Examples with TypeSystemDescription org.apache.uima.resource.metadata.TypeSystemDescription used on opensource projects

Example 21 with TypeSystemDescription

use of org.apache.uima.resource.metadata.TypeSystemDescription in project webanno by webanno.

the class MergeCasTest method simpleRelGovStackedTest.

@Test
public void simpleRelGovStackedTest() throws Exception {
    TypeSystemDescription customeTypesSpan = DiffUtils.createCustomTypeSystem(SPAN_TYPE, "webanno.custom.Multivalspan", asList("f1", "f2"), null);
    TypeSystemDescription customeTypesRel = DiffUtils.createCustomTypeSystem(RELATION_TYPE, "webanno.custom.Multivalrel", asList("rel1", "rel2"), "webanno.custom.Multivalspan");
    List<TypeSystemDescription> customTypes = new ArrayList<>();
    customTypes.add(customeTypesSpan);
    customTypes.add(customeTypesRel);
    TypeSystemDescription customType = CasCreationUtils.mergeTypeSystems(customTypes);
    Map<String, List<JCas>> casByUser = DiffUtils.loadWebAnnoTSV(customType, "mergecas/multivalspanrel/tale.tsv", "mergecas/multivalspanrel/tale.tsv");
    List<String> entryTypes = asList("webanno.custom.Multivalspan", "webanno.custom.Multivalrel");
    List<? extends DiffAdapter> diffAdapters = asList(new ArcDiffAdapter("webanno.custom.Multivalrel", "Dependent", "Governor", "rel1", "rel2"), new SpanDiffAdapter("webanno.custom.Multivalspan", "f1", "f2"));
    addRandomMergeCas(casByUser);
    DiffResult result = CasDiff2.doDiff(entryTypes, diffAdapters, LinkCompareBehavior.LINK_TARGET_AS_LABEL, casByUser);
    JCas mergeCas = MergeCas.reMergeCas(result, getSingleCasByUser(casByUser));
    casByUser = new HashMap<>();
    JCas actual = DiffUtils.readWebAnnoTSV("mergecas/multivalspanrel/tale2.tsv", customType);
    casByUser.put("actual", asList(actual));
    casByUser.put("merge", asList(mergeCas));
    result = CasDiff2.doDiff(entryTypes, diffAdapters, LinkCompareBehavior.LINK_TARGET_AS_LABEL, casByUser);
    assertEquals(0, result.getDifferingConfigurationSets().size());
    assertEquals(0, result.getIncompleteConfigurationSets().size());
}

Example 22 with TypeSystemDescription

use of org.apache.uima.resource.metadata.TypeSystemDescription in project webanno by webanno.

the class MergeCasTest method relStackedTest.

@Test
public void relStackedTest() throws Exception {
    TypeSystemDescription customeTypesSpan = DiffUtils.createCustomTypeSystem(SPAN_TYPE, "webanno.custom.Multivalspan", asList("f1", "f2"), null);
    TypeSystemDescription customeTypesRel = DiffUtils.createCustomTypeSystem(RELATION_TYPE, "webanno.custom.Multivalrel", asList("rel1", "rel2"), "webanno.custom.Multivalspan");
    List<TypeSystemDescription> customTypes = new ArrayList<>();
    customTypes.add(customeTypesSpan);
    customTypes.add(customeTypesRel);
    TypeSystemDescription customType = CasCreationUtils.mergeTypeSystems(customTypes);
    Map<String, List<JCas>> casByUser = DiffUtils.loadXMI(customType, "mergecas/multivalspanrel/stackedrel1.xmi", "mergecas/multivalspanrel/stackedrel2.xmi");
    List<String> entryTypes = asList("webanno.custom.Multivalspan", "webanno.custom.Multivalrel");
    List<? extends DiffAdapter> diffAdapters = asList(new ArcDiffAdapter("webanno.custom.Multivalrel", "Dependent", "Governor", "rel1", "rel2"), new SpanDiffAdapter("webanno.custom.Multivalspan", "f1", "f2"));
    addRandomMergeCas(casByUser);
    DiffResult result = CasDiff2.doDiff(entryTypes, diffAdapters, LinkCompareBehavior.LINK_TARGET_AS_LABEL, casByUser);
    JCas mergeCas = MergeCas.reMergeCas(result, getSingleCasByUser(casByUser));
    JCas actual = DiffUtils.readXMI("mergecas/multivalspanrel/stackedmerge.xmi", customType);
    Type relType = mergeCas.getTypeSystem().getType("webanno.custom.Multivalrel");
    int numRelMerge = CasUtil.select(mergeCas.getCas(), relType).size();
    int numRelActual = CasUtil.select(actual.getCas(), relType).size();
    Type spanType = mergeCas.getTypeSystem().getType("webanno.custom.Multivalspan");
    int numspanMerge = CasUtil.select(mergeCas.getCas(), spanType).size();
    int numspanActual = CasUtil.select(actual.getCas(), spanType).size();
    assertEquals(2, numRelMerge);
    assertEquals(2, numRelActual);
    assertEquals(4, numspanMerge);
    assertEquals(4, numspanActual);
}

Example 23 with TypeSystemDescription

use of org.apache.uima.resource.metadata.TypeSystemDescription in project webanno by webanno.

the class CasDiff2Test method relationStackedSpansTest.

@Test
public void relationStackedSpansTest() throws Exception {
    TypeSystemDescription global = TypeSystemDescriptionFactory.createTypeSystemDescription();
    TypeSystemDescription local = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("src/test/resources/desc/type/webannoTestTypes.xml");
    TypeSystemDescription merged = CasCreationUtils.mergeTypeSystems(asList(global, local));
    TokenBuilder<Token, Sentence> tb = new TokenBuilder<>(Token.class, Sentence.class);
    JCas jcasA = JCasFactory.createJCas(merged);
    {
        CAS casA = jcasA.getCas();
        tb.buildTokens(jcasA, "This is a test .");
        List<Token> tokensA = new ArrayList<>(select(jcasA, Token.class));
        Token t1A = tokensA.get(0);
        Token t2A = tokensA.get(tokensA.size() - 1);
        NamedEntity govA = new NamedEntity(jcasA, t1A.getBegin(), t1A.getEnd());
        govA.addToIndexes();
        // Here we add a stacked named entity!
        new NamedEntity(jcasA, t1A.getBegin(), t1A.getEnd()).addToIndexes();
        NamedEntity depA = new NamedEntity(jcasA, t2A.getBegin(), t2A.getEnd());
        depA.addToIndexes();
        Type relationTypeA = casA.getTypeSystem().getType("webanno.custom.Relation");
        AnnotationFS fs1A = casA.createAnnotation(relationTypeA, depA.getBegin(), depA.getEnd());
        FSUtil.setFeature(fs1A, "Governor", govA);
        FSUtil.setFeature(fs1A, "Dependent", depA);
        FSUtil.setFeature(fs1A, "value", "REL");
        casA.addFsToIndexes(fs1A);
    }
    JCas jcasB = JCasFactory.createJCas(merged);
    {
        CAS casB = jcasB.getCas();
        tb.buildTokens(jcasB, "This is a test .");
        List<Token> tokensB = new ArrayList<>(select(jcasB, Token.class));
        Token t1B = tokensB.get(0);
        Token t2B = tokensB.get(tokensB.size() - 1);
        NamedEntity govB = new NamedEntity(jcasB, t1B.getBegin(), t1B.getEnd());
        govB.addToIndexes();
        NamedEntity depB = new NamedEntity(jcasB, t2B.getBegin(), t2B.getEnd());
        depB.addToIndexes();
        Type relationTypeB = casB.getTypeSystem().getType("webanno.custom.Relation");
        AnnotationFS fs1B = casB.createAnnotation(relationTypeB, depB.getBegin(), depB.getEnd());
        FSUtil.setFeature(fs1B, "Governor", govB);
        FSUtil.setFeature(fs1B, "Dependent", depB);
        FSUtil.setFeature(fs1B, "value", "REL");
        casB.addFsToIndexes(fs1B);
    }
    Map<String, List<JCas>> casByUser = new LinkedHashMap<>();
    casByUser.put("user1", asList(jcasA));
    casByUser.put("user2", asList(jcasB));
    List<String> entryTypes = asList("webanno.custom.Relation");
    List<? extends DiffAdapter> diffAdapters = asList(new ArcDiffAdapter("webanno.custom.Relation", WebAnnoConst.FEAT_REL_TARGET, WebAnnoConst.FEAT_REL_SOURCE, "value"));
    DiffResult diff = CasDiff2.doDiff(entryTypes, diffAdapters, LinkCompareBehavior.LINK_TARGET_AS_LABEL, casByUser);
    diff.print(System.out);
    assertEquals(1, diff.size());
    assertEquals(0, diff.getDifferingConfigurationSets().size());
    assertEquals(0, diff.getIncompleteConfigurationSets().size());
    // Check against new impl
    AgreementResult agreement = AgreementUtils.getCohenKappaAgreement(diff, "webanno.custom.Relation", "value", casByUser);
    // Asserts
    System.out.printf("Agreement: %s%n", agreement.toString());
    AgreementUtils.dumpAgreementStudy(System.out, agreement);
    assertEquals(1, agreement.getPluralitySets().size());
}

Example 24 with TypeSystemDescription

use of org.apache.uima.resource.metadata.TypeSystemDescription in project webanno by webanno.

the class MiraAutomationServiceImpl method readInitialCas.

@Override
public JCas readInitialCas(TrainingDocument aDocument) throws CASException, ResourceInitializationException, IOException {
    JCas jcas = CasCreationUtils.createCas((TypeSystemDescription) null, null, null).getJCas();
    CasPersistenceUtils.readSerializedCas(jcas, getCasFile(aDocument));
    automationCasStorageService.analyzeAndRepair(aDocument, jcas.getCas());
    return jcas;
}

Example 25 with TypeSystemDescription

use of org.apache.uima.resource.metadata.TypeSystemDescription in project webanno by webanno.

the class DiffUtils method createMultiLinkWithRoleTestTypeSytem.

public static TypeSystemDescription createMultiLinkWithRoleTestTypeSytem(String... aFeatures) throws Exception {
    List<TypeSystemDescription> typeSystems = new ArrayList<>();
    TypeSystemDescription tsd = new TypeSystemDescription_impl();
    // Link type
    TypeDescription linkTD = tsd.addType(LINK_TYPE, "", CAS.TYPE_NAME_TOP);
    linkTD.addFeature("role", "", CAS.TYPE_NAME_STRING);
    linkTD.addFeature("target", "", Token.class.getName());
    // Link host
    TypeDescription hostTD = tsd.addType(HOST_TYPE, "", CAS.TYPE_NAME_ANNOTATION);
    hostTD.addFeature("links", "", CAS.TYPE_NAME_FS_ARRAY, linkTD.getName(), false);
    for (String feature : aFeatures) {
        hostTD.addFeature(feature, "", CAS.TYPE_NAME_STRING);
    }
    typeSystems.add(tsd);
    typeSystems.add(TypeSystemDescriptionFactory.createTypeSystemDescription());
    return CasCreationUtils.mergeTypeSystems(typeSystems);
}