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 <[email protected]> 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 <[email protected]> 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 <[email protected]> > > 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 <[email protected]> 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=" Dr. > > >> Nutritious Medical Nutrition Therapy for > > >> Hyperlipidemia Referral from: Julie Tester, RD, LD, > > >> CNSD Phone contact: (555) 555-1212 Height: 144 cm > > >> Current Weight: 45 kg Date of current weight: 02-29-2001 Admit > > Weight: > > >> 53 kg BMI: 18 kg/m2 Diet: General Daily Calorie > > needs > > >> (kcals): 1500 calories, assessed as HB + 20% for > > activity. Daily > > >> Protein needs: 40 grams, assessed as 1.0 g/kg. 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. "/> > > >> <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 > > >> > > >
