Marshall,
It seems I post reply crossing paths with yours.
Your comment makes me realize what is wrong and
I think you don't need to run what I sent for about 10 minutes ago.
I will try editing codes and report again.
Thanks for now,
Isaac
On Nov 21, 2007 12:56 AM, Marshall Schor <[EMAIL PROTECTED]> wrote:
> Hi Issac,
>
> Thanks for sending the trace (although, as Thilo says, the source
> doesn't line up with the trace line numbers for some reason...)
>
> The logic of the code looks like you may have multiple CAS instances
> being used, from different Analysis engines. I see that when you start
> the application, the main constructor calls the method
> extractKeioPersonWikipedia, and this reads in a UIMA description,
> complete with its type system, builds an analysis engine (I'm guessing
> here a bit, from the name of one of your classes, AnalysisEngineUtil)
> and runs it. This returns a CAS/JCas in line 168. You then call
> createPersonList, returning a list of JCas object instances for the
> persons in that CAS.
>
> Then you iterate over this list in extractNamedentity, calling
> extractNeeFromWebdoc. This starts up another analysis engine (which
> could have a completely different type system, etc.), and line 93
> returns its jcas, which is completely unrelated to the cas/jcas which
> has the "person" annotations in it.
>
> Line 112 looks invalid in that it is trying to set a value into a field
> which is a reference to a Cas object that belongs to a different CAS.
> This isn't supported.
>
>
> -Marshall
>
>
> ISAO Isaac Saito wrote:
> > Thanks Marshall,
> > I attach the stack trace and java code below.
> >
> > <exception>
> > Exception in thread "main" java.lang.NullPointerException
> > at org.apache.uima.cas.impl.CASImpl.ll_getFSForRef(CASImpl.java:2745)
> > at
> > jp.ac.keio.dmc.context.srw.types.PersonWikip.getCompany_related(PersonWikip.java:233)
> > at
> > jp.ac.keio.dmc.context.srw.SRWikipediaMain.extractNeeFromText(SRWikipediaMain.java:120)
> > at
> > jp.ac.keio.dmc.context.srw.SRWikipediaMain.extractNeeFromWebdoc(SRWikipediaMain.java:85)
> > at
> > jp.ac.keio.dmc.context.srw.SRWikipediaMain.extractNamedentity(SRWikipediaMain.java:67)
> > at
> > jp.ac.keio.dmc.context.srw.SRWikipediaMain.<init>(SRWikipediaMain.java:47)
> > at
> > jp.ac.keio.dmc.context.srw.SRWikipediaMain.main(SRWikipediaMain.java:210)
> > </exception>
> >
> >
> > - PersonWikip.java
> > I don't attach because it is nothing special that is generated
> > automatically after defining Type System Definition on Component
> > descriptor editor.
> >
> >
> > - whole code of SRWikipediaMain.java
> > # You might feel the code verbose because I paste the whole...
> >
> > <SRWikipediaMain.java>
> > 1: package jp.ac.keio.dmc.context.srw;
> > 2:
> > 3: import java.io.IOException;
> > 4: import java.util.LinkedList;
> > 5:
> > 6: import jp.ac.keio.dmc.context.srw.types.PersonWikip;
> > 7: import jp.ac.keio.dmc.context.util.http.DMCHttpClient;
> > 8: import net.lateeye.util.uima.AnalysisEngineUtil;
> > 9:
> > 10: import org.apache.uima.analysis_engine.AnalysisEngine;
> > 11: import org.apache.uima.cas.FSIndex;
> > 12: import org.apache.uima.cas.FSIterator;
> > 13: import org.apache.uima.jcas.JCas;
> > 14: import org.apache.uima.jcas.cas.StringArray;
> > 15: import org.apache.uima.util.XMLInputSource;
> > 16:
> > 17: import com.ibm.omnifind.ne.types.Company;
> > 18: import com.ibm.omnifind.ne.types.Org;
> > 19:
> > 20: public class SRWikipediaMain {
> > 21: private static String path_eclipseWorkspace_root =
> > "C:/data/app/workspace_eclipse/";
> > 22: private static String path_ibmNeeDesc = path_eclipseWorkspace_root
> > 23: + "tae_nee_apacheUima/" + "desc/";
> > 24: private static String path_srwAeDesc = path_eclipseWorkspace_root
> > 25: + "srwikipedia/" + "descriptor/";
> > 26: private static String uimaDesc_personWikip = path_srwAeDesc
> > 27: + "KeioWikipAnnotatorDescriptor.xml";
> > 28: private static String uimaDesc_ibmNee = path_ibmNeeDesc
> > 29: + "NamedEntityAnnotatorDescriptor.xml";
> > 30: private static String uimaDesc_wikipPersonNee = path_srwAeDesc
> > 31: + "WikipPersonNeeAnnotatorDescriptor.xml";
> > 32: // private LinkedList<PersonWikip> personList = null;
> > 33: private DMCHttpClient dhc = new DMCHttpClient();
> > 34:
> > 35: public SRWikipediaMain() {
> > 36: // extract keio person from wikipedia
> > 37: LinkedList<PersonWikip> personList =
> > this.extractKeioPersonWikipedia();
> > 38:
> > 39: // extract NEs using personList
> > 40: personList = this.extractNamedentity(personList);
> > 41:
> > 42: // update 2 RDB
> > 43: this.update_SRW_db(personList);
> > 44: }
> > 45:
> > 46: private void update_SRW_db(LinkedList<PersonWikip> persons) {
> > 47: // TODO Auto-generated method stub
> > 48: }
> > 49:
> > 50: private LinkedList<PersonWikip> extractNamedentity(
> > 51: LinkedList<PersonWikip> persons) {
> > 52:
> > 53: LinkedList<PersonWikip> newList = new
> > LinkedList<PersonWikip>();
> > 54: for (int i = 0; i < persons.size(); i++) {
> > 55: PersonWikip person = persons.get(i);
> > 56:
> > 57: System.out.println("SRWikipediaMain:extractNE: "
> > 58: + person.getPersonname().getLex());
> > 59:
> > 60: person = this.extractNeeFromWebdoc(person,
> > person.getUrl_wikip());
> > 61:
> > 62: // 2007nov19/130s/for saving memory
> > 63: // newList.add(person);
> > 64: person = null;
> > 65: }
> > 66: return newList;
> > 67: }
> > 68:
> > 69: private PersonWikip extractNeeFromWebdoc(PersonWikip person, String
> > uri) {
> > 70:
> > 71: String htmlBody = null;
> > 72: try {
> > 73: htmlBody = this.dhc.doGetBody(uri);
> > 74: } catch (IllegalArgumentException e) {
> > 75: // occur when the person name is not enclosed by <a>
> > tag.
> > 76: }
> > 77:
> > 78: return this.extractNeeFromText(person, htmlBody);
> > 79: }
> > 80:
> > 81: private PersonWikip extractNeeFromText(PersonWikip person, String
> > htmlBody) {
> > 82: if (htmlBody != null) {
> > 83: // read component descriptor for IBM NEE
> > 84: XMLInputSource in = null;
> > 85: try {
> > 86: in = new
> > XMLInputSource(SRWikipediaMain.uimaDesc_ibmNee);
> > 87: } catch (IOException e) {
> > 88: e.printStackTrace();
> > 89: }
> > 90:
> > 91: // give html to analysis engine
> > 92: AnalysisEngine ae =
> > AnalysisEngineUtil.getAeInstance(in);
> > 93: JCas jcas = AnalysisEngineUtil
> > 94: .analyzeByAnalysisEngine(ae,
> > htmlBody);
> > 95:
> > 96: // set firm
> > 97: System.out.print(" - firm: ");
> > 98:
> > 99: FSIndex index =
> > jcas.getJFSIndexRepository().getAnnotationIndex(
> > 100: Company.type);
> > 101: FSIterator compIter = index.iterator();
> > 102:
> > 103: StringArray compArray = new StringArray(jcas,
> > index.size());
> > 104: int num_company = 0;
> > 105: while (compIter.hasNext()) {
> > 106: Company annot = (Company) compIter.next();
> > 107: compArray.set(num_company, annot.getLex());
> > 108: // TODO remove redundunt values
> > 109:
> > 110: num_company++;
> > 111: }
> > 112: person.setCompany_related(compArray);
> > 113:
> > System.out.print(person.getCompany_related().toArray() + " ");
> > 114:
> > 115: // set org
> > 116: System.out.println("");
> > 117: System.out.print(" - org: ");
> > 118:
> > 119: FSIterator orgIter = jcas.getJFSIndexRepository()
> > 120:
> > .getAnnotationIndex(Org.type).iterator();
> > 121: StringArray orgArray = new StringArray(jcas, 100);
> > 122: int order_org = 0;
> > 123: while (orgIter.hasNext()) {
> > 124: Org annot = (Org) orgIter.next();
> > 125: orgArray.set(order_org, annot.getLex());
> > 126:
> > 127: order_org++;
> > 128: }
> > 129: person.setCompany_related(orgArray);
> > 130: System.out.print(person.getOrg_related().toArray() +
> > " ");
> > 131:
> > 132: // read component descriptor for WikipPerson NEE
> > 133: in = null;
> > 134: jcas = null;
> > 135: try {
> > 136: in = new
> > XMLInputSource(SRWikipediaMain.uimaDesc_wikipPersonNee);
> > 137: } catch (IOException e) {
> > 138: e.printStackTrace();
> > 139: }
> > 140: // give html to analysis engine
> > 141: jcas = AnalysisEngineUtil.analyzeByAnalysisEngine(
> > 142: AnalysisEngineUtil.getAeInstance(in),
> > htmlBody);
> > 143:
> > 144: // set faculty
> > 145: // set schoold graduated
> > 146: // set pref. candidate from
> > 147: System.out.println("");
> > 148: }
> > 149:
> > 150: // TODO write 2 data base
> > 151:
> > 152: return person;
> > 153: }
> > 154:
> > 155: private String url_keiopersons_wikipedia =
> > "http://ja.wikipedia.org/wiki/%E6%85%B6%E6%87%89%E7%BE%A9%E5%A1%BE%E5%A4%A7%E5%AD%A6%E3%81%AE%E4%BA%BA%E7%89%A9%E4%B8%80%E8%A6%A7";;
> > 156:
> > 157: private LinkedList<PersonWikip> extractKeioPersonWikipedia() {
> > 158:
> > 159: XMLInputSource in = null;
> > 160: try {
> > 161: in = new
> > XMLInputSource(SRWikipediaMain.uimaDesc_personWikip);
> > 162: } catch (IOException e) {
> > 163: e.printStackTrace();
> > 164: }
> > 165: // create a JCas, given an Analysis Engine (ae)
> > 166: AnalysisEngine ae = AnalysisEngineUtil.getAeInstance(in);
> > 167: String docBody =
> > this.dhc.doGetBody(this.url_keiopersons_wikipedia);
> > 168: JCas jcas = AnalysisEngineUtil.analyzeByAnalysisEngine(ae,
> > docBody);
> > 169:
> > 170: LinkedList<PersonWikip> personList =
> > this.createPersonList(jcas);
> > 171: System.out.println("extractKeioPersonWikipedia: " +
> > personList.size());
> > 172:
> > 173: // 2007nov15/130s/this caused fatal error!!!
> > 174: // jcas.reset();
> > 175:
> > 176: return personList;
> > 177: }
> > 178:
> > 179: private LinkedList<PersonWikip> createPersonList(JCas jcas) {
> > 180: LinkedList<PersonWikip> persons = new
> > LinkedList<PersonWikip>();
> > 181:
> > 182: FSIterator personIter = jcas.getJFSIndexRepository()
> > 183:
> > .getAnnotationIndex(PersonWikip.type).iterator();
> > 184: int counter = 0;
> > 185: while (personIter.hasNext()) {
> > 186: PersonWikip p = (PersonWikip) personIter.next();
> > 187: persons.add(p);
> > 188: System.out
> > 189:
> > .println("SRWikipediaMain:createPersonList: "
> > 190: +
> > p.getPersonname().getLex() + ", URL: "
> > 191: + p.getUrl_wikip());
> > 192: counter++;
> > 193: }
> > 194: return persons;
> > 195: }
> > 196:
> > 197: public static void main(String[] args) {
> > 198: new SRWikipediaMain();
> > 199: }
> > 200: }
> > </SRWikipediaMain.java>
> >
> > Isaac
> >
> >
> > On 11/20/07, Marshall Schor <[EMAIL PROTECTED]> wrote:
> >
> >> Can you please post the stack trace so we can see the nesting of method
> >> calls leading to the null pointer exception?
> >>
> >> Thanks. -Marshall
> >>
> >> ISAO Isaac Saito wrote:
> >>
> >>> Thilo,
> >>>
> >>> Thank you for the comment.
> >>> I took following steps but the result is the same.
> >>>
> >>> 1. set /uimaj-2.2.0-incubating-bin/apache-uima/lib as a classpath
> >>> 2. clean compiled classes and build
> >>>
> >>> any comments will be appreciated.
> >>>
> >>> Isaac
> >>>
> >>> On 11/20/07, Thilo Goetz <[EMAIL PROTECTED]> wrote:
> >>>
> >>>
> >>>> Hi,
> >>>>
> >>>> this looks like you may be referring to an old version
> >>>> of your JCas classes in your classpath. The invocation
> >>>> exception may be caused because the old version of the
> >>>> Person class doesn't have the company feature yet. Please
> >>>> check your classpath and make sure the classes you run
> >>>> with are the same ones you compile against.
> >>>>
> >>>> --Thilo
> >>>>
> >>>> ISAO Isaac Saito wrote:
> >>>>
> >>>>
> >>>>> Hi all,
> >>>>>
> >>>>> Could anybody has a solution to the problem I describe below?
> >>>>>
> >>>>> Thanks in adv,
> >>>>> Isaac
> >>>>>
> >>>>>
> >>>>> - What I Want:
> >>>>> set an array of String as a feature and get them
> >>>>>
> >>>>>
> >>>>> - Phenomenon:
> >>>>>
> >>>>> -- Exception occurs and application terminates after executing
> >>>>> System.out.print(person.getCompany_related().toArray())
> >>>>>
> >>>>> Exception in thread "main" java.lang.NullPointerException
> >>>>> at
> >>>>> org.apache.uima.cas.impl.CASImpl.ll_getFSForRef(CASImpl.java:2745)
> >>>>>
> >>>>>
> >>>>> -- the content of variable shows "com.sun.jdi.InvocationException
> >>>>> occurred invoking method." after executing
> >>>>> person.setCompany_related(compArray).
> >>>>> This can be seen by using eclipse' debug mode.
> >>>>>
> >>>>>
> >>>>> - java code
> >>>>>
> >>>>> private void extractNeeFromText(String descpath, String htmlBody,
> >>>>> Annotation person) {
> >>>>> XMLInputSource in = null;
> >>>>> try {
> >>>>> in = new XMLInputSource(descpath);
> >>>>> } catch (IOException e) {
> >>>>> e.printStackTrace();
> >>>>> }
> >>>>> AnalysisEngine ae = AnalysisEngineUtil.getAeInstance(in);
> >>>>> ResourceSpecifier specifier = null;
> >>>>> AnalysisEngine ae = null;
> >>>>> try {
> >>>>> specifier =
> >>>>> UIMAFramework.getXMLParser().parseResourceSpecifier(
> >>>>> desc);
> >>>>> ae = UIMAFramework.produceAnalysisEngine(specifier);
> >>>>> } catch (InvalidXMLException e) {
> >>>>> e.printStackTrace();
> >>>>> } catch (ResourceInitializationException e) {
> >>>>> e.printStackTrace();
> >>>>> }
> >>>>> JCas jcas =
> >>>>> AnalysisEngineUtil.analyzeByAnalysisEngine(ae, htmlBody);
> >>>>> FSIndex index = jcas.getJFSIndexRepository().getAnnotationIndex(
> >>>>> Company.type);
> >>>>> StringArray compArray = new StringArray(jcas, index.size());
> >>>>> FSIterator compIter = index.iterator();
> >>>>> int num_company = 0;
> >>>>> while (compIter.hasNext()) {
> >>>>> Company annot = (Company) compIter.next();
> >>>>> compArray.set(num_company, annot.getLex());
> >>>>> // TODO remove redundunt values
> >>>>> num_company++;
> >>>>> }
> >>>>> person.setCompany_related(compArray);
> >>>>> System.out.println(person.getCompany_related().toArray());
> >>>>> }
> >>>>>
> >>>>>
> >>>>> - type system desctiption
> >>>>>
> >>>>> <?xml version="1.0" encoding="UTF-8"?>
> >>>>> <typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier";>
> >>>>> <name>Person-Wikip_TypeSystemDescriptor</name>
> >>>>> <description></description>
> >>>>> <version>1.0</version>
> >>>>> <vendor>ISAAC</vendor>
> >>>>> <imports>
> >>>>> <import
> >>>>> location="../../tae_nee_apacheUima/desc/NamedEntityTypeSystemDescriptor.xml"/>
> >>>>> </imports>
> >>>>> <types>
> >>>>> <typeDescription>
> >>>>> <name>jp.ac.keio.dmc.context.srw.types.PersonWikip</name>
> >>>>> <description>w</description>
> >>>>> <supertypeName>uima.tcas.Annotation</supertypeName>
> >>>>> <features>
> >>>>> <featureDescription>
> >>>>> <name>company_related</name>
> >>>>> <description></description>
> >>>>> <rangeTypeName>uima.cas.StringArray</rangeTypeName>
> >>>>> </featureDescription>
> >>>>> </features>
> >>>>> </typeDescription>
> >>>>> </types>
> >>>>> </typeSystemDescription>
> >>>>>
> >>>>>
> >>>>> - Referred conversation
> >>>>> http://www.ibm.com/developerworks/forums/thread.jspa?threadID=129534
> >>>>>
> >>>>>
