[kepler-users] Using NCBI Entrez web services

Panickos Neophytou panickos at gmail.com
Mon Sep 14 00:23:46 PDT 2009 

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
>>>
>>>
>

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