[kepler-users] add an actor to the local repository

Mon Jul 19 15:31:59 PDT 2010

Hi Chris,

    I can re-produce this error by turning off network access. I fired a 
bug for it (http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5098). 
I'll have a look at it.

Best wishes

Sincerely yours

Jianwu Wang
jianwu at sdsc.edu
http://users.sdsc.edu/~jianwu/

Assistant Project Scientist
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.

On 7/19/2010 3:00 PM, chrisweed at gmail.com wrote:
> I think the problem I am having is that it is trying to validate the 
> XML against
> http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd, and my proxy
> is probably in the way. Although I set the proxy in the kepler.bat 
> file on the
> command-line. I am not sure why it isn't going through.
> Chris
>
> [null] java.net.ConnectException: Connection timed out: connect
> [null] at java.net.PlainSocketImpl.socketConnect(Native Method)
> [null] at java.net.PlainSocketImpl.doConnect(Unknown Source)
> [null] at java.net.PlainSocketImpl.connectToAddress(Unknown Source)
> [null] at java.net.PlainSocketImpl.connect(Unknown Source)
> [null] at java.net.SocksSocketImpl.connect(Unknown Source)
> [null] at java.net.Socket.connect(Unknown Source)
> [null] at java.net.Socket.connect(Unknown Source)
> [null] at sun.net.NetworkClient.doConnect(Unknown Source)
> [null] at sun.net.www.http.HttpClient.openServer(Unknown Source)
> [null] at sun.net.www.http.HttpClient.openServer(Unknown Source)
> [null] at sun.net.www.http.HttpClient.<init>(Unknown Source)
> [null] at sun.net.www.http.HttpClient.New(Unknown Source)
> [null] at sun.net.www.http.HttpClient.New(Unknown Source)
> [null] at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(
> Unknown Source)
> [null] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unkn
> own Source)
> [null] at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown S
> ource)
> [null] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Un
> known Source)
> [null] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Un
> known Source)
> [null] at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown S
> ource)
> [null] at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknow
> n Source)
> [null] at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unkno
> wn Source)
> [null] at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.d
> ispatch(Unknown Source)
> [null] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDoc
> ument(Unknown Source)
> [null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown So
> urce)
> [null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown So
> urce)
> [null] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> [null] at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
> [null] at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Sour
> ce)
> [null] at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(
> KeplerMetadataExtractor.java:101)
> [null] at org.kepler.objectmanager.cache.ActorCacheObject.<init>(ActorC
> acheObject.java:141)
> [null] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(Ac
> torMetadataKAREntryHandler.java:169)
> [null] at org.kepler.kar.KARFile.cache(KARFile.java:876)
> [null] at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:591)
> [null] at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:184)
> [null] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(Export
> ArchiveAction.java:344)
> [null] at javax.swing.AbstractButton.fireActionPerformed(Unknown Source
> )
> [null] at javax.swing.AbstractButton$Handler.actionPerformed(Unknown So
> urce)
> [null] at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown So
> urce)
> [null] at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
> [null] at javax.swing.AbstractButton.doClick(Unknown Source)
> [null] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source
> )
> [null] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(
> Unknown Source)
> [null] at java.awt.Component.processMouseEvent(Unknown Source)
> [null] at javax.swing.JComponent.processMouseEvent(Unknown Source)
> [null] at java.awt.Component.processEvent(Unknown Source)
> [null] at java.awt.Container.processEvent(Unknown Source)
> [null] at java.awt.Component.dispatchEventImpl(Unknown Source)
> [null] at java.awt.Container.dispatchEventImpl(Unknown Source)
> [null] at java.awt.Component.dispatchEvent(Unknown Source)
> [null] at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Sou
> rce)
> [null] at java.awt.LightweightDispatcher.processMouseEvent(Unknown Sour
> ce)
> [null] at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
> [null] at java.awt.Container.dispatchEventImpl(Unknown Source)
> [null] at java.awt.Window.dispatchEventImpl(Unknown Source)
> [null] at java.awt.Component.dispatchEvent(Unknown Source)
> [null] at java.awt.EventQueue.dispatchEvent(Unknown Source)
> [null] at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown S
> ource)
> [null] at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Sour
> ce)
> [null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown S
> ource)
> [null] at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> [null] at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> [null] at java.awt.EventDispatchThread.run(Unknown Source)
> [null] Error parsing Actor KAR DOM "<?xml version="1.0"?>
> [null] <!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN"
> [null] "http://ptolemy.e...": Connection timed out: connect
> [null] WARN (org.kepler.objectmanager.cache.CacheManager:insertObject:237)
> KAREntry has no lsid: null
>
> On Jul 19, 2010 5:50pm, chrisweed at gmail.com wrote:
> > Thanks, I'll try that.
> > Chris
> >
> > On Jul 19, 2010 5:49pm, Jianwu Wang jianwu at sdsc.edu> wrote:
> > >
> > >
> > >
> > >
> > >
> > >
> > > Hi Chris,
> > >
> > >
> > >
> > >     If you right-click the actor and choose 'Save Archive (KAR)...', a
> > > dialog called 'Add Semantic Types?' will show up. If you click 'yes',
> > > you can choose corresponding semantic type for this actor. Then 
> another
> > > dialog will show up to save the kar file of this actor. The default
> > > location is at $KeplerData/workflows/MyWorkflows. If you save the kar
> > > file in $KeplerData/workflows/MyWorkflows directory, you can 
> search and
> > > find the actor in the ontology-tree window. It will show up under both
> > > its ontology annotations and MyWorkflows icon.
> > >
> > > Best wishes
> > >
> > > Sincerely yours
> > >
> > > Jianwu Wang
> > > jianwu at sdsc.edu
> > > http://users.sdsc.edu/~jianwu/
> > >
> > > Assistant Project Scientist
> > > Scientific Workflow Automation Technologies (SWAT) Laboratory
> > > San Diego Supercomputer Center
> > > University of California, San Diego
> > > San Diego, CA, U.S.A.
> > >
> > >
> > > On 7/19/2010 2:34 PM, chrisweed at gmail.com wrote:
> > > What is the correct method for adding an actor to the
> > > local repository, so it shows up in the ontology-tree window?
> > >
> > > I didn't see how to do this in the user guide. I tried the old "upload
> > > to repository" method, but that didn't seem to do anything.
> > >
> > > Chris
> > >
> > >
> > > _______________________________________________
> > > Kepler-users mailing list
> > > Kepler-users at kepler-project.org
> > > http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
> > >
> > >
> > >
> > > 