From groscurt at mpiz-koeln.mpg.de Sat Mar 1 03:12:14 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Sat, 01 Mar 2008 09:12:14 +0100 Subject: [MOBY-dev] Dashboard can't connect to Registries In-Reply-To: <000601c87a45$892f2700$9b8d7500$@de> References: <000601c87a45$892f2700$9b8d7500$@de> Message-ID: <47C90FDE.7030808@mpiz-koeln.mpg.de> Hi Michael, sorry thats my fault - I offer for Eclipse user the .classpath file, but unfortunatley I had some problems with the plone software and it didnt update the file. Please download the .classpath file from the tutorial again and refresh your project - this should remove your first problem. For the second... I cant check that now - but this should work when you copy the build.properties.template to build.properties and change their the proxy settings in that file (there should be poperties for that) Best andreas Michael Gerlich wrote: > Hi there, > > First of all thanks for your tutorials about setting up Biomoby with Eclipse > and for the newly created Known errors site at > > http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step > /writing-biomoby-web-services/known-errors-and-problems, > they helped me a lot and I finally have successful Builds with the Ant > Scripts (using JDK 1.5). > > But there are some things I still have problems with. > > 1) Eclipse keeps reporting that it misses required libraries, even though > the initeclipse script says Build successful. Are these errors some kind of > artifacts or should I check the ant scripts or checkout JMoby again? > > micge at linux-vm:~/eclipse> ./eclipse -vmargs > -Djava.home=/usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/ > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > > Severity and Description > Project 'moby' is missing required library: 'lib/activation.jar' > > Project 'moby' is missing required library: 'lib/adenine.jar' > Project 'moby' is missing required library: 'lib/alltools2.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-antlr.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-bcel.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-bsf.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-log4j.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-oro.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-regexp.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-resolver.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-commons-logging.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-commons-net.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-contrib.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-icontract.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jai.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-javamail.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-jdepend.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jmf.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jsch.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-junit.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-launcher.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-netrexx.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-nodeps.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-starteam.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-stylebook.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-swing.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-trax.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-vaj.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-weblogic.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-xalan1.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-xslp.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/xercesImpl.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/xml-apis.jar' > > Project 'moby' is missing required library: 'lib/axis-ant.jar' > Project 'moby' is missing required library: 'lib/axis.jar' > Project 'moby' is missing required library: 'lib/castor-0.9.5.jar' > > Project 'moby' is missing required library: 'lib/commons-codec-1.3.jar' > > Project 'moby' is missing required library: > 'lib/commons-collections-2.1.jar' > Project 'moby' is missing required library: 'lib/commons-dbcp-1.1.jar' > > Project 'moby' is missing required library: 'lib/commons-discovery-0.2.jar' > > Project 'moby' is missing required library: > 'lib/commons-httpclient-3.0-rc2.jar' > Project 'moby' is missing required library: 'lib/commons-io-1.0.jar' > > Project 'moby' is missing required library: 'lib/commons-lang-2.1.jar' > > Project 'moby' is missing required library: 'lib/commons-logging-1.0.4.jar' > > Project 'moby' is missing required library: 'lib/commons-pool-1.1.jar' > > Project 'moby' is missing required library: 'lib/concurrent.jar' > > Project 'moby' is missing required library: 'lib/dnsjava-1.3.2.jar' > > Project 'moby' is missing required library: 'lib/icis-pedigree.jar' > > Project 'moby' is missing required library: 'lib/icu4j.jar' > Project 'moby' is missing required library: 'lib/jakarta-oro-2.0.5.jar' > > Project 'moby' is missing required library: 'lib/jaxen-core.jar' > > Project 'moby' is missing required library: 'lib/jaxen-jdom.jar' > > Project 'moby' is missing required library: 'lib/jaxrpc.jar' > Project 'moby' is missing required library: 'lib/jcalendar.jar' > Project 'moby' is missing required library: 'lib/jdom.jar' > Project 'moby' is missing required library: 'lib/jena.jar' > Project 'moby' is missing required library: 'lib/jfcunit.jar' > Project 'moby' is missing required library: 'lib/jodconverter-2.2.0.jar' > > Project 'moby' is missing required library: 'lib/junit.jar' > Project 'moby' is missing required library: 'lib/log4j-1.2.12.jar' > > Project 'moby' is missing required library: 'lib/lsid-client-1.1.2.jar' > > Project 'moby' is missing required library: 'lib/lsid-server-1.1.2.jar' > > Project 'moby' is missing required library: 'lib/mail.jar' > Project 'moby' is missing required library: 'lib/mailapi_1_3_1.jar' > > Project 'moby' is missing required library: > 'lib/mysql-connector-java-3.1.7-bin.jar' > Project 'moby' is missing required library: 'lib/rdf-api-2001-01-19.jar' > > Project 'moby' is missing required library: 'lib/saaj.jar' > Project 'moby' is missing required library: 'lib/saxpath.jar' > Project 'moby' is missing required library: 'lib/servlet.jar' > Project 'moby' is missing required library: 'lib/taverna.jar' > Project 'moby' is missing required library: 'lib/wsdl4j-1.5.1.jar' > > Project 'moby' is missing required library: 'lib/xalan.jar' > Project 'moby' is missing required library: 'lib/xercesImpl.jar' > > Project 'moby' is missing required library: 'lib/xercesSamples.jar' > > Project 'moby' is missing required library: 'lib/xml-apis.jar' > Project 'moby' is missing required library: 'lib/xmlParserAPIs.jar' > > Project build error Cannot find parent: org.biomoby:jmoby for project: > org.biomoby:jmoby-core:jar:1.0.0 moby/src/main pom.xml line 1 > 1204224268317 133440 > Project build error Cannot find parent: org.biomoby:jmoby for project: > org.biomoby:jmoby-plugins:jar:1.0.0 moby/src/samples pom.xml line > 1 1204224267905 133439 > The project cannot be built until build path errors are resolved > moby > > > > 2) I'am behind a proxy server, so I had to edit proxy settings in > net.properties of JDK 1.5 (http_proxy environment variable is set, but > without effect to Java). With this, all the ant scripts work without any > problems, but when I run Dashboard, all I got are empty lists and the > following messages: > > Inside Eclipse: > --------------- > Buildfile: /home/micge/workspace/moby/build.xml > checkmaven: > initmaven: > init: > config: > compile: > moses-init: > samples-init: > dashboard-init: > dashboard-config: > dashboard: > [Dashboard] libxcb: WARNING! Program tries to unlock a connection without > having acquired > [Dashboard] a lock first, which indicates a programming error. > [Dashboard] There will be no further warnings about this issue. > [Dashboard] libxcb: WARNING! Program tries to lock an already locked > connection, > [Dashboard] which indicates a programming error. > [Dashboard] There will be no further warnings about this issue. > [Dashboard] 192616 [Thread-6] WARN CentralDigestCachedImpl - Error with > Services RDF > [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== > [Dashboard] Fault details: > [Dashboard] Fault string: java.net.ConnectException: Connection timed out > [Dashboard] Fault code: > {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > [Dashboard] Fault actor: null > [Dashboard] When calling: > [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl > [Dashboard] =========== > [Dashboard] at > org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) > [Dashboard] at > org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) > [Dashboard] at > org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest > CachedImpl.java:216) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa > chedImpl.java:243) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm > pl.java:709) > [Dashboard] at > org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 > 61) > [Dashboard] at > org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 > ) > [Dashboard] at > org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) > [Dashboard] at java.lang.Thread.run(Thread.java:595) > [Dashboard] Caused by: java.net.ConnectException: Connection timed out > [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) > [Dashboard] at > org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: > 32) > [Dashboard] at > org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) > [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) > [Dashboard] at > org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) > [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) > [Dashboard] at > org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) > [Dashboard] ... 9 more > [Dashboard] Caused by: java.net.ConnectException: Connection timed out > [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) > [Dashboard] at > java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) > [Dashboard] at > java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) > [Dashboard] at > java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) > [Dashboard] at > java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) > [Dashboard] at java.net.Socket.connect(Socket.java:520) > [Dashboard] at java.net.Socket.connect(Socket.java:470) > [Dashboard] at java.net.Socket.(Socket.java:367) > [Dashboard] at java.net.Socket.(Socket.java:180) > [Dashboard] at > org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact > ory.java:149) > [Dashboard] at > org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact > ory.java:120) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) > [Dashboard] ... 18 more > [Dashboard] 193461 [Thread-7] WARN CentralDigestCachedImpl - Error with > Services RDF > [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== > [Dashboard] Fault details: > [Dashboard] Fault string: java.net.ConnectException: Connection timed out > [Dashboard] Fault code: > {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > [Dashboard] Fault actor: null > [Dashboard] When calling: > [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl > [Dashboard] =========== > [Dashboard] at > org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) > [Dashboard] at > org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) > [Dashboard] at > org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest > CachedImpl.java:216) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa > chedImpl.java:243) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm > pl.java:709) > [Dashboard] at > org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 > 61) > [Dashboard] at > org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 > ) > [Dashboard] at > org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) > [Dashboard] at java.lang.Thread.run(Thread.java:595) > [Dashboard] Caused by: java.net.ConnectException: Connection timed out > [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) > [Dashboard] at > org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: > 32) > [Dashboard] at > org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) > [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) > [Dashboard] at > org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) > [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) > [Dashboard] at > org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) > [Dashboard] ... 9 more > [Dashboard] Caused by: java.net.ConnectException: Connection timed out > [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) > [Dashboard] at > java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) > [Dashboard] at > java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) > [Dashboard] at > java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) > [Dashboard] at > java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) > [Dashboard] at java.net.Socket.connect(Socket.java:520) > [Dashboard] at java.net.Socket.connect(Socket.java:470) > [Dashboard] at java.net.Socket.(Socket.java:367) > [Dashboard] at java.net.Socket.(Socket.java:180) > [Dashboard] at > org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact > ory.java:149) > [Dashboard] at > org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact > ory.java:120) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) > [Dashboard] ... 18 more > BUILD SUCCESSFUL > > > > >From Dashboard (after one minute) > -------------- > ===Error=== > Fault details: > Fault string: java.net.ConnectException: Connection timed out > Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > Fault actor: null > when calling: > http://moby.uralgary.ca/moby/MOBY-Central.pl > > Is this a problem with the proxy settings I made in net.properties or is it > inside Dashboard? > > > Regards, > Michael > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From martin.senger at gmail.com Sun Mar 2 12:25:16 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 01:25:16 +0800 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <200802291151.22060.groscurt@mpiz-koeln.mpg.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> > starting dashboard from console gives me I hope that I fixed all the recent (reported) problems with Dashboard, after changes caused by using Maven. I am still working on few details (e.g. on Eclipse problems) before I upload jMoby version 1.0.0 to the Maven repository. I would appreciate if you tell me if something is not working as it is supposed to work. The recent changes are summarized (as usual) here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ChangeLog (look what has been changed during and since our last meeting in Biohackhatlon). Please try, for example, the new 'ant install' (doing it in a fresh check-out may reveal more) - it should do everything, an then it starts Dashboard. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Sun Mar 2 12:35:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 01:35:21 +0800 Subject: [MOBY-dev] Dashboard can't connect to Registries In-Reply-To: <000601c87a45$892f2700$9b8d7500$@de> References: <000601c87a45$892f2700$9b8d7500$@de> Message-ID: <4d93f07c0803020935j3a2b419am70b062d7db47d5c2@mail.gmail.com> My few comments to: http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step > /writing-biomoby-web-services/known-errors-and-problems > , * "Open the *pom.xml*... and change..." Don't do, ever. The pom.xml is a generated file and will be overwritten regularly. It is generated from xmls/project.pom. But that one is shared and under cvs. Better tell me when this problem happens and I will try to solve it (even though I am trying to avoid Windows and Eclipse, but sometimes there is no detour...) * "The datatype and skeleton generation via dashboard failes in a NullPointerException" It should be fixed now. Make a new CVS update and tell me if it is not fixed please. * "The registration of my service via dashboard does not work" It works for me fine. Tell me details please if it still occurs. * "The deployment of my service via dashboard failes" I hope that I fixed it. It works for me now, at least. But I am working on other improvements in service deployment, so any comments about something not working in deployment would be very appreciated just now. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Mar 3 03:37:35 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 03 Mar 2008 09:37:35 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> Message-ID: <47CBB8CF.80303@mpiz-koeln.mpg.de> Hi Martin, it seems to work for me now with a new check out. What was the reason to start dashboard directly in the ant install task ? I stopped to update our tutorial as long as version 1.0.0. comes out... is hard to redo a lot of things if changes are still in progress ;-) Best andreas Martin Senger wrote: >> starting dashboard from console gives me >> > > > I hope that I fixed all the recent (reported) problems with Dashboard, after > changes caused by using Maven. I am still working on few details (e.g. on > Eclipse problems) before I upload jMoby version 1.0.0 to the Maven > repository. I would appreciate if you tell me if something is not working as > it is supposed to work. > > The recent changes are summarized (as usual) here: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ChangeLog (look > what has been changed during and since our last meeting in Biohackhatlon). > > Please try, for example, the new 'ant install' (doing it in a fresh > check-out may reveal more) - it should do everything, an then it starts > Dashboard. > > Cheers, > Martin > > From martin.senger at gmail.com Mon Mar 3 03:52:59 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 16:52:59 +0800 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <47CBB8CF.80303@mpiz-koeln.mpg.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> <47CBB8CF.80303@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803030052p1348df39ke4a7bfe8240be77@mail.gmail.com> > What was the reason to > start dashboard directly in the ant install task ? > Sounded like a good idea, I do not know. Any problems with it? The most advantages you witness when you do it really from a clean beginning. Which means not only not having yet build.properties file (the install script creates it and adds there property 'registry.cache.dir'), but also without (yet) any dashboard preferences (which is a bit harder to remove them in windows: you have to go to the windows registry and remove the key 'cache/directory'; that's why I have an option in 'settings' - 'manage my dashboard' - but it is not yet implemented). > I stopped to update our tutorial as long as version 1.0.0. comes out... It's real close. The only still missing pieces (AFAIK) are to test more deployment parts, and to refresh the Eclipse tutorial. Will be done this week (and then I will start working on version 1.1.0 which means adding async services and document/literal style). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Mar 3 04:10:18 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 03 Mar 2008 10:10:18 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <4d93f07c0803030052p1348df39ke4a7bfe8240be77@mail.gmail.com> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> <47CBB8CF.80303@mpiz-koeln.mpg.de> <4d93f07c0803030052p1348df39ke4a7bfe8240be77@mail.gmail.com> Message-ID: <47CBC07A.9060008@mpiz-koeln.mpg.de> Martin Senger wrote: >> What was the reason to >> start dashboard directly in the ant install task ? >> >> > > Sounded like a good idea, I do not know. Any problems with it? > Martin no, no problem with that ... just surprised seeing starting dashboard ;-) i think thats quite convenient because most people will work with dashboard and if, as you described, the script now takes a lot of responsibilites, its much better. >* "Open the *pom.xml*... and change..." > Don't do, ever. The pom.xml is a generated file and will be overwritten >regularly. It is generated from xmls/project.pom. But that one is shared and >under cvs. Better tell me when this problem happens and I will try to solve >it (even though I am trying to avoid Windows and Eclipse, but sometimes >there is no detour...) the problem about that is what also Eddie encountered... when the java.home is pointing to the jdk folder and not to the jre inside the jdk folder the expression ${java.home}/../lib/tools.jar is wrong. After changing it to ${java.home}/lib/tools.jar it works. thats why I added it. Best and keep on working *g Andreas From groscurt at mpiz-koeln.mpg.de Mon Mar 3 06:46:27 2008 From: groscurt at mpiz-koeln.mpg.de (groscurt) Date: Mon, 3 Mar 2008 12:46:27 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <47CBC07A.9060008@mpiz-koeln.mpg.de> Message-ID: <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> Hi, sorry for bothering again.... when i start dashboard with a fresh checkout i get dashboard: [Dashboard] Mar 3, 2008 12:43:34 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/RegistryPanel/prefs.xml [Dashboard] Mar 3, 2008 12:43:34 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/RegistryPanel/registryEndpoint/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:34 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/RegistryPanel/registryNamespace/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:34 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/RegistryPanel/cacheDirectory/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:36 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/ResultsPanel/prefs.xml [Dashboard] Mar 3, 2008 12:43:36 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/SimpleClientPanel/serviceEndpoint/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:36 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/SimpleClientPanel/serviceImplClass/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:37 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/SimpleClientPanel/prefs.xml [Dashboard] Mar 3, 2008 12:43:37 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/SimpleClientPanel/sc-inputFile/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:45 PM java.util.prefs.FileSystemPreferences syncWorld [Dashboard] WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: java.lang.IllegalArgumentException: Not supported: indent-number is this a dashboard issue or something local ? And on the start of dashboard the fields of Endpoint and URI are empty (for default). When switch to any other central they show up, also when i switch back to default.. its just on the first startup. Best andreas From martin.senger at gmail.com Mon Mar 3 07:08:40 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 20:08:40 +0800 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> References: <47CBC07A.9060008@mpiz-koeln.mpg.de> <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803030408v13746ae3j1548251a77424d16@mail.gmail.com> > sorry for bothering again.... Not at all. > when i start dashboard with a fresh checkout i > get Interesting; never seen it on my kubuntu. Please again: what java version are you using? It says that something is happening to your ~/.java/.userPrefs directory. Try to google it (e.g. http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751540) a bit. Try to remove the whole .java directory (your preferences disappear and you will recreate them again in dashboard). is this a dashboard issue or something local ? I hope it is local but I can't be sure. From jMoby, only Dashboard saves preference this way. > And on the start of dashboard the fields of Endpoint and URI are empty > (for > default). When switch to any other central they show up, also when i > switch > back to default.. its just on the first startup. Yes, this is how it should be. However, more important is the value in the 'cache directory'. If there are no previous preferences stored, it should be filled with the value of the registry.cache.dir (as given in 'ant install', or taken from build.properties). How does this field look like in your Dash? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Mar 3 07:26:11 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 03 Mar 2008 13:26:11 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <4d93f07c0803030408v13746ae3j1548251a77424d16@mail.gmail.com> References: <47CBC07A.9060008@mpiz-koeln.mpg.de> <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> <4d93f07c0803030408v13746ae3j1548251a77424d16@mail.gmail.com> Message-ID: <47CBEE63.2030506@mpiz-koeln.mpg.de> Martin Senger wrote: > Interesting; never seen it on my kubuntu. Please again: what java version > are you using? It says that something is happening to your > ~/.java/.userPrefs directory. Try to google it (e.g. > http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751540) a bit. Try to > remove the whole .java directory (your preferences disappear and you will > recreate them again in dashboard). > I use java version "1.6.0_04" Java(TM) SE Runtime Environment (build 1.6.0_04-b12) Java HotSpot(TM) Client VM (build 10.0-b19, mixed mode, sharing) i will google a bit :) > >> And on the start of dashboard the fields of Endpoint and URI are empty >> (for >> default). When switch to any other central they show up, also when i >> switch >> back to default.. its just on the first startup. >> > > > Yes, this is how it should be. However, more important is the value in the > 'cache directory'. If there are no previous preferences stored, it should be > filled with the value of the registry.cache.dir (as given in 'ant install', > or taken from build.properties). > > How does this field look like in your Dash? > how you described... in my old checkout I had another entry there and it complained, I changed it to the one used during the installation and it worked. With the new checkout the entry was correctly set up when dashboard started. best andreas From martin.senger at gmail.com Mon Mar 3 07:36:10 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 20:36:10 +0800 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <47CBEE63.2030506@mpiz-koeln.mpg.de> References: <47CBC07A.9060008@mpiz-koeln.mpg.de> <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> <4d93f07c0803030408v13746ae3j1548251a77424d16@mail.gmail.com> <47CBEE63.2030506@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803030436o9591a44p6412759d002fbd13@mail.gmail.com> > I use > java version "1.6.0_04" > Java(TM) SE Runtime Environment (build 1.6.0_04-b12) > Java HotSpot(TM) Client VM (build 10.0-b19, mixed mode, sharing) > I will try with 1.6 myself later. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Mon Mar 3 11:20:18 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 03 Mar 2008 17:20:18 +0100 Subject: [MOBY-dev] I am a believer... Message-ID: <47CC2542.9030600@bsc.es> Hello everybody! I'd like to continue to discuss (even in a monologue mode :-)) document/literal encoding. I have prepared an example how it would be implemented in JMoby (!). It demands a few changes in MoSeS generator to implement it. Unfortunately, because JMoby is not JAXB based, ;-), there is no possibility to generate the WSDL automatically (JAX-WS), so one must be generated somehow (by the MoSeS). I'm using JBoss 4.2.2 with JBoss WS-3.0 (METRO). Unfortunately it doesn't deploy Provider Based JAX-WS endpoints, so I use ejb3 as an example... Here is the complete example: The class that implements a "proxy" between a JAX-WS Provider and JMoby BaseService (nothing especial - just converts Source <-> String) ***************************************************** package es.bsc.inb.ejb.jmoby; import java.io.*; import javax.xml.transform.*; import javax.xml.transform.stream.*; import javax.xml.ws.Provider; import org.biomoby.service.BaseService; import org.biomoby.shared.parser.MobyPackage; public abstract class ExtendedMobyBase extends BaseService implements Provider { // provider method that is called by the JAX-WS public Source invoke(Source request) { try { TransformerFactory f = TransformerFactory.newInstance(); Transformer tr = f.newTransformer(); StringWriter sw = new StringWriter(); StreamResult result = new StreamResult(sw); tr.transform(request, result); String response = runMyService(sw.toString()); return new StreamSource(new StringReader(response)); } catch(Exception ex) { ex.printStackTrace(); } // need to generate SOAP Exception... (shouldn't fail and... this is a demo...) return null; } // JMoby (MoSeS) generated method public String runMyService(String data) { MobyPackage mobyOutput = null; try { // reading the whole input MobyPackage mobyInput = MobyPackage.createFromXML (data, "AminoAcidSequence"); // prepare an output object mobyOutput = prepareOutput (mobyInput); // do the main job processIt (mobyInput, mobyOutput); // and return an XML back return mobyOutput.toXML(); } catch (Throwable e) { boolean mobyException = (e instanceof org.biomoby.shared.MobyException); java.io.StringWriter sw = new java.io.StringWriter (500); if (e.getCause() != null || (! mobyException)) e.printStackTrace (new java.io.PrintWriter (sw)); return error (e.getMessage() + "\n" + sw.toString(), mobyOutput); } } } ***************************************************** Empty (dummy) local interface, just t o comply to ejb3 specs... ***************************************************** package es.bsc.inb.ejb.jmoby; import javax.ejb.Local; @Local public interface JMobyDocumentLiteralDemoServiceLocal {} ***************************************************** Here is the service itself. It implements processIt() method from BaseService JMoby class... ***************************************************** package es.bsc.inb.ejb.jmoby; import javax.ejb.Stateless; import javax.xml.transform.Source; import javax.xml.ws.*; import org.biomoby.shared.MobyException; import org.biomoby.shared.datatypes.MobyObject; import org.biomoby.shared.parser.*; @WebServiceProvider(serviceName="JMobyDocumentLiteralDemoService", portName="JMobyDocumentLiteralDemoPort", targetNamespace="urn:JMobyDocumentLiteralDemoService/wsdl", wsdlLocation = "META-INF/wsdl/JMobyDocumentLiteralDemoService.wsdl") @javax.xml.ws.ServiceMode(value=javax.xml.ws.Service.Mode.PAYLOAD) @Stateless public class JMobyDocumentLiteralDemoService extends ExtendedMobyBase implements JMobyDocumentLiteralDemoServiceLocal, Provider { @Override public void processIt(MobyJob request, MobyJob response, MobyPackage arg2) throws MobyException { // echo... MobyObject object = request.getData(); response.setData(object); } } ***************************************************** And finally we MUST provide the WSDL file (in the correct location as in "META-INF/wsdl/JMobyDocumentLiteralDemoService.wsdl") ***************************************************** ***************************************************** Note, that this is a Document/Literal XML Schema based web-service that use JMoby as an implementation. Unfortunately, there is no client from JMoby yet to call the service... :-( The schema () is the same for any Moby web-service (no ontology included). Yours, Dmitry. P.S. As always appreciate your opinions (aggressive and negative included :-) ). From gordonp at ucalgary.ca Mon Mar 3 12:01:12 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 03 Mar 2008 10:01:12 -0700 Subject: [MOBY-dev] I am a believer... In-Reply-To: <47CC2542.9030600@bsc.es> References: <47CC2542.9030600@bsc.es> Message-ID: <47CC2ED8.8050003@ucalgary.ca> Hi Dmitry, I can't comment on the server side of things, because I don't use MoSeS, but I am planning on adding client-side support for Document/Literal in the next couple of weeks, so you'll actually be able to use it. :-) Regards, Paul > > > Note, that this is a Document/Literal XML Schema based web-service > that use JMoby as an implementation. > Unfortunately, there is no client from JMoby yet to call the > service... :-( > > The schema () is the same for any Moby web-service (no > ontology included). > > Yours, > > Dmitry. > > P.S. As always appreciate your opinions (aggressive and negative > included :-) ). > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,47cc2ae710950453915731! > > > From dmitry.repchevski at bsc.es Mon Mar 3 12:25:25 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 03 Mar 2008 18:25:25 +0100 Subject: [MOBY-dev] I am a believer... In-Reply-To: <47CC2ED8.8050003@ucalgary.ca> References: <47CC2ED8.8050003@ucalgary.ca> Message-ID: <47CC3485.1090300@bsc.es> Hello Paul, So no discussion so far... ;-) The question is not that I can not use it (my API can support it), but THE WAY it supposed to be implemented. If you look into http://inb.bsc.es/java/moby_ejb3_example.html you can see the my point of view. I would be happy to see MobyMessage as a BARE PAYLOAD of the document/literal service: ************************************************************** AGHFJHGDKHGJKADGHJGDJH ************************************************************** On the server side it gives an opportunity to use a STANDARD JAX-WS protocol stack. On the client side it gives an opportunity to use a STANDARD JAX-WS protocol stack. The given example was to show that just modifying a little bit JMoby BaseService class (adding public Source invoke(Source request) method and implementing Provider interface) will add such a support to JMoby WITHOUT breaking "old" soap-encoding sertvices. It would cost virtually nothing to convert the "old" ones to the doc/literal, because this way the only thing for the service provider to do is to update JMoby version and put some (STANDARD) annotations to the service. And by the way get rid of AXIS ;-) Sicerely Yours, Dmitry, P.S. > I can now go Axis-free in > MobyRequest (except for there being no Central implementation without > Axis... hint hint). ;-) Done. http://inb.bsc.es/java/moby_central.html From groscurt at mpiz-koeln.mpg.de Fri Mar 7 10:12:59 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 07 Mar 2008 16:12:59 +0100 Subject: [MOBY-dev] [Fwd: Problem with xercexImpl-2.6.2.jar] Message-ID: <47D15B7B.4030706@mpiz-koeln.mpg.de> hi, I write biomoby service with eclipse. and now the maven 2.0 finds wished libraries and downloads it automatically . But I have problem with xercexImpl-2.6.2.jar , because it has older version SAXParserFactory. So the above jar files should be removed from class path. else I get an Exception like this: Exception in thread "main" java.lang.UnsupportedOperationException: This parser does not support specification "null" version "null". I can simply remove this jar from lib of my biomoby project before, but now maven try to download and install it every time after I removed it from maven repository in my local directory. how should I do , so that maven doesn't download it by default? Should I change the dependency relationship in pom.xml ? thank you for your help in advance? regrads hao chen From martin.senger at gmail.com Fri Mar 7 10:58:22 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 7 Mar 2008 23:58:22 +0800 Subject: [MOBY-dev] [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47D15B7B.4030706@mpiz-koeln.mpg.de> References: <47D15B7B.4030706@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803070758j176a25f0o2a035938d5e29258@mail.gmail.com> Hi, Exception in thread "main" java.lang.UnsupportedOperationException: This > parser does not support specification "null" version "null". > You have to trace what jar file is loading it (as its dependency) and then apply the same trick that is already once used in jmoby/xmls/project.pom: commons-configuration commons-configuration 1.5 xerces xerces When you find it, change the xmls/project.pom and please commit it back to jMoby. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Sat Mar 8 05:21:06 2008 From: martin.senger at gmail.com (Martin Senger) Date: Sat, 8 Mar 2008 18:21:06 +0800 Subject: [MOBY-dev] looking for asynchronous service specification... Message-ID: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> ...and cannot find it on biomoby.org pages. Can anybody send here the latest version of it please? I am ready to implement it into MoSeS but somehow without the spec it is a bit difficult... :-) Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Mar 10 08:56:43 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 10 Mar 2008 13:56:43 +0100 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> Message-ID: <47D5300B.4010301@mpiz-koeln.mpg.de> Hi, is it deliberately that while deploying via dashboard (started from eclipse) on a remote machine - dashboard does not take the value of the 'Tomcat home directory' the user specified, but the CATALINA_HOME variable of the user ? We had the problem that whatever value we specified in this field it always used the value of the system variable - which is probably (and in our case definitely *g) different on the remote machine. As always - local problems or a general one ;-) Best andreas From jmrodriguez at cnio.es Mon Mar 10 09:15:14 2008 From: jmrodriguez at cnio.es (Jose Manuel rodriguez) Date: Mon, 10 Mar 2008 14:15:14 +0100 Subject: [MOBY-dev] looking for asynchronous service specification... In-Reply-To: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> Message-ID: <47D53462.8090401@cnio.es> Hello Martin, In the next root of CVS you can find the asynchronous proposal cvs.open-bio.org:/home/repository/moby/moby-live/Docs/asyncDocs/ Best Regards, Jos?. Martin Senger wrote: > ...and cannot find it on biomoby.org pages. Can anybody send here the latest > version of it please? I am ready to implement it into MoSeS but somehow > without the spec it is a bit difficult... :-) > > Thanks, > Martin > > -- Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From jmrodriguez at cnio.es Mon Mar 10 09:15:14 2008 From: jmrodriguez at cnio.es (Jose Manuel rodriguez) Date: Mon, 10 Mar 2008 14:15:14 +0100 Subject: [MOBY-dev] looking for asynchronous service specification... In-Reply-To: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> Message-ID: <47D53462.8090401@cnio.es> Hello Martin, In the next root of CVS you can find the asynchronous proposal cvs.open-bio.org:/home/repository/moby/moby-live/Docs/asyncDocs/ Best Regards, Jos?. Martin Senger wrote: > ...and cannot find it on biomoby.org pages. Can anybody send here the latest > version of it please? I am ready to implement it into MoSeS but somehow > without the spec it is a bit difficult... :-) > > Thanks, > Martin > > -- Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From groscurt at mpiz-koeln.mpg.de Mon Mar 10 09:38:10 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 10 Mar 2008 14:38:10 +0100 Subject: [MOBY-dev] General deployment question Message-ID: <47D539C2.1010608@mpiz-koeln.mpg.de> Hiho, another thing we wonder is - the ant task 'deploy' copies all libs and jars correctly to Tomcat.. why doesnt it copy also the implementing class ? I tried it with entering the impl class of the service in the field 'Pattern for implementation class names' (something which someone can please shortly explain what that is for ?) - but I always have to copy the the implementation class? is this just the way or do we forget something ? best and thanks andreas From martin.senger at gmail.com Mon Mar 10 16:47:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Mar 2008 04:47:21 +0800 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <47D5300B.4010301@mpiz-koeln.mpg.de> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> <47D5300B.4010301@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> > is it deliberately that while deploying via dashboard (started from > eclipse) on a remote machine - dashboard does not take the value of the > 'Tomcat home directory' the user specified, but the CATALINA_HOME > variable of the user ? Hard to say if it was deliberately or not (I do not remember it). But I spotted this last week, too (when I was testing it again because of changes done due to the jMoby mavenization). And I almost concluded that it should be almost in all cases the 'localhost' value. This means the value that is used on the remote machine to talk to that remote machine. But generally, you are right: if the help says that this field is used, it should be used. Do you wish me to fix it? [I mean to fix the behaviour, not just to fix the help page.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Mon Mar 10 16:49:56 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Mar 2008 04:49:56 +0800 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D539C2.1010608@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> > another thing we wonder is - the ant task 'deploy' copies all libs and > jars correctly to Tomcat.. why doesnt it copy also the implementing > class ? Because it does not know where the implementing class is (it just knows its name). You have to jar it first (probably together with adding other libraries needed) and then to tell dashboard where to take it from (using the user library/directory field). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Tue Mar 11 03:43:02 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 11 Mar 2008 08:43:02 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> Message-ID: <47D63806.3000107@mpiz-koeln.mpg.de> Hi Martin, this i dont get. The implementing class is compiled into other/samples. In dashboard you have to enter the full package name (at least in the 'Implemented by class' field) - so this should give all information ?! or what do i miss here ? and also - can you (or anyone) shortly explain what the 'Pattern for implementation class names' is ? i never use it and everything works, but still wondering what it is for. Best andreas Martin Senger wrote: >> another thing we wonder is - the ant task 'deploy' copies all libs and >> jars correctly to Tomcat.. why doesnt it copy also the implementing >> class ? >> > > > Because it does not know where the implementing class is (it just knows its > name). You have to jar it first (probably together with adding other > libraries needed) and then to tell dashboard where to take it from (using > the user library/directory field). > > Cheers, > Martin > > From groscurt at mpiz-koeln.mpg.de Tue Mar 11 03:46:27 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 11 Mar 2008 08:46:27 +0100 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> <47D5300B.4010301@mpiz-koeln.mpg.de> <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> Message-ID: <47D638D3.1050908@mpiz-koeln.mpg.de> Hi Martin, it would be great if you can fix it. E.g. on my local machine tomcat can be found under /local/groscurt/tomcat/. This value is also set as CATALINA_HOME in my .bashrc. But if I want to deploy on our test production server, on which the Tomcat can be found under /opt/tomcat, of course I enter /opt/tomcat in the 'Tomcat home directory". Deploying it will result with the current code that it tries to deploy to /local/groscurt/tomcat which failes of course on the test production server. so for me this is something to be fixed. Thanks Andreas Martin Senger wrote: > But generally, you are right: if the help says that this field is used, it > should be used. Do you wish me to fix it? [I mean to fix the behaviour, not > just to fix the help page.] > > Cheers, > Martin > > From martin.senger at gmail.com Tue Mar 11 07:35:38 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Mar 2008 07:35:38 -0400 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D63806.3000107@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> > this i dont get. The implementing class is compiled into other/samples. > In dashboard you have to enter the full package name (at least in the > 'Implemented by class' field) - so this should give all information ?! I have not known that you were referring to the 'samples'. The 'samples' are a bit special: they are on the CLASSPATH when Dashboard starts - which allows users to use them immediately in the Simple client panel. But they are still not considered when deploying to a Tomcat. If I do so (and it is easy to change it) then every user will have the samples deployed into his/her Tomcat. I considered it wrong. I prefer to let a user to decide - and if he/she wants to have the samples deployed, he/she can specify the samples directory in the "Directory with the user's jar files". So the quetsion now is: should I add the samples to the deployed jar files , as well? Regarding the package name: in that fields you specify a full package name - but it is not its location, so Dashboard cannot use it to find the place where the class physically sits. and also - can you (or anyone) shortly explain what the 'Pattern for > implementation class names' is ? i never use it and everything works, > but still wondering what it is for. It is for deploying to Axis (which is, so far, the only way we deploy jMoby services). The Axis engine needs to know the class name that represents each service (it uses it in its own configuration file server-config.wsdd where all service names are mapped to their class names). You need, therefore, specify for each service a class name in the table in the column "Implemented by class". You can do it manually - in which case you do not need to use anything in the "Pattern..." field. But the Pattern field helps you fill it the column at the beginning, before you start editing it. If you name your implementing classes, using some pattern that is the same for all your services, except the part where is the service name itself, usage of Pattern helps you that you need less editing (ideally no editing, at all). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Tue Mar 11 07:58:26 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 11 Mar 2008 12:58:26 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> Message-ID: <47D673E2.8040101@mpiz-koeln.mpg.de> Martin Senger wrote: >> this i dont get. The implementing class is compiled into other/samples. >> In dashboard you have to enter the full package name (at least in the >> 'Implemented by class' field) - so this should give all information ? >> I have not known that you were referring to the 'samples'. The 'samples' are >> a bit special: they are on the CLASSPATH when Dashboard starts - which >> allows users to use them immediately in the Simple client panel. But they >> are still not considered when deploying to a Tomcat. If I do so (and it is >> easy to change it) then every user will have the samples deployed into >> his/her Tomcat. I considered it wrong. I prefer to let a user to decide - >> and if he/she wants to have the samples deployed, he/she can specify the >> samples directory in the "Directory with the user's jar files". So the >> quetsion now is: should I add the samples to the deployed jar files , as >> well? >> not quite sure if we talk about the same ;-) > But they are still not considered when deploying to a Tomcat why ? the sample is my web service implementation class - of course i want to have to in Tomcat... > then every user will have the samples deployed into his/her Tomcat in my project with my samples folder there are only my developed web services, so my samples... what is the problem ? we should try to figure out whether we talk about the same or if someone (probably me *g) misses something ;-) >> Regarding the package name: in that fields you specify a full package name - >> but it is not its location, so Dashboard cannot use it to find the place >> where the class physically sits. >> >> assuming the default classloader the packname is identical to the location... and the implementing class is inside build/others/samples - so sorry still not getting the problem ;-) >> and also - can you (or anyone) shortly explain what the 'Pattern for >> >> implementation class names' is ? i never use it and everything works, >> but still wondering what it is for. >> > > It is for deploying to Axis (which is, so far, the only way we deploy jMoby > services). The Axis engine needs to know the class name that represents each > service (it uses it in its own configuration file server-config.wsdd where > all service names are mapped to their class names). You need, therefore, > specify for each service a class name in the table in the column > "Implemented by class". You can do it manually - in which case you do not > need to use anything in the "Pattern..." field. But the Pattern field helps > you fill it the column at the beginning, before you start editing it. If you > name your implementing classes, using some pattern that is the same for all > your services, except the part where is the service name itself, usage of > Pattern helps you that you need less editing (ideally no editing, at all). > ok - this means all my web services have the de.mpg.mpiz_koeln.*Impl so I can use that pattern instead to type in each servicename ? Is the pattern then de.mpg.mpiz_koeln.${SERVICE}Impl ? Thx much for your help Andreas From martin.senger at gmail.com Tue Mar 11 21:21:56 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Mar 2008 21:21:56 -0400 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D673E2.8040101@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> > not quite sure if we talk about the same ;-) Okay, tell me again what you want. > assuming the default classloader the packname is identical to the > location... No, not true. The package name is identical to the last part of the full path of the file where the class is written into. But it does not tell what is the full path. ok - this means all my web services have the de.mpg.mpiz_koeln.*Impl so > I can use that pattern instead to type in each servicename ? Yes. > Is the pattern then de.mpg.mpiz_koeln.${SERVICE}Impl ? Probably. It depends what you meant by the star in "de.mpg.mpiz_koeln.*Impl". This is how the help page explains it: "the ${SERVICE} token is replaced by a real service name, and ${Service} token by a real service name with the first letter changed to upper-case". Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Mar 12 08:55:05 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 13:55:05 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> Message-ID: <47D7D2A9.7080207@mpiz-koeln.mpg.de> Martin Senger wrote: >> assuming the default classloader the packname is identical to the >> location... >> > > No, not true. The package name is identical to the last part of the full > path of the file where the class is written into. But it does not tell what > is the full path. > How do you generate the skeletons then ? from my point of view thats the same situation. Skeletons sources are put into generated/skeletons and the compilation are put into build/other/skeletons. You know this paths and put them into a jar. For the samples it is identical... sources are found in src/samples and the compilation are in build/others/samples. I dont get the difference. and samples are (for me and others) the web services.... How do you get the compilations from build/other/skeletons - and why is that no problem, but build/other/samples is one ? Again - my implementation of the Web Service is inside src/samples and the compilation is in build/others/samples. My Service is de.mpg.mpiz_koeln.SERVICEImpl, so ergo you find the class in build/others/samples/de/mpg/mpiz_koeln/SERVICEImpl. I still dont understand why this is not accessible, when the skeletons or datatypes are.... What I love to see is that the implementation classes I enter in dashboard when I give the pattern or enter it for each service are copied into CATALINA_HOME/webapps/axis/WEB-INF/classes, just as the generated jars are copied into CATALINA_HOME/webapps/axis/WEB-INF/lib. >> Is the pattern then de.mpg.mpiz_koeln.${SERVICE}Impl ? >> > > > Probably. It depends what you meant by the star in "de.mpg.mpiz_koeln.*Impl". > This is how the help page explains it: > "the ${SERVICE} token is replaced by a real service name, and ${Service} > token by a real service name with the first letter changed to upper-case". > cool - the * was the real service name - thx. Best andreas Andreas From martin.senger at gmail.com Wed Mar 12 09:09:31 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 09:09:31 -0400 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D7D2A9.7080207@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> > How do you generate the skeletons then ? from my point of view thats the > same situation. No, it isn't. When I generate something I can choose where to put it (and I can remember that knowledge until I deploy to Tomcat). When I want something to take as an input (that I have not created) somebody must tell me where it is. > For the samples it is identical... sources are > found in src/samples and the compilation are in build/others/samples. I > dont get the difference. > I can find the samples, I admit it. But I am not sure if it is a good idea to deploy samples every time anybody does the deployment. I already asked if it was what you were suggesting. Were you? Is it really wise to deploy things that are not needed for those who do not provide sample services, at all? > How do you get the compilations from build/other/skeletons - and why is > that no problem, but build/other/samples is one ? I think it was answered above. Was it? Again - my implementation of the Web Service is inside src/samples and > the compilation is in build/others/samples. But that's just your case, not everybody does it like that. I may have my implementation in a totally different Eclipse project - and I have to tell Dashboard "Hey, here are my jar files". What I love to see is that the implementation classes I enter in > dashboard when I give the pattern or enter it for each service are > copied into CATALINA_HOME/webapps/axis/WEB-INF/classes That's generally impossible, unless we have some conventions (e.g. take samples by default, as you are suggesting). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Mar 12 09:28:51 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 14:28:51 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> Message-ID: <47D7DA93.2030809@mpiz-koeln.mpg.de> Finally i think we get along with what we are talking about ;-) I do understand your points... *cheer* Martin Senger wrote: >> I can find the samples, I admit it. But I am not sure if it is a good idea >> to deploy samples every time anybody does the deployment. I already asked if >> it was what you were suggesting. Were you? Is it really wise to deploy >> things that are not needed for those who do not provide sample services, at >> all >> Yes thats what I asked for... see answer below > Again - my implementation of the Web Service is inside src/samples and >> the compilation is in build/others/samples. >> > > But that's just your case, not everybody does it like that. I may have my > implementation in a totally different Eclipse project - and I have to tell > Dashboard "Hey, here are my jar files". > > Now I do get the essentiell point. But for my whole BioMoby life I was told... my Web Services HAVE to be in src/samples and will be compiled to build/others/samples. and honestly we tell that every person form all workshops now for years (so that was not only my view of this). Now that I know that the samples folder is not automatically the implementation folder (which makes sense, but why was I told so ;-) ) I understand your objection and therefore you are right. With assuming the classes in samples are not automatically the web services it is not wise to deploy them its just horrible - people doing this now for quite a while.... Best and thx andreas > What I love to see is that the implementation classes I enter in > >> dashboard when I give the pattern or enter it for each service are >> copied into CATALINA_HOME/webapps/axis/WEB-INF/classes >> > > > That's generally impossible, unless we have some conventions (e.g. take > samples by default, as you are suggesting). > > Cheers, > Martin > > From groscurt at mpiz-koeln.mpg.de Wed Mar 12 09:39:30 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 14:39:30 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> Message-ID: <47D7DD12.1010509@mpiz-koeln.mpg.de> but some additions. so as far as i know and as i said, lot people develop there services with the class inside samples. You said you can access the samples, so why not copying not all samples, but the class which was entered in dashboard ? So no one has any unwanted samples deployed - just the one(s) from his/her service ? if this is possible - i like to have it .... objections? andreas From martin.senger at gmail.com Wed Mar 12 09:55:00 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 09:55:00 -0400 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <47D638D3.1050908@mpiz-koeln.mpg.de> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> <47D5300B.4010301@mpiz-koeln.mpg.de> <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> <47D638D3.1050908@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803120655j1de1fe10h2f4b99f4bd752c37@mail.gmail.com> Hi, I was looking at the problem how to assign some properties for the remote deployment from Dashboard. I could not replicate the problem but I found a missing piece in the help. Here is how it works (but please let me know if you experienced different behaviour): 1) The Dashboard takes the information as entered in the fields "Tomcat home directory", AAxis relative path in tomcat", "Hostname", "port" and "path of axis admin servlet" and tries to use them in the newly created build.xmlfile that will be used on the remote machine. So far, so good. 2) But doing the above, Dashboard may be also influenced by properties defined in your build.properties file (because Dashboard uses Ant to do the job). The properties in question are: cross.tomcat.home cross.tomcat.host cross.tomcat.host If you have them defined in your build.properties, they will take, unfortunately, precedence over the field values entered in Dashboard. Andreas, could you please confirm that it is your case? 3) The same may happen, if you have set the CATALINA_HOME environment variable. Again, this may (I say 'may' because I have not tried this alternative now) take precedence over the field values in Dashboard. At the moment, I do not know how to fix it (easily), or if to fix it at all. It is, of course, possible, but could we live with just mentioning these consequences in the help? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Mar 12 10:03:25 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 10:03:25 -0400 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D7DD12.1010509@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> <47D7DD12.1010509@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803120703u206ab042t7a3441acde9fac40@mail.gmail.com> > You said you can access the samples, so why not copying not all samples, > but the class which was entered in dashboard ? When I was writing my answer, this alternative came to my mind - and I was just telling myself "don't worry, nobody will think about it" :-) Seriously, this is not a right solution because this would bring just one class to the Tomcat - but the implementation may require more classes (the ones the main class depends on). I would say, we either let it as it is now, or we add all samples to deployment. Because you are explaining now how important the samples directory had and have been, perhaps I should take it as a hint and not to be too concerned about having these classes deployed, after all. Which means I am (being influenced by you) changing my mind now - so should I go ahead and add samples there? [Perhaps I will do it using some property defining a conditional inclusion, with its default value as true?] Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Mar 12 10:25:04 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 15:25:04 +0100 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <4d93f07c0803120655j1de1fe10h2f4b99f4bd752c37@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> <47D5300B.4010301@mpiz-koeln.mpg.de> <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> <47D638D3.1050908@mpiz-koeln.mpg.de> <4d93f07c0803120655j1de1fe10h2f4b99f4bd752c37@mail.gmail.com> Message-ID: <47D7E7C0.2090000@mpiz-koeln.mpg.de> Martin Senger wrote: > If you have them defined in your build.properties, they will take, > unfortunately, precedence over the field values entered in Dashboard. > Andreas, could you please confirm that it is your case? > > in our case it was not point 2) we never set any variables in the build.properties, but point 3) is our case. If the CATALINA_HOME environment variable is set, this one is used. > At the moment, I do not know how to fix it (easily), or if to fix it at all. > It is, of course, possible, but could we live with just mentioning these > consequences in the help? > Thanks for investigating - if this is really a hardy, then mention it in the help - preferable would be to have solved this, but i also see this as not the most urgent issue. At least it has to be written somewhere that people can read it up ;-) Thx andreas From groscurt at mpiz-koeln.mpg.de Wed Mar 12 10:31:34 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 15:31:34 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803120703u206ab042t7a3441acde9fac40@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> <47D7DD12.1010509@mpiz-koeln.mpg.de> <4d93f07c0803120703u206ab042t7a3441acde9fac40@mail.gmail.com> Message-ID: <47D7E946.20707@mpiz-koeln.mpg.de> Martin Senger wrote: >> You said you can access the samples, so why not copying not all samples, >> but the class which was entered in dashboard ? >> > > > When I was writing my answer, this alternative came to my mind - and I was > just telling myself "don't worry, nobody will think about it" :-) > hehe ;-) > Seriously, this is not a right solution because this would bring just one > class to the Tomcat - but the implementation may require more classes (the > ones the main class depends on). I would say, we either let it as it is now, > or we add all samples to deployment. Because you are explaining now how > important the samples directory had and have been, perhaps I should take it > as a hint and not to be too concerned about having these classes deployed, > after all. Which means I am (being influenced by you) changing my mind now - > so should I go ahead and add samples there? [Perhaps I will do it using some > property defining a conditional inclusion, with its default value as true?] > maybe we wait some hours if the guys from Canada want something to say :) I'm still convinced that you should deploy all classes in samples (because yes, you are right, web service might a) have several classes and b) these classes might be in different packages), with excluding org.biomoby.tutorial.*. The idea of a property for that sounds good to me, so the people can decide which way they want to go. thx for that discussion Martin :) Andreas From haase_dirk at web.de Wed Mar 12 10:11:00 2008 From: haase_dirk at web.de (Dirk Haase) Date: Wed, 12 Mar 2008 15:11:00 +0100 Subject: [MOBY-dev] General deployment question Message-ID: <982046343@web.de> > > But that's just your case, not everybody does it like that. I may have my > > implementation in a totally different Eclipse project - and I have to tell > > Dashboard "Hey, here are my jar files". > > > > > Now I do get the essentiell point. But for my whole BioMoby life I was > told... my Web Services HAVE to be in src/samples and will be compiled > to build/others/samples. and honestly we tell that every person form all > workshops now for years (so that was not only my view of this). Oh, who told you so? Just by coincidence, I know of a jMoby tutorial which actually recommends to use a separate Eclipse project ;-) See here: http://tinyurl.com/2yl8l2 (2nd sentence) Cheers, dirk From groscurt at mpiz-koeln.mpg.de Wed Mar 12 10:55:53 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 15:55:53 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <982046343@web.de> References: <982046343@web.de> Message-ID: <47D7EEF9.6010707@mpiz-koeln.mpg.de> Dirk Haase wrote: > Oh, who told you so? Just by coincidence, I know of a jMoby tutorial which > actually recommends to use a separate Eclipse project ;-) > > See here: http://tinyurl.com/2yl8l2 (2nd sentence) > > Cheers, > dirk cant remember that, but at least at the last workshop we told people so and neither Mark nor Eddie objected (probably they didnt realize that)... If this is really not intended that people do so - I would be fine to stay with the current system. But I dont see a problem for those cases that people do write their services in samples to enable that these classes are automatically deployed and that would be possible by given such property (which might be set to false by default instead of true). And if this is really the way it should be used... I need to update my tutorial ;-) thx andreas From martin.senger at gmail.com Wed Mar 12 14:34:30 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 14:34:30 -0400 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <200802291151.22060.groscurt@mpiz-koeln.mpg.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803121134v4ceafcan5f0d273abcaae53e@mail.gmail.com> Andreas, starting dashboard from console gives me > > Warning: Reference moses.build.classpath has not been set at runtime, but > was > found during build file parsing, attempting to resolve. Future versions of > Ant may support referencing ids defined in non-executed targets. > Can this issue be considered solved/closed, or you are still getting it? Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Mar 12 14:46:09 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 14:46:09 -0400 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <1205177598.16508.14.camel@linux-iug0.site> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> Message-ID: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Hi jMobyers, I have committed a change in jMoby dependency file that excludes xerces from all included 3rd-party libraries (especially from jena, commons-dbcp and jaxen). I have tested it a bit but please make your own tests (those of you whose parts rely on these components) and let us know if I broke something. I hope it should be okay - actually quite opposite: with having the old xerces parser there, the newer XML parser in Java would not be used and some features would be missing. Thanks to Hao Chen for making this change. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Mar 13 04:25:53 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Mar 2008 09:25:53 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <4d93f07c0803121134v4ceafcan5f0d273abcaae53e@mail.gmail.com> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> <4d93f07c0803121134v4ceafcan5f0d273abcaae53e@mail.gmail.com> Message-ID: <47D8E511.207@mpiz-koeln.mpg.de> Havent had or havent seen that problem anymore... so consider it as solved/closed :-) best andreas Martin Senger wrote: > Andreas, > > starting dashboard from console gives me > >> Warning: Reference moses.build.classpath has not been set at runtime, but >> was >> found during build file parsing, attempting to resolve. Future versions of >> Ant may support referencing ids defined in non-executed targets. >> >> > > Can this issue be considered solved/closed, or you are still getting it? > > Martin > > From groscurt at mpiz-koeln.mpg.de Thu Mar 13 06:06:48 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Mar 2008 11:06:48 +0100 Subject: [MOBY-dev] Web Services in a secure World In-Reply-To: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Message-ID: <47D8FCB8.7060607@mpiz-koeln.mpg.de> Hi everyone, I like to start a discussion or ask for your knowledge about the possibilty of using secure BioMoby Web Service. The scenario is to register Web Services which work on https and only people with a specific certificate are allowed to call this Web Service. Another scenario is that people with different certificates can call the same Web Service, but based on their certificate the Web Service does behave differntly (like given out different data, working on different databases or so). Unfortunately I'm not that familiar with the whole https and java - http communication, so I like to ask you to give me some input about my ideas. Establishing a https connection is not difficult, I'm currently thinking about how to enable that different certificates are treated differently. One possibility is to work on the level of the apache and do have different authenifications for the certificates. Based on this authentification people are directed to the corresponding service. But this solution sound aweful, because you have to offer for each certificate a service and this services have to be physically be different so that not person A with certificate A can call service B with some detours. So for me this is a really messy solution. Is this correct or do I have an error in my scenario. The other idea is that based on the certificate the Web Service checks who has actually called. I tried with the current moby API to retrieve any information about the certificate which was used for the calling process, but I couldnt find any method which gives me such information. So ist here any method which is or could return me any information. Another idea was, because the certificate is actually non binary one could send it as secondary. Is this reasonable to do so and is it sufficient to do a simple equals in the web service or is any more complex operation based on the certificate required. Thanks for reading and thanks for any input, comments and suggestions Andreas PS: just to verify - this is nothing which came up just in my mind - it is a request from several EU-SOL partners ;-) From groscurt at mpiz-koeln.mpg.de Thu Mar 13 07:38:51 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Mar 2008 12:38:51 +0100 Subject: [MOBY-dev] Web Services in a secure World In-Reply-To: <47D8FCB8.7060607@mpiz-koeln.mpg.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> Message-ID: <47D9124B.2050304@mpiz-koeln.mpg.de> Hi, funny to have written an email and then later while searching the web and discussing stuff with Mark Fiers here - we think to have a nice solution based on the description here http://www.impetus.us/~rjmooney/projects/misc/clientcertauth.html. with different services depending on which certificate was used. So - in our view this is solved, but feel free to add something :-) best andreas Andreas Groscurth wrote: > Hi everyone, > > I like to start a discussion or ask for your knowledge about the > possibilty of using secure BioMoby Web Service. > > The scenario is to register Web Services which work on https and only > people with a specific certificate are allowed to call this Web Service. > > Another scenario is that people with different certificates can call > the same Web Service, but based on their certificate the Web Service > does behave differntly (like given out different data, working on > different databases or so). > > Unfortunately I'm not that familiar with the whole https and java - > http communication, so I like to ask you to give me some input about > my ideas. > > Establishing a https connection is not difficult, I'm currently > thinking about how to enable that different certificates are treated > differently. > > One possibility is to work on the level of the apache and do have > different authenifications for the certificates. Based on this > authentification people are directed to the corresponding service. But > this solution sound aweful, because you have to offer for each > certificate a service and this services have to be physically be > different so that not person A with certificate A can call service B > with some detours. So for me this is a really messy solution. > > Is this correct or do I have an error in my scenario. > > The other idea is that based on the certificate the Web Service checks > who has actually called. I tried with the current moby API to retrieve > any information about the certificate which was used for the calling > process, but I couldnt find any method which gives me such information. > > So ist here any method which is or could return me any information. > > Another idea was, because the certificate is actually non binary one > could send it as secondary. Is this reasonable to do so and is it > sufficient to do a simple equals in the web service or is any more > complex operation based on the certificate required. > > Thanks for reading and thanks for any input, comments and suggestions > Andreas > > PS: just to verify - this is nothing which came up just in my mind - > it is a request from several EU-SOL partners ;-) > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From sneumann at ipb-halle.de Thu Mar 13 09:25:36 2008 From: sneumann at ipb-halle.de (sneumann) Date: Thu, 13 Mar 2008 14:25:36 +0100 Subject: [MOBY-dev] Web Services in a secure World In-Reply-To: <47D9124B.2050304@mpiz-koeln.mpg.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> <47D9124B.2050304@mpiz-koeln.mpg.de> Message-ID: <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> On Do, 2008-03-13 at 12:38 +0100, Andreas Groscurth wrote: > with different services depending on which certificate was used. but that was not part of the simple tutorial, was it ?! > So - in our view this is solved, but feel free to add something :-) So what is the use case solved here ? You have a service -- say a database/repository -- which includes data produced by -- say three -- different consortia, and should also serve data (for which the protection phase has expired) to the public without any certificate. How do pass the cert information down to the retrieval layer ? Or do you use apache to demultiplex / route the same query to a given (virtual) service to the appropriate instance based on the certificate ? This probably doesn't scale very well. What happens if some remote machine/user belongs to two consortia (or in fact the administrator needs access to all consortium data), then he needs to choose the appropriate cert ? Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 191 bytes Desc: This is a digitally signed message part URL: From martin.senger at gmail.com Thu Mar 13 12:59:58 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 13 Mar 2008 12:59:58 -0400 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user Message-ID: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> Dear all, I have uploaded jMoby (version 1.0.0) to our Maven repository (you can see it at and use it from http://biomoby.org/m2repo/org/biomoby/jmoby/). The next versions will follow as new features are added and bugs fixed. I have a request for the Eclipse users: I have not found time (as I planned) to make sure that jMoby works smoothly both within and outside the Eclipse (I know for sure that it works fine outside the Eclipse). What is needed now is to provide a file .classpath.template that can serve as a template for a file .classpath (this file should not have any absolute path - which may happen when created on some platforms), and that reflects the same environment (eg. building classes into 'build' directory and not the 'bin' directory) as defined in the Ant's build.xml file. This file (.classpath.template) should be committed to jMoby. Also the documentation on using jMoby from Eclipse should be updated to reflect the existence and usage of this new file. [Perhaps, we can have also a template .project.template - but that is less important.] Is there anybody to do it please? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Mar 13 13:44:03 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Mar 2008 18:44:03 +0100 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> Message-ID: <47D967E3.3050604@mpiz-koeln.mpg.de> Hi, I can do that tomorrow - got such .classpath file already as download from our tutorial page. best andreas PS: .project is not necessary to provide. PPS: What i also will provide then in the docs is how to get the maven plugin for eclipse if wanted Martin Senger wrote: > Dear all, > > I have uploaded jMoby (version 1.0.0) to our Maven repository (you can see > it at and use it from http://biomoby.org/m2repo/org/biomoby/jmoby/). The > next versions will follow as new features are added and bugs fixed. > > I have a request for the Eclipse users: I have not found time (as I planned) > to make sure that jMoby works smoothly both within and outside the Eclipse > (I know for sure that it works fine outside the Eclipse). What is needed now > is to provide a file .classpath.template that can serve as a template for a > file .classpath (this file should not have any absolute path - which may > happen when created on some platforms), and that reflects the same > environment (eg. building classes into 'build' directory and not the 'bin' > directory) as defined in the Ant's build.xml file. This file > (.classpath.template) should be committed to jMoby. Also the documentation > on using jMoby from Eclipse should be updated to reflect the existence and > usage of this new file. [Perhaps, we can have also a template > .project.template - but that is less important.] > > Is there anybody to do it please? > > Cheers, > Martin > > From gordonp at ucalgary.ca Thu Mar 13 18:54:12 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 13 Mar 2008 16:54:12 -0600 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Message-ID: <47D9B094.2020001@ucalgary.ca> Never mind, I see that the ant task names have changed... Martin Senger wrote: > Hi jMobyers, > > I have committed a change in jMoby dependency file that excludes xerces from > all included 3rd-party libraries (especially from jena, commons-dbcp and > jaxen). I have tested it a bit but please make your own tests (those of you > whose parts rely on these components) and let us know if I broke something. > I hope it should be okay - actually quite opposite: with having the old > xerces parser there, the newer XML parser in Java would not be used and some > features would be missing. > > Thanks to Hao Chen for making this change. > > Cheers, > Martin > > From gordonp at ucalgary.ca Thu Mar 13 18:46:43 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 13 Mar 2008 16:46:43 -0600 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Message-ID: <47D9AED3.5060500@ucalgary.ca> Hi Martin, This may be related: when I do an ant celan, then try to run some of my JUnit tests... moses-clean: [delete] Deleting directory /export/home/gordonp/projects/moby-live/Java/build/others/datatypes [delete] Deleting directory /export/home/gordonp/projects/moby-live/Java/build/others/skeletons clean-services: moses-init: [mkdir] Created dir: /export/home/gordonp/projects/moby-live/Java/build/others/datatypes [mkdir] Created dir: /export/home/gordonp/projects/moby-live/Java/build/others/skeletons generate-datatypes: [Data Types] Generating data types into '/export/home/gordonp/projects/moby-live/Java/generated/datatypes'... [Data Types] Reading data type definitions... [Data Types] ===ERROR=== [Data Types] org/apache/xerces/util/XMLChar [Data Types] =========== Which brings up another issue. Why is the build file making the MoSeS classes when my unit tests have nothing to do with MoSeS? Have some new superfluous dependencies been added? Cheers, Paul Martin Senger wrote: > Hi jMobyers, > > I have committed a change in jMoby dependency file that excludes xerces from > all included 3rd-party libraries (especially from jena, commons-dbcp and > jaxen). I have tested it a bit but please make your own tests (those of you > whose parts rely on these components) and let us know if I broke something. > I hope it should be okay - actually quite opposite: with having the old > xerces parser there, the newer XML parser in Java would not be used and some > features would be missing. > > Thanks to Hao Chen for making this change. > > Cheers, > Martin > > From martin.senger at gmail.com Thu Mar 13 21:26:37 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 13 Mar 2008 20:26:37 -0500 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47D9AED3.5060500@ucalgary.ca> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D9AED3.5060500@ucalgary.ca> Message-ID: <4d93f07c0803131826l1da8b372hbf8f0bcf5d025114@mail.gmail.com> > Which brings up another issue. Why is the build file making the MoSeS > classes when my unit tests have nothing to do with MoSeS? Your junit test not, but mine yes. If you run 'ant test-junit' then *all* junit tests are run, including those that are testing MoSeS. The 'test-junit' task is an umbrella covering two separate groups of junit tests: tasks 'do-junit' and 'do-junit-2'. The former are your tests, the latter mine. So if you prefer to run only your tests, call 'ant do-junit'. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Fri Mar 14 05:30:54 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 10:30:54 +0100 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Message-ID: <47DA45CE.2000708@mpiz-koeln.mpg.de> Hi, with a fresh checkout I get during install ant task dashboard-config: [jar] Building jar: C:\workspace\Moby_cvs\build\lib\dashboard-config.jar [Local cache] [Local cache] The jMoby is now creating a local cache. Depending [Local cache] on the network speed, it may take several minutes [Local cache] (usually it should be done within about a minute). [Local cache] [Local cache] [You can check the progress in the jMoby.log file.] [Local cache] [Local cache] Retrieving namespaces... 0:00:38.422 [Local cache] ===ERROR=== [Local cache] org/apache/xerces/util/XMLChar [Local cache] =========== Retrieving data types... BUILD FAILED C:\workspace\Moby_cvs\xmls\install.xml:99: Java returned: 1 in eclipse and on console, windows, java 1.6 best andreas Martin Senger wrote: > Hi jMobyers, > > I have committed a change in jMoby dependency file that excludes xerces from > all included 3rd-party libraries (especially from jena, commons-dbcp and > jaxen). I have tested it a bit but please make your own tests (those of you > whose parts rely on these components) and let us know if I broke something. > I hope it should be okay - actu > ally quite opposite: with having the old > xerces parser there, the newer XML parser in Java would not be used and some > features would be missing. > > Thanks to Hao Chen for making this change. > > Cheers, > Martin > > From groscurt at mpiz-koeln.mpg.de Fri Mar 14 05:50:15 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 10:50:15 +0100 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47DA45CE.2000708@mpiz-koeln.mpg.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> Message-ID: <47DA4A57.4060006@mpiz-koeln.mpg.de> Running install on console under linux i get dashboard-config: [jar] Building jar: /home/pcb/groscurt/moby-live/Java/build/lib/dashboard-config.jar [Local cache] [Local cache] The jMoby is now creating a local cache. Depending [Local cache] on the network speed, it may take several minutes [Local cache] (usually it should be done within about a minute). [Local cache] [Local cache] [You can check the progress in the jMoby.log file.] [Local cache] [Local cache] ===ERROR=== [Local cache] Provider org.apache.xerces.jaxp.DocumentBuilderFactoryImpl not found [Local cache] =========== Retrieving namespaces... BUILD FAILED /home/pcb/groscurt/moby-live/Java/xmls/install.xml:99: Java returned: 1 best andreas Andreas Groscurth wrote: > Hi, > > with a fresh checkout I get during install ant task > > dashboard-config: > [jar] Building jar: > C:\workspace\Moby_cvs\build\lib\dashboard-config.jar > [Local cache] > [Local cache] The jMoby is now creating a local cache. Depending > [Local cache] on the network speed, it may take several minutes > [Local cache] (usually it should be done within about a minute). > [Local cache] > [Local cache] [You can check the progress in the jMoby.log file.] > [Local cache] [Local cache] Retrieving namespaces... 0:00:38.422 > [Local cache] ===ERROR=== > [Local cache] org/apache/xerces/util/XMLChar > [Local cache] =========== > Retrieving data types... > BUILD FAILED > C:\workspace\Moby_cvs\xmls\install.xml:99: Java returned: 1 > > in eclipse and on console, windows, java 1.6 > > best > andreas > > Martin Senger wrote: >> Hi jMobyers, >> >> I have committed a change in jMoby dependency file that excludes >> xerces from >> all included 3rd-party libraries (especially from jena, commons-dbcp and >> jaxen). I have tested it a bit but please make your own tests (those >> of you >> whose parts rely on these components) and let us know if I broke >> something. >> I hope it should be okay - actu > >> ally quite opposite: with having the old >> xerces parser there, the newer XML parser in Java would not be used >> and some >> features would be missing. >> >> Thanks to Hao Chen for making this change. >> >> Cheers, >> Martin >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Fri Mar 14 06:00:32 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 11:00:32 +0100 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <47D967E3.3050604@mpiz-koeln.mpg.de> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> Message-ID: <47DA4CC0.3080605@mpiz-koeln.mpg.de> Hi, before I check it in - I added .classpath.template in the basedir of the project and edit the initeclipse task so that the .classpath.template file is copied into .classpath file. The only thing which could me problematic is that I have to use overwrite="true" so that i will overwrite the existing one which eclipse automatically generates. If someone later calls this task again and might have changed the .classpath it will again be overwritten. Other solution is to tell the user to first delete the .classpath generated by Eclipse. Suggestions? Andreas PS: Will update also the docs today Andreas Groscurth wrote: > Hi, > > I can do that tomorrow - got such .classpath file already as download > from our tutorial page. > > best > andreas > > PS: .project is not necessary to provide. > > PPS: What i also will provide then in the docs is how to get the maven > plugin for eclipse if wanted > > Martin Senger wrote: >> Dear all, >> >> I have uploaded jMoby (version 1.0.0) to our Maven repository (you >> can see >> it at and use it from http://biomoby.org/m2repo/org/biomoby/jmoby/). The >> next versions will follow as new features are added and bugs fixed. >> >> I have a request for the Eclipse users: I have not found time (as I >> planned) >> to make sure that jMoby works smoothly both within and outside the >> Eclipse >> (I know for sure that it works fine outside the Eclipse). What is >> needed now >> is to provide a file .classpath.template that can serve as a template >> for a >> file .classpath (this file should not have any absolute path - which may >> happen when created on some platforms), and that reflects the same >> environment (eg. building classes into 'build' directory and not the >> 'bin' >> directory) as defined in the Ant's build.xml file. This file >> (.classpath.template) should be committed to jMoby. Also the >> documentation >> on using jMoby from Eclipse should be updated to reflect the >> existence and >> usage of this new file. [Perhaps, we can have also a template >> .project.template - but that is less important.] >> >> Is there anybody to do it please? >> >> Cheers, >> Martin >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Fri Mar 14 06:39:04 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 11:39:04 +0100 Subject: [MOBY-dev] Web Services in a secure World In-Reply-To: <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> <47D9124B.2050304@mpiz-koeln.mpg.de> <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <47DA55C8.4040208@mpiz-koeln.mpg.de> sneumann wrote: > On Do, 2008-03-13 at 12:38 +0100, Andreas Groscurth wrote: > >> with different services depending on which certificate was used. >> > but that was not part of the simple tutorial, was it ?! > no the simple tutorial, which i took down today, does not cover that. As soon as we tested at here in EU-SOL I will put up the turial up again. Otherwise its dangerous that it will be changed over the next weeks over and over again >> So - in our view this is solved, but feel free to add something :-) >> > So what is the use case solved here ? > Use case is that you offer Web services which shall be only called by elected persons identified by a certificate. We assume that the servlet container is not accessible for public. The solution we think of is that the clients retrieving a certificate signed by an CA and have to use this files in the clients to call BioMoby Web Services. On the server side the apache will take care of the authentification and depending on the certificates redirect to the corresponding servlet container E.g. Certificate-A-user -> axis_a/services/.... Certificate-B-user -> axis_b/services/... of course it has to be ensured that these redirects are not accessible without any authentification And although this might have the problem of implementing several services more than once - at least in Java you can easily use avoid this by using facade patterns. > You have a service -- say a database/repository -- which includes > data produced by -- say three -- different consortia, and should also > serve data (for which the protection phase has expired) to the public > without any certificate. How do pass the cert information down to the > retrieval layer ? > so as describes - apache will do that > Or do you use apache to demultiplex / route the same query > to a given (virtual) service to the appropriate instance > based on the certificate ? This probably doesn't scale very well. > didnt get that - if this is the way as described above - why yo think it doesnt scala very well ? > What happens if some remote machine/user belongs to two consortia > (or in fact the administrator needs access to all consortium data), > then he needs to choose the appropriate cert ? > This is definitely a point we have to think of. This has to be differences. One - what happens if a person with two certificates calls a service, which one is used ? a solution (at least in java) could be that the client has several keystore in which the certificates are stored and he selectes the one he wants to use currently. The other one is if one has access to all data, although from different consortium. In this case I would use a different certificate. Thanks for your input - I'm glad if you have anything to add here. best andreas > Yours, > Steffen > > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From martin.senger at gmail.com Fri Mar 14 07:37:53 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 07:37:53 -0400 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <47DA4CC0.3080605@mpiz-koeln.mpg.de> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> > before I check it in - I added .classpath.template in the basedir of the > project and edit the initeclipse task so that the .classpath.template > file is copied into .classpath file. No, don't do it please. Just leave the copying to the users. The same as they do with other templates (except the .cvsignore.template - but hat is less important template). The users will have quite often a different .classpath because they may be testing new things in Eclipse and they even do not know that the .classpath is changing. No, I definitely would keep the initeclipse task untouched. But please go ahead and commit the .classpath.template. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Mar 14 07:41:58 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 07:41:58 -0400 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47DA45CE.2000708@mpiz-koeln.mpg.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> > [Local cache] ===ERROR=== > [Local cache] org/apache/xerces/util/XMLChar > [Local cache] =========== Good that you found this. I was worried that something like this might happen. I will investigate and fix it - but it may be only the next week (I am going to travel later today back to Philippines from the US and I may not have time to fix it before it). Paul, do you know why is this happening? You know much more about XML parsers libraries than I do. I thought that Java 1.5 has already an XML parser - so why does it complain about xerces? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From mark.fiers at wur.nl Fri Mar 14 07:29:23 2008 From: mark.fiers at wur.nl (Fiers, Mark) Date: Fri, 14 Mar 2008 12:29:23 +0100 Subject: [MOBY-dev] error in java moby request References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> <47D9124B.2050304@mpiz-koeln.mpg.de> <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> <47DA55C8.4040208@mpiz-koeln.mpg.de> Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> Hi, I'm trying to write a moby client program in java, using the testing repository: Central worker = new CentralImpl( "http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl", "http://bioinfo.icapture.ubc.ca/MOBY/Central"); and subsequently call a service I'm trying to develop, but that ends in an error. Appearantly the code is looking at the default registry, as the script prints: Fetching data type ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects ... done What am I doing wrong? Or is this a bug? regards Mark Fiers -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 2995 bytes Desc: not available URL: From martin.senger at gmail.com Fri Mar 14 07:50:57 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 07:50:57 -0400 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> Message-ID: <4d93f07c0803140450i7d725805r1dd2f57fc7c744d1@mail.gmail.com> Eddie, the problem reported by Andreas is caused in the Jena package (Jena needs the XMLChar library). Could you look why this class is not part of the Java 1.5? Can it be found elsewhere than in xerces? [The xerces itself caused problems from other reasons - see previous emails about it if you wish, or I can re-send them.] The full stack (with a command-line how you can replicate it) is here: senger at sherekhan:~/jMoby$ build/run/run-cache-client -fill -cachedir anotherMyCache/ -v -stack Retrieving namespaces... 0:00:02.384 Retrieving data types... ===ERROR=== java.lang.NoClassDefFoundError: org/apache/xerces/util/XMLChar at com.hp.hpl.jena.rdf.model.impl.Util.notNameChar(Util.java:87) at com.hp.hpl.jena.rdf.model.impl.Util.splitNamespace(Util.java:67) at com.hp.hpl.jena.graph.Node_URI.getLocalName(Node_URI.java:55) at com.hp.hpl.jena.rdf.model.impl.ResourceImpl.getLocalName( ResourceImpl.java:126) at com.hp.hpl.jena.rdf.model.impl.PropertyImpl.checkLocalName( PropertyImpl.java:78) at com.hp.hpl.jena.rdf.model.impl.PropertyImpl.( PropertyImpl.java:86) at com.hp.hpl.jena.rdf.model.ResourceFactory$Impl.createProperty( ResourceFactory.java:244) at com.hp.hpl.jena.rdf.model.ResourceFactory.createProperty( ResourceFactory.java:120) at com.hp.hpl.jena.vocabulary.RDF.property(RDF.java:32) at com.hp.hpl.jena.vocabulary.RDF.(RDF.java:45) at com.hp.hpl.jena.ontology.impl.OntResourceImpl.( OntResourceImpl.java:63) at com.hp.hpl.jena.enhanced.BuiltinPersonalities.( BuiltinPersonalities.java:28) at com.hp.hpl.jena.rdf.model.impl.ModelCom.(ModelCom.java:51) at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel( ModelFactory.java:124) at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel( ModelFactory.java:118) at org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF( DataTypeParser.java:156) at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache( CentralDigestCachedImpl.java:125) at org.biomoby.client.CentralDigestCachedImpl.getDataTypes( CentralDigestCachedImpl.java:769) at CacheRegistryClient.main(CacheRegistryClient.java:85) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Fri Mar 14 07:53:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 12:53:55 +0100 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> Message-ID: <47DA6753.8000108@mpiz-koeln.mpg.de> Martin Senger wrote: >> before I check it in - I added .classpath.template in the basedir of the >> project and edit the initeclipse task so that the .classpath.template >> file is copied into .classpath file. >> > > > No, don't do it please. Just leave the copying to the users. The same as > they do with other templates (except the .cvsignore.template - but hat is > less important template). The users will have quite often a different > .classpath because they may be testing new things in Eclipse and they even > do not know that the .classpath is changing. No, I definitely would keep the > initeclipse task untouched. > > But please go ahead and commit the .classpath.template. > > Cheers, > Martin > > oki... it is coming to cvs :) - the initeclipse is now virginal again. will update the docs also today andreas From martin.senger at gmail.com Fri Mar 14 07:56:42 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 07:56:42 -0400 Subject: [MOBY-dev] error in java moby request In-Reply-To: <33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> <47D9124B.2050304@mpiz-koeln.mpg.de> <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> <47DA55C8.4040208@mpiz-koeln.mpg.de> <33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> Message-ID: <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> > and subsequently call a service I'm trying to develop, but that ends in an > error. > > Appearantly the code is looking at the default registry, as the script > prints: > > Fetching data type ontology from > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > ... done > What does your code do (what method of CentralImpl is it trying to call) when it fails? Knowing this will help me to reproduce the problem. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Mar 14 08:04:56 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 08:04:56 -0400 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <47DA6753.8000108@mpiz-koeln.mpg.de> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> <47DA6753.8000108@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803140504s55f44dbblc2dabdb373121cb2@mail.gmail.com> Thanks for the .classpath.template. I still have an Eclipse question (I am not sure, however, if my formulating it is correct, so perhaps I am not looking only for an answer but also for a better question :-)): There are other files, configuration files, that are needed in build/classes. For jMoby, it is logging configuration file log4j.propertiesand a directory 'templates' (uses for MoSeS). All these files are copied there by 'ant config'. Is it a way that they can be either copied there by Eclipse (perhaps by mentioning them in the .classpath), or, at least, not to be removed by Eclipse when I press F5 (refresh) in Eclipse? Eclipse seems to be very rude to all files in build/classes that it was not put there by her (is the Eclipse female gender in English :-)). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From mark.fiers at wur.nl Fri Mar 14 08:36:42 2008 From: mark.fiers at wur.nl (Fiers, Mark) Date: Fri, 14 Mar 2008 13:36:42 +0100 Subject: [MOBY-dev] error in java moby request References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow><1205177598.16508.14.camel@linux-iug0.site><4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com><47D8FCB8.7060607@mpiz-koeln.mpg.de><47D9124B.2050304@mpiz-koeln.mpg.de><1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de><47DA55C8.4040208@mpiz-koeln.mpg.de><33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAE950191@scomp0039.wurnet.nl> Hi Martin, The code is attached and the exact error message is: Fetching data type ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects ... done Fetching namespace ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Namespaces Exception in thread "main" org.biomoby.shared.MobyException: Attempted to build a composite MOBY object from XML, but the tag (MSCmlspectUrl) does not correspond to an existing data type in the registry (default). Please check the spelling and capitalization of the XML tag, to match a registered data type. at org.biomoby.shared.data.MobyDataComposite.(MobyDataComposite.java:42) at org.biomoby.shared.data.MobyDataObject.createInstanceFromDOM(MobyDataObject.java:215) at org.biomoby.shared.data.MobyDataObject.createInstanceFromDOM(MobyDataObject.java:178) at org.biomoby.shared.data.MobyContentInstance.parseDataGroup(MobyContentInstance.java:245) at org.biomoby.shared.data.MobyContentInstance.(MobyContentInstance.java:130) at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument(MobyDataUtils.java:236) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:306) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275) at biomoby_clients.TestXcmsGetPeaks.main(TestXcmsGetPeaks.java:66) hopefully that helps, and thanks! Mark -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger Sent: Fri 3/14/2008 12:56 PM To: Core developer announcements Subject: Re: [MOBY-dev] error in java moby request > and subsequently call a service I'm trying to develop, but that ends in an > error. > > Appearantly the code is looking at the default registry, as the script > prints: > > Fetching data type ontology from > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > ... done > What does your code do (what method of CentralImpl is it trying to call) when it fails? Knowing this will help me to reproduce the problem. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 7145 bytes Desc: not available URL: From mark.fiers at wur.nl Fri Mar 14 08:54:12 2008 From: mark.fiers at wur.nl (Fiers, Mark) Date: Fri, 14 Mar 2008 13:54:12 +0100 Subject: [MOBY-dev] error in java moby request References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow><1205177598.16508.14.camel@linux-iug0.site><4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com><47D8FCB8.7060607@mpiz-koeln.mpg.de><47D9124B.2050304@mpiz-koeln.mpg.de><1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de><47DA55C8.4040208@mpiz-koeln.mpg.de><33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAE950192@scomp0039.wurnet.nl> Hi Martin, One more thing: the fact that the code is complaining about the object MSCmlspectUrl and not about MSRawCdfUrl might very well be bacause the latter object is registered at the default moby central (and the first one is not) with best regards Mark -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger Sent: Fri 3/14/2008 12:56 PM To: Core developer announcements Subject: Re: [MOBY-dev] error in java moby request > and subsequently call a service I'm trying to develop, but that ends in an > error. > > Appearantly the code is looking at the default registry, as the script > prints: > > Fetching data type ontology from > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > ... done > What does your code do (what method of CentralImpl is it trying to call) when it fails? Knowing this will help me to reproduce the problem. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3534 bytes Desc: not available URL: From groscurt at mpiz-koeln.mpg.de Fri Mar 14 09:08:53 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 14:08:53 +0100 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <4d93f07c0803140504s55f44dbblc2dabdb373121cb2@mail.gmail.com> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> <47DA6753.8000108@mpiz-koeln.mpg.de> <4d93f07c0803140504s55f44dbblc2dabdb373121cb2@mail.gmail.com> Message-ID: <47DA78E5.9050701@mpiz-koeln.mpg.de> Hi Martin, so do i understand that correctly - jmoby requires the log4j.properties and the templates folder in the build/classes folder. When you hit refresh in eclipse on your project - eclipse deletes this folder and this file ? mhm - I do have these files/folders but eclipse keeps them neverthless how hard i hit refresh. best andreas Martin Senger wrote: > Thanks for the .classpath.template. > > I still have an Eclipse question (I am not sure, however, if my formulating > it is correct, so perhaps I am not looking only for an answer but also for a > better question :-)): > > There are other files, configuration files, that are needed in > build/classes. For jMoby, it is logging configuration file > log4j.propertiesand a directory 'templates' (uses for MoSeS). All > these files are copied > there by 'ant config'. Is it a way that they can be either copied there by > Eclipse (perhaps by mentioning them in the .classpath), or, at least, not to > be removed by Eclipse when I press F5 (refresh) in Eclipse? Eclipse seems to > be very rude to all files in build/classes that it was not put there by her > (is the Eclipse female gender in English :-)). > > Cheers, > Martin > > From edward.kawas at gmail.com Fri Mar 14 09:26:53 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 14 Mar 2008 06:26:53 -0700 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803140450i7d725805r1dd2f57fc7c744d1@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> <4d93f07c0803140450i7d725805r1dd2f57fc7c744d1@mail.gmail.com> Message-ID: <47da7d24.06ec720a.52e4.ffffda19@mx.google.com> I found that class in other packages, org.apache.jasper.xmlparsers, org.apache.axis.utils, etc. I didn't find anyone with the same package as the one that we need though. I also couldn't find why it was not included in java 5, although, I did find http://jcs.mobile-utopia.com/jcs/53280_XMLChar.java and it makes you think that the class is part of the package com.sun.org.apache.xcerces.internal.util. I will keep looking, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: March-14-08 4:51 AM To: Core developer announcements; Eddie Kawas Subject: Re: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] Eddie, the problem reported by Andreas is caused in the Jena package (Jena needs the XMLChar library). Could you look why this class is not part of the Java 1.5? Can it be found elsewhere than in xerces? [The xerces itself caused problems from other reasons - see previous emails about it if you wish, or I can re-send them.] The full stack (with a command-line how you can replicate it) is here: senger at sherekhan:~/jMoby$ build/run/run-cache-client -fill -cachedir anotherMyCache/ -v -stack Retrieving namespaces... 0:00:02.384 Retrieving data types... ===ERROR=== java.lang.NoClassDefFoundError: org/apache/xerces/util/XMLChar at com.hp.hpl.jena.rdf.model.impl.Util.notNameChar(Util.java:87) at com.hp.hpl.jena.rdf.model.impl.Util.splitNamespace(Util.java:67) at com.hp.hpl.jena.graph.Node_URI.getLocalName(Node_URI.java:55) at com.hp.hpl.jena.rdf.model.impl.ResourceImpl.getLocalName( ResourceImpl.java:126) at com.hp.hpl.jena.rdf.model.impl.PropertyImpl.checkLocalName( PropertyImpl.java:78) at com.hp.hpl.jena.rdf.model.impl.PropertyImpl.( PropertyImpl.java:86) at com.hp.hpl.jena.rdf.model.ResourceFactory$Impl.createProperty( ResourceFactory.java:244) at com.hp.hpl.jena.rdf.model.ResourceFactory.createProperty( ResourceFactory.java:120) at com.hp.hpl.jena.vocabulary.RDF.property(RDF.java:32) at com.hp.hpl.jena.vocabulary.RDF.(RDF.java:45) at com.hp.hpl.jena.ontology.impl.OntResourceImpl.( OntResourceImpl.java:63) at com.hp.hpl.jena.enhanced.BuiltinPersonalities.( BuiltinPersonalities.java:28) at com.hp.hpl.jena.rdf.model.impl.ModelCom.(ModelCom.java:51) at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel( ModelFactory.java:124) at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel( ModelFactory.java:118) at org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF( DataTypeParser.java:156) at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache( CentralDigestCachedImpl.java:125) at org.biomoby.client.CentralDigestCachedImpl.getDataTypes( CentralDigestCachedImpl.java:769) at CacheRegistryClient.main(CacheRegistryClient.java:85) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ 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 Fri Mar 14 09:40:47 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 14 Mar 2008 07:40:47 -0600 Subject: [MOBY-dev] error in java moby request In-Reply-To: <33AFFE3255BCA043AF09514A6F6BFBAE950192@scomp0039.wurnet.nl> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow><1205177598.16508.14.camel@linux-iug0.site><4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com><47D8FCB8.7060607@mpiz-koeln.mpg.de><47D9124B.2050304@mpiz-koeln.mpg.de><1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de><47DA55C8.4040208@mpiz-koeln.mpg.de><33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> <33AFFE3255BCA043AF09514A6F6BFBAE950192@scomp0039.wurnet.nl> Message-ID: <47DA805F.9030904@ucalgary.ca> Hi Mark, I'll look into this for you today... Fiers, Mark wrote: > Hi Martin, > > One more thing: the fact that the code is complaining about the object MSCmlspectUrl and not about MSRawCdfUrl might very well be bacause the latter object is registered at the default moby central (and the first one is not) > > with best regards > Mark > > > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger > Sent: Fri 3/14/2008 12:56 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] error in java moby request > > >> and subsequently call a service I'm trying to develop, but that ends in an >> error. >> >> Appearantly the code is looking at the default registry, as the script >> prints: >> >> Fetching data type ontology from >> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects >> ... done >> >> > > What does your code do (what method of CentralImpl is it trying to call) > when it fails? Knowing this will help me to reproduce the problem. > > Thanks, > Martin > > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47da757110950789310626! > From mark.fiers at wur.nl Fri Mar 14 10:41:43 2008 From: mark.fiers at wur.nl (Fiers, Mark) Date: Fri, 14 Mar 2008 15:41:43 +0100 Subject: [MOBY-dev] error in java moby request References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow><1205177598.16508.14.camel@linux-iug0.site><4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com><47D8FCB8.7060607@mpiz-koeln.mpg.de><47D9124B.2050304@mpiz-koeln.mpg.de><1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de><47DA55C8.4040208@mpiz-koeln.mpg.de><33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> <33AFFE3255BCA043AF09514A6F6BFBAE950192@scomp0039.wurnet.nl> <47DA805F.9030904@ucalgary.ca> Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAE95019D@scomp0039.wurnet.nl> Thank you! -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Paul Gordon Sent: Fri 3/14/2008 2:40 PM To: Core developer announcements Subject: Re: [MOBY-dev] error in java moby request Hi Mark, I'll look into this for you today... Fiers, Mark wrote: > Hi Martin, > > One more thing: the fact that the code is complaining about the object MSCmlspectUrl and not about MSRawCdfUrl might very well be bacause the latter object is registered at the default moby central (and the first one is not) > > with best regards > Mark > > > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger > Sent: Fri 3/14/2008 12:56 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] error in java moby request > > >> and subsequently call a service I'm trying to develop, but that ends in an >> error. >> >> Appearantly the code is looking at the default registry, as the script >> prints: >> >> Fetching data type ontology from >> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects >> ... done >> >> > > What does your code do (what method of CentralImpl is it trying to call) > when it fails? Knowing this will help me to reproduce the problem. > > Thanks, > Martin > > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47da757110950789310626! > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3790 bytes Desc: not available URL: From martin.senger at gmail.com Fri Mar 14 17:55:05 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 17:55:05 -0400 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47da7d24.06ec720a.52e4.ffffda19@mx.google.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> <4d93f07c0803140450i7d725805r1dd2f57fc7c744d1@mail.gmail.com> <47da7d24.06ec720a.52e4.ffffda19@mx.google.com> Message-ID: <4d93f07c0803141455r5da67aa9j56b636e6e2894d3a@mail.gmail.com> Thank you for investigating. At the end, please make a decision what jar should we include in jMoby's project.pom. When you tell me, I will do it and upload an updated jMoby version. This is quite urgent issue because nobody can fill the cache without this probem being solved. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Mar 14 18:01:32 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 18:01:32 -0400 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <47DA78E5.9050701@mpiz-koeln.mpg.de> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> <47DA6753.8000108@mpiz-koeln.mpg.de> <4d93f07c0803140504s55f44dbblc2dabdb373121cb2@mail.gmail.com> <47DA78E5.9050701@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803141501l6c837552wb3cbf24f39e9a96b@mail.gmail.com> > When you hit refresh in eclipse on your project - eclipse deletes this > folder and this file ? > > mhm - I do have these files/folders but eclipse keeps them neverthless > how hard i hit refresh. > I thing that it depends when (after what action) you hit the Refresh button. I will try to make my request more accurate when I am back in my office where I can try Eclipse my easier. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Fri Mar 14 18:04:16 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 14 Mar 2008 15:04:16 -0700 Subject: [MOBY-dev] Unit testing of BioMoby Services Message-ID: Hi all, During the hackathon I was working on the OWL classes and predicates we need for the ability to create unit tests in the Service metadata coming from the Service provider. I just finished working things out with the myGrid team, and here are the predicates and classes we have agreed on: Namespace: http://www.mygrid.org.uk/mygrid-moby-service# Class: #unitTest usage: can have one or more unitTests per service #operation ObjectProperty: #hasUnitTest domain: #operation range: #unitTest DatatypeProperty: #exampleInput domain: #unitTest range: xsd#string content: the full SOAP payload XML of an invocation message DatatypeProperty: #validOutputXML domain: #unitTest range: xsd#string content: the full SOAP payload of the associated output message DatatypeProperty: #validREGEX domain: #unitTest range: xsd#string content: a regular expression that should match against the output SOAP Payload of this unitTest DatatypeProperty: #validXPath domain: #unitTest range: xsd#string content: an XPath expression that should match against the output SOAP Payload of this unitTest An example can be seen in the antirrhinum.net,getDragonAlleleLocus service, whose signature RDF is available here: http://moby.ucalgary.ca/signatures/antirrhinum.rdf I'm almost finished writing a little Perl script that will go through and test the services based on the Unit Test data - I'll put it in the CVS as soon as it's done. Cheers all! Mark -- -- Mark Wilkinson iCAPTURE Centre From martin.senger at gmail.com Fri Mar 14 19:35:58 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 19:35:58 -0400 Subject: [MOBY-dev] Problem with xercexImpl fixed (for jMoby users) Message-ID: <4d93f07c0803141635p2183436fn5db83c5f45628c68@mail.gmail.com> Hi all, After an emergency (thanks very much to those you reported the problem), I have put back (into our dependency file xmls/project.pom) the xercesImpl.jar- but now its newer version ( 2.7.1.). This fixes the reported problem (a class not found). Please cvs update and type 'ant clean compile' (that should bring the new library to your machine). After I create more junit tests (in order to spot a similar emergency in time, next time) I will upload the newer version of jMoby to the Maven repository (it will be vesion 1.0.1). But, of course, I do not know if the newer xercesImpl version is suitable for those users you complained about xerces in the first place (that was a reason why I removed the xerces dependency). Please try your code and if you have again problems we can discuss the options. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Mon Mar 17 18:29:19 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 17 Mar 2008 16:29:19 -0600 Subject: [MOBY-dev] LSIDs for secondary data types? Message-ID: <47DEF0BF.5010103@ucalgary.ca> Hi all, Can we define formally LSIDs for the secondary parameter datatypes? e.g. urn:lsid:biomoby.org:secondaryParamClass:Integer: urn:lsid:biomoby.org:secondaryParamClass:String: urn:lsid:biomoby.org:secondaryParamClass:Float: urn:lsid:biomoby.org:secondaryParamClass:Boolean: This would help me with my Semantic Annotations for WSDL work... Objections? Paul From markw at illuminae.com Mon Mar 17 18:52:02 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 17 Mar 2008 15:52:02 -0700 Subject: [MOBY-dev] LSIDs for secondary data types? In-Reply-To: <47DEF0BF.5010103@ucalgary.ca> References: <47DEF0BF.5010103@ucalgary.ca> Message-ID: No objections here. I assume you need them to resolve? If so, to what on the data-side and to what on the metadata side? M On Mon, 17 Mar 2008 15:29:19 -0700, Paul Gordon wrote: > Hi all, > > Can we define formally LSIDs for the secondary parameter datatypes? e.g. > > urn:lsid:biomoby.org:secondaryParamClass:Integer: > urn:lsid:biomoby.org:secondaryParamClass:String: > urn:lsid:biomoby.org:secondaryParamClass:Float: > urn:lsid:biomoby.org:secondaryParamClass:Boolean: > > This would help me with my Semantic Annotations for WSDL work... > > Objections? > > Paul > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From gordonp at ucalgary.ca Tue Mar 18 09:51:31 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 18 Mar 2008 07:51:31 -0600 Subject: [MOBY-dev] LSIDs for secondary data types? In-Reply-To: References: <47DEF0BF.5010103@ucalgary.ca> Message-ID: <47DFC8E3.7030009@ucalgary.ca> No data resolution (there is no obligation to provide both, e.g. we have no "data" for urn:lsid:biomoby.org:objectclass:DNASequence:), just metadata with a description of what it is. Mark Wilkinson wrote: > No objections here. > > I assume you need them to resolve? If so, to what on the data-side > and to what on the metadata side? > > M > > > > On Mon, 17 Mar 2008 15:29:19 -0700, Paul Gordon > wrote: > >> Hi all, >> >> Can we define formally LSIDs for the secondary parameter datatypes? e.g. >> >> urn:lsid:biomoby.org:secondaryParamClass:Integer: >> urn:lsid:biomoby.org:secondaryParamClass:String: >> urn:lsid:biomoby.org:secondaryParamClass:Float: >> urn:lsid:biomoby.org:secondaryParamClass:Boolean: >> >> This would help me with my Semantic Annotations for WSDL work... >> >> Objections? >> >> Paul >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From darin.london at duke.edu Tue Mar 18 14:17:00 2008 From: darin.london at duke.edu (darin.london at duke.edu) Date: Tue, 18 Mar 2008 13:17:00 -0500 Subject: [MOBY-dev] BOSC 2008 Announcement and Call For Submissions Message-ID: <200803181817.m2IIH0Ai007305@tenero.duhs.duke.edu> BOSC 2008 Call for Abstracts The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many Open Source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall theme for the conference this year is "Tackling Hard Problems with Emerging Technologies". Topics under this umbrella include cyberinfrastructure, grid computing and workflow management and discovery, and visualization. We will also have a series of update talks about the main Open Source Bioinformatics Software suites. One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done. This year, BOSC is accepting abstract submissions on the conference theme "Tackling Hard Problems with Emerging Technologies". The conference theme reflects that there are new technologies emerging on both the scientific front (new sequencing technologies, etc.) and the IT front (workflows, mashup/web 2.0, improvements in all of the major programming languages, etc.), which may allow the open source community to solve problems that were previously intractable. Abstracts may be submitted for the following topics. 1. Cyberinfrastructure - We are interested in presentations on topics dealing with the development of infrastructure on the web to facilitate software and data re-use (mashups, or traditional), interoperability and inter-process communication, system/service discovery, and data movement and modeling in distributed systems. This may include peer-to-peer systems of data transfer, Web Services, various flavors of data representation (SOAP, JSON, XML, others), and technologies commonly referred to under the Web 2.0 paradigm (e.g. folksonomies/tagging, user-based content generation, content feeds, and Social Networking). 2. Grid Computing and Workflow Management and Discovery - We particularly invite talks that report progress in making workflow systems easier to use and on how to do distributed-collaborative research , e.g. workflows that encompass the coordination of systems running in different parts of the world. 3. Visualization - Visualization is a maturing area of open source software development. We particularly invite talks that demonstrate innovative visualization systems in the context of workflows. 4. Open Source Software - Speakers will present talks on the use, development, or philosophy of open source software in bioinformatics. 5. Bio* Open Source Project Updates - We invite abstracts from the representatives of the open source projects sponsored by or affiliated to the O|B|F (see Projects). Please consult the official BOSC 2008 website at http://www.open-bio.org/wiki/Upcoming_BOSC_conference for all updates and extra information. Submission Process: All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t Important Dates: May 11: Abstract submission deadline. June 2: Notification of accepted talks. June 4: Early registration discount cut-off. July 18-19: BOSC 2008! We hope to see you at BOSC 2008! Kam Dahlquist and Darin London BOSC 2008 Co-organizers From Sebastien.Carrere at toulouse.inra.fr Thu Mar 27 07:43:09 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 27 Mar 2008 12:43:09 +0100 Subject: [MOBY-dev] deregister time out on Test Registry Message-ID: <47EB884D.4000304@toulouse.inra.fr> Bonjour, Does anyone else encounter problems when trying to de-register a service reisterd in the Test registry ? (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl) I'va got a time out message:"Failed with status:500 Server closed connection without sending any data back" The service seems to be removed (because when I try to de-register it again, I've got the correct message "No services in the registry match the given URL and the signatureURL didn\'t contain any services. The RDF agent was called, but found nothing useful." Anyone has an idea ? I use the Perl API. NB: this time-out does not occur on the production registry. Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From ola.spjuth at farmbio.uu.se Fri Mar 28 17:07:24 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 28 Mar 2008 22:07:24 +0100 Subject: [MOBY-dev] Caching revisited Message-ID: <8DC04FBC-A3BD-4DCB-BE94-097EF4CED5DA@farmbio.uu.se> Hi, I just can't get caching to work properly with jMoby! it has cost me so many hours and I still can't figure it out. I want to cache as much as possible in the background on first start, then on second start everything should be as fast as possible. I am able to cache the registry (thanks to previous discussion here and Pauls assistance), but even so I I still get the annoying Fetching data type ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects when I invoke a service. What am I doing wrong? I have attached a Java snippet with a main() that demonstrates this. It seems it is the invokeService() that always downloads the data type ontology. Am I calling this wrong or is it a bug? Thanks, .../Ola ? From gordonp at ucalgary.ca Fri Mar 28 17:55:47 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Mar 2008 15:55:47 -0600 Subject: [MOBY-dev] Caching revisited In-Reply-To: <8DC04FBC-A3BD-4DCB-BE94-097EF4CED5DA@farmbio.uu.se> References: <8DC04FBC-A3BD-4DCB-BE94-097EF4CED5DA@farmbio.uu.se> Message-ID: <47ED6963.6020605@ucalgary.ca> Hi Ola, We decided to create a single caching mechanism in jMoby, and Eddie implemented this at the BioHackathon last month. I have yet to change MobyRequest to use this, but it's on my shortlist (It relates to the problem Mark Fiers was having last week). Your trouble gives me incentive to switch it over sooner, as in the next couple of days. :-) In any case, the existing code shouldn't refetch the ontology unless you either don't call loadDataTypes(yourCacheURL) when you start your JVM, or you are specifying a different registry argument. Regards, Paul Ola Spjuth wrote: > Hi, > > I just can't get caching to work properly with jMoby! it has cost me > so many hours and I still can't figure it out. I want to cache as much > as possible in the background on first start, then on second start > everything should be as fast as possible. I am able to cache the > registry (thanks to previous discussion here and Pauls assistance), > but even so I I still get the annoying Fetching data type ontology > from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects when I invoke a > service. What am I doing wrong? I have attached a Java snippet with a > main() that demonstrates this. > > It seems it is the invokeService() that always downloads the data type > ontology. Am I calling this wrong or is it a bug? > > Thanks, > > .../Ola > > > ------------------------------------------------------------------------ > From wlalexander at gmail.com Mon Mar 31 21:37:31 2008 From: wlalexander at gmail.com (Wendy Alexander) Date: Mon, 31 Mar 2008 18:37:31 -0700 Subject: [MOBY-dev] Eclipse, Maven and JDK Message-ID: <52a28ae20803311837m28afe66ag7b7759b4306b5ca1@mail.gmail.com> Hi all, I am having a heck of a time trying to get Eclipse to recognize a JDK so that it can use the Maven libraries. I have several JDKs installed. In Eclipse, I set my installed JREs to my JDK directories. I set my path to include JDK 1.5. I set JAVA_HOME to my JDK directory. I selected JDK 1.5as my project Jave Library. I added a -vm line to eclipse.ini directing it to my JDK. I still get a message on Eclipse start-up saying, "The Maven Integration requires that Eclipse be running a JDK, because a number of Maven core plugins use jars from the JDK. Please make sure the -vm option in eclipse.ini is pointing to a JDK and verify that Installed JREs are also using a JDK." I have no idea what I'm doing wrong. Please help! Thanks! W From groscurt at mpiz-koeln.mpg.de Sat Mar 1 08:12:14 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Sat, 01 Mar 2008 09:12:14 +0100 Subject: [MOBY-dev] Dashboard can't connect to Registries In-Reply-To: <000601c87a45$892f2700$9b8d7500$@de> References: <000601c87a45$892f2700$9b8d7500$@de> Message-ID: <47C90FDE.7030808@mpiz-koeln.mpg.de> Hi Michael, sorry thats my fault - I offer for Eclipse user the .classpath file, but unfortunatley I had some problems with the plone software and it didnt update the file. Please download the .classpath file from the tutorial again and refresh your project - this should remove your first problem. For the second... I cant check that now - but this should work when you copy the build.properties.template to build.properties and change their the proxy settings in that file (there should be poperties for that) Best andreas Michael Gerlich wrote: > Hi there, > > First of all thanks for your tutorials about setting up Biomoby with Eclipse > and for the newly created Known errors site at > > http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step > /writing-biomoby-web-services/known-errors-and-problems, > they helped me a lot and I finally have successful Builds with the Ant > Scripts (using JDK 1.5). > > But there are some things I still have problems with. > > 1) Eclipse keeps reporting that it misses required libraries, even though > the initeclipse script says Build successful. Are these errors some kind of > artifacts or should I check the ant scripts or checkout JMoby again? > > micge at linux-vm:~/eclipse> ./eclipse -vmargs > -Djava.home=/usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/ > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings > (Datei oder Verzeichnis nicht gefunden) > > Severity and Description > Project 'moby' is missing required library: 'lib/activation.jar' > > Project 'moby' is missing required library: 'lib/adenine.jar' > Project 'moby' is missing required library: 'lib/alltools2.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-antlr.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-bcel.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-bsf.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-log4j.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-oro.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-regexp.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-apache-resolver.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-commons-logging.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-commons-net.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-contrib.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-icontract.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jai.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-javamail.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-jdepend.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jmf.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jsch.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-junit.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-launcher.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-netrexx.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-nodeps.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-starteam.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-stylebook.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-swing.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-trax.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-vaj.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-weblogic.jar' > Project 'moby' is missing required library: > 'lib/ant_home/lib/ant-xalan1.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/ant-xslp.jar' > > Project 'moby' is missing required library: 'lib/ant_home/lib/ant.jar' > > Project 'moby' is missing required library: > 'lib/ant_home/lib/xercesImpl.jar' > Project 'moby' is missing required library: 'lib/ant_home/lib/xml-apis.jar' > > Project 'moby' is missing required library: 'lib/axis-ant.jar' > Project 'moby' is missing required library: 'lib/axis.jar' > Project 'moby' is missing required library: 'lib/castor-0.9.5.jar' > > Project 'moby' is missing required library: 'lib/commons-codec-1.3.jar' > > Project 'moby' is missing required library: > 'lib/commons-collections-2.1.jar' > Project 'moby' is missing required library: 'lib/commons-dbcp-1.1.jar' > > Project 'moby' is missing required library: 'lib/commons-discovery-0.2.jar' > > Project 'moby' is missing required library: > 'lib/commons-httpclient-3.0-rc2.jar' > Project 'moby' is missing required library: 'lib/commons-io-1.0.jar' > > Project 'moby' is missing required library: 'lib/commons-lang-2.1.jar' > > Project 'moby' is missing required library: 'lib/commons-logging-1.0.4.jar' > > Project 'moby' is missing required library: 'lib/commons-pool-1.1.jar' > > Project 'moby' is missing required library: 'lib/concurrent.jar' > > Project 'moby' is missing required library: 'lib/dnsjava-1.3.2.jar' > > Project 'moby' is missing required library: 'lib/icis-pedigree.jar' > > Project 'moby' is missing required library: 'lib/icu4j.jar' > Project 'moby' is missing required library: 'lib/jakarta-oro-2.0.5.jar' > > Project 'moby' is missing required library: 'lib/jaxen-core.jar' > > Project 'moby' is missing required library: 'lib/jaxen-jdom.jar' > > Project 'moby' is missing required library: 'lib/jaxrpc.jar' > Project 'moby' is missing required library: 'lib/jcalendar.jar' > Project 'moby' is missing required library: 'lib/jdom.jar' > Project 'moby' is missing required library: 'lib/jena.jar' > Project 'moby' is missing required library: 'lib/jfcunit.jar' > Project 'moby' is missing required library: 'lib/jodconverter-2.2.0.jar' > > Project 'moby' is missing required library: 'lib/junit.jar' > Project 'moby' is missing required library: 'lib/log4j-1.2.12.jar' > > Project 'moby' is missing required library: 'lib/lsid-client-1.1.2.jar' > > Project 'moby' is missing required library: 'lib/lsid-server-1.1.2.jar' > > Project 'moby' is missing required library: 'lib/mail.jar' > Project 'moby' is missing required library: 'lib/mailapi_1_3_1.jar' > > Project 'moby' is missing required library: > 'lib/mysql-connector-java-3.1.7-bin.jar' > Project 'moby' is missing required library: 'lib/rdf-api-2001-01-19.jar' > > Project 'moby' is missing required library: 'lib/saaj.jar' > Project 'moby' is missing required library: 'lib/saxpath.jar' > Project 'moby' is missing required library: 'lib/servlet.jar' > Project 'moby' is missing required library: 'lib/taverna.jar' > Project 'moby' is missing required library: 'lib/wsdl4j-1.5.1.jar' > > Project 'moby' is missing required library: 'lib/xalan.jar' > Project 'moby' is missing required library: 'lib/xercesImpl.jar' > > Project 'moby' is missing required library: 'lib/xercesSamples.jar' > > Project 'moby' is missing required library: 'lib/xml-apis.jar' > Project 'moby' is missing required library: 'lib/xmlParserAPIs.jar' > > Project build error Cannot find parent: org.biomoby:jmoby for project: > org.biomoby:jmoby-core:jar:1.0.0 moby/src/main pom.xml line 1 > 1204224268317 133440 > Project build error Cannot find parent: org.biomoby:jmoby for project: > org.biomoby:jmoby-plugins:jar:1.0.0 moby/src/samples pom.xml line > 1 1204224267905 133439 > The project cannot be built until build path errors are resolved > moby > > > > 2) I'am behind a proxy server, so I had to edit proxy settings in > net.properties of JDK 1.5 (http_proxy environment variable is set, but > without effect to Java). With this, all the ant scripts work without any > problems, but when I run Dashboard, all I got are empty lists and the > following messages: > > Inside Eclipse: > --------------- > Buildfile: /home/micge/workspace/moby/build.xml > checkmaven: > initmaven: > init: > config: > compile: > moses-init: > samples-init: > dashboard-init: > dashboard-config: > dashboard: > [Dashboard] libxcb: WARNING! Program tries to unlock a connection without > having acquired > [Dashboard] a lock first, which indicates a programming error. > [Dashboard] There will be no further warnings about this issue. > [Dashboard] libxcb: WARNING! Program tries to lock an already locked > connection, > [Dashboard] which indicates a programming error. > [Dashboard] There will be no further warnings about this issue. > [Dashboard] 192616 [Thread-6] WARN CentralDigestCachedImpl - Error with > Services RDF > [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== > [Dashboard] Fault details: > [Dashboard] Fault string: java.net.ConnectException: Connection timed out > [Dashboard] Fault code: > {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > [Dashboard] Fault actor: null > [Dashboard] When calling: > [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl > [Dashboard] =========== > [Dashboard] at > org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) > [Dashboard] at > org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) > [Dashboard] at > org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest > CachedImpl.java:216) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa > chedImpl.java:243) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm > pl.java:709) > [Dashboard] at > org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 > 61) > [Dashboard] at > org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 > ) > [Dashboard] at > org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) > [Dashboard] at java.lang.Thread.run(Thread.java:595) > [Dashboard] Caused by: java.net.ConnectException: Connection timed out > [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) > [Dashboard] at > org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: > 32) > [Dashboard] at > org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) > [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) > [Dashboard] at > org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) > [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) > [Dashboard] at > org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) > [Dashboard] ... 9 more > [Dashboard] Caused by: java.net.ConnectException: Connection timed out > [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) > [Dashboard] at > java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) > [Dashboard] at > java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) > [Dashboard] at > java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) > [Dashboard] at > java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) > [Dashboard] at java.net.Socket.connect(Socket.java:520) > [Dashboard] at java.net.Socket.connect(Socket.java:470) > [Dashboard] at java.net.Socket.(Socket.java:367) > [Dashboard] at java.net.Socket.(Socket.java:180) > [Dashboard] at > org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact > ory.java:149) > [Dashboard] at > org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact > ory.java:120) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) > [Dashboard] ... 18 more > [Dashboard] 193461 [Thread-7] WARN CentralDigestCachedImpl - Error with > Services RDF > [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== > [Dashboard] Fault details: > [Dashboard] Fault string: java.net.ConnectException: Connection timed out > [Dashboard] Fault code: > {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > [Dashboard] Fault actor: null > [Dashboard] When calling: > [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl > [Dashboard] =========== > [Dashboard] at > org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) > [Dashboard] at > org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) > [Dashboard] at > org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest > CachedImpl.java:216) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa > chedImpl.java:243) > [Dashboard] at > org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm > pl.java:709) > [Dashboard] at > org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 > 61) > [Dashboard] at > org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 > ) > [Dashboard] at > org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) > [Dashboard] at java.lang.Thread.run(Thread.java:595) > [Dashboard] Caused by: java.net.ConnectException: Connection timed out > [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) > [Dashboard] at > org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: > 32) > [Dashboard] at > org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) > [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) > [Dashboard] at > org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) > [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) > [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) > [Dashboard] at > org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) > [Dashboard] ... 9 more > [Dashboard] Caused by: java.net.ConnectException: Connection timed out > [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) > [Dashboard] at > java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) > [Dashboard] at > java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) > [Dashboard] at > java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) > [Dashboard] at > java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) > [Dashboard] at java.net.Socket.connect(Socket.java:520) > [Dashboard] at java.net.Socket.connect(Socket.java:470) > [Dashboard] at java.net.Socket.(Socket.java:367) > [Dashboard] at java.net.Socket.(Socket.java:180) > [Dashboard] at > org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact > ory.java:149) > [Dashboard] at > org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact > ory.java:120) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) > [Dashboard] at > org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) > [Dashboard] ... 18 more > BUILD SUCCESSFUL > > > > >From Dashboard (after one minute) > -------------- > ===Error=== > Fault details: > Fault string: java.net.ConnectException: Connection timed out > Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > Fault actor: null > when calling: > http://moby.uralgary.ca/moby/MOBY-Central.pl > > Is this a problem with the proxy settings I made in net.properties or is it > inside Dashboard? > > > Regards, > Michael > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From martin.senger at gmail.com Sun Mar 2 17:25:16 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 01:25:16 +0800 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <200802291151.22060.groscurt@mpiz-koeln.mpg.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> > starting dashboard from console gives me I hope that I fixed all the recent (reported) problems with Dashboard, after changes caused by using Maven. I am still working on few details (e.g. on Eclipse problems) before I upload jMoby version 1.0.0 to the Maven repository. I would appreciate if you tell me if something is not working as it is supposed to work. The recent changes are summarized (as usual) here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ChangeLog (look what has been changed during and since our last meeting in Biohackhatlon). Please try, for example, the new 'ant install' (doing it in a fresh check-out may reveal more) - it should do everything, an then it starts Dashboard. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Sun Mar 2 17:35:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 01:35:21 +0800 Subject: [MOBY-dev] Dashboard can't connect to Registries In-Reply-To: <000601c87a45$892f2700$9b8d7500$@de> References: <000601c87a45$892f2700$9b8d7500$@de> Message-ID: <4d93f07c0803020935j3a2b419am70b062d7db47d5c2@mail.gmail.com> My few comments to: http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step > /writing-biomoby-web-services/known-errors-and-problems > , * "Open the *pom.xml*... and change..." Don't do, ever. The pom.xml is a generated file and will be overwritten regularly. It is generated from xmls/project.pom. But that one is shared and under cvs. Better tell me when this problem happens and I will try to solve it (even though I am trying to avoid Windows and Eclipse, but sometimes there is no detour...) * "The datatype and skeleton generation via dashboard failes in a NullPointerException" It should be fixed now. Make a new CVS update and tell me if it is not fixed please. * "The registration of my service via dashboard does not work" It works for me fine. Tell me details please if it still occurs. * "The deployment of my service via dashboard failes" I hope that I fixed it. It works for me now, at least. But I am working on other improvements in service deployment, so any comments about something not working in deployment would be very appreciated just now. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Mar 3 08:37:35 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 03 Mar 2008 09:37:35 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> Message-ID: <47CBB8CF.80303@mpiz-koeln.mpg.de> Hi Martin, it seems to work for me now with a new check out. What was the reason to start dashboard directly in the ant install task ? I stopped to update our tutorial as long as version 1.0.0. comes out... is hard to redo a lot of things if changes are still in progress ;-) Best andreas Martin Senger wrote: >> starting dashboard from console gives me >> > > > I hope that I fixed all the recent (reported) problems with Dashboard, after > changes caused by using Maven. I am still working on few details (e.g. on > Eclipse problems) before I upload jMoby version 1.0.0 to the Maven > repository. I would appreciate if you tell me if something is not working as > it is supposed to work. > > The recent changes are summarized (as usual) here: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ChangeLog (look > what has been changed during and since our last meeting in Biohackhatlon). > > Please try, for example, the new 'ant install' (doing it in a fresh > check-out may reveal more) - it should do everything, an then it starts > Dashboard. > > Cheers, > Martin > > From martin.senger at gmail.com Mon Mar 3 08:52:59 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 16:52:59 +0800 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <47CBB8CF.80303@mpiz-koeln.mpg.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> <47CBB8CF.80303@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803030052p1348df39ke4a7bfe8240be77@mail.gmail.com> > What was the reason to > start dashboard directly in the ant install task ? > Sounded like a good idea, I do not know. Any problems with it? The most advantages you witness when you do it really from a clean beginning. Which means not only not having yet build.properties file (the install script creates it and adds there property 'registry.cache.dir'), but also without (yet) any dashboard preferences (which is a bit harder to remove them in windows: you have to go to the windows registry and remove the key 'cache/directory'; that's why I have an option in 'settings' - 'manage my dashboard' - but it is not yet implemented). > I stopped to update our tutorial as long as version 1.0.0. comes out... It's real close. The only still missing pieces (AFAIK) are to test more deployment parts, and to refresh the Eclipse tutorial. Will be done this week (and then I will start working on version 1.1.0 which means adding async services and document/literal style). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Mar 3 09:10:18 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 03 Mar 2008 10:10:18 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <4d93f07c0803030052p1348df39ke4a7bfe8240be77@mail.gmail.com> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> <4d93f07c0803020925u33f300d3v91b452b7a9b74737@mail.gmail.com> <47CBB8CF.80303@mpiz-koeln.mpg.de> <4d93f07c0803030052p1348df39ke4a7bfe8240be77@mail.gmail.com> Message-ID: <47CBC07A.9060008@mpiz-koeln.mpg.de> Martin Senger wrote: >> What was the reason to >> start dashboard directly in the ant install task ? >> >> > > Sounded like a good idea, I do not know. Any problems with it? > Martin no, no problem with that ... just surprised seeing starting dashboard ;-) i think thats quite convenient because most people will work with dashboard and if, as you described, the script now takes a lot of responsibilites, its much better. >* "Open the *pom.xml*... and change..." > Don't do, ever. The pom.xml is a generated file and will be overwritten >regularly. It is generated from xmls/project.pom. But that one is shared and >under cvs. Better tell me when this problem happens and I will try to solve >it (even though I am trying to avoid Windows and Eclipse, but sometimes >there is no detour...) the problem about that is what also Eddie encountered... when the java.home is pointing to the jdk folder and not to the jre inside the jdk folder the expression ${java.home}/../lib/tools.jar is wrong. After changing it to ${java.home}/lib/tools.jar it works. thats why I added it. Best and keep on working *g Andreas From groscurt at mpiz-koeln.mpg.de Mon Mar 3 11:46:27 2008 From: groscurt at mpiz-koeln.mpg.de (groscurt) Date: Mon, 3 Mar 2008 12:46:27 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <47CBC07A.9060008@mpiz-koeln.mpg.de> Message-ID: <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> Hi, sorry for bothering again.... when i start dashboard with a fresh checkout i get dashboard: [Dashboard] Mar 3, 2008 12:43:34 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/RegistryPanel/prefs.xml [Dashboard] Mar 3, 2008 12:43:34 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/RegistryPanel/registryEndpoint/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:34 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/RegistryPanel/registryNamespace/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:34 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/RegistryPanel/cacheDirectory/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:36 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/ResultsPanel/prefs.xml [Dashboard] Mar 3, 2008 12:43:36 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/SimpleClientPanel/serviceEndpoint/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:36 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/SimpleClientPanel/serviceImplClass/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:37 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/SimpleClientPanel/prefs.xml [Dashboard] Mar 3, 2008 12:43:37 PM java.util.prefs.FileSystemPreferences$7 run [Dashboard] WARNING: Prefs file removed in background /home/ubuntu/.java/.userPrefs/org/biomoby/service/dashboard/SimpleClientPanel/sc-inputFile/AAQnNpPKBSRk-history/prefs.xml [Dashboard] Mar 3, 2008 12:43:45 PM java.util.prefs.FileSystemPreferences syncWorld [Dashboard] WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: java.lang.IllegalArgumentException: Not supported: indent-number is this a dashboard issue or something local ? And on the start of dashboard the fields of Endpoint and URI are empty (for default). When switch to any other central they show up, also when i switch back to default.. its just on the first startup. Best andreas From martin.senger at gmail.com Mon Mar 3 12:08:40 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 20:08:40 +0800 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> References: <47CBC07A.9060008@mpiz-koeln.mpg.de> <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803030408v13746ae3j1548251a77424d16@mail.gmail.com> > sorry for bothering again.... Not at all. > when i start dashboard with a fresh checkout i > get Interesting; never seen it on my kubuntu. Please again: what java version are you using? It says that something is happening to your ~/.java/.userPrefs directory. Try to google it (e.g. http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751540) a bit. Try to remove the whole .java directory (your preferences disappear and you will recreate them again in dashboard). is this a dashboard issue or something local ? I hope it is local but I can't be sure. From jMoby, only Dashboard saves preference this way. > And on the start of dashboard the fields of Endpoint and URI are empty > (for > default). When switch to any other central they show up, also when i > switch > back to default.. its just on the first startup. Yes, this is how it should be. However, more important is the value in the 'cache directory'. If there are no previous preferences stored, it should be filled with the value of the registry.cache.dir (as given in 'ant install', or taken from build.properties). How does this field look like in your Dash? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Mar 3 12:26:11 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 03 Mar 2008 13:26:11 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <4d93f07c0803030408v13746ae3j1548251a77424d16@mail.gmail.com> References: <47CBC07A.9060008@mpiz-koeln.mpg.de> <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> <4d93f07c0803030408v13746ae3j1548251a77424d16@mail.gmail.com> Message-ID: <47CBEE63.2030506@mpiz-koeln.mpg.de> Martin Senger wrote: > Interesting; never seen it on my kubuntu. Please again: what java version > are you using? It says that something is happening to your > ~/.java/.userPrefs directory. Try to google it (e.g. > http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751540) a bit. Try to > remove the whole .java directory (your preferences disappear and you will > recreate them again in dashboard). > I use java version "1.6.0_04" Java(TM) SE Runtime Environment (build 1.6.0_04-b12) Java HotSpot(TM) Client VM (build 10.0-b19, mixed mode, sharing) i will google a bit :) > >> And on the start of dashboard the fields of Endpoint and URI are empty >> (for >> default). When switch to any other central they show up, also when i >> switch >> back to default.. its just on the first startup. >> > > > Yes, this is how it should be. However, more important is the value in the > 'cache directory'. If there are no previous preferences stored, it should be > filled with the value of the registry.cache.dir (as given in 'ant install', > or taken from build.properties). > > How does this field look like in your Dash? > how you described... in my old checkout I had another entry there and it complained, I changed it to the one used during the installation and it worked. With the new checkout the entry was correctly set up when dashboard started. best andreas From martin.senger at gmail.com Mon Mar 3 12:36:10 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 3 Mar 2008 20:36:10 +0800 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <47CBEE63.2030506@mpiz-koeln.mpg.de> References: <47CBC07A.9060008@mpiz-koeln.mpg.de> <04f9dd7706fccee14c9e9ecd856be7ec@mpizmail.mpiz-koeln.mpg.de> <4d93f07c0803030408v13746ae3j1548251a77424d16@mail.gmail.com> <47CBEE63.2030506@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803030436o9591a44p6412759d002fbd13@mail.gmail.com> > I use > java version "1.6.0_04" > Java(TM) SE Runtime Environment (build 1.6.0_04-b12) > Java HotSpot(TM) Client VM (build 10.0-b19, mixed mode, sharing) > I will try with 1.6 myself later. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Mon Mar 3 16:20:18 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 03 Mar 2008 17:20:18 +0100 Subject: [MOBY-dev] I am a believer... Message-ID: <47CC2542.9030600@bsc.es> Hello everybody! I'd like to continue to discuss (even in a monologue mode :-)) document/literal encoding. I have prepared an example how it would be implemented in JMoby (!). It demands a few changes in MoSeS generator to implement it. Unfortunately, because JMoby is not JAXB based, ;-), there is no possibility to generate the WSDL automatically (JAX-WS), so one must be generated somehow (by the MoSeS). I'm using JBoss 4.2.2 with JBoss WS-3.0 (METRO). Unfortunately it doesn't deploy Provider Based JAX-WS endpoints, so I use ejb3 as an example... Here is the complete example: The class that implements a "proxy" between a JAX-WS Provider and JMoby BaseService (nothing especial - just converts Source <-> String) ***************************************************** package es.bsc.inb.ejb.jmoby; import java.io.*; import javax.xml.transform.*; import javax.xml.transform.stream.*; import javax.xml.ws.Provider; import org.biomoby.service.BaseService; import org.biomoby.shared.parser.MobyPackage; public abstract class ExtendedMobyBase extends BaseService implements Provider { // provider method that is called by the JAX-WS public Source invoke(Source request) { try { TransformerFactory f = TransformerFactory.newInstance(); Transformer tr = f.newTransformer(); StringWriter sw = new StringWriter(); StreamResult result = new StreamResult(sw); tr.transform(request, result); String response = runMyService(sw.toString()); return new StreamSource(new StringReader(response)); } catch(Exception ex) { ex.printStackTrace(); } // need to generate SOAP Exception... (shouldn't fail and... this is a demo...) return null; } // JMoby (MoSeS) generated method public String runMyService(String data) { MobyPackage mobyOutput = null; try { // reading the whole input MobyPackage mobyInput = MobyPackage.createFromXML (data, "AminoAcidSequence"); // prepare an output object mobyOutput = prepareOutput (mobyInput); // do the main job processIt (mobyInput, mobyOutput); // and return an XML back return mobyOutput.toXML(); } catch (Throwable e) { boolean mobyException = (e instanceof org.biomoby.shared.MobyException); java.io.StringWriter sw = new java.io.StringWriter (500); if (e.getCause() != null || (! mobyException)) e.printStackTrace (new java.io.PrintWriter (sw)); return error (e.getMessage() + "\n" + sw.toString(), mobyOutput); } } } ***************************************************** Empty (dummy) local interface, just t o comply to ejb3 specs... ***************************************************** package es.bsc.inb.ejb.jmoby; import javax.ejb.Local; @Local public interface JMobyDocumentLiteralDemoServiceLocal {} ***************************************************** Here is the service itself. It implements processIt() method from BaseService JMoby class... ***************************************************** package es.bsc.inb.ejb.jmoby; import javax.ejb.Stateless; import javax.xml.transform.Source; import javax.xml.ws.*; import org.biomoby.shared.MobyException; import org.biomoby.shared.datatypes.MobyObject; import org.biomoby.shared.parser.*; @WebServiceProvider(serviceName="JMobyDocumentLiteralDemoService", portName="JMobyDocumentLiteralDemoPort", targetNamespace="urn:JMobyDocumentLiteralDemoService/wsdl", wsdlLocation = "META-INF/wsdl/JMobyDocumentLiteralDemoService.wsdl") @javax.xml.ws.ServiceMode(value=javax.xml.ws.Service.Mode.PAYLOAD) @Stateless public class JMobyDocumentLiteralDemoService extends ExtendedMobyBase implements JMobyDocumentLiteralDemoServiceLocal, Provider { @Override public void processIt(MobyJob request, MobyJob response, MobyPackage arg2) throws MobyException { // echo... MobyObject object = request.getData(); response.setData(object); } } ***************************************************** And finally we MUST provide the WSDL file (in the correct location as in "META-INF/wsdl/JMobyDocumentLiteralDemoService.wsdl") ***************************************************** ***************************************************** Note, that this is a Document/Literal XML Schema based web-service that use JMoby as an implementation. Unfortunately, there is no client from JMoby yet to call the service... :-( The schema () is the same for any Moby web-service (no ontology included). Yours, Dmitry. P.S. As always appreciate your opinions (aggressive and negative included :-) ). From gordonp at ucalgary.ca Mon Mar 3 17:01:12 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 03 Mar 2008 10:01:12 -0700 Subject: [MOBY-dev] I am a believer... In-Reply-To: <47CC2542.9030600@bsc.es> References: <47CC2542.9030600@bsc.es> Message-ID: <47CC2ED8.8050003@ucalgary.ca> Hi Dmitry, I can't comment on the server side of things, because I don't use MoSeS, but I am planning on adding client-side support for Document/Literal in the next couple of weeks, so you'll actually be able to use it. :-) Regards, Paul > > > Note, that this is a Document/Literal XML Schema based web-service > that use JMoby as an implementation. > Unfortunately, there is no client from JMoby yet to call the > service... :-( > > The schema () is the same for any Moby web-service (no > ontology included). > > Yours, > > Dmitry. > > P.S. As always appreciate your opinions (aggressive and negative > included :-) ). > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,47cc2ae710950453915731! > > > From dmitry.repchevski at bsc.es Mon Mar 3 17:25:25 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 03 Mar 2008 18:25:25 +0100 Subject: [MOBY-dev] I am a believer... In-Reply-To: <47CC2ED8.8050003@ucalgary.ca> References: <47CC2ED8.8050003@ucalgary.ca> Message-ID: <47CC3485.1090300@bsc.es> Hello Paul, So no discussion so far... ;-) The question is not that I can not use it (my API can support it), but THE WAY it supposed to be implemented. If you look into http://inb.bsc.es/java/moby_ejb3_example.html you can see the my point of view. I would be happy to see MobyMessage as a BARE PAYLOAD of the document/literal service: ************************************************************** AGHFJHGDKHGJKADGHJGDJH ************************************************************** On the server side it gives an opportunity to use a STANDARD JAX-WS protocol stack. On the client side it gives an opportunity to use a STANDARD JAX-WS protocol stack. The given example was to show that just modifying a little bit JMoby BaseService class (adding public Source invoke(Source request) method and implementing Provider interface) will add such a support to JMoby WITHOUT breaking "old" soap-encoding sertvices. It would cost virtually nothing to convert the "old" ones to the doc/literal, because this way the only thing for the service provider to do is to update JMoby version and put some (STANDARD) annotations to the service. And by the way get rid of AXIS ;-) Sicerely Yours, Dmitry, P.S. > I can now go Axis-free in > MobyRequest (except for there being no Central implementation without > Axis... hint hint). ;-) Done. http://inb.bsc.es/java/moby_central.html From groscurt at mpiz-koeln.mpg.de Fri Mar 7 15:12:59 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 07 Mar 2008 16:12:59 +0100 Subject: [MOBY-dev] [Fwd: Problem with xercexImpl-2.6.2.jar] Message-ID: <47D15B7B.4030706@mpiz-koeln.mpg.de> hi, I write biomoby service with eclipse. and now the maven 2.0 finds wished libraries and downloads it automatically . But I have problem with xercexImpl-2.6.2.jar , because it has older version SAXParserFactory. So the above jar files should be removed from class path. else I get an Exception like this: Exception in thread "main" java.lang.UnsupportedOperationException: This parser does not support specification "null" version "null". I can simply remove this jar from lib of my biomoby project before, but now maven try to download and install it every time after I removed it from maven repository in my local directory. how should I do , so that maven doesn't download it by default? Should I change the dependency relationship in pom.xml ? thank you for your help in advance? regrads hao chen From martin.senger at gmail.com Fri Mar 7 15:58:22 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 7 Mar 2008 23:58:22 +0800 Subject: [MOBY-dev] [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47D15B7B.4030706@mpiz-koeln.mpg.de> References: <47D15B7B.4030706@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803070758j176a25f0o2a035938d5e29258@mail.gmail.com> Hi, Exception in thread "main" java.lang.UnsupportedOperationException: This > parser does not support specification "null" version "null". > You have to trace what jar file is loading it (as its dependency) and then apply the same trick that is already once used in jmoby/xmls/project.pom: commons-configuration commons-configuration 1.5 xerces xerces When you find it, change the xmls/project.pom and please commit it back to jMoby. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Sat Mar 8 10:21:06 2008 From: martin.senger at gmail.com (Martin Senger) Date: Sat, 8 Mar 2008 18:21:06 +0800 Subject: [MOBY-dev] looking for asynchronous service specification... Message-ID: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> ...and cannot find it on biomoby.org pages. Can anybody send here the latest version of it please? I am ready to implement it into MoSeS but somehow without the spec it is a bit difficult... :-) Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Mar 10 12:56:43 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 10 Mar 2008 13:56:43 +0100 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> Message-ID: <47D5300B.4010301@mpiz-koeln.mpg.de> Hi, is it deliberately that while deploying via dashboard (started from eclipse) on a remote machine - dashboard does not take the value of the 'Tomcat home directory' the user specified, but the CATALINA_HOME variable of the user ? We had the problem that whatever value we specified in this field it always used the value of the system variable - which is probably (and in our case definitely *g) different on the remote machine. As always - local problems or a general one ;-) Best andreas From jmrodriguez at cnio.es Mon Mar 10 13:15:14 2008 From: jmrodriguez at cnio.es (Jose Manuel rodriguez) Date: Mon, 10 Mar 2008 14:15:14 +0100 Subject: [MOBY-dev] looking for asynchronous service specification... In-Reply-To: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> Message-ID: <47D53462.8090401@cnio.es> Hello Martin, In the next root of CVS you can find the asynchronous proposal cvs.open-bio.org:/home/repository/moby/moby-live/Docs/asyncDocs/ Best Regards, Jos?. Martin Senger wrote: > ...and cannot find it on biomoby.org pages. Can anybody send here the latest > version of it please? I am ready to implement it into MoSeS but somehow > without the spec it is a bit difficult... :-) > > Thanks, > Martin > > -- Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From jmrodriguez at cnio.es Mon Mar 10 13:15:14 2008 From: jmrodriguez at cnio.es (Jose Manuel rodriguez) Date: Mon, 10 Mar 2008 14:15:14 +0100 Subject: [MOBY-dev] looking for asynchronous service specification... In-Reply-To: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> Message-ID: <47D53462.8090401@cnio.es> Hello Martin, In the next root of CVS you can find the asynchronous proposal cvs.open-bio.org:/home/repository/moby/moby-live/Docs/asyncDocs/ Best Regards, Jos?. Martin Senger wrote: > ...and cannot find it on biomoby.org pages. Can anybody send here the latest > version of it please? I am ready to implement it into MoSeS but somehow > without the spec it is a bit difficult... :-) > > Thanks, > Martin > > -- Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From groscurt at mpiz-koeln.mpg.de Mon Mar 10 13:38:10 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 10 Mar 2008 14:38:10 +0100 Subject: [MOBY-dev] General deployment question Message-ID: <47D539C2.1010608@mpiz-koeln.mpg.de> Hiho, another thing we wonder is - the ant task 'deploy' copies all libs and jars correctly to Tomcat.. why doesnt it copy also the implementing class ? I tried it with entering the impl class of the service in the field 'Pattern for implementation class names' (something which someone can please shortly explain what that is for ?) - but I always have to copy the the implementation class? is this just the way or do we forget something ? best and thanks andreas From martin.senger at gmail.com Mon Mar 10 20:47:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Mar 2008 04:47:21 +0800 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <47D5300B.4010301@mpiz-koeln.mpg.de> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> <47D5300B.4010301@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> > is it deliberately that while deploying via dashboard (started from > eclipse) on a remote machine - dashboard does not take the value of the > 'Tomcat home directory' the user specified, but the CATALINA_HOME > variable of the user ? Hard to say if it was deliberately or not (I do not remember it). But I spotted this last week, too (when I was testing it again because of changes done due to the jMoby mavenization). And I almost concluded that it should be almost in all cases the 'localhost' value. This means the value that is used on the remote machine to talk to that remote machine. But generally, you are right: if the help says that this field is used, it should be used. Do you wish me to fix it? [I mean to fix the behaviour, not just to fix the help page.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Mon Mar 10 20:49:56 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Mar 2008 04:49:56 +0800 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D539C2.1010608@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> > another thing we wonder is - the ant task 'deploy' copies all libs and > jars correctly to Tomcat.. why doesnt it copy also the implementing > class ? Because it does not know where the implementing class is (it just knows its name). You have to jar it first (probably together with adding other libraries needed) and then to tell dashboard where to take it from (using the user library/directory field). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Tue Mar 11 07:43:02 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 11 Mar 2008 08:43:02 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> Message-ID: <47D63806.3000107@mpiz-koeln.mpg.de> Hi Martin, this i dont get. The implementing class is compiled into other/samples. In dashboard you have to enter the full package name (at least in the 'Implemented by class' field) - so this should give all information ?! or what do i miss here ? and also - can you (or anyone) shortly explain what the 'Pattern for implementation class names' is ? i never use it and everything works, but still wondering what it is for. Best andreas Martin Senger wrote: >> another thing we wonder is - the ant task 'deploy' copies all libs and >> jars correctly to Tomcat.. why doesnt it copy also the implementing >> class ? >> > > > Because it does not know where the implementing class is (it just knows its > name). You have to jar it first (probably together with adding other > libraries needed) and then to tell dashboard where to take it from (using > the user library/directory field). > > Cheers, > Martin > > From groscurt at mpiz-koeln.mpg.de Tue Mar 11 07:46:27 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 11 Mar 2008 08:46:27 +0100 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> <47D5300B.4010301@mpiz-koeln.mpg.de> <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> Message-ID: <47D638D3.1050908@mpiz-koeln.mpg.de> Hi Martin, it would be great if you can fix it. E.g. on my local machine tomcat can be found under /local/groscurt/tomcat/. This value is also set as CATALINA_HOME in my .bashrc. But if I want to deploy on our test production server, on which the Tomcat can be found under /opt/tomcat, of course I enter /opt/tomcat in the 'Tomcat home directory". Deploying it will result with the current code that it tries to deploy to /local/groscurt/tomcat which failes of course on the test production server. so for me this is something to be fixed. Thanks Andreas Martin Senger wrote: > But generally, you are right: if the help says that this field is used, it > should be used. Do you wish me to fix it? [I mean to fix the behaviour, not > just to fix the help page.] > > Cheers, > Martin > > From martin.senger at gmail.com Tue Mar 11 11:35:38 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Mar 2008 07:35:38 -0400 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D63806.3000107@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> > this i dont get. The implementing class is compiled into other/samples. > In dashboard you have to enter the full package name (at least in the > 'Implemented by class' field) - so this should give all information ?! I have not known that you were referring to the 'samples'. The 'samples' are a bit special: they are on the CLASSPATH when Dashboard starts - which allows users to use them immediately in the Simple client panel. But they are still not considered when deploying to a Tomcat. If I do so (and it is easy to change it) then every user will have the samples deployed into his/her Tomcat. I considered it wrong. I prefer to let a user to decide - and if he/she wants to have the samples deployed, he/she can specify the samples directory in the "Directory with the user's jar files". So the quetsion now is: should I add the samples to the deployed jar files , as well? Regarding the package name: in that fields you specify a full package name - but it is not its location, so Dashboard cannot use it to find the place where the class physically sits. and also - can you (or anyone) shortly explain what the 'Pattern for > implementation class names' is ? i never use it and everything works, > but still wondering what it is for. It is for deploying to Axis (which is, so far, the only way we deploy jMoby services). The Axis engine needs to know the class name that represents each service (it uses it in its own configuration file server-config.wsdd where all service names are mapped to their class names). You need, therefore, specify for each service a class name in the table in the column "Implemented by class". You can do it manually - in which case you do not need to use anything in the "Pattern..." field. But the Pattern field helps you fill it the column at the beginning, before you start editing it. If you name your implementing classes, using some pattern that is the same for all your services, except the part where is the service name itself, usage of Pattern helps you that you need less editing (ideally no editing, at all). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Tue Mar 11 11:58:26 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 11 Mar 2008 12:58:26 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> Message-ID: <47D673E2.8040101@mpiz-koeln.mpg.de> Martin Senger wrote: >> this i dont get. The implementing class is compiled into other/samples. >> In dashboard you have to enter the full package name (at least in the >> 'Implemented by class' field) - so this should give all information ? >> I have not known that you were referring to the 'samples'. The 'samples' are >> a bit special: they are on the CLASSPATH when Dashboard starts - which >> allows users to use them immediately in the Simple client panel. But they >> are still not considered when deploying to a Tomcat. If I do so (and it is >> easy to change it) then every user will have the samples deployed into >> his/her Tomcat. I considered it wrong. I prefer to let a user to decide - >> and if he/she wants to have the samples deployed, he/she can specify the >> samples directory in the "Directory with the user's jar files". So the >> quetsion now is: should I add the samples to the deployed jar files , as >> well? >> not quite sure if we talk about the same ;-) > But they are still not considered when deploying to a Tomcat why ? the sample is my web service implementation class - of course i want to have to in Tomcat... > then every user will have the samples deployed into his/her Tomcat in my project with my samples folder there are only my developed web services, so my samples... what is the problem ? we should try to figure out whether we talk about the same or if someone (probably me *g) misses something ;-) >> Regarding the package name: in that fields you specify a full package name - >> but it is not its location, so Dashboard cannot use it to find the place >> where the class physically sits. >> >> assuming the default classloader the packname is identical to the location... and the implementing class is inside build/others/samples - so sorry still not getting the problem ;-) >> and also - can you (or anyone) shortly explain what the 'Pattern for >> >> implementation class names' is ? i never use it and everything works, >> but still wondering what it is for. >> > > It is for deploying to Axis (which is, so far, the only way we deploy jMoby > services). The Axis engine needs to know the class name that represents each > service (it uses it in its own configuration file server-config.wsdd where > all service names are mapped to their class names). You need, therefore, > specify for each service a class name in the table in the column > "Implemented by class". You can do it manually - in which case you do not > need to use anything in the "Pattern..." field. But the Pattern field helps > you fill it the column at the beginning, before you start editing it. If you > name your implementing classes, using some pattern that is the same for all > your services, except the part where is the service name itself, usage of > Pattern helps you that you need less editing (ideally no editing, at all). > ok - this means all my web services have the de.mpg.mpiz_koeln.*Impl so I can use that pattern instead to type in each servicename ? Is the pattern then de.mpg.mpiz_koeln.${SERVICE}Impl ? Thx much for your help Andreas From martin.senger at gmail.com Wed Mar 12 01:21:56 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Mar 2008 21:21:56 -0400 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D673E2.8040101@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> > not quite sure if we talk about the same ;-) Okay, tell me again what you want. > assuming the default classloader the packname is identical to the > location... No, not true. The package name is identical to the last part of the full path of the file where the class is written into. But it does not tell what is the full path. ok - this means all my web services have the de.mpg.mpiz_koeln.*Impl so > I can use that pattern instead to type in each servicename ? Yes. > Is the pattern then de.mpg.mpiz_koeln.${SERVICE}Impl ? Probably. It depends what you meant by the star in "de.mpg.mpiz_koeln.*Impl". This is how the help page explains it: "the ${SERVICE} token is replaced by a real service name, and ${Service} token by a real service name with the first letter changed to upper-case". Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Mar 12 12:55:05 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 13:55:05 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> Message-ID: <47D7D2A9.7080207@mpiz-koeln.mpg.de> Martin Senger wrote: >> assuming the default classloader the packname is identical to the >> location... >> > > No, not true. The package name is identical to the last part of the full > path of the file where the class is written into. But it does not tell what > is the full path. > How do you generate the skeletons then ? from my point of view thats the same situation. Skeletons sources are put into generated/skeletons and the compilation are put into build/other/skeletons. You know this paths and put them into a jar. For the samples it is identical... sources are found in src/samples and the compilation are in build/others/samples. I dont get the difference. and samples are (for me and others) the web services.... How do you get the compilations from build/other/skeletons - and why is that no problem, but build/other/samples is one ? Again - my implementation of the Web Service is inside src/samples and the compilation is in build/others/samples. My Service is de.mpg.mpiz_koeln.SERVICEImpl, so ergo you find the class in build/others/samples/de/mpg/mpiz_koeln/SERVICEImpl. I still dont understand why this is not accessible, when the skeletons or datatypes are.... What I love to see is that the implementation classes I enter in dashboard when I give the pattern or enter it for each service are copied into CATALINA_HOME/webapps/axis/WEB-INF/classes, just as the generated jars are copied into CATALINA_HOME/webapps/axis/WEB-INF/lib. >> Is the pattern then de.mpg.mpiz_koeln.${SERVICE}Impl ? >> > > > Probably. It depends what you meant by the star in "de.mpg.mpiz_koeln.*Impl". > This is how the help page explains it: > "the ${SERVICE} token is replaced by a real service name, and ${Service} > token by a real service name with the first letter changed to upper-case". > cool - the * was the real service name - thx. Best andreas Andreas From martin.senger at gmail.com Wed Mar 12 13:09:31 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 09:09:31 -0400 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D7D2A9.7080207@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> > How do you generate the skeletons then ? from my point of view thats the > same situation. No, it isn't. When I generate something I can choose where to put it (and I can remember that knowledge until I deploy to Tomcat). When I want something to take as an input (that I have not created) somebody must tell me where it is. > For the samples it is identical... sources are > found in src/samples and the compilation are in build/others/samples. I > dont get the difference. > I can find the samples, I admit it. But I am not sure if it is a good idea to deploy samples every time anybody does the deployment. I already asked if it was what you were suggesting. Were you? Is it really wise to deploy things that are not needed for those who do not provide sample services, at all? > How do you get the compilations from build/other/skeletons - and why is > that no problem, but build/other/samples is one ? I think it was answered above. Was it? Again - my implementation of the Web Service is inside src/samples and > the compilation is in build/others/samples. But that's just your case, not everybody does it like that. I may have my implementation in a totally different Eclipse project - and I have to tell Dashboard "Hey, here are my jar files". What I love to see is that the implementation classes I enter in > dashboard when I give the pattern or enter it for each service are > copied into CATALINA_HOME/webapps/axis/WEB-INF/classes That's generally impossible, unless we have some conventions (e.g. take samples by default, as you are suggesting). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Mar 12 13:28:51 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 14:28:51 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> Message-ID: <47D7DA93.2030809@mpiz-koeln.mpg.de> Finally i think we get along with what we are talking about ;-) I do understand your points... *cheer* Martin Senger wrote: >> I can find the samples, I admit it. But I am not sure if it is a good idea >> to deploy samples every time anybody does the deployment. I already asked if >> it was what you were suggesting. Were you? Is it really wise to deploy >> things that are not needed for those who do not provide sample services, at >> all >> Yes thats what I asked for... see answer below > Again - my implementation of the Web Service is inside src/samples and >> the compilation is in build/others/samples. >> > > But that's just your case, not everybody does it like that. I may have my > implementation in a totally different Eclipse project - and I have to tell > Dashboard "Hey, here are my jar files". > > Now I do get the essentiell point. But for my whole BioMoby life I was told... my Web Services HAVE to be in src/samples and will be compiled to build/others/samples. and honestly we tell that every person form all workshops now for years (so that was not only my view of this). Now that I know that the samples folder is not automatically the implementation folder (which makes sense, but why was I told so ;-) ) I understand your objection and therefore you are right. With assuming the classes in samples are not automatically the web services it is not wise to deploy them its just horrible - people doing this now for quite a while.... Best and thx andreas > What I love to see is that the implementation classes I enter in > >> dashboard when I give the pattern or enter it for each service are >> copied into CATALINA_HOME/webapps/axis/WEB-INF/classes >> > > > That's generally impossible, unless we have some conventions (e.g. take > samples by default, as you are suggesting). > > Cheers, > Martin > > From groscurt at mpiz-koeln.mpg.de Wed Mar 12 13:39:30 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 14:39:30 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> Message-ID: <47D7DD12.1010509@mpiz-koeln.mpg.de> but some additions. so as far as i know and as i said, lot people develop there services with the class inside samples. You said you can access the samples, so why not copying not all samples, but the class which was entered in dashboard ? So no one has any unwanted samples deployed - just the one(s) from his/her service ? if this is possible - i like to have it .... objections? andreas From martin.senger at gmail.com Wed Mar 12 13:55:00 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 09:55:00 -0400 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <47D638D3.1050908@mpiz-koeln.mpg.de> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> <47D5300B.4010301@mpiz-koeln.mpg.de> <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> <47D638D3.1050908@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803120655j1de1fe10h2f4b99f4bd752c37@mail.gmail.com> Hi, I was looking at the problem how to assign some properties for the remote deployment from Dashboard. I could not replicate the problem but I found a missing piece in the help. Here is how it works (but please let me know if you experienced different behaviour): 1) The Dashboard takes the information as entered in the fields "Tomcat home directory", AAxis relative path in tomcat", "Hostname", "port" and "path of axis admin servlet" and tries to use them in the newly created build.xmlfile that will be used on the remote machine. So far, so good. 2) But doing the above, Dashboard may be also influenced by properties defined in your build.properties file (because Dashboard uses Ant to do the job). The properties in question are: cross.tomcat.home cross.tomcat.host cross.tomcat.host If you have them defined in your build.properties, they will take, unfortunately, precedence over the field values entered in Dashboard. Andreas, could you please confirm that it is your case? 3) The same may happen, if you have set the CATALINA_HOME environment variable. Again, this may (I say 'may' because I have not tried this alternative now) take precedence over the field values in Dashboard. At the moment, I do not know how to fix it (easily), or if to fix it at all. It is, of course, possible, but could we live with just mentioning these consequences in the help? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Mar 12 14:03:25 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 10:03:25 -0400 Subject: [MOBY-dev] General deployment question In-Reply-To: <47D7DD12.1010509@mpiz-koeln.mpg.de> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> <47D7DD12.1010509@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803120703u206ab042t7a3441acde9fac40@mail.gmail.com> > You said you can access the samples, so why not copying not all samples, > but the class which was entered in dashboard ? When I was writing my answer, this alternative came to my mind - and I was just telling myself "don't worry, nobody will think about it" :-) Seriously, this is not a right solution because this would bring just one class to the Tomcat - but the implementation may require more classes (the ones the main class depends on). I would say, we either let it as it is now, or we add all samples to deployment. Because you are explaining now how important the samples directory had and have been, perhaps I should take it as a hint and not to be too concerned about having these classes deployed, after all. Which means I am (being influenced by you) changing my mind now - so should I go ahead and add samples there? [Perhaps I will do it using some property defining a conditional inclusion, with its default value as true?] Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Mar 12 14:25:04 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 15:25:04 +0100 Subject: [MOBY-dev] Deploying on a remote machine in dashboard In-Reply-To: <4d93f07c0803120655j1de1fe10h2f4b99f4bd752c37@mail.gmail.com> References: <4d93f07c0803080221o1dc64640g931aa0cad79c091b@mail.gmail.com> <47D5300B.4010301@mpiz-koeln.mpg.de> <4d93f07c0803101347v500f747al66444678581481a6@mail.gmail.com> <47D638D3.1050908@mpiz-koeln.mpg.de> <4d93f07c0803120655j1de1fe10h2f4b99f4bd752c37@mail.gmail.com> Message-ID: <47D7E7C0.2090000@mpiz-koeln.mpg.de> Martin Senger wrote: > If you have them defined in your build.properties, they will take, > unfortunately, precedence over the field values entered in Dashboard. > Andreas, could you please confirm that it is your case? > > in our case it was not point 2) we never set any variables in the build.properties, but point 3) is our case. If the CATALINA_HOME environment variable is set, this one is used. > At the moment, I do not know how to fix it (easily), or if to fix it at all. > It is, of course, possible, but could we live with just mentioning these > consequences in the help? > Thanks for investigating - if this is really a hardy, then mention it in the help - preferable would be to have solved this, but i also see this as not the most urgent issue. At least it has to be written somewhere that people can read it up ;-) Thx andreas From groscurt at mpiz-koeln.mpg.de Wed Mar 12 14:31:34 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 15:31:34 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <4d93f07c0803120703u206ab042t7a3441acde9fac40@mail.gmail.com> References: <47D539C2.1010608@mpiz-koeln.mpg.de> <4d93f07c0803101349m2e87a4b3ge5516ca35992bd49@mail.gmail.com> <47D63806.3000107@mpiz-koeln.mpg.de> <4d93f07c0803110435l75f98b5boe4f7c21c4f26c479@mail.gmail.com> <47D673E2.8040101@mpiz-koeln.mpg.de> <4d93f07c0803111821q6fd83253y4b0ff41821d57958@mail.gmail.com> <47D7D2A9.7080207@mpiz-koeln.mpg.de> <4d93f07c0803120609h5035ffccnf481c171dc4dd045@mail.gmail.com> <47D7DD12.1010509@mpiz-koeln.mpg.de> <4d93f07c0803120703u206ab042t7a3441acde9fac40@mail.gmail.com> Message-ID: <47D7E946.20707@mpiz-koeln.mpg.de> Martin Senger wrote: >> You said you can access the samples, so why not copying not all samples, >> but the class which was entered in dashboard ? >> > > > When I was writing my answer, this alternative came to my mind - and I was > just telling myself "don't worry, nobody will think about it" :-) > hehe ;-) > Seriously, this is not a right solution because this would bring just one > class to the Tomcat - but the implementation may require more classes (the > ones the main class depends on). I would say, we either let it as it is now, > or we add all samples to deployment. Because you are explaining now how > important the samples directory had and have been, perhaps I should take it > as a hint and not to be too concerned about having these classes deployed, > after all. Which means I am (being influenced by you) changing my mind now - > so should I go ahead and add samples there? [Perhaps I will do it using some > property defining a conditional inclusion, with its default value as true?] > maybe we wait some hours if the guys from Canada want something to say :) I'm still convinced that you should deploy all classes in samples (because yes, you are right, web service might a) have several classes and b) these classes might be in different packages), with excluding org.biomoby.tutorial.*. The idea of a property for that sounds good to me, so the people can decide which way they want to go. thx for that discussion Martin :) Andreas From haase_dirk at web.de Wed Mar 12 14:11:00 2008 From: haase_dirk at web.de (Dirk Haase) Date: Wed, 12 Mar 2008 15:11:00 +0100 Subject: [MOBY-dev] General deployment question Message-ID: <982046343@web.de> > > But that's just your case, not everybody does it like that. I may have my > > implementation in a totally different Eclipse project - and I have to tell > > Dashboard "Hey, here are my jar files". > > > > > Now I do get the essentiell point. But for my whole BioMoby life I was > told... my Web Services HAVE to be in src/samples and will be compiled > to build/others/samples. and honestly we tell that every person form all > workshops now for years (so that was not only my view of this). Oh, who told you so? Just by coincidence, I know of a jMoby tutorial which actually recommends to use a separate Eclipse project ;-) See here: http://tinyurl.com/2yl8l2 (2nd sentence) Cheers, dirk From groscurt at mpiz-koeln.mpg.de Wed Mar 12 14:55:53 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 12 Mar 2008 15:55:53 +0100 Subject: [MOBY-dev] General deployment question In-Reply-To: <982046343@web.de> References: <982046343@web.de> Message-ID: <47D7EEF9.6010707@mpiz-koeln.mpg.de> Dirk Haase wrote: > Oh, who told you so? Just by coincidence, I know of a jMoby tutorial which > actually recommends to use a separate Eclipse project ;-) > > See here: http://tinyurl.com/2yl8l2 (2nd sentence) > > Cheers, > dirk cant remember that, but at least at the last workshop we told people so and neither Mark nor Eddie objected (probably they didnt realize that)... If this is really not intended that people do so - I would be fine to stay with the current system. But I dont see a problem for those cases that people do write their services in samples to enable that these classes are automatically deployed and that would be possible by given such property (which might be set to false by default instead of true). And if this is really the way it should be used... I need to update my tutorial ;-) thx andreas From martin.senger at gmail.com Wed Mar 12 18:34:30 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 14:34:30 -0400 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <200802291151.22060.groscurt@mpiz-koeln.mpg.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803121134v4ceafcan5f0d273abcaae53e@mail.gmail.com> Andreas, starting dashboard from console gives me > > Warning: Reference moses.build.classpath has not been set at runtime, but > was > found during build file parsing, attempting to resolve. Future versions of > Ant may support referencing ids defined in non-executed targets. > Can this issue be considered solved/closed, or you are still getting it? Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Mar 12 18:46:09 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 12 Mar 2008 14:46:09 -0400 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <1205177598.16508.14.camel@linux-iug0.site> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> Message-ID: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Hi jMobyers, I have committed a change in jMoby dependency file that excludes xerces from all included 3rd-party libraries (especially from jena, commons-dbcp and jaxen). I have tested it a bit but please make your own tests (those of you whose parts rely on these components) and let us know if I broke something. I hope it should be okay - actually quite opposite: with having the old xerces parser there, the newer XML parser in Java would not be used and some features would be missing. Thanks to Hao Chen for making this change. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Mar 13 08:25:53 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Mar 2008 09:25:53 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <4d93f07c0803121134v4ceafcan5f0d273abcaae53e@mail.gmail.com> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <200802291151.22060.groscurt@mpiz-koeln.mpg.de> <4d93f07c0803121134v4ceafcan5f0d273abcaae53e@mail.gmail.com> Message-ID: <47D8E511.207@mpiz-koeln.mpg.de> Havent had or havent seen that problem anymore... so consider it as solved/closed :-) best andreas Martin Senger wrote: > Andreas, > > starting dashboard from console gives me > >> Warning: Reference moses.build.classpath has not been set at runtime, but >> was >> found during build file parsing, attempting to resolve. Future versions of >> Ant may support referencing ids defined in non-executed targets. >> >> > > Can this issue be considered solved/closed, or you are still getting it? > > Martin > > From groscurt at mpiz-koeln.mpg.de Thu Mar 13 10:06:48 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Mar 2008 11:06:48 +0100 Subject: [MOBY-dev] Web Services in a secure World In-Reply-To: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Message-ID: <47D8FCB8.7060607@mpiz-koeln.mpg.de> Hi everyone, I like to start a discussion or ask for your knowledge about the possibilty of using secure BioMoby Web Service. The scenario is to register Web Services which work on https and only people with a specific certificate are allowed to call this Web Service. Another scenario is that people with different certificates can call the same Web Service, but based on their certificate the Web Service does behave differntly (like given out different data, working on different databases or so). Unfortunately I'm not that familiar with the whole https and java - http communication, so I like to ask you to give me some input about my ideas. Establishing a https connection is not difficult, I'm currently thinking about how to enable that different certificates are treated differently. One possibility is to work on the level of the apache and do have different authenifications for the certificates. Based on this authentification people are directed to the corresponding service. But this solution sound aweful, because you have to offer for each certificate a service and this services have to be physically be different so that not person A with certificate A can call service B with some detours. So for me this is a really messy solution. Is this correct or do I have an error in my scenario. The other idea is that based on the certificate the Web Service checks who has actually called. I tried with the current moby API to retrieve any information about the certificate which was used for the calling process, but I couldnt find any method which gives me such information. So ist here any method which is or could return me any information. Another idea was, because the certificate is actually non binary one could send it as secondary. Is this reasonable to do so and is it sufficient to do a simple equals in the web service or is any more complex operation based on the certificate required. Thanks for reading and thanks for any input, comments and suggestions Andreas PS: just to verify - this is nothing which came up just in my mind - it is a request from several EU-SOL partners ;-) From groscurt at mpiz-koeln.mpg.de Thu Mar 13 11:38:51 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Mar 2008 12:38:51 +0100 Subject: [MOBY-dev] Web Services in a secure World In-Reply-To: <47D8FCB8.7060607@mpiz-koeln.mpg.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> Message-ID: <47D9124B.2050304@mpiz-koeln.mpg.de> Hi, funny to have written an email and then later while searching the web and discussing stuff with Mark Fiers here - we think to have a nice solution based on the description here http://www.impetus.us/~rjmooney/projects/misc/clientcertauth.html. with different services depending on which certificate was used. So - in our view this is solved, but feel free to add something :-) best andreas Andreas Groscurth wrote: > Hi everyone, > > I like to start a discussion or ask for your knowledge about the > possibilty of using secure BioMoby Web Service. > > The scenario is to register Web Services which work on https and only > people with a specific certificate are allowed to call this Web Service. > > Another scenario is that people with different certificates can call > the same Web Service, but based on their certificate the Web Service > does behave differntly (like given out different data, working on > different databases or so). > > Unfortunately I'm not that familiar with the whole https and java - > http communication, so I like to ask you to give me some input about > my ideas. > > Establishing a https connection is not difficult, I'm currently > thinking about how to enable that different certificates are treated > differently. > > One possibility is to work on the level of the apache and do have > different authenifications for the certificates. Based on this > authentification people are directed to the corresponding service. But > this solution sound aweful, because you have to offer for each > certificate a service and this services have to be physically be > different so that not person A with certificate A can call service B > with some detours. So for me this is a really messy solution. > > Is this correct or do I have an error in my scenario. > > The other idea is that based on the certificate the Web Service checks > who has actually called. I tried with the current moby API to retrieve > any information about the certificate which was used for the calling > process, but I couldnt find any method which gives me such information. > > So ist here any method which is or could return me any information. > > Another idea was, because the certificate is actually non binary one > could send it as secondary. Is this reasonable to do so and is it > sufficient to do a simple equals in the web service or is any more > complex operation based on the certificate required. > > Thanks for reading and thanks for any input, comments and suggestions > Andreas > > PS: just to verify - this is nothing which came up just in my mind - > it is a request from several EU-SOL partners ;-) > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From sneumann at ipb-halle.de Thu Mar 13 13:25:36 2008 From: sneumann at ipb-halle.de (sneumann) Date: Thu, 13 Mar 2008 14:25:36 +0100 Subject: [MOBY-dev] Web Services in a secure World In-Reply-To: <47D9124B.2050304@mpiz-koeln.mpg.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> <47D9124B.2050304@mpiz-koeln.mpg.de> Message-ID: <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> On Do, 2008-03-13 at 12:38 +0100, Andreas Groscurth wrote: > with different services depending on which certificate was used. but that was not part of the simple tutorial, was it ?! > So - in our view this is solved, but feel free to add something :-) So what is the use case solved here ? You have a service -- say a database/repository -- which includes data produced by -- say three -- different consortia, and should also serve data (for which the protection phase has expired) to the public without any certificate. How do pass the cert information down to the retrieval layer ? Or do you use apache to demultiplex / route the same query to a given (virtual) service to the appropriate instance based on the certificate ? This probably doesn't scale very well. What happens if some remote machine/user belongs to two consortia (or in fact the administrator needs access to all consortium data), then he needs to choose the appropriate cert ? Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 191 bytes Desc: This is a digitally signed message part URL: From martin.senger at gmail.com Thu Mar 13 16:59:58 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 13 Mar 2008 12:59:58 -0400 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user Message-ID: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> Dear all, I have uploaded jMoby (version 1.0.0) to our Maven repository (you can see it at and use it from http://biomoby.org/m2repo/org/biomoby/jmoby/). The next versions will follow as new features are added and bugs fixed. I have a request for the Eclipse users: I have not found time (as I planned) to make sure that jMoby works smoothly both within and outside the Eclipse (I know for sure that it works fine outside the Eclipse). What is needed now is to provide a file .classpath.template that can serve as a template for a file .classpath (this file should not have any absolute path - which may happen when created on some platforms), and that reflects the same environment (eg. building classes into 'build' directory and not the 'bin' directory) as defined in the Ant's build.xml file. This file (.classpath.template) should be committed to jMoby. Also the documentation on using jMoby from Eclipse should be updated to reflect the existence and usage of this new file. [Perhaps, we can have also a template .project.template - but that is less important.] Is there anybody to do it please? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Mar 13 17:44:03 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Mar 2008 18:44:03 +0100 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> Message-ID: <47D967E3.3050604@mpiz-koeln.mpg.de> Hi, I can do that tomorrow - got such .classpath file already as download from our tutorial page. best andreas PS: .project is not necessary to provide. PPS: What i also will provide then in the docs is how to get the maven plugin for eclipse if wanted Martin Senger wrote: > Dear all, > > I have uploaded jMoby (version 1.0.0) to our Maven repository (you can see > it at and use it from http://biomoby.org/m2repo/org/biomoby/jmoby/). The > next versions will follow as new features are added and bugs fixed. > > I have a request for the Eclipse users: I have not found time (as I planned) > to make sure that jMoby works smoothly both within and outside the Eclipse > (I know for sure that it works fine outside the Eclipse). What is needed now > is to provide a file .classpath.template that can serve as a template for a > file .classpath (this file should not have any absolute path - which may > happen when created on some platforms), and that reflects the same > environment (eg. building classes into 'build' directory and not the 'bin' > directory) as defined in the Ant's build.xml file. This file > (.classpath.template) should be committed to jMoby. Also the documentation > on using jMoby from Eclipse should be updated to reflect the existence and > usage of this new file. [Perhaps, we can have also a template > .project.template - but that is less important.] > > Is there anybody to do it please? > > Cheers, > Martin > > From gordonp at ucalgary.ca Thu Mar 13 22:54:12 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 13 Mar 2008 16:54:12 -0600 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Message-ID: <47D9B094.2020001@ucalgary.ca> Never mind, I see that the ant task names have changed... Martin Senger wrote: > Hi jMobyers, > > I have committed a change in jMoby dependency file that excludes xerces from > all included 3rd-party libraries (especially from jena, commons-dbcp and > jaxen). I have tested it a bit but please make your own tests (those of you > whose parts rely on these components) and let us know if I broke something. > I hope it should be okay - actually quite opposite: with having the old > xerces parser there, the newer XML parser in Java would not be used and some > features would be missing. > > Thanks to Hao Chen for making this change. > > Cheers, > Martin > > From gordonp at ucalgary.ca Thu Mar 13 22:46:43 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 13 Mar 2008 16:46:43 -0600 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Message-ID: <47D9AED3.5060500@ucalgary.ca> Hi Martin, This may be related: when I do an ant celan, then try to run some of my JUnit tests... moses-clean: [delete] Deleting directory /export/home/gordonp/projects/moby-live/Java/build/others/datatypes [delete] Deleting directory /export/home/gordonp/projects/moby-live/Java/build/others/skeletons clean-services: moses-init: [mkdir] Created dir: /export/home/gordonp/projects/moby-live/Java/build/others/datatypes [mkdir] Created dir: /export/home/gordonp/projects/moby-live/Java/build/others/skeletons generate-datatypes: [Data Types] Generating data types into '/export/home/gordonp/projects/moby-live/Java/generated/datatypes'... [Data Types] Reading data type definitions... [Data Types] ===ERROR=== [Data Types] org/apache/xerces/util/XMLChar [Data Types] =========== Which brings up another issue. Why is the build file making the MoSeS classes when my unit tests have nothing to do with MoSeS? Have some new superfluous dependencies been added? Cheers, Paul Martin Senger wrote: > Hi jMobyers, > > I have committed a change in jMoby dependency file that excludes xerces from > all included 3rd-party libraries (especially from jena, commons-dbcp and > jaxen). I have tested it a bit but please make your own tests (those of you > whose parts rely on these components) and let us know if I broke something. > I hope it should be okay - actually quite opposite: with having the old > xerces parser there, the newer XML parser in Java would not be used and some > features would be missing. > > Thanks to Hao Chen for making this change. > > Cheers, > Martin > > From martin.senger at gmail.com Fri Mar 14 01:26:37 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 13 Mar 2008 20:26:37 -0500 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47D9AED3.5060500@ucalgary.ca> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D9AED3.5060500@ucalgary.ca> Message-ID: <4d93f07c0803131826l1da8b372hbf8f0bcf5d025114@mail.gmail.com> > Which brings up another issue. Why is the build file making the MoSeS > classes when my unit tests have nothing to do with MoSeS? Your junit test not, but mine yes. If you run 'ant test-junit' then *all* junit tests are run, including those that are testing MoSeS. The 'test-junit' task is an umbrella covering two separate groups of junit tests: tasks 'do-junit' and 'do-junit-2'. The former are your tests, the latter mine. So if you prefer to run only your tests, call 'ant do-junit'. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Fri Mar 14 09:30:54 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 10:30:54 +0100 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> Message-ID: <47DA45CE.2000708@mpiz-koeln.mpg.de> Hi, with a fresh checkout I get during install ant task dashboard-config: [jar] Building jar: C:\workspace\Moby_cvs\build\lib\dashboard-config.jar [Local cache] [Local cache] The jMoby is now creating a local cache. Depending [Local cache] on the network speed, it may take several minutes [Local cache] (usually it should be done within about a minute). [Local cache] [Local cache] [You can check the progress in the jMoby.log file.] [Local cache] [Local cache] Retrieving namespaces... 0:00:38.422 [Local cache] ===ERROR=== [Local cache] org/apache/xerces/util/XMLChar [Local cache] =========== Retrieving data types... BUILD FAILED C:\workspace\Moby_cvs\xmls\install.xml:99: Java returned: 1 in eclipse and on console, windows, java 1.6 best andreas Martin Senger wrote: > Hi jMobyers, > > I have committed a change in jMoby dependency file that excludes xerces from > all included 3rd-party libraries (especially from jena, commons-dbcp and > jaxen). I have tested it a bit but please make your own tests (those of you > whose parts rely on these components) and let us know if I broke something. > I hope it should be okay - actu > ally quite opposite: with having the old > xerces parser there, the newer XML parser in Java would not be used and some > features would be missing. > > Thanks to Hao Chen for making this change. > > Cheers, > Martin > > From groscurt at mpiz-koeln.mpg.de Fri Mar 14 09:50:15 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 10:50:15 +0100 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47DA45CE.2000708@mpiz-koeln.mpg.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> Message-ID: <47DA4A57.4060006@mpiz-koeln.mpg.de> Running install on console under linux i get dashboard-config: [jar] Building jar: /home/pcb/groscurt/moby-live/Java/build/lib/dashboard-config.jar [Local cache] [Local cache] The jMoby is now creating a local cache. Depending [Local cache] on the network speed, it may take several minutes [Local cache] (usually it should be done within about a minute). [Local cache] [Local cache] [You can check the progress in the jMoby.log file.] [Local cache] [Local cache] ===ERROR=== [Local cache] Provider org.apache.xerces.jaxp.DocumentBuilderFactoryImpl not found [Local cache] =========== Retrieving namespaces... BUILD FAILED /home/pcb/groscurt/moby-live/Java/xmls/install.xml:99: Java returned: 1 best andreas Andreas Groscurth wrote: > Hi, > > with a fresh checkout I get during install ant task > > dashboard-config: > [jar] Building jar: > C:\workspace\Moby_cvs\build\lib\dashboard-config.jar > [Local cache] > [Local cache] The jMoby is now creating a local cache. Depending > [Local cache] on the network speed, it may take several minutes > [Local cache] (usually it should be done within about a minute). > [Local cache] > [Local cache] [You can check the progress in the jMoby.log file.] > [Local cache] [Local cache] Retrieving namespaces... 0:00:38.422 > [Local cache] ===ERROR=== > [Local cache] org/apache/xerces/util/XMLChar > [Local cache] =========== > Retrieving data types... > BUILD FAILED > C:\workspace\Moby_cvs\xmls\install.xml:99: Java returned: 1 > > in eclipse and on console, windows, java 1.6 > > best > andreas > > Martin Senger wrote: >> Hi jMobyers, >> >> I have committed a change in jMoby dependency file that excludes >> xerces from >> all included 3rd-party libraries (especially from jena, commons-dbcp and >> jaxen). I have tested it a bit but please make your own tests (those >> of you >> whose parts rely on these components) and let us know if I broke >> something. >> I hope it should be okay - actu > >> ally quite opposite: with having the old >> xerces parser there, the newer XML parser in Java would not be used >> and some >> features would be missing. >> >> Thanks to Hao Chen for making this change. >> >> Cheers, >> Martin >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Fri Mar 14 10:00:32 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 11:00:32 +0100 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <47D967E3.3050604@mpiz-koeln.mpg.de> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> Message-ID: <47DA4CC0.3080605@mpiz-koeln.mpg.de> Hi, before I check it in - I added .classpath.template in the basedir of the project and edit the initeclipse task so that the .classpath.template file is copied into .classpath file. The only thing which could me problematic is that I have to use overwrite="true" so that i will overwrite the existing one which eclipse automatically generates. If someone later calls this task again and might have changed the .classpath it will again be overwritten. Other solution is to tell the user to first delete the .classpath generated by Eclipse. Suggestions? Andreas PS: Will update also the docs today Andreas Groscurth wrote: > Hi, > > I can do that tomorrow - got such .classpath file already as download > from our tutorial page. > > best > andreas > > PS: .project is not necessary to provide. > > PPS: What i also will provide then in the docs is how to get the maven > plugin for eclipse if wanted > > Martin Senger wrote: >> Dear all, >> >> I have uploaded jMoby (version 1.0.0) to our Maven repository (you >> can see >> it at and use it from http://biomoby.org/m2repo/org/biomoby/jmoby/). The >> next versions will follow as new features are added and bugs fixed. >> >> I have a request for the Eclipse users: I have not found time (as I >> planned) >> to make sure that jMoby works smoothly both within and outside the >> Eclipse >> (I know for sure that it works fine outside the Eclipse). What is >> needed now >> is to provide a file .classpath.template that can serve as a template >> for a >> file .classpath (this file should not have any absolute path - which may >> happen when created on some platforms), and that reflects the same >> environment (eg. building classes into 'build' directory and not the >> 'bin' >> directory) as defined in the Ant's build.xml file. This file >> (.classpath.template) should be committed to jMoby. Also the >> documentation >> on using jMoby from Eclipse should be updated to reflect the >> existence and >> usage of this new file. [Perhaps, we can have also a template >> .project.template - but that is less important.] >> >> Is there anybody to do it please? >> >> Cheers, >> Martin >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Fri Mar 14 10:39:04 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 11:39:04 +0100 Subject: [MOBY-dev] Web Services in a secure World In-Reply-To: <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> <47D9124B.2050304@mpiz-koeln.mpg.de> <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <47DA55C8.4040208@mpiz-koeln.mpg.de> sneumann wrote: > On Do, 2008-03-13 at 12:38 +0100, Andreas Groscurth wrote: > >> with different services depending on which certificate was used. >> > but that was not part of the simple tutorial, was it ?! > no the simple tutorial, which i took down today, does not cover that. As soon as we tested at here in EU-SOL I will put up the turial up again. Otherwise its dangerous that it will be changed over the next weeks over and over again >> So - in our view this is solved, but feel free to add something :-) >> > So what is the use case solved here ? > Use case is that you offer Web services which shall be only called by elected persons identified by a certificate. We assume that the servlet container is not accessible for public. The solution we think of is that the clients retrieving a certificate signed by an CA and have to use this files in the clients to call BioMoby Web Services. On the server side the apache will take care of the authentification and depending on the certificates redirect to the corresponding servlet container E.g. Certificate-A-user -> axis_a/services/.... Certificate-B-user -> axis_b/services/... of course it has to be ensured that these redirects are not accessible without any authentification And although this might have the problem of implementing several services more than once - at least in Java you can easily use avoid this by using facade patterns. > You have a service -- say a database/repository -- which includes > data produced by -- say three -- different consortia, and should also > serve data (for which the protection phase has expired) to the public > without any certificate. How do pass the cert information down to the > retrieval layer ? > so as describes - apache will do that > Or do you use apache to demultiplex / route the same query > to a given (virtual) service to the appropriate instance > based on the certificate ? This probably doesn't scale very well. > didnt get that - if this is the way as described above - why yo think it doesnt scala very well ? > What happens if some remote machine/user belongs to two consortia > (or in fact the administrator needs access to all consortium data), > then he needs to choose the appropriate cert ? > This is definitely a point we have to think of. This has to be differences. One - what happens if a person with two certificates calls a service, which one is used ? a solution (at least in java) could be that the client has several keystore in which the certificates are stored and he selectes the one he wants to use currently. The other one is if one has access to all data, although from different consortium. In this case I would use a different certificate. Thanks for your input - I'm glad if you have anything to add here. best andreas > Yours, > Steffen > > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From martin.senger at gmail.com Fri Mar 14 11:37:53 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 07:37:53 -0400 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <47DA4CC0.3080605@mpiz-koeln.mpg.de> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> > before I check it in - I added .classpath.template in the basedir of the > project and edit the initeclipse task so that the .classpath.template > file is copied into .classpath file. No, don't do it please. Just leave the copying to the users. The same as they do with other templates (except the .cvsignore.template - but hat is less important template). The users will have quite often a different .classpath because they may be testing new things in Eclipse and they even do not know that the .classpath is changing. No, I definitely would keep the initeclipse task untouched. But please go ahead and commit the .classpath.template. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Mar 14 11:41:58 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 07:41:58 -0400 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47DA45CE.2000708@mpiz-koeln.mpg.de> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> > [Local cache] ===ERROR=== > [Local cache] org/apache/xerces/util/XMLChar > [Local cache] =========== Good that you found this. I was worried that something like this might happen. I will investigate and fix it - but it may be only the next week (I am going to travel later today back to Philippines from the US and I may not have time to fix it before it). Paul, do you know why is this happening? You know much more about XML parsers libraries than I do. I thought that Java 1.5 has already an XML parser - so why does it complain about xerces? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From mark.fiers at wur.nl Fri Mar 14 11:29:23 2008 From: mark.fiers at wur.nl (Fiers, Mark) Date: Fri, 14 Mar 2008 12:29:23 +0100 Subject: [MOBY-dev] error in java moby request References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> <47D9124B.2050304@mpiz-koeln.mpg.de> <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> <47DA55C8.4040208@mpiz-koeln.mpg.de> Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> Hi, I'm trying to write a moby client program in java, using the testing repository: Central worker = new CentralImpl( "http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl", "http://bioinfo.icapture.ubc.ca/MOBY/Central"); and subsequently call a service I'm trying to develop, but that ends in an error. Appearantly the code is looking at the default registry, as the script prints: Fetching data type ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects ... done What am I doing wrong? Or is this a bug? regards Mark Fiers -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 2995 bytes Desc: not available URL: From martin.senger at gmail.com Fri Mar 14 11:50:57 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 07:50:57 -0400 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> Message-ID: <4d93f07c0803140450i7d725805r1dd2f57fc7c744d1@mail.gmail.com> Eddie, the problem reported by Andreas is caused in the Jena package (Jena needs the XMLChar library). Could you look why this class is not part of the Java 1.5? Can it be found elsewhere than in xerces? [The xerces itself caused problems from other reasons - see previous emails about it if you wish, or I can re-send them.] The full stack (with a command-line how you can replicate it) is here: senger at sherekhan:~/jMoby$ build/run/run-cache-client -fill -cachedir anotherMyCache/ -v -stack Retrieving namespaces... 0:00:02.384 Retrieving data types... ===ERROR=== java.lang.NoClassDefFoundError: org/apache/xerces/util/XMLChar at com.hp.hpl.jena.rdf.model.impl.Util.notNameChar(Util.java:87) at com.hp.hpl.jena.rdf.model.impl.Util.splitNamespace(Util.java:67) at com.hp.hpl.jena.graph.Node_URI.getLocalName(Node_URI.java:55) at com.hp.hpl.jena.rdf.model.impl.ResourceImpl.getLocalName( ResourceImpl.java:126) at com.hp.hpl.jena.rdf.model.impl.PropertyImpl.checkLocalName( PropertyImpl.java:78) at com.hp.hpl.jena.rdf.model.impl.PropertyImpl.( PropertyImpl.java:86) at com.hp.hpl.jena.rdf.model.ResourceFactory$Impl.createProperty( ResourceFactory.java:244) at com.hp.hpl.jena.rdf.model.ResourceFactory.createProperty( ResourceFactory.java:120) at com.hp.hpl.jena.vocabulary.RDF.property(RDF.java:32) at com.hp.hpl.jena.vocabulary.RDF.(RDF.java:45) at com.hp.hpl.jena.ontology.impl.OntResourceImpl.( OntResourceImpl.java:63) at com.hp.hpl.jena.enhanced.BuiltinPersonalities.( BuiltinPersonalities.java:28) at com.hp.hpl.jena.rdf.model.impl.ModelCom.(ModelCom.java:51) at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel( ModelFactory.java:124) at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel( ModelFactory.java:118) at org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF( DataTypeParser.java:156) at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache( CentralDigestCachedImpl.java:125) at org.biomoby.client.CentralDigestCachedImpl.getDataTypes( CentralDigestCachedImpl.java:769) at CacheRegistryClient.main(CacheRegistryClient.java:85) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Fri Mar 14 11:53:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 12:53:55 +0100 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> Message-ID: <47DA6753.8000108@mpiz-koeln.mpg.de> Martin Senger wrote: >> before I check it in - I added .classpath.template in the basedir of the >> project and edit the initeclipse task so that the .classpath.template >> file is copied into .classpath file. >> > > > No, don't do it please. Just leave the copying to the users. The same as > they do with other templates (except the .cvsignore.template - but hat is > less important template). The users will have quite often a different > .classpath because they may be testing new things in Eclipse and they even > do not know that the .classpath is changing. No, I definitely would keep the > initeclipse task untouched. > > But please go ahead and commit the .classpath.template. > > Cheers, > Martin > > oki... it is coming to cvs :) - the initeclipse is now virginal again. will update the docs also today andreas From martin.senger at gmail.com Fri Mar 14 11:56:42 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 07:56:42 -0400 Subject: [MOBY-dev] error in java moby request In-Reply-To: <33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47D8FCB8.7060607@mpiz-koeln.mpg.de> <47D9124B.2050304@mpiz-koeln.mpg.de> <1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de> <47DA55C8.4040208@mpiz-koeln.mpg.de> <33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> Message-ID: <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> > and subsequently call a service I'm trying to develop, but that ends in an > error. > > Appearantly the code is looking at the default registry, as the script > prints: > > Fetching data type ontology from > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > ... done > What does your code do (what method of CentralImpl is it trying to call) when it fails? Knowing this will help me to reproduce the problem. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Mar 14 12:04:56 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 08:04:56 -0400 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <47DA6753.8000108@mpiz-koeln.mpg.de> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> <47DA6753.8000108@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803140504s55f44dbblc2dabdb373121cb2@mail.gmail.com> Thanks for the .classpath.template. I still have an Eclipse question (I am not sure, however, if my formulating it is correct, so perhaps I am not looking only for an answer but also for a better question :-)): There are other files, configuration files, that are needed in build/classes. For jMoby, it is logging configuration file log4j.propertiesand a directory 'templates' (uses for MoSeS). All these files are copied there by 'ant config'. Is it a way that they can be either copied there by Eclipse (perhaps by mentioning them in the .classpath), or, at least, not to be removed by Eclipse when I press F5 (refresh) in Eclipse? Eclipse seems to be very rude to all files in build/classes that it was not put there by her (is the Eclipse female gender in English :-)). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From mark.fiers at wur.nl Fri Mar 14 12:36:42 2008 From: mark.fiers at wur.nl (Fiers, Mark) Date: Fri, 14 Mar 2008 13:36:42 +0100 Subject: [MOBY-dev] error in java moby request References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow><1205177598.16508.14.camel@linux-iug0.site><4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com><47D8FCB8.7060607@mpiz-koeln.mpg.de><47D9124B.2050304@mpiz-koeln.mpg.de><1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de><47DA55C8.4040208@mpiz-koeln.mpg.de><33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAE950191@scomp0039.wurnet.nl> Hi Martin, The code is attached and the exact error message is: Fetching data type ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects ... done Fetching namespace ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Namespaces Exception in thread "main" org.biomoby.shared.MobyException: Attempted to build a composite MOBY object from XML, but the tag (MSCmlspectUrl) does not correspond to an existing data type in the registry (default). Please check the spelling and capitalization of the XML tag, to match a registered data type. at org.biomoby.shared.data.MobyDataComposite.(MobyDataComposite.java:42) at org.biomoby.shared.data.MobyDataObject.createInstanceFromDOM(MobyDataObject.java:215) at org.biomoby.shared.data.MobyDataObject.createInstanceFromDOM(MobyDataObject.java:178) at org.biomoby.shared.data.MobyContentInstance.parseDataGroup(MobyContentInstance.java:245) at org.biomoby.shared.data.MobyContentInstance.(MobyContentInstance.java:130) at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument(MobyDataUtils.java:236) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:306) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275) at biomoby_clients.TestXcmsGetPeaks.main(TestXcmsGetPeaks.java:66) hopefully that helps, and thanks! Mark -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger Sent: Fri 3/14/2008 12:56 PM To: Core developer announcements Subject: Re: [MOBY-dev] error in java moby request > and subsequently call a service I'm trying to develop, but that ends in an > error. > > Appearantly the code is looking at the default registry, as the script > prints: > > Fetching data type ontology from > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > ... done > What does your code do (what method of CentralImpl is it trying to call) when it fails? Knowing this will help me to reproduce the problem. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 7145 bytes Desc: not available URL: From mark.fiers at wur.nl Fri Mar 14 12:54:12 2008 From: mark.fiers at wur.nl (Fiers, Mark) Date: Fri, 14 Mar 2008 13:54:12 +0100 Subject: [MOBY-dev] error in java moby request References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow><1205177598.16508.14.camel@linux-iug0.site><4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com><47D8FCB8.7060607@mpiz-koeln.mpg.de><47D9124B.2050304@mpiz-koeln.mpg.de><1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de><47DA55C8.4040208@mpiz-koeln.mpg.de><33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAE950192@scomp0039.wurnet.nl> Hi Martin, One more thing: the fact that the code is complaining about the object MSCmlspectUrl and not about MSRawCdfUrl might very well be bacause the latter object is registered at the default moby central (and the first one is not) with best regards Mark -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger Sent: Fri 3/14/2008 12:56 PM To: Core developer announcements Subject: Re: [MOBY-dev] error in java moby request > and subsequently call a service I'm trying to develop, but that ends in an > error. > > Appearantly the code is looking at the default registry, as the script > prints: > > Fetching data type ontology from > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > ... done > What does your code do (what method of CentralImpl is it trying to call) when it fails? Knowing this will help me to reproduce the problem. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 3534 bytes Desc: not available URL: From groscurt at mpiz-koeln.mpg.de Fri Mar 14 13:08:53 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 14 Mar 2008 14:08:53 +0100 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <4d93f07c0803140504s55f44dbblc2dabdb373121cb2@mail.gmail.com> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> <47DA6753.8000108@mpiz-koeln.mpg.de> <4d93f07c0803140504s55f44dbblc2dabdb373121cb2@mail.gmail.com> Message-ID: <47DA78E5.9050701@mpiz-koeln.mpg.de> Hi Martin, so do i understand that correctly - jmoby requires the log4j.properties and the templates folder in the build/classes folder. When you hit refresh in eclipse on your project - eclipse deletes this folder and this file ? mhm - I do have these files/folders but eclipse keeps them neverthless how hard i hit refresh. best andreas Martin Senger wrote: > Thanks for the .classpath.template. > > I still have an Eclipse question (I am not sure, however, if my formulating > it is correct, so perhaps I am not looking only for an answer but also for a > better question :-)): > > There are other files, configuration files, that are needed in > build/classes. For jMoby, it is logging configuration file > log4j.propertiesand a directory 'templates' (uses for MoSeS). All > these files are copied > there by 'ant config'. Is it a way that they can be either copied there by > Eclipse (perhaps by mentioning them in the .classpath), or, at least, not to > be removed by Eclipse when I press F5 (refresh) in Eclipse? Eclipse seems to > be very rude to all files in build/classes that it was not put there by her > (is the Eclipse female gender in English :-)). > > Cheers, > Martin > > From edward.kawas at gmail.com Fri Mar 14 13:26:53 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 14 Mar 2008 06:26:53 -0700 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <4d93f07c0803140450i7d725805r1dd2f57fc7c744d1@mail.gmail.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> <4d93f07c0803140450i7d725805r1dd2f57fc7c744d1@mail.gmail.com> Message-ID: <47da7d24.06ec720a.52e4.ffffda19@mx.google.com> I found that class in other packages, org.apache.jasper.xmlparsers, org.apache.axis.utils, etc. I didn't find anyone with the same package as the one that we need though. I also couldn't find why it was not included in java 5, although, I did find http://jcs.mobile-utopia.com/jcs/53280_XMLChar.java and it makes you think that the class is part of the package com.sun.org.apache.xcerces.internal.util. I will keep looking, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: March-14-08 4:51 AM To: Core developer announcements; Eddie Kawas Subject: Re: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] Eddie, the problem reported by Andreas is caused in the Jena package (Jena needs the XMLChar library). Could you look why this class is not part of the Java 1.5? Can it be found elsewhere than in xerces? [The xerces itself caused problems from other reasons - see previous emails about it if you wish, or I can re-send them.] The full stack (with a command-line how you can replicate it) is here: senger at sherekhan:~/jMoby$ build/run/run-cache-client -fill -cachedir anotherMyCache/ -v -stack Retrieving namespaces... 0:00:02.384 Retrieving data types... ===ERROR=== java.lang.NoClassDefFoundError: org/apache/xerces/util/XMLChar at com.hp.hpl.jena.rdf.model.impl.Util.notNameChar(Util.java:87) at com.hp.hpl.jena.rdf.model.impl.Util.splitNamespace(Util.java:67) at com.hp.hpl.jena.graph.Node_URI.getLocalName(Node_URI.java:55) at com.hp.hpl.jena.rdf.model.impl.ResourceImpl.getLocalName( ResourceImpl.java:126) at com.hp.hpl.jena.rdf.model.impl.PropertyImpl.checkLocalName( PropertyImpl.java:78) at com.hp.hpl.jena.rdf.model.impl.PropertyImpl.( PropertyImpl.java:86) at com.hp.hpl.jena.rdf.model.ResourceFactory$Impl.createProperty( ResourceFactory.java:244) at com.hp.hpl.jena.rdf.model.ResourceFactory.createProperty( ResourceFactory.java:120) at com.hp.hpl.jena.vocabulary.RDF.property(RDF.java:32) at com.hp.hpl.jena.vocabulary.RDF.(RDF.java:45) at com.hp.hpl.jena.ontology.impl.OntResourceImpl.( OntResourceImpl.java:63) at com.hp.hpl.jena.enhanced.BuiltinPersonalities.( BuiltinPersonalities.java:28) at com.hp.hpl.jena.rdf.model.impl.ModelCom.(ModelCom.java:51) at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel( ModelFactory.java:124) at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel( ModelFactory.java:118) at org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF( DataTypeParser.java:156) at org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache( CentralDigestCachedImpl.java:125) at org.biomoby.client.CentralDigestCachedImpl.getDataTypes( CentralDigestCachedImpl.java:769) at CacheRegistryClient.main(CacheRegistryClient.java:85) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ 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 Fri Mar 14 13:40:47 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 14 Mar 2008 07:40:47 -0600 Subject: [MOBY-dev] error in java moby request In-Reply-To: <33AFFE3255BCA043AF09514A6F6BFBAE950192@scomp0039.wurnet.nl> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow><1205177598.16508.14.camel@linux-iug0.site><4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com><47D8FCB8.7060607@mpiz-koeln.mpg.de><47D9124B.2050304@mpiz-koeln.mpg.de><1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de><47DA55C8.4040208@mpiz-koeln.mpg.de><33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> <33AFFE3255BCA043AF09514A6F6BFBAE950192@scomp0039.wurnet.nl> Message-ID: <47DA805F.9030904@ucalgary.ca> Hi Mark, I'll look into this for you today... Fiers, Mark wrote: > Hi Martin, > > One more thing: the fact that the code is complaining about the object MSCmlspectUrl and not about MSRawCdfUrl might very well be bacause the latter object is registered at the default moby central (and the first one is not) > > with best regards > Mark > > > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger > Sent: Fri 3/14/2008 12:56 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] error in java moby request > > >> and subsequently call a service I'm trying to develop, but that ends in an >> error. >> >> Appearantly the code is looking at the default registry, as the script >> prints: >> >> Fetching data type ontology from >> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects >> ... done >> >> > > What does your code do (what method of CentralImpl is it trying to call) > when it fails? Knowing this will help me to reproduce the problem. > > Thanks, > Martin > > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47da757110950789310626! > From mark.fiers at wur.nl Fri Mar 14 14:41:43 2008 From: mark.fiers at wur.nl (Fiers, Mark) Date: Fri, 14 Mar 2008 15:41:43 +0100 Subject: [MOBY-dev] error in java moby request References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow><1205177598.16508.14.camel@linux-iug0.site><4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com><47D8FCB8.7060607@mpiz-koeln.mpg.de><47D9124B.2050304@mpiz-koeln.mpg.de><1205414736.11424.219.camel@lathan.ipb-sub.ipb-halle.de><47DA55C8.4040208@mpiz-koeln.mpg.de><33AFFE3255BCA043AF09514A6F6BFBAE95018F@scomp0039.wurnet.nl> <4d93f07c0803140456k7cc70b55y1f26c00f7ca53410@mail.gmail.com> <33AFFE3255BCA043AF09514A6F6BFBAE950192@scomp0039.wurnet.nl> <47DA805F.9030904@ucalgary.ca> Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAE95019D@scomp0039.wurnet.nl> Thank you! -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Paul Gordon Sent: Fri 3/14/2008 2:40 PM To: Core developer announcements Subject: Re: [MOBY-dev] error in java moby request Hi Mark, I'll look into this for you today... Fiers, Mark wrote: > Hi Martin, > > One more thing: the fact that the code is complaining about the object MSCmlspectUrl and not about MSRawCdfUrl might very well be bacause the latter object is registered at the default moby central (and the first one is not) > > with best regards > Mark > > > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger > Sent: Fri 3/14/2008 12:56 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] error in java moby request > > >> and subsequently call a service I'm trying to develop, but that ends in an >> error. >> >> Appearantly the code is looking at the default registry, as the script >> prints: >> >> Fetching data type ontology from >> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects >> ... done >> >> > > What does your code do (what method of CentralImpl is it trying to call) > when it fails? Knowing this will help me to reproduce the problem. > > Thanks, > Martin > > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47da757110950789310626! > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 3790 bytes Desc: not available URL: From martin.senger at gmail.com Fri Mar 14 21:55:05 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 17:55:05 -0400 Subject: [MOBY-dev] WG: [Fwd: Problem with xercexImpl-2.6.2.jar] In-Reply-To: <47da7d24.06ec720a.52e4.ffffda19@mx.google.com> References: <773B9ED9AC3B42138BE6822977EAEFC4@rainbow> <1205177598.16508.14.camel@linux-iug0.site> <4d93f07c0803121146w2d83323bp81d87e07b6447174@mail.gmail.com> <47DA45CE.2000708@mpiz-koeln.mpg.de> <4d93f07c0803140441r7cf4771du3a086562973f2a9b@mail.gmail.com> <4d93f07c0803140450i7d725805r1dd2f57fc7c744d1@mail.gmail.com> <47da7d24.06ec720a.52e4.ffffda19@mx.google.com> Message-ID: <4d93f07c0803141455r5da67aa9j56b636e6e2894d3a@mail.gmail.com> Thank you for investigating. At the end, please make a decision what jar should we include in jMoby's project.pom. When you tell me, I will do it and upload an updated jMoby version. This is quite urgent issue because nobody can fill the cache without this probem being solved. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Mar 14 22:01:32 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 18:01:32 -0400 Subject: [MOBY-dev] jMoby 1.0.0 finalized & request from Eclipse user In-Reply-To: <47DA78E5.9050701@mpiz-koeln.mpg.de> References: <4d93f07c0803130959i34b7f0bboe21e85f80b1becab@mail.gmail.com> <47D967E3.3050604@mpiz-koeln.mpg.de> <47DA4CC0.3080605@mpiz-koeln.mpg.de> <4d93f07c0803140437x6dae7767y2ef7e6f3a8b4e1fb@mail.gmail.com> <47DA6753.8000108@mpiz-koeln.mpg.de> <4d93f07c0803140504s55f44dbblc2dabdb373121cb2@mail.gmail.com> <47DA78E5.9050701@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0803141501l6c837552wb3cbf24f39e9a96b@mail.gmail.com> > When you hit refresh in eclipse on your project - eclipse deletes this > folder and this file ? > > mhm - I do have these files/folders but eclipse keeps them neverthless > how hard i hit refresh. > I thing that it depends when (after what action) you hit the Refresh button. I will try to make my request more accurate when I am back in my office where I can try Eclipse my easier. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Fri Mar 14 22:04:16 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 14 Mar 2008 15:04:16 -0700 Subject: [MOBY-dev] Unit testing of BioMoby Services Message-ID: Hi all, During the hackathon I was working on the OWL classes and predicates we need for the ability to create unit tests in the Service metadata coming from the Service provider. I just finished working things out with the myGrid team, and here are the predicates and classes we have agreed on: Namespace: http://www.mygrid.org.uk/mygrid-moby-service# Class: #unitTest usage: can have one or more unitTests per service #operation ObjectProperty: #hasUnitTest domain: #operation range: #unitTest DatatypeProperty: #exampleInput domain: #unitTest range: xsd#string content: the full SOAP payload XML of an invocation message DatatypeProperty: #validOutputXML domain: #unitTest range: xsd#string content: the full SOAP payload of the associated output message DatatypeProperty: #validREGEX domain: #unitTest range: xsd#string content: a regular expression that should match against the output SOAP Payload of this unitTest DatatypeProperty: #validXPath domain: #unitTest range: xsd#string content: an XPath expression that should match against the output SOAP Payload of this unitTest An example can be seen in the antirrhinum.net,getDragonAlleleLocus service, whose signature RDF is available here: http://moby.ucalgary.ca/signatures/antirrhinum.rdf I'm almost finished writing a little Perl script that will go through and test the services based on the Unit Test data - I'll put it in the CVS as soon as it's done. Cheers all! Mark -- -- Mark Wilkinson iCAPTURE Centre From martin.senger at gmail.com Fri Mar 14 23:35:58 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 19:35:58 -0400 Subject: [MOBY-dev] Problem with xercexImpl fixed (for jMoby users) Message-ID: <4d93f07c0803141635p2183436fn5db83c5f45628c68@mail.gmail.com> Hi all, After an emergency (thanks very much to those you reported the problem), I have put back (into our dependency file xmls/project.pom) the xercesImpl.jar- but now its newer version ( 2.7.1.). This fixes the reported problem (a class not found). Please cvs update and type 'ant clean compile' (that should bring the new library to your machine). After I create more junit tests (in order to spot a similar emergency in time, next time) I will upload the newer version of jMoby to the Maven repository (it will be vesion 1.0.1). But, of course, I do not know if the newer xercesImpl version is suitable for those users you complained about xerces in the first place (that was a reason why I removed the xerces dependency). Please try your code and if you have again problems we can discuss the options. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Mon Mar 17 22:29:19 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 17 Mar 2008 16:29:19 -0600 Subject: [MOBY-dev] LSIDs for secondary data types? Message-ID: <47DEF0BF.5010103@ucalgary.ca> Hi all, Can we define formally LSIDs for the secondary parameter datatypes? e.g. urn:lsid:biomoby.org:secondaryParamClass:Integer: urn:lsid:biomoby.org:secondaryParamClass:String: urn:lsid:biomoby.org:secondaryParamClass:Float: urn:lsid:biomoby.org:secondaryParamClass:Boolean: This would help me with my Semantic Annotations for WSDL work... Objections? Paul From markw at illuminae.com Mon Mar 17 22:52:02 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 17 Mar 2008 15:52:02 -0700 Subject: [MOBY-dev] LSIDs for secondary data types? In-Reply-To: <47DEF0BF.5010103@ucalgary.ca> References: <47DEF0BF.5010103@ucalgary.ca> Message-ID: No objections here. I assume you need them to resolve? If so, to what on the data-side and to what on the metadata side? M On Mon, 17 Mar 2008 15:29:19 -0700, Paul Gordon wrote: > Hi all, > > Can we define formally LSIDs for the secondary parameter datatypes? e.g. > > urn:lsid:biomoby.org:secondaryParamClass:Integer: > urn:lsid:biomoby.org:secondaryParamClass:String: > urn:lsid:biomoby.org:secondaryParamClass:Float: > urn:lsid:biomoby.org:secondaryParamClass:Boolean: > > This would help me with my Semantic Annotations for WSDL work... > > Objections? > > Paul > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From gordonp at ucalgary.ca Tue Mar 18 13:51:31 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 18 Mar 2008 07:51:31 -0600 Subject: [MOBY-dev] LSIDs for secondary data types? In-Reply-To: References: <47DEF0BF.5010103@ucalgary.ca> Message-ID: <47DFC8E3.7030009@ucalgary.ca> No data resolution (there is no obligation to provide both, e.g. we have no "data" for urn:lsid:biomoby.org:objectclass:DNASequence:), just metadata with a description of what it is. Mark Wilkinson wrote: > No objections here. > > I assume you need them to resolve? If so, to what on the data-side > and to what on the metadata side? > > M > > > > On Mon, 17 Mar 2008 15:29:19 -0700, Paul Gordon > wrote: > >> Hi all, >> >> Can we define formally LSIDs for the secondary parameter datatypes? e.g. >> >> urn:lsid:biomoby.org:secondaryParamClass:Integer: >> urn:lsid:biomoby.org:secondaryParamClass:String: >> urn:lsid:biomoby.org:secondaryParamClass:Float: >> urn:lsid:biomoby.org:secondaryParamClass:Boolean: >> >> This would help me with my Semantic Annotations for WSDL work... >> >> Objections? >> >> Paul >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From darin.london at duke.edu Tue Mar 18 18:17:00 2008 From: darin.london at duke.edu (darin.london at duke.edu) Date: Tue, 18 Mar 2008 13:17:00 -0500 Subject: [MOBY-dev] BOSC 2008 Announcement and Call For Submissions Message-ID: <200803181817.m2IIH0Ai007305@tenero.duhs.duke.edu> BOSC 2008 Call for Abstracts The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many Open Source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall theme for the conference this year is "Tackling Hard Problems with Emerging Technologies". Topics under this umbrella include cyberinfrastructure, grid computing and workflow management and discovery, and visualization. We will also have a series of update talks about the main Open Source Bioinformatics Software suites. One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done. This year, BOSC is accepting abstract submissions on the conference theme "Tackling Hard Problems with Emerging Technologies". The conference theme reflects that there are new technologies emerging on both the scientific front (new sequencing technologies, etc.) and the IT front (workflows, mashup/web 2.0, improvements in all of the major programming languages, etc.), which may allow the open source community to solve problems that were previously intractable. Abstracts may be submitted for the following topics. 1. Cyberinfrastructure - We are interested in presentations on topics dealing with the development of infrastructure on the web to facilitate software and data re-use (mashups, or traditional), interoperability and inter-process communication, system/service discovery, and data movement and modeling in distributed systems. This may include peer-to-peer systems of data transfer, Web Services, various flavors of data representation (SOAP, JSON, XML, others), and technologies commonly referred to under the Web 2.0 paradigm (e.g. folksonomies/tagging, user-based content generation, content feeds, and Social Networking). 2. Grid Computing and Workflow Management and Discovery - We particularly invite talks that report progress in making workflow systems easier to use and on how to do distributed-collaborative research , e.g. workflows that encompass the coordination of systems running in different parts of the world. 3. Visualization - Visualization is a maturing area of open source software development. We particularly invite talks that demonstrate innovative visualization systems in the context of workflows. 4. Open Source Software - Speakers will present talks on the use, development, or philosophy of open source software in bioinformatics. 5. Bio* Open Source Project Updates - We invite abstracts from the representatives of the open source projects sponsored by or affiliated to the O|B|F (see Projects). Please consult the official BOSC 2008 website at http://www.open-bio.org/wiki/Upcoming_BOSC_conference for all updates and extra information. Submission Process: All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t Important Dates: May 11: Abstract submission deadline. June 2: Notification of accepted talks. June 4: Early registration discount cut-off. July 18-19: BOSC 2008! We hope to see you at BOSC 2008! Kam Dahlquist and Darin London BOSC 2008 Co-organizers From Sebastien.Carrere at toulouse.inra.fr Thu Mar 27 11:43:09 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 27 Mar 2008 12:43:09 +0100 Subject: [MOBY-dev] deregister time out on Test Registry Message-ID: <47EB884D.4000304@toulouse.inra.fr> Bonjour, Does anyone else encounter problems when trying to de-register a service reisterd in the Test registry ? (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl) I'va got a time out message:"Failed with status:500 Server closed connection without sending any data back" The service seems to be removed (because when I try to de-register it again, I've got the correct message "No services in the registry match the given URL and the signatureURL didn\'t contain any services. The RDF agent was called, but found nothing useful." Anyone has an idea ? I use the Perl API. NB: this time-out does not occur on the production registry. Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From ola.spjuth at farmbio.uu.se Fri Mar 28 21:07:24 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 28 Mar 2008 22:07:24 +0100 Subject: [MOBY-dev] Caching revisited Message-ID: <8DC04FBC-A3BD-4DCB-BE94-097EF4CED5DA@farmbio.uu.se> Hi, I just can't get caching to work properly with jMoby! it has cost me so many hours and I still can't figure it out. I want to cache as much as possible in the background on first start, then on second start everything should be as fast as possible. I am able to cache the registry (thanks to previous discussion here and Pauls assistance), but even so I I still get the annoying Fetching data type ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects when I invoke a service. What am I doing wrong? I have attached a Java snippet with a main() that demonstrates this. It seems it is the invokeService() that always downloads the data type ontology. Am I calling this wrong or is it a bug? Thanks, .../Ola ? From gordonp at ucalgary.ca Fri Mar 28 21:55:47 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Mar 2008 15:55:47 -0600 Subject: [MOBY-dev] Caching revisited In-Reply-To: <8DC04FBC-A3BD-4DCB-BE94-097EF4CED5DA@farmbio.uu.se> References: <8DC04FBC-A3BD-4DCB-BE94-097EF4CED5DA@farmbio.uu.se> Message-ID: <47ED6963.6020605@ucalgary.ca> Hi Ola, We decided to create a single caching mechanism in jMoby, and Eddie implemented this at the BioHackathon last month. I have yet to change MobyRequest to use this, but it's on my shortlist (It relates to the problem Mark Fiers was having last week). Your trouble gives me incentive to switch it over sooner, as in the next couple of days. :-) In any case, the existing code shouldn't refetch the ontology unless you either don't call loadDataTypes(yourCacheURL) when you start your JVM, or you are specifying a different registry argument. Regards, Paul Ola Spjuth wrote: > Hi, > > I just can't get caching to work properly with jMoby! it has cost me > so many hours and I still can't figure it out. I want to cache as much > as possible in the background on first start, then on second start > everything should be as fast as possible. I am able to cache the > registry (thanks to previous discussion here and Pauls assistance), > but even so I I still get the annoying Fetching data type ontology > from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects when I invoke a > service. What am I doing wrong? I have attached a Java snippet with a > main() that demonstrates this. > > It seems it is the invokeService() that always downloads the data type > ontology. Am I calling this wrong or is it a bug? > > Thanks, > > .../Ola > > > ------------------------------------------------------------------------ >