[kepler-users] Using NCBI Entrez web services
Jianwu Wang
jianwu at sdsc.edu
Mon Sep 14 09:10:42 PDT 2009
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
>>>>
>>>>
>>>>
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