/tutorial/service
Added Files:
TestServiceNotesImpl.java
Log Message:
moby-live/Java/src/samples/org/jmoby/tutorial/service TestServiceNotesImpl.java,NONE,1.1
From senger at dev.open-bio.org Mon May 21 00:56:46 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 20 May 2007 20:56:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705210056.l4L0uk56008472@dev.open-bio.org>
senger
Sun May 20 20:56:46 EDT 2007
Update of /home/repository/moby/moby-live/Java/data
In directory dev.open-bio.org:/tmp/cvs-serv8457/data
Added Files:
TestServiceNotes-input.xml
Log Message:
moby-live/Java/data TestServiceNotes-input.xml,NONE,1.1
From mwilkinson at dev.open-bio.org Thu May 24 17:50:37 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 24 May 2007 13:50:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705241750.l4OHobdk021458@dev.open-bio.org>
mwilkinson
Thu May 24 13:50:36 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv21439/MOBY-S_API/Perl
Modified Files:
DiscoverService.html
Log Message:
fixed error in docs
moby-live/Docs/MOBY-S_API/Perl DiscoverService.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/DiscoverService.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/DiscoverService.html 2007/02/19 22:36:12 1.2
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/DiscoverService.html 2007/05/24 17:50:36 1.3
@@ -73,7 +73,7 @@
use MOBY::Client::Central;
my $m = MOBY::Client::Central->new;
-my ($serv_instances, $reg) = $findService->(
+my ($serv_instances, $reg) = $m->findService(
authURI => "mydomain.mycompany.org",
serviceName => "getGoTerm");
From mwilkinson at dev.open-bio.org Thu May 24 19:46:38 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 24 May 2007 15:46:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705241946.l4OJkcYu021627@dev.open-bio.org>
mwilkinson
Thu May 24 15:46:38 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv21608/MOBY-S_API/Perl
Modified Files:
ExecuteSyncService.html
Log Message:
fixed error in docs
moby-live/Docs/MOBY-S_API/Perl ExecuteSyncService.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/02/19 22:36:12 1.2
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/24 19:46:38 1.3
@@ -105,7 +105,7 @@
# we now have the WSDL description of the Service
# we use this to create a MOBY::Client::Service object
-my $SERV = MOBY::Client::Service->new(service => $SI);
+my $SERV = MOBY::Client::Service->new(service => $wsdl);
# the $SERV object knows everything it needs to know to interact with
# that Moby Service, so all we have to do it provide the correct data
From mwilkinson at dev.open-bio.org Thu May 24 19:56:48 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 24 May 2007 15:56:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705241956.l4OJumEY021668@dev.open-bio.org>
mwilkinson
Thu May 24 15:56:47 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv21649/MOBY-S_API/Perl
Modified Files:
ExecuteSyncService.html
Log Message:
fixed error in docs
moby-live/Docs/MOBY-S_API/Perl ExecuteSyncService.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/24 19:46:38 1.3
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/24 19:56:47 1.4
@@ -116,8 +116,8 @@
@single_invocation = ([$articleName, $inputdata1]);
@multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2])
-my $result1 = $SERV->execute(XMLInputList => \@single_invocation);
-my $result2 = $SERV->execute(XMLInputList => \@multiple_invocation);
+my $result1 = $SERV->execute(XMLinputlist => \@single_invocation);
+my $result2 = $SERV->execute(XMLinputlist => \@multiple_invocation);
# The content of $result is the raw XML of whatever the service provider
# gave us. There are a variety of ways to deal with this data, or you
From mwilkinson at dev.open-bio.org Fri May 25 13:22:56 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 25 May 2007 09:22:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705251322.l4PDMuWc023386@dev.open-bio.org>
mwilkinson
Fri May 25 09:22:56 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv23367/MOBY
Modified Files:
CommonSubs.pm
Log Message:
fixed documentation error
moby-live/Perl/MOBY CommonSubs.pm,1.96,1.97
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.96
retrieving revision 1.97
diff -u -r1.96 -r1.97
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2007/02/09 00:27:07 1.96
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2007/05/25 13:22:56 1.97
@@ -38,7 +38,7 @@
my $responses = serviceResponseParser($resp); # returns MOBY objects
foreach my $queryID(keys %$responses){
- $this_invocation = $inputs->{$queryID}; # this is the block with this queryID
+ $this_invocation = $responses->{$queryID}; # this is the block with this queryID
my $this_output = "";
if (my $data = $this_invocation->{'responseArticleName'}){
From mwilkinson at dev.open-bio.org Fri May 25 13:25:14 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 25 May 2007 09:25:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705251325.l4PDPEAR023426@dev.open-bio.org>
mwilkinson
Fri May 25 09:25:14 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv23407/MOBY-S_API/Perl
Modified Files:
ExecuteSyncService.html
Log Message:
fixed doc rendering of XML
moby-live/Docs/MOBY-S_API/Perl ExecuteSyncService.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/24 19:56:47 1.4
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/25 13:25:14 1.5
@@ -110,8 +110,8 @@
# that Moby Service, so all we have to do it provide the correct data
my $articleName =
-my $inputdata1 = "";
-my $inputdata2 = "";
+my $inputdata1 = ">Object namespace='GO' id='0050789'>";
+my $inputdata2 = ">Object namespace='GO' id='0050789'>";
@single_invocation = ([$articleName, $inputdata1]);
@multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2])
From mwilkinson at dev.open-bio.org Fri May 25 13:48:50 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 25 May 2007 09:48:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705251348.l4PDmoYh023955@dev.open-bio.org>
mwilkinson
Fri May 25 09:48:50 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv23936/MOBY/Client
Modified Files:
SimpleArticle.pm
Log Message:
namespacing of attributes was not being read properly
moby-live/Perl/MOBY/Client SimpleArticle.pm,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2006/10/02 23:31:20 1.16
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2007/05/25 13:48:50 1.17
@@ -275,6 +275,7 @@
$self->articleName( "" );
$self->objectType( "" );
my $attr = $dom->getAttributeNode( 'articleName' );
+ $attr ||= $dom->getAttributeNode( 'moby:articleName' );
my $articleName = $attr ? $attr->getValue : "";
$attr = $dom->getAttributeNode( 'lsid' );
my $lsid = $attr ? $attr->getValue : "";
From mwilkinson at dev.open-bio.org Fri May 25 13:57:23 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 25 May 2007 09:57:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705251357.l4PDvNNV024337@dev.open-bio.org>
mwilkinson
Fri May 25 09:57:23 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv24300/MOBY
Modified Files:
CommonSubs.pm
Log Message:
documentation errors
moby-live/Perl/MOBY CommonSubs.pm,1.97,1.98
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.97
retrieving revision 1.98
diff -u -r1.97 -r1.98
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2007/05/25 13:22:56 1.97
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2007/05/25 13:57:23 1.98
@@ -41,11 +41,13 @@
$this_invocation = $responses->{$queryID}; # this is the block with this queryID
my $this_output = "";
- if (my $data = $this_invocation->{'responseArticleName'}){
+ if (my $data = $this_invocation->{'responseArticleName'}){ # whatever your articleName is...
# $data is a MOBY::Client::Simple|Collection|ParameterArticle
my ($namespace) = @{$data->namespaces};
my $id = $data->id;
- my $XML_LibXML = $input->XML_DOM; # get access to the DOM
+ my $XML_LibXML = $data->XML_DOM; # get access to the DOM
+ # assuming that you have an element of type "String"
+ # with articleName "Description"
my $desc = getNodeContentWithArticle($XML_LibXML, "String", "Description");
###################
# DO SOMETHING TO RESPOSE DATA HERE
From mwilkinson at dev.open-bio.org Fri May 25 13:58:51 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 25 May 2007 09:58:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705251358.l4PDwpVd024437@dev.open-bio.org>
mwilkinson
Fri May 25 09:58:51 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv24414/MOBY/Client
Modified Files:
CollectionArticle.pm SecondaryArticle.pm
Log Message:
more namespace parsing errors
moby-live/Perl/MOBY/Client CollectionArticle.pm,1.16,1.17 SecondaryArticle.pm,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2006/05/30 18:56:16 1.16
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm 2007/05/25 13:58:51 1.17
@@ -263,6 +263,7 @@
$self->articleName( "" );
$self->Simples( [] );
my $attr = $dom->getAttributeNode( 'articleName' );
+ $attr ||= $dom->getAttributeNode( 'moby:articleName' );
my $articleName = "";
$articleName = $attr->getValue if $attr;
$self->articleName( $articleName );
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2007/02/07 01:21:24 1.13
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2007/05/25 13:58:51 1.14
@@ -255,6 +255,7 @@
$self->articleName( "" );
$self->objectType( "" );
my $attr = $dom->getAttributeNode( 'articleName' );
+ $attr ||= $dom->getAttributeNode( 'moby:articleName' );
$self->articleName( $attr ? $attr->getValue : "" );
if ( @{ $dom->getElementsByLocalName( 'Value' ) }[0] ) {
return $self->_createInstantiatedArticle( $dom );
From mwilkinson at dev.open-bio.org Fri May 25 14:23:47 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 25 May 2007 10:23:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705251423.l4PENlwo024516@dev.open-bio.org>
mwilkinson
Fri May 25 10:23:47 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv24497/MOBY/Client
Modified Files:
SimpleArticle.pm
Log Message:
more namespace parsing errors
moby-live/Perl/MOBY/Client SimpleArticle.pm,1.17,1.18
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2007/05/25 13:48:50 1.17
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm 2007/05/25 14:23:47 1.18
@@ -325,8 +325,10 @@
next unless $child->nodeType == ELEMENT_NODE;
$self->objectType( $child->localname );
my $attr = $child->getAttributeNode( 'namespace' );
+ $attr ||= $child->getAttributeNode( 'moby:namespace' );
$self->addNamespace( $attr->getValue ) if $attr;
my $id = $child->getAttributeNode( 'id' );
+ $id ||= $child->getAttributeNode( 'moby:id' );
$self->id( $id->getValue ) if $id;
}
return $self;
From senger at dev.open-bio.org Sun May 27 19:18:17 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 27 May 2007 15:18:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705271918.l4RJIHG3026911@dev.open-bio.org>
senger
Sun May 27 15:18:17 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv26856/src/samples/org/jmoby/tutorial/service
Modified Files:
TestServiceNotesImpl.java
Log Message:
moby-live/Java/src/samples/org/jmoby/tutorial/service TestServiceNotesImpl.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java 2007/05/21 00:56:15 1.1
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java 2007/05/27 19:18:17 1.2
@@ -37,13 +37,31 @@
throws MobyException {
MobyDateTime input = get_input_date (request);
String date = input.getValue();
- outputContext.setServiceNotes ("This is a general service note.");
outputContext.addException (ServiceException.info ("Input date was " + date),
request);
+
+ StringBuilder buf = new StringBuilder();
+ buf.append ("This is a general service note.\n");
+ buf.append ("HTTP Headers:\n");
+ buf.append ("-------------\n");
+ buf.append (getHTTPHeaders().toString());
+ buf.append ("\n");
+ buf.append ("Length: ");
+ buf.append (getRequestLength() + "\n");
+ try {
+ buf.append ("Request URL: ");
+ buf.append (getServletRequest().getRequestURL().toString());
+ buf.append ("\n");
+ } catch (NullPointerException e) {
+ // can happen if the servlet request is not available
+ }
+ outputContext.setServiceNotes (buf.toString());
+
SimpleDateFormat sdf = new SimpleDateFormat (MobyDateTime.FULL_FORMAT);
MobyDateTime output = new MobyDateTime ();
output.setValue (sdf.format (new Date()));
set_output_date (response, output);
+
}
}
From senger at dev.open-bio.org Sun May 27 19:18:17 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 27 May 2007 15:18:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705271918.l4RJIHVp026893@dev.open-bio.org>
senger
Sun May 27 15:18:17 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv26856/src/main/org/biomoby/service
Modified Files:
BaseService.java
Log Message:
moby-live/Java/src/main/org/biomoby/service BaseService.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java 2006/04/29 21:22:30 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java 2007/05/27 19:18:17 1.8
@@ -21,9 +21,11 @@
import org.apache.axis.MessageContext;
import javax.servlet.http.HttpServletRequest;
-import java.util.Vector;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Properties;
import java.util.Enumeration;
+import java.util.Properties;
/**
* A base class for all Biomoby services (if their providers choose to
@@ -160,13 +162,11 @@
// but I want to keep the constructor of this class without
// any throwing exception, so I simulate here what toolkit can do
if (toolkit == null) {
- Vector v = new Vector();
+ List v = new ArrayList();
Properties props = System.getProperties();
for (Enumeration en = props.propertyNames(); en.hasMoreElements(); )
- v.addElement (en.nextElement());
- String[] results = new String [v.size()];
- v.copyInto (results);
- return results;
+ v.add ((String)en.nextElement());
+ return v.toArray (new String[] {});
}
return toolkit.getAttributeNames();
}
@@ -204,6 +204,22 @@
}
/**************************************************************************
+ * Returns a servlet request instance - the one that delivered a
+ * request to this service.
+ *
+ * @return a servlet request, or null if the request is not
+ * available
+ *************************************************************************/
+ public HttpServletRequest getServletRequest() {
+ MessageContext ctx = MessageContext.getCurrentContext();
+ if (ctx == null)
+ return null;
+ HttpServletRequest req =
+ (HttpServletRequest)ctx.getProperty (HTTPConstants.MC_HTTP_SERVLETREQUEST);
+ return req;
+ }
+
+ /**************************************************************************
* Returns the Internet Protocol (IP) address of the client or
* last proxy that sent the request.
*
@@ -219,6 +235,57 @@
}
/**************************************************************************
+ * Returns HTTP headers that were used when delivering a request
+ * to this services.
+ *
+ * @return a set of name-value pairs representinh HTTP headers; if
+ * the headers are not accessible, an empty set is returned (never
+ * null)
+ *************************************************************************/
+ public Properties getHTTPHeaders() {
+ Properties headers = new Properties();
+ MessageContext ctx = MessageContext.getCurrentContext();
+ if (ctx == null)
+ return headers;
+ HttpServletRequest req =
+ (HttpServletRequest)ctx.getProperty (HTTPConstants.MC_HTTP_SERVLETREQUEST);
+ if (req == null)
+ return headers;
+ for (Enumeration en = req.getHeaderNames(); en.hasMoreElements(); ) {
+ String headerName = (String)en.nextElement();
+ String headerValue = req.getHeader (headerName);
+ if (headerValue != null)
+ headers.put (headerName, headerValue);
+ }
+ return headers;
+ }
+
+ /**************************************************************************
+ * Returns length (in bytes) of the request coming to this service.
+ *
+ * The length is taken from the HTTP headers. This is only a
+ * convenient method extracting one header from those available by
+ * the {@link #getHTTPHeaders getHTTPHeaders}. >p>
+ *
+ * @return a length of the request, or zero if the request length
+ * is not available
+ *************************************************************************/
+ public int getRequestLength() {
+ MessageContext ctx = MessageContext.getCurrentContext();
+ if (ctx == null)
+ return 0;
+ HttpServletRequest req =
+ (HttpServletRequest)ctx.getProperty (HTTPConstants.MC_HTTP_SERVLETREQUEST);
+ if (req == null)
+ return 0;
+ try {
+ return new Integer (req.getHeader ("content-length")).intValue();
+ } catch (Exception e) {
+ return 0;
+ }
+ }
+
+ /**************************************************************************
* A utility method returning true if 'value' is neither null nor
* a string consisting only from whitespaces.
*************************************************************************/
From senger at dev.open-bio.org Sun May 27 19:18:17 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 27 May 2007 15:18:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705271918.l4RJIHGA026875@dev.open-bio.org>
senger
Sun May 27 15:18:17 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv26856/docs
Modified Files:
ChangeLog
Log Message:
moby-live/Java/docs ChangeLog,1.78,1.79
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.78
retrieving revision 1.79
diff -u -r1.78 -r1.79
--- /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/21 00:56:14 1.78
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/27 19:18:17 1.79
@@ -1,3 +1,9 @@
+2007-05-27 Martin Senger
+
+ * Added: BaseService got new methods to access HTTP headers and
+ servlet environment of the request (getRequestLength(),
+ getHTTPHeaders(), getServletRequest()).
+
2007-05-20 Martin Senger
* Fixed: the date format of MobyDateTime is now fully compliant
From senger at dev.open-bio.org Tue May 29 03:51:46 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 28 May 2007 23:51:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705290351.l4T3pkPx029134@dev.open-bio.org>
senger
Mon May 28 23:51:46 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv29045/src/main/org/biomoby/client
Modified Files:
BaseClient.java CentralDigestCachedImpl.java
CentralDigestImpl.java CentralImpl.java
Log Message:
moby-live/Java/src/main/org/biomoby/client BaseClient.java,1.11,1.12 CentralDigestCachedImpl.java,1.18,1.19 CentralDigestImpl.java,1.12,1.13 CentralImpl.java,1.47,1.48
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java 2006/07/07 04:12:39 1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java 2007/05/29 03:51:46 1.12
@@ -21,6 +21,8 @@
import org.tulsoft.tools.soap.axis.AxisCall;
import org.tulsoft.shared.GException;
+import org.apache.commons.lang.StringUtils;
+
import org.jdom.input.SAXBuilder;
import org.jdom.Document;
import org.jdom.Element;
@@ -59,10 +61,10 @@
*
*************************************************************************/
static protected boolean notEmpty (String value) {
- return ( value != null && ! "".equals (value.trim()) );
+ return StringUtils.isNotBlank (value);
}
static protected boolean isEmpty (String value) {
- return ! notEmpty (value);
+ return StringUtils.isBlank (value);
}
/**************************************************************************
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2006/04/28 00:13:40 1.18
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2007/05/29 03:51:46 1.19
@@ -556,7 +556,9 @@
if (! currentFiles.contains (authority)) {
// missing file: fetch it from a registry
fireEvent (AUTHORITY_LOADING, authority);
- String xml = getServicesAsXML (new MobyService (MobyService.DUMMY_NAME, authority), null, true, true);
+ MobyService pattern = new MobyService (MobyService.DUMMY_NAME, authority);
+ pattern.setCategory ("");
+ String xml = getServicesAsXML (pattern, null, true, true);
store (servicesCache, authority, xml);
fireEvent (AUTHORITY_LOADED, authority);
if (stopS) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestImpl.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestImpl.java 2006/07/07 04:12:39 1.12
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestImpl.java 2007/05/29 03:51:46 1.13
@@ -174,7 +174,9 @@
fireEvent (AUTHORITY_LOADING, authority);
String[] names = (String[])entry.getValue();
for (int i = 0; i < names.length; i++) {
- MobyService[] servs = findService (new MobyService (names[i], authority));
+ MobyService pattern = new MobyService (names[i], authority);
+ pattern.setCategory ("");
+ MobyService[] servs = findService (pattern);
for (int j = 0; j < servs.length; j++)
v.addElement (servs[j]);
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2006/11/21 13:04:15 1.47
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2007/05/29 03:51:46 1.48
@@ -385,8 +385,10 @@
boolean expandObjects,
boolean expandServices,
boolean authoritative) {
- if (service == null)
+ if (service == null) {
service = new MobyService ("dummy");
+ service.setCategory ("");
+ }
StringBuffer buf = new StringBuffer();
buf.append ("\n\n");
@@ -1430,6 +1432,7 @@
if (serviceType == null)
return new MobyService[] {};
MobyService pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
pattern.setType (serviceType);
return findService (pattern, null);
}
@@ -1469,8 +1472,10 @@
boolean includeChildrenServiceTypes,
boolean includeParentDataTypes)
throws MobyException {
- if (pattern == null)
+ if (pattern == null) {
pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ }
String result =
getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes);
From senger at dev.open-bio.org Tue May 29 03:51:46 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 28 May 2007 23:51:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705290351.l4T3pkG6029086@dev.open-bio.org>
senger
Mon May 28 23:51:46 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv29045/src/Clients
Modified Files:
CreateMobyInput.java MobyCmdLineClient.java
Log Message:
moby-live/Java/src/Clients CreateMobyInput.java,1.8,1.9 MobyCmdLineClient.java,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/CreateMobyInput.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/Clients/CreateMobyInput.java 2006/02/12 18:47:38 1.8
+++ /home/repository/moby/moby-live/Java/src/Clients/CreateMobyInput.java 2007/05/29 03:51:46 1.9
@@ -206,8 +206,9 @@
if (service != null) {
MobyService mobyService = null;
if (cachedir == null) {
- MobyService[] services =
- worker.findService (new MobyService (service));
+ MobyService pattern = new MobyService (service);
+ pattern.setCategory ("");
+ MobyService[] services = worker.findService (pattern);
if (services.length > 0)
mobyService = services[0];
} else {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2005/10/27 04:15:23 1.13
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2007/05/29 03:51:46 1.14
@@ -519,13 +519,19 @@
decorationLn ("--------------------");
int pos = param.indexOf (",");
MobyService[] services;
- if (pos == -1)
- services = worker.findService (new MobyService (param));
- else if (pos == param.length() - 1)
- services = worker.findService (new MobyService (param.substring (0, pos)));
- else {
- MobyService pattern = new MobyService (param.substring (0, pos));
+ MobyService pattern = null;
+ if (pos == -1) {
+ pattern = new MobyService (param);
+ pattern.setCategory ("");
+ services = worker.findService (pattern);
+ } else if (pos == param.length() - 1) {
+ pattern = new MobyService (param.substring (0, pos));
+ pattern.setCategory ("");
+ services = worker.findService (pattern);
+ } else {
+ pattern = new MobyService (param.substring (0, pos));
pattern.setAuthority (param.substring (pos+1));
+ pattern.setCategory ("");
services = worker.findService (pattern);
}
printServices (services, cmd.hasOption ("-on"));
@@ -541,15 +547,26 @@
decorationLn ("Looking for services of type '" + param + "':");
decorationLn ("----------------------------");
MobyService pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
pattern.setType (param);
printServices (worker.findService (pattern, null, !cmd.hasOption ("-nc"), true),
cmd.hasOption ("-on"));
}
+ if ((param = cmd.getParam ("-fc")) != null ) {
+ decorationLn ("Looking for services of category '" + param + "':");
+ decorationLn ("--------------------------------");
+ MobyService pattern = new MobyService ("dummy");
+ pattern.setCategory (param);
+ printServices (worker.findService (pattern, null, !cmd.hasOption ("-nc"), true),
+ cmd.hasOption ("-on"));
+ }
+
if (cmd.hasParam ("-fs-type") || cmd.hasParam ("-fs-auth") ||
cmd.hasParam ("-fs-in") || cmd.hasParam ("-fs-out")) {
decorationLn ("Looking for services with the following pattern:");
MobyService pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
pattern.setType (cmd.getParam ("-fs-type"));
pattern.setAuthority (cmd.getParam ("-fs-auth"));
if ((param = cmd.getParam ("-fs-in")) != null ) {
@@ -613,16 +630,23 @@
String serviceName = null;
int pos = params[0].indexOf (",");
MobyService[] services;
+ MobyService pattern = null;
if (pos == -1) {
serviceName = params[0];
- services = worker.findService (new MobyService (params[0]));
+ pattern = new MobyService (serviceName);
+ pattern.setCategory ("");
+ services = worker.findService (pattern);
+
} else if (pos == params[0].length() - 1) {
serviceName = params[0].substring (0, pos);
- services = worker.findService (new MobyService (serviceName));
+ pattern = new MobyService (serviceName);
+ pattern.setCategory ("");
+ services = worker.findService (pattern);
} else {
serviceName = params[0].substring (0, pos);
- MobyService pattern = new MobyService (serviceName);
+ pattern = new MobyService (serviceName);
pattern.setAuthority (params[0].substring (pos+1));
+ pattern.setCategory ("");
services = worker.findService (pattern);
}
if (services != null && services.length > 0) {
@@ -693,7 +717,7 @@
if (services != null) {
for (int i = 0; i < services.length; i++) {
if (onlyNames)
- System.out.println (services[i].getName());
+ System.out.println (services[i].getUniqueName());
else
System.out.println (services[i]);
}
From senger at dev.open-bio.org Tue May 29 03:51:46 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 28 May 2007 23:51:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705290351.l4T3pkNh029064@dev.open-bio.org>
senger
Mon May 28 23:51:45 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv29045/docs
Modified Files:
ChangeLog
Log Message:
moby-live/Java/docs ChangeLog,1.79,1.80
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.79
retrieving revision 1.80
diff -u -r1.79 -r1.80
--- /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/27 19:18:17 1.79
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/29 03:51:45 1.80
@@ -1,3 +1,15 @@
+2007-05-29 Martin Senger
+
+ * Fixed: on various place where a service was looking for, the
+ used service pattern has now category empty (so not only services
+ with the default 'moby' category are found).
+
+ * Changed: the output list with names of found services (created
+ by MobyCmdLineClient) contains now also service authority.
+
+ * Added: MobyCmdLineClient has a new option -fc for finding
+ services by category.
+
2007-05-27 Martin Senger
* Added: BaseService got new methods to access HTTP headers and
From senger at dev.open-bio.org Tue May 29 03:51:46 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 28 May 2007 23:51:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705290351.l4T3pk3b029184@dev.open-bio.org>
senger
Mon May 28 23:51:46 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv29045/src/samples/org/jmoby/tutorial/service
Modified Files:
TestServiceNotesImpl.java
Log Message:
moby-live/Java/src/samples/org/jmoby/tutorial/service TestServiceNotesImpl.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java 2007/05/27 19:18:17 1.2
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java 2007/05/29 03:51:46 1.3
@@ -61,7 +61,6 @@
MobyDateTime output = new MobyDateTime ();
output.setValue (sdf.format (new Date()));
set_output_date (response, output);
-
}
}
From senger at dev.open-bio.org Tue May 29 03:51:46 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 28 May 2007 23:51:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705290351.l4T3pkgM029104@dev.open-bio.org>
senger
Mon May 28 23:51:46 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory dev.open-bio.org:/tmp/cvs-serv29045/src/Clients/help
Modified Files:
MobyCmdLineClient_usage.txt
Log Message:
moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2005/09/04 13:45:37 1.10
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2007/05/29 03:51:46 1.11
@@ -66,6 +66,9 @@
-ft
find services of the given service type
+ -fc
+ find services of the given category
+
-f
find services by keywords (apply logical OR if more keywords);
is a comma-delimited lists of keywords
From senger at dev.open-bio.org Tue May 29 03:51:46 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 28 May 2007 23:51:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705290351.l4T3pkkr029160@dev.open-bio.org>
senger
Mon May 28 23:51:46 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator
In directory dev.open-bio.org:/tmp/cvs-serv29045/src/main/org/biomoby/service/generator
Modified Files:
ServicesGenerator.java
Log Message:
moby-live/Java/src/main/org/biomoby/service/generator ServicesGenerator.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2005/11/07 07:03:50 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2007/05/29 03:51:46 1.4
@@ -235,6 +235,7 @@
if (filteredIn (names[i], wantedService)) {
MobyService patternService = new MobyService (names[i]);
patternService.setAuthority (authority);
+ patternService.setCategory ("");
MobyService[] services = findService (patternService, worker, allServices);
for (int s = 0; s < services.length; s++)
generateService (services[s], props, allServices, allDataTypes, serviceCount);
From gordonp at dev.open-bio.org Tue May 29 23:49:32 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Tue, 29 May 2007 19:49:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705292349.l4TNnWQN031209@dev.open-bio.org>
gordonp
Tue May 29 19:49:32 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv31174/src/main/org/biomoby/shared/data
Modified Files:
MobyDataDateTime.java
Log Message:
Updates to fix timezone offsets from Zulu, which are now maintained. Ditched SimpleDateFormat and replaced with homegrown formatter.
moby-live/Java/src/main/org/biomoby/shared/data MobyDataDateTime.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataDateTime.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataDateTime.java 2007/04/03 02:27:33 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataDateTime.java 2007/05/29 23:49:32 1.8
@@ -46,7 +46,7 @@
* @param stringISO8601 if null, the current local date and time is used
*/
public MobyDataDateTime(String articleName, String stringISO8601) throws IllegalArgumentException{
- super(articleName, stringISO8601);
+ super(articleName);
setDataType(MobyDataType.getDataType("DateTime"));
value = parseISO8601(stringISO8601);
}
@@ -59,7 +59,6 @@
super(articleName, "");
setDataType(MobyDataType.getDataType("DateTime"));
value = cal;
- ((StringBuffer) super.getObject()).append(toString()); // set string representation in case super.toXML() is called explicitly
}
public MobyDataDateTime(GregorianCalendar cal){
@@ -171,21 +170,25 @@
}
boolean plus = tok.equals("+");
if (! st.hasMoreTokens()) {
- throw new IllegalArgumentException("Missing hour field");
+ throw new IllegalArgumentException("Missing hour field in timezone offset");
}
- int tzhour = Integer.parseInt(st.nextToken());
- int tzmin = 0;
+ String tzhour = st.nextToken();
+ String tzmin = "00";
if (check(st, ":") && (st.hasMoreTokens())) {
- tzmin = Integer.parseInt(st.nextToken());
+ tzmin = st.nextToken();
} else {
- throw new IllegalArgumentException("Missing minute field");
+ throw new IllegalArgumentException("Missing minute field in timezone offset");
}
if (plus) {
- calendar.add(Calendar.HOUR, tzhour);
- calendar.add(Calendar.MINUTE, tzmin);
+ calendar.setTimeZone(TimeZone.getTimeZone("GMT+"+tzhour+":"+tzmin));
+ calendar.add(Calendar.HOUR, Integer.parseInt(tzhour));
+ calendar.add(Calendar.MINUTE, Integer.parseInt(tzmin));
+ calendar.set(Calendar.DST_OFFSET, 0); //ISO8601 does not deal with DST
} else {
- calendar.add(Calendar.HOUR, -tzhour);
- calendar.add(Calendar.MINUTE, -tzmin);
+ calendar.setTimeZone(TimeZone.getTimeZone("GMT-"+tzhour+":"+tzmin));
+ calendar.add(Calendar.HOUR, Integer.parseInt("-"+tzhour));
+ calendar.add(Calendar.MINUTE, Integer.parseInt("-"+tzmin));
+ calendar.set(Calendar.DST_OFFSET, 0);
}
}
} catch (NumberFormatException ex) {
@@ -228,39 +231,39 @@
* <simon at jasmine.org.uk>. Does not yet deal with fractions
* of seconds.
*************************************************************************/
- public static String getString (GregorianCalendar value) {
+ public static String getString (GregorianCalendar cvalue) {
- String timef = "'T'hh:mm:ss";
+ String timef = "'T'HH:mm:ss";
String datef = "yyyy-MM-dd";
- String bothf = "yyyy-MM-dd'T'hh:mm:ss";
+ String bothf = "yyyy-MM-dd'T'HH:mm:ss";
boolean doTimeZone = true;
String format = bothf; // initially assume this is a date/time
- if((value.isSet(Calendar.DAY_OF_MONTH) == false || value.get(Calendar.DAY_OF_MONTH) == 1) &&
- (value.isSet(Calendar.MONTH) == false || value.get(Calendar.MONTH) == 0) &&
- (value.isSet(Calendar.YEAR) == false || value.get(Calendar.YEAR) == 1970)){
+ if((cvalue.isSet(Calendar.DAY_OF_MONTH) == false || cvalue.get(Calendar.DAY_OF_MONTH) == 1) &&
+ (cvalue.isSet(Calendar.MONTH) == false || cvalue.get(Calendar.MONTH) == 0) &&
+ (cvalue.isSet(Calendar.YEAR) == false || cvalue.get(Calendar.YEAR) == 1970)){
// it's highly probable that we're
// looking at a time-of-day.
format = timef;
}
else{
- if((value.isSet(Calendar.HOUR) == false || value.get(Calendar.HOUR) == 0) &&
- (value.isSet(Calendar.MINUTE) == false || value.get(Calendar.MINUTE) == 0) &&
- (value.isSet(Calendar.SECOND) == false || value.get(Calendar.SECOND) == 0)){
+ if((cvalue.isSet(Calendar.HOUR) == false || cvalue.get(Calendar.HOUR) == 0) &&
+ (cvalue.isSet(Calendar.MINUTE) == false || cvalue.get(Calendar.MINUTE) == 0) &&
+ (cvalue.isSet(Calendar.SECOND) == false || cvalue.get(Calendar.SECOND) == 0)){
// It's highly probable that we're looking at a date
format = datef;
doTimeZone = false;
}
}
- StringBuffer result = new StringBuffer((new SimpleDateFormat(format)).format(value.getTime()));
+ StringBuffer result = new StringBuffer((new SimpleDateFormat(format)).format(cvalue.getTime()));
// We don't need to worry about timezone in date only strings but otherwise we do...
if (doTimeZone){
- int offsetTotalMillis = value.get(java.util.Calendar.ZONE_OFFSET);
+ int offsetTotalMillis = cvalue.getTimeZone().getOffset(cvalue.getTime().getTime());
- // UTC
+ // UTC, a.k.a. Zulu time
if (offsetTotalMillis == 0){
result.append("Z");
}
@@ -269,24 +272,39 @@
DecimalFormat decf = new DecimalFormat("00");
int offsetTotalMinutes = offsetTotalMillis/60000;
- int offsetMinutes = Math.abs( offsetTotalMinutes % 60);
- int offsetHours = Math.abs( offsetTotalMinutes / 60);
- String offsetString = "+";
-
- if (offsetTotalMinutes < 0){
- offsetString = "-";
- }
- result.append(offsetString).append(decf.format(offsetHours));
-
- if (offsetMinutes > 0){
- result.append(decf.format(offsetMinutes));
- }
+ int offsetMinutes = offsetTotalMinutes % 60;
+ int offsetHours = offsetTotalMinutes / 60;
+ String offsetString = offsetTotalMinutes < 0 ? "-":"+";
+
+ // We will maintain the time zone data, so roll back/forward the clock to GMT, and append
+ // the offset data to the representation
+ cvalue.add(Calendar.MINUTE, -offsetMinutes);
+ cvalue.add(Calendar.HOUR_OF_DAY, -offsetHours);
+ result = new StringBuffer(formatDateTime(cvalue));
+ // Reset, so we don't mess things up permanently for the given calendar
+ cvalue.add(Calendar.MINUTE, offsetMinutes);
+ cvalue.add(Calendar.HOUR_OF_DAY, offsetHours);
+
+ result.append(offsetString).append(decf.format(Math.abs(offsetHours)));
+ result.append(":"+decf.format(Math.abs(offsetMinutes)));
}
}
return result.toString();
}
+ protected static String formatDateTime(Calendar ctime){
+ DecimalFormat decf = new DecimalFormat("00");
+ return
+ ctime.get(Calendar.YEAR)+"-"+
+ decf.format(ctime.get(Calendar.MONTH)+1)+"-"+
+ decf.format(ctime.get(Calendar.DAY_OF_MONTH))+"T"+
+ decf.format(ctime.get(Calendar.HOUR_OF_DAY))+":"+
+ decf.format(ctime.get(Calendar.MINUTE))+":"+
+ decf.format(ctime.get(Calendar.SECOND));
+ }
+
+
public Object clone(){
MobyDataDateTime copy = new MobyDataDateTime(getName(), getValue());
copy.setDataType(getDataType());
From gordonp at dev.open-bio.org Tue May 29 23:49:51 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Tue, 29 May 2007 19:49:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705292349.l4TNnpgm031251@dev.open-bio.org>
gordonp
Tue May 29 19:49:51 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/test
In directory dev.open-bio.org:/tmp/cvs-serv31217/src/main/org/biomoby/shared/data/test
Log Message:
Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/test added to the repository
moby-live/Java/src/main/org/biomoby/shared/data/test - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/test/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/test/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/test/RCS/directory,v: No such file or directory
From gordonp at dev.open-bio.org Tue May 29 23:52:14 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Tue, 29 May 2007 19:52:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705292352.l4TNqEQD031311@dev.open-bio.org>
gordonp
Tue May 29 19:52:14 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/test
In directory dev.open-bio.org:/tmp/cvs-serv31280/src/main/org/biomoby/shared/data/test
Added Files:
MobyDataDateTimeTestCase.java
Log Message:
Test cases for MobyDataDateTime, built after timezone issues discovered by Ivan Parraga Garcia. Checks Central European and Newfoundland times, standard and daylight savings.
moby-live/Java/src/main/org/biomoby/shared/data/test MobyDataDateTimeTestCase.java,NONE,1.1
From gordonp at dev.open-bio.org Wed May 30 17:44:19 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 30 May 2007 13:44:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705301744.l4UHiJQG000345@dev.open-bio.org>
gordonp
Wed May 30 13:44:19 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv309/src/main/org/biomoby/shared/parser
Modified Files:
ServiceException.java
Log Message:
Changed exception printing to toXMLString() so as not to collide with Martin's toXML(), which returns a DOM object
moby-live/Java/src/main/org/biomoby/shared/parser ServiceException.java,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java 2007/05/21 00:56:15 1.12
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java 2007/05/30 17:44:19 1.13
@@ -479,26 +479,26 @@
return ex;
}
-// public String toXML(){
-// StringBuffer xml = new StringBuffer(" \n");
-
-// xml.append(""+code+"");
-
-// if(getMessage() != null){
-// xml.append(" "+getMessage()+"");
-// }
+ public String toXMLString(){
+ StringBuffer xml = new StringBuffer(" \n");
+
+ xml.append(""+code+"");
+
+ if(getMessage() != null){
+ xml.append(" "+getMessage()+"");
+ }
-// xml.append(" ");
+ xml.append(" ");
-// return xml.toString();
-// }
+ return xml.toString();
+ }
}
From gordonp at dev.open-bio.org Wed May 30 17:44:19 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 30 May 2007 13:44:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705301744.l4UHiJIl000363@dev.open-bio.org>
gordonp
Wed May 30 13:44:19 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv309/src/main/org/biomoby/shared/data
Modified Files:
MobyContentInstance.java
Log Message:
Changed exception printing to toXMLString() so as not to collide with Martin's toXML(), which returns a DOM object
moby-live/Java/src/main/org/biomoby/shared/data MobyContentInstance.java,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java 2007/03/30 19:48:37 1.10
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java 2007/05/30 17:44:19 1.11
@@ -412,7 +412,7 @@
xml.append(""+serviceNotes +"");
}
for(int i = 0; i < exs.length; i++){
- xml.append(exs[i].toXML());
+ xml.append(exs[i].toXMLString());
}
xml.append("");
}
From senger at dev.open-bio.org Thu May 31 13:42:51 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 31 May 2007 09:42:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705311342.l4VDgphl001912@dev.open-bio.org>
senger
Thu May 31 09:42:51 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory dev.open-bio.org:/tmp/cvs-serv1857/src/Clients/help
Modified Files:
MobyCmdLineClient_usage.txt
Log Message:
starting addign support for async services
moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2007/05/29 03:51:46 1.11
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2007/05/31 13:42:51 1.12
@@ -18,6 +18,10 @@
-uri is a URI defining Moby registry's namespace
(default: http://mobycentral.icapture.ubc.ca/MOBY/Central)
+ or
+ -registry
+ is a convenient way to specify a known registry;
+ the list of known registries can be obtained by the -lr option
where specify what to ask a Moby registry to do:
@@ -30,6 +34,8 @@
-ln ... list names and descriptions of all namespaces
-ld ... list names and descriptions of all data types
-lu ... list URLs of RDF documents describing this registry
+ -lr ... list of known BioMoby registries
+ (with -on prints only names/synonyms of the registries)
To get entities by their names:
@@ -214,5 +220,7 @@
format of : service-name[,service-authority]
+[Undocumented and 'in-the-progress' options: -async, -url .]
+
[Note: You can also use -argsfile to read arguments from a
file. See details in src/Client/help/argsfile.example.]
From senger at dev.open-bio.org Thu May 31 13:42:51 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 31 May 2007 09:42:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705311342.l4VDgpj9001973@dev.open-bio.org>
senger
Thu May 31 09:42:51 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv1857/src/main/org/biomoby/shared
Modified Files:
MobyService.java
Log Message:
starting addign support for async services
moby-live/Java/src/main/org/biomoby/shared MobyService.java,1.17,1.18
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2007/03/29 19:41:37 1.17
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2007/05/31 13:42:51 1.18
@@ -40,7 +40,7 @@
static public final String BIOMOBY_SERVICE_URI = "http://biomoby.org/";
protected String name;
- protected String category = "moby";
+ protected String category = CATEGORY_MOBY;
protected String authority = "";
protected String emailContact = "";
protected String type = "";
@@ -61,6 +61,17 @@
public static final int TESTED = 8; // Gives a valid answer to a valid test input provided by the service
protected int serviceStatus = UNCHECKED;
protected int statusChecks = UNCHECKED;
+
+ /** Name of a default category for BioMoby services. */
+ public static final String CATEGORY_MOBY = "moby";
+
+ /** Name of a category for asynchornous BioMoby services. */
+ public static final String CATEGORY_MOBY_ASYNC = "moby-async";
+
+ /** A suffix added to a service name in order to make a method
+ * name that submits input to an asynchronous service.
+ */
+ public static final String SUBMIT_ACTION_SUFFIX = "_submit";
// We need both, because you can't synchrinize on a null array
protected static MobyService[] uninitializedServices = new MobyService[0];
@@ -196,7 +207,7 @@
return category;
}
public void setCategory (String value) {
- category = (value == null ? "moby" : value);
+ category = (value == null ? CATEGORY_MOBY : value);
}
public String getDescription() {
@@ -529,6 +540,6 @@
}
public boolean isAsynchronous(){
- return category.equals("moby-async");
+ return category.equals (CATEGORY_MOBY_ASYNC);
}
}
From senger at dev.open-bio.org Thu May 31 13:42:51 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 31 May 2007 09:42:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705311342.l4VDgpgD001955@dev.open-bio.org>
senger
Thu May 31 09:42:51 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta
In directory dev.open-bio.org:/tmp/cvs-serv1857/src/main/org/biomoby/registry/meta
Modified Files:
Registry.java
Log Message:
starting addign support for async services
moby-live/Java/src/main/org/biomoby/registry/meta Registry.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java 2006/10/02 17:57:49 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java 2007/05/31 13:42:51 1.2
@@ -68,7 +68,7 @@
*
********************************************************************/
public String toString() {
- StringBuffer buf = new StringBuffer (200);
+ StringBuilder buf = new StringBuilder (200);
String title = "Information about '" + getSynonym() + "' registry:";
buf.append (title);
buf.append ("\n");
@@ -80,7 +80,7 @@
buf.append ("Contact: " + getContact() + "\n");
buf.append ("Public: " + new Boolean (isPublic()).toString() + "\n\n");
buf.append ("Description:\n" + getDescription() + "\n");
- return new String (buf);
+ return buf.toString();
}
/*********************************************************************
From senger at dev.open-bio.org Thu May 31 13:42:51 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 31 May 2007 09:42:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705311342.l4VDgpMF001876@dev.open-bio.org>
senger
Thu May 31 09:42:51 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv1857/docs
Modified Files:
ChangeLog
Log Message:
starting addign support for async services
moby-live/Java/docs ChangeLog,1.80,1.81
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.80
retrieving revision 1.81
diff -u -r1.80 -r1.81
--- /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/29 03:51:45 1.80
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/31 13:42:51 1.81
@@ -1,5 +1,16 @@
+2007-05-31 Martin Senger
+
+ * Added: few new constants into MobyService for async services
+ support
+
+ * Added: starting to add support for the async services into
+ MobyCmdLineClient
+
2007-05-29 Martin Senger
+ * Added: new options -lt and -registry to the MobyCmdLineClient
+ for easier selection which registry to use.
+
* Fixed: on various place where a service was looking for, the
used service pattern has now category empty (so not only services
with the default 'moby' category are found).
From senger at dev.open-bio.org Thu May 31 13:42:51 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 31 May 2007 09:42:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705311342.l4VDgpim001936@dev.open-bio.org>
senger
Thu May 31 09:42:51 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv1857/src/main/org/biomoby/client
Modified Files:
AsyncClient.java CentralImpl.java
Log Message:
starting addign support for async services
moby-live/Java/src/main/org/biomoby/client AsyncClient.java,1.1,1.2 CentralImpl.java,1.48,1.49
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/AsyncClient.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/AsyncClient.java 2007/03/30 21:17:27 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/AsyncClient.java 2007/05/31 13:42:51 1.2
@@ -35,7 +35,6 @@
public static final String WSRP_PROPERTY_TAG_NAME = "ResourceProperty";
public static final String MOBY_SERVICE_INVOC_ID_TAG_NAME = "ServiceInvocationId";
- public static final String MOBY_SUBMIT_ACTION_CMD_SUFFIX = "_submit";
public static final String MOBY_RESULT_PROPERTY_PREFIX = "result_";
public static EndpointReference sendRequest(MobyService service, MobyContentInstance contents) throws Exception{
@@ -72,7 +71,7 @@
// Populate the body
// Create the main element and namespace
SOAPElement bodyElement = body.addChildElement(envelope.createName(
- servicename + MOBY_SUBMIT_ACTION_CMD_SUFFIX,
+ servicename + MobyService.SUBMIT_ACTION_SUFFIX,
MobyPrefixResolver.MOBY_TRANSPORT_PREFIX,
MobyPrefixResolver.MOBY_TRANSPORT_NAMESPACE));
// Add content
@@ -97,7 +96,7 @@
httpConn.setRequestProperty("Content-Type", CONTENT_TYPE);
httpConn.setRequestProperty("User-agent", USER_AGENT);
httpConn.setRequestProperty("SOAPAction", MobyPrefixResolver.MOBY_TRANSPORT_NAMESPACE+"#"
- + servicename + MOBY_SUBMIT_ACTION_CMD_SUFFIX);
+ + servicename + MobyService.SUBMIT_ACTION_SUFFIX);
httpConn.setRequestMethod("POST");
httpConn.setDoOutput(true);
httpConn.setDoInput(true);
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2007/05/29 03:51:46 1.48
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2007/05/31 13:42:51 1.49
@@ -24,6 +24,7 @@
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.DocumentBuilder;
+import javax.xml.namespace.QName;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NamedNodeMap;
@@ -35,6 +36,7 @@
import org.apache.axis.client.Service;
import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
@@ -219,7 +221,12 @@
} catch (AxisFault e) {
throw new MobyException
- (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
+ (formatFault (e,
+ endpoint.toString(),
+ (call == null ? null : call.getOperationName())),
+ e);
+// (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
+
} catch (Exception e) {
throw new MobyException (e.toString(), e);
// e.printStackTrace();
@@ -1873,5 +1880,46 @@
return (buffer == null) ? str : buffer.toString();
}
+ /*************************************************************************
+ * Format an exception.
+ *************************************************************************/
+ public static String formatFault (AxisFault e, String endpoint, QName method) {
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ formatFault (e, new PrintStream (baos), endpoint, method);
+ return baos.toString();
+ }
+
+ /*************************************************************************
+ * Format an exception.
+ *************************************************************************/
+ public static void formatFault (AxisFault e, PrintStream out,
+ String endpoint, QName method) {
+
+ out.println ("===ERROR===");
+ out.println ("Fault details:");
+ // for some obvious errors I do not print all details (with a lenghty trace stack)
+ String faultString = e.getFaultString();
+ if ( (! faultString.startsWith ("java.net.ConnectException")) &&
+ (faultString.indexOf ("Could not find class for the service named:") == -1)
+ ) {
+ org.w3c.dom.Element[] details = e.getFaultDetails();
+ for (int i = 0; i < details.length; i++) {
+ String s = details[i].toString().replaceAll ("<", "<");
+ s = s.replaceAll (">", ">");
+ out.println (s);
+ }
+ }
+ out.println ("Fault string: " + faultString);
+ out.println ("Fault code: " + e.getFaultCode());
+ out.println ("Fault actor: " + e.getFaultActor());
+ if (endpoint != null || method != null)
+ out.println ("When calling:");
+ if (endpoint != null)
+ out.println ("\t" + endpoint);
+ if (method != null)
+ out.println ("\t" + method);
+ out.println ("===========");
+ }
+
}
From senger at dev.open-bio.org Thu May 31 13:42:51 2007
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 31 May 2007 09:42:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200705311342.l4VDgplS001894@dev.open-bio.org>
senger
Thu May 31 09:42:51 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv1857/src/Clients
Modified Files:
MobyCmdLineClient.java
Log Message:
starting addign support for async services
moby-live/Java/src/Clients MobyCmdLineClient.java,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2007/05/29 03:51:46 1.14
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2007/05/31 13:42:51 1.15
@@ -13,6 +13,10 @@
import org.tulsoft.shared.StringUtils;
import org.tulsoft.shared.GException;
+import org.biomoby.registry.meta.RegistriesList;
+import org.biomoby.registry.meta.Registries;
+import org.biomoby.registry.meta.Registry;
+
import java.util.*;
import java.io.*;
@@ -80,11 +84,23 @@
}
verbose = !cmd.hasOption ("-q");
+ String param;
// where is a Moby registry
- Central worker = new CentralImpl (cmd.getParam ("-e"),
- cmd.getParam ("-uri"));
- String param;
+ Central worker = null;
+ if ((param = cmd.getParam ("-registry")) == null) {
+ worker = new CentralImpl (cmd.getParam ("-e"),
+ cmd.getParam ("-uri"));
+ } else {
+ final Registries regList = RegistriesList.getInstance();
+ Registry reg = regList.get (param);
+ if (reg == null) {
+ System.err.println ("ERROR: Failed to find registry " + param);
+ System.exit (1);
+ }
+ worker = new CentralImpl (reg.getEndpoint(),
+ reg.getNamespace());
+ }
if (cmd.hasOption ("-debug")) {
worker.setDebug (true);
@@ -185,6 +201,16 @@
}
}
+ if (cmd.hasOption ("-lr")) {
+ boolean onlyNames = cmd.hasOption ("-on");
+ decorationLn ("Known BioMoby Registries:");
+ decorationLn ("-------------------------");
+ final Registries regList = RegistriesList.getInstance();
+ for (Registry reg: regList.getAll()) {
+ System.out.println (onlyNames ? reg.getSynonym() : reg.toString());
+ }
+ }
+
//
// retrieval of more complex entities
//
@@ -625,43 +651,51 @@
if ((params = cmd.getParam ("-scall", 2)) != null ) {
if (params[0] != null && params[1] != null) {
- // find URL of the wanted service
- decorationLn ("Looking for service '" + params[0] + "':");
+ // find name and URL of the wanted service
String serviceName = null;
+ String authority = null;
int pos = params[0].indexOf (",");
- MobyService[] services;
- MobyService pattern = null;
if (pos == -1) {
serviceName = params[0];
- pattern = new MobyService (serviceName);
- pattern.setCategory ("");
- services = worker.findService (pattern);
-
} else if (pos == params[0].length() - 1) {
serviceName = params[0].substring (0, pos);
- pattern = new MobyService (serviceName);
- pattern.setCategory ("");
- services = worker.findService (pattern);
} else {
serviceName = params[0].substring (0, pos);
- pattern = new MobyService (serviceName);
- pattern.setAuthority (params[0].substring (pos+1));
+ authority = params[0].substring (pos+1);
+ }
+ String serviceURL = null;
+ String category = MobyService.CATEGORY_MOBY;
+ if ((serviceURL = cmd.getParam ("-url")) == null) {
+ // look in the registry
+ decorationLn ("Looking for service '" + params[0] + "':");
+ MobyService pattern = new MobyService (serviceName, authority);
pattern.setCategory ("");
- services = worker.findService (pattern);
+ MobyService[] services = worker.findService (pattern);
+ if (services != null && services.length > 0) {
+ serviceURL = services[0].getURL();
+ category = services[0].getCategory();
+ }
}
- if (services != null && services.length > 0) {
- String serviceURL = services[0].getURL();
- if (! serviceURL.equals ("")) {
-
- // call the service
- decorationLn ("Calling service '" + serviceName + "' with the input from '" + params[1] + "':");
- if (new File (params[1]).exists())
- params[1] = FileUtils.getFile (params[1]);
- decorationLn (params[1]);
- decorationLn ("---------------");
- Central serviceWorker = new CentralImpl (serviceURL, "http://biomoby.org/");
- System.out.println (serviceWorker.call (serviceName, params[1]));
+
+ if (! "".equals (serviceURL)) {
+ String methodName = null;
+
+ if (MobyService.CATEGORY_MOBY_ASYNC.equals (category) ||
+ cmd.hasOption ("-async")) {
+ methodName = serviceName + MobyService.SUBMIT_ACTION_SUFFIX;
+ } else {
+ methodName = serviceName;
}
+
+ // call the service
+ decorationLn ("Calling '" + methodName +
+ "' with the input from '" + params[1] + "':");
+ if (new File (params[1]).exists())
+ params[1] = FileUtils.getFile (params[1]);
+ decorationLn (params[1]);
+ decorationLn ("---------------");
+ Central serviceWorker = new CentralImpl (serviceURL, "http://biomoby.org/");
+ System.out.println (serviceWorker.call (methodName, params[1]));
}
}
}