You are viewing a plain text version of this content. The canonical link for it is here.
Posted to user@uima.apache.org by ISAO Isaac Saito <13...@1995.sfc.ne.jp> on 2007/11/19 12:34:39 UTC
Question: Array of String as a feature
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
Re: Question: Array of String as a feature
Posted by ISAO Isaac Saito <13...@1995.sfc.ne.jp>.
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 <ms...@schor.com> 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 <ms...@schor.com> 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 <tw...@gmx.de> 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
> >>>>>
> >>>>>
Re: Question: Array of String as a feature
Posted by Marshall Schor <ms...@schor.com>.
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 <ms...@schor.com> 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 <tw...@gmx.de> 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
>>>>>
>>>>>
>>>
>>>
>
>
>
Re: Question: Array of String as a feature
Posted by ISAO Isaac Saito <13...@1995.sfc.ne.jp>.
Thilo and Marshall,
Sorry for several inconviniences.
Here is the executable resources.
http://bruch.sfc.keio.ac.jp:5130/dsweb/Get/Document-17966/srw_debugger.tar.gz
The gz file includes following files and folders:
- ./documentAnalyzer.bat : classpath is customized
- ./src/
- ./classes/
- ./descriptor/
- ./collection/ : sample html file to be analyzed
After running documentAnalyzer.bat and press analyze, you will see the
exception.
# source codes are actually different from what I posted here before,
# but the result seems same.
The annotator is specialized for japanese language, so the sample
collection is also jpn, UTF-8. I am afraid it might occur another
problem at your environment...
Thanks for your help and patience,
Isaac
On Nov 20, 2007 5:13 PM, Thilo Goetz <tw...@gmx.de> wrote:
> Hm, does the stack trace you posted match the source?
> Line 85, for example, doesn't contain any executable
> code.
>
> What would really help here is if you could put together
> a test case that we can run. Unless Marshall can see
> the issue just from looking at the code, that is really
> your best option. Create a test case, zip it up, and
> attach it to a Jira issue (with instructions on how to
> run and reproduce the problem).
>
> Thanks,
>
> Thilo
>
> 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 <ms...@schor.com> 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 <tw...@gmx.de> 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
> >>>>>
> >>>
> >>>
Re: Question: Array of String as a feature
Posted by Thilo Goetz <tw...@gmx.de>.
Hm, does the stack trace you posted match the source?
Line 85, for example, doesn't contain any executable
code.
What would really help here is if you could put together
a test case that we can run. Unless Marshall can see
the issue just from looking at the code, that is really
your best option. Create a test case, zip it up, and
attach it to a Jira issue (with instructions on how to
run and reproduce the problem).
Thanks,
Thilo
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 <ms...@schor.com> 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 <tw...@gmx.de> 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
>>>>>
>>>
>>>
Re: Question: Array of String as a feature
Posted by ISAO Isaac Saito <13...@1995.sfc.ne.jp>.
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 <ms...@schor.com> 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 <tw...@gmx.de> 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
> >>>
> >
> >
> >
Re: Question: Array of String as a feature
Posted by Marshall Schor <ms...@schor.com>.
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 <tw...@gmx.de> 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
>>>
>
>
>
Re: Question: Array of String as a feature
Posted by ISAO Isaac Saito <13...@1995.sfc.ne.jp>.
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 <tw...@gmx.de> 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
>
Re: Question: Array of String as a feature
Posted by Thilo Goetz <tw...@gmx.de>.
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