Hi Panickos,
We are planning to publish Kepler 2.0. But currently you have to use
nightly build Kepler 1.x to use the actor. You can follow the steps at
https://kepler-project.org/developers/teams/build/documentation/build-system-instructions
to install Kepler.
Best wishes
Sincerely yours
Jianwu Wang
jianwu at sdsc.edu
http://users.sdsc.edu/~jianwu/
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.
Panickos Neophytou wrote:
> Thanks for the info.
> I am using version 1.0 of Kepler.
>
> I tried what you said from the menu Tools->Instantiate Component and I
> got the exception which I'm adding at the end of this email.
>
> So I guess I need to upgrade. Is there a stable version I can use?
> Should I use the kepler1.0Dev installation? Or some king of nightly
> build? Where can I find these? So far I've been looking in here:
> http://dist.kepler-project.org/dist/
>
> Thanks again,
> Panickos
>
>
> com.microstar.xml.XmlException: XML element "entity" triggers
> exception. in [external stream] at line 1 and column 193
> Caused by:
> ptolemy.kernel.util.IllegalActionException: Cannot find class:
> org.kepler.actor.rest.RESTService
> Because:
> expected character (found "/") (expected "<") in
> https://code.kepler-project.org/code/kepler/trunk/modules/actors/src/org/kepler/actor/rest/RESTService.java
> at line 1 and column 5
> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:3291)
> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)
> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)
> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)
> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)
> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1318)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1446)
> at ptolemy.moml.MoMLChangeRequest._execute(MoMLChangeRequest.java:270)
> at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:139)
> at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:697)
> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1668)
> at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1187)
> at
> ptolemy.vergil.actor.ActorGraphFrame$InstantiateEntityAction.actionPerformed(ActorGraphFrame.java:670)
> at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
> at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
> at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
> at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1051)
> at apple.laf.CUIAquaMenuItem.doClick(CUIAquaMenuItem.java:119)
> at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1092)
> at java.awt.Component.processMouseEvent(Component.java:5602)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
> at java.awt.Component.processEvent(Component.java:5367)
> at java.awt.Container.processEvent(Container.java:2010)
> at java.awt.Component.dispatchEventImpl(Component.java:4068)
> at java.awt.Container.dispatchEventImpl(Container.java:2068)
> at java.awt.Component.dispatchEvent(Component.java:3903)
> at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
> at java.awt.Container.dispatchEventImpl(Container.java:2054)
> at java.awt.Window.dispatchEventImpl(Window.java:1801)
> at java.awt.Component.dispatchEvent(Component.java:3903)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> at
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
> Caused by: ptolemy.kernel.util.IllegalActionException: Cannot find
> class: org.kepler.actor.rest.RESTService
> Because:
> expected character (found "/") (expected "<") in
> https://code.kepler-project.org/code/kepler/trunk/modules/actors/src/org/kepler/actor/rest/RESTService.java
> at line 1 and column 5
> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3701)
> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2379)
> ... 41 more
> Caused by: com.microstar.xml.XmlException: expected character (found
> "/") (expected "<") in
> https://code.kepler-project.org/code/kepler/trunk/modules/actors/src/org/kepler/actor/rest/RESTService.java
> at line 1 and column 5
> at ptolemy.moml.MoMLParser.error(MoMLParser.java:1025)
> at com.microstar.xml.XmlParser.error(XmlParser.java:448)
> at com.microstar.xml.XmlParser.error(XmlParser.java:459)
> at com.microstar.xml.XmlParser.require(XmlParser.java:2317)
> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:480)
> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1334)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1292)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1265)
> at ptolemy.moml.MoMLParser._findOrParse(MoMLParser.java:4420)
> at ptolemy.moml.MoMLParser._attemptToFindMoMLClass(MoMLParser.java:3498)
> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3696)
> ... 42 more
> Caused by: ptolemy.kernel.util.IllegalActionException: Cannot find
> class: org.kepler.actor.rest.RESTService
> Because:
> expected character (found "/") (expected "<") in
> https://code.kepler-project.org/code/kepler/trunk/modules/actors/src/org/kepler/actor/rest/RESTService.java
> at line 1 and column 5
> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3701)
> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2379)
> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)
> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)
> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)
> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)
> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1318)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1446)
> at ptolemy.moml.MoMLChangeRequest._execute(MoMLChangeRequest.java:270)
> at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:139)
> at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:697)
> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1668)
> at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1187)
> at
> ptolemy.vergil.actor.ActorGraphFrame$InstantiateEntityAction.actionPerformed(ActorGraphFrame.java:670)
> at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
> at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
> at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
> at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1051)
> at apple.laf.CUIAquaMenuItem.doClick(CUIAquaMenuItem.java:119)
> at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1092)
> at java.awt.Component.processMouseEvent(Component.java:5602)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
> at java.awt.Component.processEvent(Component.java:5367)
> at java.awt.Container.processEvent(Container.java:2010)
> at java.awt.Component.dispatchEventImpl(Component.java:4068)
> at java.awt.Container.dispatchEventImpl(Container.java:2068)
> at java.awt.Component.dispatchEvent(Component.java:3903)
> at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2054)
> at java.awt.Window.dispatchEventImpl(Window.java:1801)
> at java.awt.Component.dispatchEvent(Component.java:3903)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> at
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
> Caused by: com.microstar.xml.XmlException: expected character (found
> "/") (expected "<") in
> https://code.kepler-project.org/code/kepler/trunk/modules/actors/src/org/kepler/actor/rest/RESTService.java
> at line 1 and column 5
> at ptolemy.moml.MoMLParser.error(MoMLParser.java:1025)
> at com.microstar.xml.XmlParser.error(XmlParser.java:448)
> at com.microstar.xml.XmlParser.error(XmlParser.java:459)
> at com.microstar.xml.XmlParser.require(XmlParser.java:2317)
> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:480)
> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1334)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1292)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1265)
> at ptolemy.moml.MoMLParser._findOrParse(MoMLParser.java:4420)
> at ptolemy.moml.MoMLParser._attemptToFindMoMLClass(MoMLParser.java:3498)
> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3696)
> ... 42 more
> Caused by: com.microstar.xml.XmlException: expected character (found
> "/") (expected "<") in
> https://code.kepler-project.org/code/kepler/trunk/modules/actors/src/org/kepler/actor/rest/RESTService.java
> at line 1 and column 5
> at ptolemy.moml.MoMLParser.error(MoMLParser.java:1025)
> at com.microstar.xml.XmlParser.error(XmlParser.java:448)
> at com.microstar.xml.XmlParser.error(XmlParser.java:459)
> at com.microstar.xml.XmlParser.require(XmlParser.java:2317)
> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:480)
> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1334)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1292)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1265)
> at ptolemy.moml.MoMLParser._findOrParse(MoMLParser.java:4420)
> at ptolemy.moml.MoMLParser._attemptToFindMoMLClass(MoMLParser.java:3498)
> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3696)
> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2379)
> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)
> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)
> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)
> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)
> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1318)
> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1446)
> at ptolemy.moml.MoMLChangeRequest._execute(MoMLChangeRequest.java:270)
> at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:139)
> at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:697)
> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1668)
> at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1187)
> at
> ptolemy.vergil.actor.ActorGraphFrame$InstantiateEntityAction.actionPerformed(ActorGraphFrame.java:670)
> at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
> at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
> at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
> at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1051)
> at apple.laf.CUIAquaMenuItem.doClick(CUIAquaMenuItem.java:119)
> at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1092)
> at java.awt.Component.processMouseEvent(Component.java:5602)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
> at java.awt.Component.processEvent(Component.java:5367)
> at java.awt.Container.processEvent(Container.java:2010)
> at java.awt.Component.dispatchEventImpl(Component.java:4068)
> at java.awt.Container.dispatchEventImpl(Container.java:2068)
> at java.awt.Component.dispatchEvent(Component.java:3903)
> at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
> at java.awt.Container.dispatchEventImpl(Container.java:2054)
> at java.awt.Window.dispatchEventImpl(Window.java:1801)
> at java.awt.Component.dispatchEvent(Component.java:3903)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> at
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
>
> On Mon, Sep 14, 2009 at 12:06 AM, Jianwu Wang <jianwu at sdsc.edu> wrote:
>
>> Hi Panickos,
>>
>> Which Kepler version are you using? This actor is not in Kepler 1.0, only
>> in Kepler trunk. The java class for this actor is
>> org.kepler.actor.rest.RESTService (its url at kepler-trunk is
>> https://code.kepler-project.org/code/kepler/trunk/modules/actors/src/org/kepler/actor/rest/RESTService.java),
>> you can try to use 'initiate the component' item to initiate the actor. If
>> you still can not get it, please update your Kepler.
>>
>> Best wishes
>>
>> Sincerely yours
>>
>> Jianwu Wang
>> jianwu at sdsc.edu
>> http://users.sdsc.edu/~jianwu/
>>
>> Scientific Workflow Automation Technologies (SWAT) Laboratory
>> San Diego Supercomputer Center University of California, San Diego
>> San Diego, CA, U.S.A.
>>
>>
>> Panickos Neophytou wrote:
>>
>>> Hi Jianwu,
>>>
>>> I searched for this but couldn't find something relevant. Maybe I'm
>>> looking at the wrong place or just skipped it... Can you tell me the
>>> exact name of the Actor I should be looking for?
>>>
>>> Thanks,
>>> Panickos
>>>
>>> On Sun, Sep 13, 2009 at 11:42 PM, Jianwu Wang <jianwu at sdsc.edu> wrote:
>>>
>>>
>>>> Hi Panickos,
>>>>
>>>> There is a RESTful Service actor in Kepler trunk. You should be able
>>>> to
>>>> find it by searching 'Service'.
>>>>
>>>> Best wishes
>>>>
>>>> Sincerely yours
>>>>
>>>> Jianwu Wang
>>>> jianwu at sdsc.edu
>>>> http://users.sdsc.edu/~jianwu/
>>>>
>>>> Scientific Workflow Automation Technologies (SWAT) Laboratory
>>>> San Diego Supercomputer Center
>>>> University of California, San Diego
>>>> San Diego, CA, U.S.A.
>>>>
>>>> Panickos Neophytou wrote:
>>>>
>>>> Thanks Daniel,
>>>>
>>>> I was wondering if there's any way to use the REST method, using just
>>>> the URL with some query parameters. Is there an actor for doing this?
>>>> And maybe have the query part of the URL be generated somehow by the
>>>> upstream actors of the workflow...
>>>>
>>>> If this is not possible, then how long do you think it is going to
>>>> take to fix the Web Service Actor? Should I pause this and wait for
>>>> your update or should I try something different?
>>>>
>>>> Cheers,
>>>> Panickos
>>>>
>>>> On Sat, Sep 12, 2009 at 9:42 PM, Daniel Crawl <crawl at sdsc.edu> wrote:
>>>>
>>>>
>>>> Hi Panickos,
>>>>
>>>> I'm in the process of updating the web service actor to
>>>> work with the NCBI web services. I'll let you know when
>>>> I'm done.
>>>>
>>>> --dan
>>>>
>>>>
>>>>
>>>> Panickos Neophytou wrote:
>>>>
>>>>
>>>> Hi,
>>>>
>>>> I'm new to kepler and I was wondering if anyone has a sample workflow
>>>> using eSearch and eFetch for some any of their databases. I tried a
>>>> few thing and I also didn't find anything on the web about this.
>>>>
>>>> Thanks,
>>>> Panickos
>>>> _______________________________________________
>>>> Kepler-users mailing list
>>>> Kepler-users at kepler-project.org
>>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Kepler-users mailing list
>>>> Kepler-users at kepler-project.org
>>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>
>>>>
>>>>
