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 > >> >
