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 >>
