[kepler-users] visualization of data provenance in kepler

Fri Jun 29 13:01:05 PDT 2012

Hi Derik,

Thank you for your help. I tried two of my workflows and both of them
failed. One failed when copy filename.xml CON: and got an error message
"Not enough storage is available to process this command." The other one
was successfully copied, but had an exception when I tried the opm2dot
command. I have pasted the exception below. I will try a couple of other
things later. Thank you again for your help.

Yujia

opmToolbox>bin\opm2dot soil.xml soil.dot soil.pdf
Exception in thread "main" javax.xml.bind.UnmarshalException: unexpected
element
 (uri:"http://openprovenance.org/model/v1.01.a", local:"opmGraph").
Expected ele
ments are <{http://openprovenance.org/model/opmx#}annotation>,<{
http://openprove
nance.org/model/opmx#}label>,<{
http://openprovenance.org/model/opmx#}opmGraph>,<
{http://openprovenance.org/model/opmx#}pname>,<{
http://openprovenance.org/model/
opmx#}profile>,<{http://openprovenance.org/model/opmx#}type>,<{
http://openproven
ance.org/model/opmx#}value>
        at
com.sun.xml.bind.v2.runtime.unmarshaller.UnmarshallingContext.handleE
vent(UnmarshallingContext.java:642)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.Loader.reportError(Loader.ja
va:254)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.Loader.reportError(Loader.ja
va:249)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.Loader.reportUnexpectedChild
Element(Loader.java:116)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.UnmarshallingContext$Default
RootLoader.childElement(UnmarshallingContext.java:1049)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.UnmarshallingContext._startE
lement(UnmarshallingContext.java:478)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.UnmarshallingContext.startEl
ement(UnmarshallingContext.java:459)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.SAXConnector.startElement(SA
XConnector.java:148)
        at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown
Sour
ce)
        at
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unkn
own Source)
        at
org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.s
canRootElementHook(Unknown Source)
        at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContent
Dispatcher.dispatch(Unknown Source)
        at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Un
known Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown
Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown
Sour
ce)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(
UnmarshallerImpl.java:211)
        at
com.sun.xml.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(U
nmarshallerImpl.java:184)
        at
javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(Unknown Sou
rce)
        at
javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(Unknown Sou
rce)
        at
javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(Unknown Sou
rce)
        at
javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(Unknown Sou
rce)
        at
org.openprovenance.model.OPMDeserialiser.deserialiseOPMGraph(OPMDeser
ialiser.java:70)
        at org.openprovenance.model.OPMToDot.convert(OPMToDot.java:164)
        at org.openprovenance.model.OPMToDot.main(OPMToDot.java:48)

On Fri, Jun 29, 2012 at 3:11 PM, Derik Barseghian <barseghian at nceas.ucsb.edu
> wrote:

> Hi Yujia,
> By default provenance records to a local HSQL database using the
> "SQL-SPA-8" format, but other options are available. Turn off the default
> style of recording by clicking the P button in the toolbar (so it's red),
> and dragging to workflow canvas a Provenance Recorder. Double-click on it
> to configure it, and change Recording Type to OPM XML.
> Derik
>
> On Jun 29, 2012, at 11:56 AM, Yujia Zhou wrote:
>
> > Hi Derik,
> >
> > Thank you very much! I'm trying the OPM toolbox since my workflow is not
> a comad workflow.
> > I have installed the OPM box and I am able to run its demos. But how can
> I make the kepler provenance module record to OPM?
> >
> > Yujia
> >
> > On Thu, Jun 28, 2012 at 3:21 PM, Derik Barseghian <
> barseghian at nceas.ucsb.edu> wrote:
> > Hi Yujia,
> > There are actually two different provenance subsystems available in
> Kepler, the released provenance suite, and a provenance system that I
> believe was designed to work with the comad add-on(s).
> >
> > The released provenance suite doesn't have a data visualization
> capability, though it does allow recording to OPM, and the OPM toolbox has
> a tool to convert these OPM graphs to graphviz, but a co-worker gave that a
> try this morning without success. It does seem like it may be possible
> though. This is what I would pursue if you are interested.
> >
> > The comad provenance system has a provenance browser for data
> visualization. A screenshot of it is here:
> >
> https://kepler-project.org/developers/interest-groups/provenance-interest-group/keplerprovbrowserui.png/view?searchterm=provenance%20browser
> > You'll see the provenance-browser module in:
> https://code.kepler-project.org/code/kepler/trunk/modules/
> >
> > I gave it a very quick try just now, and got errors when trying to open
> some the included example trace files. I don't think this project is being
> maintained, and I believe it is restrictive to comad workflows. I saw this
> browser working in the distant past and it looked useful, it would be nice
> if it were made to work with the released provenance module.
> >
> > Derik
> >
> >
> > On Jun 28, 2012, at 6:51 AM, Yujia Zhou wrote:
> >
> > > Hi,
> > >
> > > I want to build a provenance diagram in Kepler. I have installed the
> provenance module and I am able to query the database successfully. But I'm
> wondering if there's a way for Kepler to produce a nice graph to visualize
> the data provenance? Thank you very much.
> > >
> > > Yujia
> > > _______________________________________________
> > > Kepler-users mailing list
> > > Kepler-users at kepler-project.org
> > > http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
> >
> >
>
>
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