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From Yi-Wen Liu <yiwen...@usc.edu>
Subject Re: run fails but has output
Date Tue, 17 Nov 2015 22:18:51 GMT
Hi,

The ducc.log didn't show running:
2015.11.16 23:29:26 Mon Received
2015.11.16 23:29:26 Mon WaitingForDriver
2015.11.16 23:29:54 Mon WaitingForResources
2015.11.16 23:30:04 Mon Assigned
2015.11.16 23:30:14 Mon Initializing
2015.11.16 23:34:48 Mon Completing
2015.11.16 23:35:18 Mon Completed
2015.11.16 23:35:18 Mon completion type: CanceledByDriver
2015.11.16 23:35:18 Mon rationale: unspecified

And I didn't find error in all_in_one local:

[1] Loading model:

[1] ...

[1] Loading model:

[1] .

[1] Loading configuration.

[1] Loading feature templates.

[1] Loading lexica.

[1] Loading model:

[1] ................................

[1] Loading model:

[1] .............................

[1] 17 Nov 2015 13:49:33  INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip

[1] 17 Nov 2015 13:49:35  INFO JdbcConnectionResourceImpl - Connection
established to:
jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/umls2011ab/umls

[1] 17 Nov 2015 13:49:35  INFO JdbcConnectionResourceImpl - Connection
established to:
jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls

[1] 17 Nov 2015 13:49:35  INFO JdbcConnectionResourceImpl - Connection
established to:
jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/orange_book_hsqldb/umls

[1] 17 Nov 2015 13:49:35  INFO UmlsDictionaryLookupAnnotator - Parsing
descriptor:
/Users/ducc/src/apache-ctakes-3.2.2/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml

[1] 17 Nov 2015 13:49:35  INFO FirstTokenPermLookupInitializerImpl -
Exclusion tagset loaded: [dt, to, rp, ls, pos, md, vbd, vbg, vb, ex, vbp,
vbn, pdt, vbz, wp, wrb, in, wps, pp$, prp$, wdt, prp, pp, cc, cd]

[1] 17 Nov 2015 13:49:35  INFO FirstTokenPermLookupInitializerImpl -
Exclusion tagset loaded: [to, dt, rp, ex, vbp, ls, vbn, pdt, wp, vbz, wrb,
in, pos, wps, md, wdt, pp$, vbd, vb, vbg, pp, cc, cd]

[1] 17 Nov 2015 13:49:35  INFO UmlsDictionaryLookupAnnotator - Using
ctakes.umlsaddr: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser:
yiwenliu

[1] 17 Nov 2015 13:49:39  INFO LvgCmdApiResourceImpl - Loading NLM Norm and
Lvg with config file =
/Users/ducc/src/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties

[1] 17 Nov 2015 13:49:39  INFO LvgCmdApiResourceImpl -   config file
absolute path =
/Users/ducc/src/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties

[1] 17 Nov 2015 13:49:39  INFO LvgCmdApiResourceImpl - cwd = /Users/ducc/src

[1] 17 Nov 2015 13:49:39  INFO LvgCmdApiResourceImpl - cd
/Users/ducc/src/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/

[1] 17 Nov 2015 13:49:40  INFO LvgCmdApiResourceImpl - cd /Users/ducc/src

It looks like it suddenly canceled by driver and no more output on screen.
Another log file shows connection refused so I checked driver logs, and
found the three errors in first email.

Is that error org.xml.sax.SAXParseException; Trying to serialize non-XML
1.0 character caused by invalid space and characters in Xml, or it's more
like syntax error of CR Xml?

Thanks,
Yi-Wen

On Tue, Nov 17, 2015 at 1:36 PM, Lou DeGenaro <lou.degenaro@gmail.com>
wrote:

> Hi Yi-Wen,
>
> Does your CR function correctly outside of DUCC?  Have you tired debugging
> using DUCC's All-In-One feature as suggested previously by Eddie?
>
> Lou.
>
> On Tue, Nov 17, 2015 at 3:54 PM, Yi-Wen Liu <yiwenliu@usc.edu> wrote:
>
> > Hi,
> >
> > I tried to remove redundant white spaces but it doesn't work, and I
> didn't
> > add any other special characters in CR.
> >
> > Is that error caused by invalid space and characters in Xml, or it's more
> > like syntax error of CR Xml?
> >
> >
> >
> > Thanks,
> > Yi-Wen
> >
> > > On Nov 17, 2015, at 5:37 AM, Lou DeGenaro <lou.degenaro@gmail.com>
> > wrote:
> > >
> > > Yi-Wen,
> > >
> > > The DUCC Job first visits the Initialization state.  This is when the
> Job
> > > Driver (JD) initializes your UIMA CollecitonReader (CR). The CR that
> you
> > > specified in your DUCC Job submission is constructed and its getTotal()
> > > method is invoked to determine the number of work items.  But I think
> > your
> > > Job made it past the Initialization state and into the Running state.
> > > Looking at the log snippits that you posted, I see:
> > >
> > > 16 Nov 2015 23:34:38,353  INFO JobDriver - T[18] advanceJdState
> > > current=Initializing request=Active result=Active
> > >
> > > This means the JD has exited its Initializing state and is now Active
> and
> > > is fetching work items.  Further evidence is the entry:
> > >
> > > 16 Nov 2015 23:34:39,066 ERROR CasManager - T[17] getMetaCas
> > >
> > > What do the contents of the file ducc.log in your Job's log directory
> > > show?  You should see "Initializing" followed by "Running".
> > >
> > > It looks like the root cause of your problem is that your CR's
> getNext()
> > is
> > > trying to produce work items for the JD but is failing:
> > >
> > > org.xml.sax.SAXParseException; Trying to serialize non-XML 1.0
> > > character: , 0x0
> > >        at
> > org.apache.uima.util.XMLSerializer$CharacterValidatingContentHand
> > > ler.checkForInvalidXmlChars(XMLSerializer.java:254)
> > >
> > > I recommend determining why your CR is broken, fixing, and
> re-submitting
> > > your Job to DUCC.
> > >
> > > Lou.
> > >
> > >> On Tue, Nov 17, 2015 at 2:46 AM, Yi-Wen Liu <yiwenliu@usc.edu> wrote:
> > >>
> > >> Hello,
> > >>
> > >> I am still stuck in the following error of DUCC and job always got
> > canceled
> > >> by driver:
> > >>
> > >> 16 Nov 2015 23:34:38,353  INFO JobDriver - T[18] advanceJdState
> > >> current=Initializing request=Active result=Active
> > >> 16 Nov 2015 23:34:39,066 ERROR ProxyLogger - T[17] loggify
> > >> org.xml.sax.SAXParseException; Trying to serialize non-XML 1.0
> > >> character: , 0x0
> > >>        at
> > >>
> >
> org.apache.uima.util.XMLSerializer$CharacterValidatingContentHandler.checkForInvalidXmlChars(XMLSerializer.java:254)
> > >>
> > >> 16 Nov 2015 23:34:39,066 ERROR CasManager - T[17] getMetaCas
> > >> org.apache.uima.ducc.container.common.classloader.ProxyException
> > >>        at
> > >>
> >
> org.apache.uima.ducc.container.jd.classload.ProxyJobDriverCollectionReader.getMetaCas(ProxyJobDriverCollectionReader.java:127)
> > >>        at
> > >>
> >
> org.apache.uima.ducc.container.jd.cas.CasManager.getMetaCas(CasManager.java:65)
> > >>        at
> > >>
> >
> org.apache.uima.ducc.container.jd.fsm.wi.ActionGet.engage(ActionGet.java:118)
> > >>        at
> > >> org.apache.uima.ducc.container.common.fsm.Fsm.transition(Fsm.java:172)
> > >>
> > >> 16 Nov 2015 23:34:39,068 ERROR ActionGet - T[17] engage
> > >> org.apache.uima.ducc.container.jd.JobDriverException
> > >>        at
> > >>
> >
> org.apache.uima.ducc.container.jd.cas.CasManager.getMetaCas(CasManager.java:74)
> > >>        at
> > >>
> >
> org.apache.uima.ducc.container.jd.fsm.wi.ActionGet.engage(ActionGet.java:118)
> > >>
> > >>
> > >> However, when I looked into output directory, there were output (much
> > >> omitted from below):
> > >>
> > >> <?xml version="1.0" encoding="UTF-8"?><CAS version="2">
> > >>    <uima.cas.Sofa _indexed="0" _id="1" sofaNum="1"
> sofaID="_InitialView"
> > >> mimeType="text" sofaString="&#13;&#10;Dr.
> > >> Nutritious&#13;&#10;&#13;&#10;Medical Nutrition Therapy
for
> > >> Hyperlipidemia&#13;&#10;&#13;&#10;Referral from: Julie
Tester, RD, LD,
> > >> CNSD&#13;&#10;Phone contact: (555) 555-1212&#13;&#10;Height:
144 cm
> > >> Current Weight: 45 kg   Date of current weight: 02-29-2001   Admit
> > Weight:
> > >> 53 kg   BMI: 18 kg/m2&#13;&#10;Diet: General&#13;&#10;Daily
Calorie
> > needs
> > >> (kcals): 1500 calories, assessed as HB + 20% for
> > activity.&#13;&#10;Daily
> > >> Protein needs: 40 grams,  assessed as 1.0 g/kg.&#13;&#10;Pt has
been
> on
> > a
> > >> 3-day calorie count and has had an average intake of 1100 calories.
> She
> > >> was instructed to drink 2-3 cans of liquid supplement to help promote
> > >> weight gain.  She agrees with the plan and has my number for further
> > >> assessment. May want a Resting Metabolic Rate as well. She takes an
> > aspirin
> > >> a day for knee pain.&#13;&#10;"/>
> > >>    <org.apache.ctakes.typesystem.type.structured.DocumentID
> _indexed="1"
> > >> _id="8" documentID="testpatient_plaintext_1.txt"/>
> > >>    <uima.tcas.DocumentAnnotation _indexed="1" _id="10" _ref_sofa="1"
> > >> begin="0" end="735" language="x-unspecified"/>
> > >>    <org.apache.ctakes.typesystem.type.textspan.Segment _indexed="1"
> > >> _id="15" _ref_sofa="1" begin="0" end="735" id="SIMPLE_SEGMENT"/>
> > >>    <org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1"
> > >> _id="21" _ref_sofa="1" begin="2" end="16" sentenceNumber="0"/>
> > >> ..
> > >> ..
> > >> ..
> > >>    <org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="2975"
> > >> codingScheme="SNOMED" code="103733002" oid="103733002#SNOMED"
> > score="0.0"
> > >> disambiguated="false" cui="C0087111" tui="T061"/>
> > >>    <uima.cas.FSArray _id="3005" size="4">
> > >>        <i>2975</i>
> > >>        <i>2985</i>
> > >>        <i>2965</i>
> > >>        <i>2995</i>
> > >>    </uima.cas.FSArray>
> > >>    <org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="2924"
> > >> codingScheme="SNOMED" code="243121000" oid="243121000#SNOMED"
> > score="0.0"
> > >> disambiguated="false" cui="C0418981" tui="T061"/>
> > >>    <uima.cas.FSArray _id="2934" size="1">
> > >>        <i>2924</i>
> > >>    </uima.cas.FSArray>
> > >>    <org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="2870"
> > >> codingScheme="RXNORM" code="1191" oid="1191#RXNORM" score="0.0"
> > >> disambiguated="false" cui="C0004057" tui="T121"/>
> > >>    <org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="2880"
> > >> codingScheme="RXNORM" code="1191" oid="1191#RXNORM" score="0.0"
> > >> disambiguated="false" cui="C0004057" tui="T109"/>
> > >>    <uima.cas.FSArray _id="2890" size="2">
> > >>        <i>2880</i>
> > >>        <i>2870</i>
> > >>    </uima.cas.FSArray>
> > >> </CAS>
> > >>
> > >>
> > >> I am not sure what's going on here, the job wasn't in running stage
> but
> > has
> > >> output...
> > >> It always got canceled by driver and showed run fails after
> > initializing,
> > >> so I didn't expect there would have any output file.
> > >> And I also doubt whether the content in output file is correct....any
> > >> suggestion is appreciated!
> > >>
> > >> Thanks,
> > >> Yi-Wen
> > >>
> >
>

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