From py at pingoured.fr Mon Mar 29 07:27:59 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Mon, 29 Mar 2010 13:27:59 +0200 Subject: [MOBY-dev] Javadoc down ? Message-ID: <1269862079.10177.9.camel@localhost.localdomain> Hi, I am trying to reach (without success) the javadoc at: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/index.html Has someone more luck than me ? I am trying to find the object to put a composite (not string, int or boolean) object in a MobyDataInstance. Any ideas ? Thanks, Pierre From edward.kawas at gmail.com Mon Mar 29 09:49:44 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 29 Mar 2010 06:49:44 -0700 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269862079.10177.9.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> Message-ID: <002301cacf46$b0981e20$11c85a60$@gmail.com> I think that it has something to do with a recent commit, because the script that builds the javadoc is reporting compile problems. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > Sent: Monday, March 29, 2010 4:28 AM > To: 'Core developer announcements' > Subject: [MOBY-dev] Javadoc down ? > > Hi, > > I am trying to reach (without success) the javadoc at: > http://biomoby.open-bio.org/CVS_CONTENT/moby- > live/Java/docs/API/index.html > > Has someone more luck than me ? > > > I am trying to find the object to put a composite (not string, int or > boolean) object in a MobyDataInstance. Any ideas ? > > > Thanks, > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Mar 29 10:22:54 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 08:22:54 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269862079.10177.9.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> Message-ID: <4BB0B7BE.1030908@ucalgary.ca> Salut Pierre, I've put the javadocs online here: http://www.visualgenomics.ca/gordonp/mobyjavadocs/API/ I'm not completely sure I understand your question...do you mean a MobyContentInstance? Pierre-Yves Chibon wrote: > Hi, > > I am trying to reach (without success) the javadoc at: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/index.html > > Has someone more luck than me ? > > > I am trying to find the object to put a composite (not string, int or > boolean) object in a MobyDataInstance. Any ideas ? > > > Thanks, > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From gordonp at ucalgary.ca Mon Mar 29 10:27:36 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 08:27:36 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269862079.10177.9.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> Message-ID: <4BB0B8D8.4000500@ucalgary.ca> A MobyDataComposite? This holds anything that is not a primitive datatype... Pierre-Yves Chibon wrote: > Hi, > > I am trying to reach (without success) the javadoc at: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/index.html > > Has someone more luck than me ? > > > I am trying to find the object to put a composite (not string, int or > boolean) object in a MobyDataInstance. Any ideas ? > > > Thanks, > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From py at pingoured.fr Mon Mar 29 11:18:41 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Mon, 29 Mar 2010 17:18:41 +0200 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB0B8D8.4000500@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <4BB0B8D8.4000500@ucalgary.ca> Message-ID: <1269875922.10177.16.camel@localhost.localdomain> Thanks for pulling up the javadoc. On Mon, 2010-03-29 at 08:27 -0600, Paul Gordon wrote: > A MobyDataComposite? This holds anything that is not a primitive > datatype... I am looking at this object but I have a collection of GeneticMarker: java.lang.Object extended byorg.biomoby.shared.datatypes.MobyObject extended byorg.biomoby.shared.datatypes.Marker extended byorg.biomoby.shared.datatypes.GeneticMarker I am trying to put it in a MobyDataComposite, but this one only accepts MobyDataType (and not MobyObject). Then I will put these collection of MobyDataComposite into an vector of MobyDataInstance to be sent to the service. Am I doing this correctly ? Thanks, Pierre From gordonp at ucalgary.ca Mon Mar 29 11:49:55 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 09:49:55 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269875922.10177.16.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> <4BB0B8D8.4000500@ucalgary.ca> <1269875922.10177.16.camel@localhost.localdomain> Message-ID: <4BB0CC23.9010909@ucalgary.ca> Hi Pierre, Unfortunately, no. There are two ways to create data in Moby: using the generated classes (as you are doing), and generic classes (those in org.biomoby.shared.data). You cannot mix the two (since the generated classes do not inherit from MobyData). Maybe Eddie can help you with the generated classes? If you want to just use the generic classes, the code would look something like this: /* Find the service */ Central central = new CentralImpl(); MobyService templateService = new MobyService("MyServiceName"); MobyService[] validServices = central.findService(templateService); /* Prepare the input */ MobyDataType markerType = central.getDataType("GeneticMarker"); MobyDataObjectSet gmCollection = new MobyDataObjectSet(); // a collection for(/* loop over your native marker info set */){ gmCollection.add(new MobyDataComposite(markerType, null, null, fieldName1, fieldValue1, fieldName2, fieldValue2...)); // create the collection members } MobyContentInstance request = new MobyContentInstance(gmCollection, "myServiceParamName"); // build a request envelope /* Call the service */ MobyRequest requester = new MobyRequest(central); // the thing that calls Moby services requester.setService(validServices[0]); MobyContentInstance response = requester.invokeService(request); //synchronous call to service I don't see GeneticMarker in the Object registry, so I can't give you more specific info on the MobyDataComposite c-tor... Regards, Paul Pierre-Yves Chibon wrote: > Thanks for pulling up the javadoc. > > On Mon, 2010-03-29 at 08:27 -0600, Paul Gordon wrote: > >> A MobyDataComposite? This holds anything that is not a primitive >> datatype... >> > I am looking at this object but I have a collection of GeneticMarker: > java.lang.Object > extended byorg.biomoby.shared.datatypes.MobyObject > extended byorg.biomoby.shared.datatypes.Marker > extended byorg.biomoby.shared.datatypes.GeneticMarker > > I am trying to put it in a MobyDataComposite, but this one only accepts > MobyDataType (and not MobyObject). Then I will put these collection of > MobyDataComposite into an vector of MobyDataInstance to be sent to the service. > Am I doing this correctly ? > > Thanks, > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From py at pingoured.fr Mon Mar 29 12:11:15 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Mon, 29 Mar 2010 18:11:15 +0200 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB0CC23.9010909@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <4BB0B8D8.4000500@ucalgary.ca> <1269875922.10177.16.camel@localhost.localdomain> <4BB0CC23.9010909@ucalgary.ca> Message-ID: <1269879075.4829.0.camel@localhost.localdomain> On Mon, 2010-03-29 at 09:49 -0600, Paul Gordon wrote: > I don't see GeneticMarker in the Object registry, so I can't give you > more specific info on the MobyDataComposite c-tor... That is already quite some help. I will look into this. Thanks, Pierre From martin.senger at gmail.com Mon Mar 29 15:41:48 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 20:41:48 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <002301cacf46$b0981e20$11c85a60$@gmail.com> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> Message-ID: <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> > I think that it has something to do with a recent commit, because the > script > that builds the javadoc is reporting compile problems. > Paul, can you look at it please - so we can compile again? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From gordonp at ucalgary.ca Mon Mar 29 16:01:19 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 14:01:19 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> Message-ID: <4BB1070F.7030604@ucalgary.ca> Hmm..of course it all compiles fine for me here, so I've just committed all the changes I have locally. Hopefully this fixes it. Can I get the error details, or do I need to do a whole new CVS checkout? Martin Senger wrote: >> I think that it has something to do with a recent commit, because the >> script >> that builds the javadoc is reporting compile problems. >> >> > > Paul, can you look at it please - so we can compile again? > > Thanks, > Martin > > From martin.senger at gmail.com Mon Mar 29 16:09:32 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 21:09:32 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB1070F.7030604@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> <4BB1070F.7030604@ucalgary.ca> Message-ID: <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> Paul, thanks for a very fast reaction. It compiles fine now. Perhaps I was too fast with my email - the problem might have been in the corrupted jar files in the maven repository. When I removed them they were fetched again and compilation succeeded. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From martin.senger at gmail.com Mon Mar 29 16:16:39 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 21:16:39 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> <4BB1070F.7030604@ucalgary.ca> <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> Message-ID: <4d93f07c1003291316h5ee494cq337350612be9886d@mail.gmail.com> [cont.] ... however,... Paul, Eddie, can you remind me what was our last decision on Java version? Is it officially 1.6 or still 1.5? Or, are the compilation errors (in seahawk classes; see below) I got on biomoby.org not related to Java version? Cheers, Martin compile: [javac] Compiling 368 source files to /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/build/classes [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:426: cannot find symbol [javac] symbol : class Desktop [javac] location: class ca.ucalgary.seahawk.gui.MobyContentPane [javac] Desktop desktop = Desktop.getDesktop(); [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:426: cannot find symbol [javac] symbol : variable Desktop [javac] location: class ca.ucalgary.seahawk.gui.MobyContentPane [javac] Desktop desktop = Desktop.getDesktop(); [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:427: package Desktop does not exist [javac] if(!desktop.isSupported(Desktop.Action.BROWSE)) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:180: cannot find symbol [javac] symbol : method isEmpty() [javac] location: class java.lang.String [javac] if(this.getText().isEmpty()) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:178: method does not override a method from its superclass [javac] @Override [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:187: cannot find symbol [javac] symbol : method isEmpty() [javac] location: class java.lang.String [javac] if(this.getText().isEmpty()) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:185: method does not override a method from its superclass [javac] @Override [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:214: cannot find symbol [javac] symbol : method isEmpty() [javac] location: class java.lang.String [javac] if(this.getText().isEmpty()) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:212: method does not override a method from its superclass [javac] @Override [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:221: cannot find symbol [javac] symbol : method isEmpty() [javac] location: class java.lang.String [javac] if(this.getText().isEmpty()) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:219: method does not override a method from its superclass [javac] @Override [javac] ^ [javac] Note: /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.javauses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 11 errors -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From gordonp at ucalgary.ca Mon Mar 29 16:23:52 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 14:23:52 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4d93f07c1003291316h5ee494cq337350612be9886d@mail.gmail.com> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> <4BB1070F.7030604@ucalgary.ca> <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> <4d93f07c1003291316h5ee494cq337350612be9886d@mail.gmail.com> Message-ID: <4BB10C58.3060309@ucalgary.ca> Hmm..I thought we decided 1.6... Martin Senger wrote: > [cont.] ... however,... > > Paul, Eddie, can you remind me what was our last decision on Java version? > Is it officially 1.6 or still 1.5? Or, are the compilation errors (in > seahawk classes; see below) I got on biomoby.org not related to Java > version? > > Cheers, > Martin > > compile: > [javac] Compiling 368 source files to /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/build/classes > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:426: > cannot find symbol > [javac] symbol : class > Desktop > > [javac] location: class > ca.ucalgary.seahawk.gui.MobyContentPane > > [javac] Desktop desktop = > Desktop.getDesktop(); > > [javac] > ^ > > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:426: > cannot find symbol > [javac] symbol : variable > Desktop > > [javac] location: class > ca.ucalgary.seahawk.gui.MobyContentPane > > [javac] Desktop desktop = > Desktop.getDesktop(); > > [javac] > ^ > > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:427: > package Desktop does not exist > [javac] if(!desktop.isSupported(Desktop.Action.BROWSE)) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:180: > cannot find symbol > [javac] symbol : method isEmpty() > [javac] location: class java.lang.String > [javac] if(this.getText().isEmpty()) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:178: > method does not override a method from its superclass > [javac] @Override > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:187: > cannot find symbol > [javac] symbol : method isEmpty() > [javac] location: class java.lang.String > [javac] if(this.getText().isEmpty()) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:185: > method does not override a method from its superclass > [javac] @Override > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:214: > cannot find symbol > [javac] symbol : method isEmpty() > [javac] location: class java.lang.String > [javac] if(this.getText().isEmpty()) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:212: > method does not override a method from its superclass > [javac] @Override > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:221: > cannot find symbol > [javac] symbol : method isEmpty() > [javac] location: class java.lang.String > [javac] if(this.getText().isEmpty()) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:219: > method does not override a method from its superclass > [javac] @Override > [javac] ^ > [javac] Note: /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.javauses > or overrides a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [javac] Note: Some input files use unchecked or unsafe operations. > [javac] Note: Recompile with -Xlint:unchecked for details. > [javac] 11 errors > > > From martin.senger at gmail.com Mon Mar 29 16:26:11 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 21:26:11 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB10C58.3060309@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> <4BB1070F.7030604@ucalgary.ca> <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> <4d93f07c1003291316h5ee494cq337350612be9886d@mail.gmail.com> <4BB10C58.3060309@ucalgary.ca> Message-ID: <4d93f07c1003291326q50b720dby9a4e4ed135996859@mail.gmail.com> > > Hmm..I thought we decided 1.6... 1.6 is fine with me. Anybody opposing? Anyway, meanwhile, I am going to install Java 1.6. on biomoby.org so it will compile. Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From martin.senger at gmail.com Mon Mar 29 16:47:04 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 21:47:04 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269862079.10177.9.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> Message-ID: <4d93f07c1003291347w640f2b0bg45bacf1f1cc1789c@mail.gmail.com> > I am trying to reach (without success) the javadoc at: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/index.html > It is back. As Eddie already said, the problem was with the compilation. Once that was solved, the docs is back. Cheers, Martin PS for Paul, Eddie (and perhaps me): It would be nice to fix these warnings: docs: [javadoc] Generating Javadoc [javadoc] Javadoc execution [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataRecorder.java:2127: warning - @param argument "responseURL" is not a parameter name. [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java:142: warning - @param argument "t" is not a parameter name. [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java:94: warning - @param argument "url" is not a parameter name. [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/client/MobyRequestEvent.java:60: warning - @param argument "inputXML" is not a parameter name. [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/inb/biomoby/central/gui/model/MobyObjectPropertiesTableModel.java:72: warning - @return tag has no arguments. -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From py at pingoured.fr Tue Mar 30 05:26:52 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 30 Mar 2010 11:26:52 +0200 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB0CC23.9010909@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <4BB0B8D8.4000500@ucalgary.ca> <1269875922.10177.16.camel@localhost.localdomain> <4BB0CC23.9010909@ucalgary.ca> Message-ID: <1269941212.8363.64.camel@localhost.localdomain> On Mon, 2010-03-29 at 09:49 -0600, Paul Gordon wrote: > Maybe Eddie can help you with > the generated classes? Out of curiosity I would not mind to see some example code. I believe this is the mechanism which is used by the web-service when we send back the output, isn't it ? Using a similar approach, can't the output from a service be easily parsed to its object (the generated one not the generic one). At the moment I use a couple of while into each other, it does the job but I wonder if there is not easier way. Thanks, Regards, Pierre From py at pingoured.fr Mon Mar 29 11:27:59 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Mon, 29 Mar 2010 13:27:59 +0200 Subject: [MOBY-dev] Javadoc down ? Message-ID: <1269862079.10177.9.camel@localhost.localdomain> Hi, I am trying to reach (without success) the javadoc at: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/index.html Has someone more luck than me ? I am trying to find the object to put a composite (not string, int or boolean) object in a MobyDataInstance. Any ideas ? Thanks, Pierre From edward.kawas at gmail.com Mon Mar 29 13:49:44 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 29 Mar 2010 06:49:44 -0700 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269862079.10177.9.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> Message-ID: <002301cacf46$b0981e20$11c85a60$@gmail.com> I think that it has something to do with a recent commit, because the script that builds the javadoc is reporting compile problems. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > Sent: Monday, March 29, 2010 4:28 AM > To: 'Core developer announcements' > Subject: [MOBY-dev] Javadoc down ? > > Hi, > > I am trying to reach (without success) the javadoc at: > http://biomoby.open-bio.org/CVS_CONTENT/moby- > live/Java/docs/API/index.html > > Has someone more luck than me ? > > > I am trying to find the object to put a composite (not string, int or > boolean) object in a MobyDataInstance. Any ideas ? > > > Thanks, > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Mar 29 14:22:54 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 08:22:54 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269862079.10177.9.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> Message-ID: <4BB0B7BE.1030908@ucalgary.ca> Salut Pierre, I've put the javadocs online here: http://www.visualgenomics.ca/gordonp/mobyjavadocs/API/ I'm not completely sure I understand your question...do you mean a MobyContentInstance? Pierre-Yves Chibon wrote: > Hi, > > I am trying to reach (without success) the javadoc at: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/index.html > > Has someone more luck than me ? > > > I am trying to find the object to put a composite (not string, int or > boolean) object in a MobyDataInstance. Any ideas ? > > > Thanks, > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From gordonp at ucalgary.ca Mon Mar 29 14:27:36 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 08:27:36 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269862079.10177.9.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> Message-ID: <4BB0B8D8.4000500@ucalgary.ca> A MobyDataComposite? This holds anything that is not a primitive datatype... Pierre-Yves Chibon wrote: > Hi, > > I am trying to reach (without success) the javadoc at: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/index.html > > Has someone more luck than me ? > > > I am trying to find the object to put a composite (not string, int or > boolean) object in a MobyDataInstance. Any ideas ? > > > Thanks, > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From py at pingoured.fr Mon Mar 29 15:18:41 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Mon, 29 Mar 2010 17:18:41 +0200 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB0B8D8.4000500@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <4BB0B8D8.4000500@ucalgary.ca> Message-ID: <1269875922.10177.16.camel@localhost.localdomain> Thanks for pulling up the javadoc. On Mon, 2010-03-29 at 08:27 -0600, Paul Gordon wrote: > A MobyDataComposite? This holds anything that is not a primitive > datatype... I am looking at this object but I have a collection of GeneticMarker: java.lang.Object extended byorg.biomoby.shared.datatypes.MobyObject extended byorg.biomoby.shared.datatypes.Marker extended byorg.biomoby.shared.datatypes.GeneticMarker I am trying to put it in a MobyDataComposite, but this one only accepts MobyDataType (and not MobyObject). Then I will put these collection of MobyDataComposite into an vector of MobyDataInstance to be sent to the service. Am I doing this correctly ? Thanks, Pierre From gordonp at ucalgary.ca Mon Mar 29 15:49:55 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 09:49:55 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269875922.10177.16.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> <4BB0B8D8.4000500@ucalgary.ca> <1269875922.10177.16.camel@localhost.localdomain> Message-ID: <4BB0CC23.9010909@ucalgary.ca> Hi Pierre, Unfortunately, no. There are two ways to create data in Moby: using the generated classes (as you are doing), and generic classes (those in org.biomoby.shared.data). You cannot mix the two (since the generated classes do not inherit from MobyData). Maybe Eddie can help you with the generated classes? If you want to just use the generic classes, the code would look something like this: /* Find the service */ Central central = new CentralImpl(); MobyService templateService = new MobyService("MyServiceName"); MobyService[] validServices = central.findService(templateService); /* Prepare the input */ MobyDataType markerType = central.getDataType("GeneticMarker"); MobyDataObjectSet gmCollection = new MobyDataObjectSet(); // a collection for(/* loop over your native marker info set */){ gmCollection.add(new MobyDataComposite(markerType, null, null, fieldName1, fieldValue1, fieldName2, fieldValue2...)); // create the collection members } MobyContentInstance request = new MobyContentInstance(gmCollection, "myServiceParamName"); // build a request envelope /* Call the service */ MobyRequest requester = new MobyRequest(central); // the thing that calls Moby services requester.setService(validServices[0]); MobyContentInstance response = requester.invokeService(request); //synchronous call to service I don't see GeneticMarker in the Object registry, so I can't give you more specific info on the MobyDataComposite c-tor... Regards, Paul Pierre-Yves Chibon wrote: > Thanks for pulling up the javadoc. > > On Mon, 2010-03-29 at 08:27 -0600, Paul Gordon wrote: > >> A MobyDataComposite? This holds anything that is not a primitive >> datatype... >> > I am looking at this object but I have a collection of GeneticMarker: > java.lang.Object > extended byorg.biomoby.shared.datatypes.MobyObject > extended byorg.biomoby.shared.datatypes.Marker > extended byorg.biomoby.shared.datatypes.GeneticMarker > > I am trying to put it in a MobyDataComposite, but this one only accepts > MobyDataType (and not MobyObject). Then I will put these collection of > MobyDataComposite into an vector of MobyDataInstance to be sent to the service. > Am I doing this correctly ? > > Thanks, > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From py at pingoured.fr Mon Mar 29 16:11:15 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Mon, 29 Mar 2010 18:11:15 +0200 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB0CC23.9010909@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <4BB0B8D8.4000500@ucalgary.ca> <1269875922.10177.16.camel@localhost.localdomain> <4BB0CC23.9010909@ucalgary.ca> Message-ID: <1269879075.4829.0.camel@localhost.localdomain> On Mon, 2010-03-29 at 09:49 -0600, Paul Gordon wrote: > I don't see GeneticMarker in the Object registry, so I can't give you > more specific info on the MobyDataComposite c-tor... That is already quite some help. I will look into this. Thanks, Pierre From martin.senger at gmail.com Mon Mar 29 19:41:48 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 20:41:48 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <002301cacf46$b0981e20$11c85a60$@gmail.com> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> Message-ID: <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> > I think that it has something to do with a recent commit, because the > script > that builds the javadoc is reporting compile problems. > Paul, can you look at it please - so we can compile again? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From gordonp at ucalgary.ca Mon Mar 29 20:01:19 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 14:01:19 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> Message-ID: <4BB1070F.7030604@ucalgary.ca> Hmm..of course it all compiles fine for me here, so I've just committed all the changes I have locally. Hopefully this fixes it. Can I get the error details, or do I need to do a whole new CVS checkout? Martin Senger wrote: >> I think that it has something to do with a recent commit, because the >> script >> that builds the javadoc is reporting compile problems. >> >> > > Paul, can you look at it please - so we can compile again? > > Thanks, > Martin > > From martin.senger at gmail.com Mon Mar 29 20:09:32 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 21:09:32 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB1070F.7030604@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> <4BB1070F.7030604@ucalgary.ca> Message-ID: <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> Paul, thanks for a very fast reaction. It compiles fine now. Perhaps I was too fast with my email - the problem might have been in the corrupted jar files in the maven repository. When I removed them they were fetched again and compilation succeeded. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From martin.senger at gmail.com Mon Mar 29 20:16:39 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 21:16:39 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> <4BB1070F.7030604@ucalgary.ca> <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> Message-ID: <4d93f07c1003291316h5ee494cq337350612be9886d@mail.gmail.com> [cont.] ... however,... Paul, Eddie, can you remind me what was our last decision on Java version? Is it officially 1.6 or still 1.5? Or, are the compilation errors (in seahawk classes; see below) I got on biomoby.org not related to Java version? Cheers, Martin compile: [javac] Compiling 368 source files to /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/build/classes [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:426: cannot find symbol [javac] symbol : class Desktop [javac] location: class ca.ucalgary.seahawk.gui.MobyContentPane [javac] Desktop desktop = Desktop.getDesktop(); [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:426: cannot find symbol [javac] symbol : variable Desktop [javac] location: class ca.ucalgary.seahawk.gui.MobyContentPane [javac] Desktop desktop = Desktop.getDesktop(); [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:427: package Desktop does not exist [javac] if(!desktop.isSupported(Desktop.Action.BROWSE)) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:180: cannot find symbol [javac] symbol : method isEmpty() [javac] location: class java.lang.String [javac] if(this.getText().isEmpty()) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:178: method does not override a method from its superclass [javac] @Override [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:187: cannot find symbol [javac] symbol : method isEmpty() [javac] location: class java.lang.String [javac] if(this.getText().isEmpty()) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:185: method does not override a method from its superclass [javac] @Override [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:214: cannot find symbol [javac] symbol : method isEmpty() [javac] location: class java.lang.String [javac] if(this.getText().isEmpty()) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:212: method does not override a method from its superclass [javac] @Override [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:221: cannot find symbol [javac] symbol : method isEmpty() [javac] location: class java.lang.String [javac] if(this.getText().isEmpty()) { [javac] ^ [javac] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:219: method does not override a method from its superclass [javac] @Override [javac] ^ [javac] Note: /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.javauses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 11 errors -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From gordonp at ucalgary.ca Mon Mar 29 20:23:52 2010 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Mar 2010 14:23:52 -0600 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4d93f07c1003291316h5ee494cq337350612be9886d@mail.gmail.com> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> <4BB1070F.7030604@ucalgary.ca> <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> <4d93f07c1003291316h5ee494cq337350612be9886d@mail.gmail.com> Message-ID: <4BB10C58.3060309@ucalgary.ca> Hmm..I thought we decided 1.6... Martin Senger wrote: > [cont.] ... however,... > > Paul, Eddie, can you remind me what was our last decision on Java version? > Is it officially 1.6 or still 1.5? Or, are the compilation errors (in > seahawk classes; see below) I got on biomoby.org not related to Java > version? > > Cheers, > Martin > > compile: > [javac] Compiling 368 source files to /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/build/classes > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:426: > cannot find symbol > [javac] symbol : class > Desktop > > [javac] location: class > ca.ucalgary.seahawk.gui.MobyContentPane > > [javac] Desktop desktop = > Desktop.getDesktop(); > > [javac] > ^ > > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:426: > cannot find symbol > [javac] symbol : variable > Desktop > > [javac] location: class > ca.ucalgary.seahawk.gui.MobyContentPane > > [javac] Desktop desktop = > Desktop.getDesktop(); > > [javac] > ^ > > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java:427: > package Desktop does not exist > [javac] if(!desktop.isSupported(Desktop.Action.BROWSE)) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:180: > cannot find symbol > [javac] symbol : method isEmpty() > [javac] location: class java.lang.String > [javac] if(this.getText().isEmpty()) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:178: > method does not override a method from its superclass > [javac] @Override > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:187: > cannot find symbol > [javac] symbol : method isEmpty() > [javac] location: class java.lang.String > [javac] if(this.getText().isEmpty()) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:185: > method does not override a method from its superclass > [javac] @Override > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:214: > cannot find symbol > [javac] symbol : method isEmpty() > [javac] location: class java.lang.String > [javac] if(this.getText().isEmpty()) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:212: > method does not override a method from its superclass > [javac] @Override > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:221: > cannot find symbol > [javac] symbol : method isEmpty() > [javac] location: class java.lang.String > [javac] if(this.getText().isEmpty()) { > [javac] ^ > [javac] /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/WorkflowPreviewDialog.java:219: > method does not override a method from its superclass > [javac] @Override > [javac] ^ > [javac] Note: /home/websites/ > biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.javauses > or overrides a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [javac] Note: Some input files use unchecked or unsafe operations. > [javac] Note: Recompile with -Xlint:unchecked for details. > [javac] 11 errors > > > From martin.senger at gmail.com Mon Mar 29 20:26:11 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 21:26:11 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB10C58.3060309@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <002301cacf46$b0981e20$11c85a60$@gmail.com> <4d93f07c1003291241p8c094d5x3823f6c8d8928a8d@mail.gmail.com> <4BB1070F.7030604@ucalgary.ca> <4d93f07c1003291309s10371b9al2ad054fbd0bd71a4@mail.gmail.com> <4d93f07c1003291316h5ee494cq337350612be9886d@mail.gmail.com> <4BB10C58.3060309@ucalgary.ca> Message-ID: <4d93f07c1003291326q50b720dby9a4e4ed135996859@mail.gmail.com> > > Hmm..I thought we decided 1.6... 1.6 is fine with me. Anybody opposing? Anyway, meanwhile, I am going to install Java 1.6. on biomoby.org so it will compile. Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From martin.senger at gmail.com Mon Mar 29 20:47:04 2010 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Mar 2010 21:47:04 +0100 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <1269862079.10177.9.camel@localhost.localdomain> References: <1269862079.10177.9.camel@localhost.localdomain> Message-ID: <4d93f07c1003291347w640f2b0bg45bacf1f1cc1789c@mail.gmail.com> > I am trying to reach (without success) the javadoc at: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/index.html > It is back. As Eddie already said, the problem was with the compilation. Once that was solved, the docs is back. Cheers, Martin PS for Paul, Eddie (and perhaps me): It would be nice to fix these warnings: docs: [javadoc] Generating Javadoc [javadoc] Javadoc execution [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataRecorder.java:2127: warning - @param argument "responseURL" is not a parameter name. [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java:142: warning - @param argument "t" is not a parameter name. [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java:94: warning - @param argument "url" is not a parameter name. [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/client/MobyRequestEvent.java:60: warning - @param argument "inputXML" is not a parameter name. [javadoc] /home/websites/ biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/inb/biomoby/central/gui/model/MobyObjectPropertiesTableModel.java:72: warning - @return tag has no arguments. -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From py at pingoured.fr Tue Mar 30 09:26:52 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 30 Mar 2010 11:26:52 +0200 Subject: [MOBY-dev] Javadoc down ? In-Reply-To: <4BB0CC23.9010909@ucalgary.ca> References: <1269862079.10177.9.camel@localhost.localdomain> <4BB0B8D8.4000500@ucalgary.ca> <1269875922.10177.16.camel@localhost.localdomain> <4BB0CC23.9010909@ucalgary.ca> Message-ID: <1269941212.8363.64.camel@localhost.localdomain> On Mon, 2010-03-29 at 09:49 -0600, Paul Gordon wrote: > Maybe Eddie can help you with > the generated classes? Out of curiosity I would not mind to see some example code. I believe this is the mechanism which is used by the web-service when we send back the output, isn't it ? Using a similar approach, can't the output from a service be easily parsed to its object (the generated one not the generic one). At the moment I use a couple of while into each other, it does the job but I wonder if there is not easier way. Thanks, Regards, Pierre