Examples with AnnotationFeature de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature used on opensource projects

Example 36 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class AutomationUtil method repeateRelationAnnotation.

public static void repeateRelationAnnotation(AnnotatorState aState, DocumentService aDocumentService, CorrectionDocumentService aCorrectionDocumentService, AnnotationSchemaService aAnnotationService, AnnotationFS fs, AnnotationFeature aFeature, String aValue) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    for (SourceDocument d : aDocumentService.listSourceDocuments(aState.getProject())) {
        loadDocument(d, aAnnotationService, aDocumentService, aCorrectionDocumentService, aState.getUser());
        JCas jCas = aCorrectionDocumentService.readCorrectionCas(d);
        ArcAdapter adapter = (ArcAdapter) aAnnotationService.getAdapter(aFeature.getLayer());
        String sourceFName = adapter.getSourceFeatureName();
        String targetFName = adapter.getTargetFeatureName();
        Type type = getType(jCas.getCas(), aFeature.getLayer().getName());
        Type spanType = getType(jCas.getCas(), adapter.getAttachTypeName());
        Feature arcSpanFeature = spanType.getFeatureByBaseName(adapter.getAttachFeatureName());
        Feature dependentFeature = type.getFeatureByBaseName(targetFName);
        Feature governorFeature = type.getFeatureByBaseName(sourceFName);
        AnnotationFS dependentFs = null;
        AnnotationFS governorFs = null;
        if (adapter.getAttachFeatureName() != null) {
            dependentFs = (AnnotationFS) fs.getFeatureValue(dependentFeature).getFeatureValue(arcSpanFeature);
            governorFs = (AnnotationFS) fs.getFeatureValue(governorFeature).getFeatureValue(arcSpanFeature);
        } else {
            dependentFs = (AnnotationFS) fs.getFeatureValue(dependentFeature);
            governorFs = (AnnotationFS) fs.getFeatureValue(governorFeature);
        }
        if (adapter.isCrossMultipleSentence()) {
            List<AnnotationFS> mSpanAnnos = new ArrayList<>(getAllAnnoFss(jCas, governorFs.getType()));
            repeatRelation(aState, 0, jCas.getDocumentText().length() - 1, aFeature, aValue, jCas, adapter, dependentFs, governorFs, mSpanAnnos);
        } else {
            for (Sentence sent : select(jCas, Sentence.class)) {
                List<AnnotationFS> spanAnnos = selectCovered(governorFs.getType(), sent);
                repeatRelation(aState, sent.getBegin(), sent.getEnd(), aFeature, aValue, jCas, adapter, dependentFs, governorFs, spanAnnos);
            }
        }
        aCorrectionDocumentService.writeCorrectionCas(jCas, d);
    }
}

Example 37 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class ImportExportServiceImpl method exportCasToFile.

/**
 * A new directory is created using UUID so that every exported file will reside in its own
 * directory. This is useful as the written file can have multiple extensions based on the
 * Writer class used.
 */
@Override
public File exportCasToFile(CAS cas, SourceDocument aDocument, String aFileName, @SuppressWarnings("rawtypes") Class aWriter, boolean aStripExtension) throws IOException, UIMAException {
    // Update the source file name in case it is changed for some reason. This is necessary
    // for the writers to create the files under the correct names.
    Project project = aDocument.getProject();
    File currentDocumentUri = new File(dir.getAbsolutePath() + "/" + PROJECT_FOLDER + "/" + project.getId() + "/" + DOCUMENT_FOLDER + "/" + aDocument.getId() + "/" + SOURCE_FOLDER);
    DocumentMetaData documentMetadata = DocumentMetaData.get(cas.getJCas());
    documentMetadata.setDocumentUri(new File(currentDocumentUri, aFileName).toURI().toURL().toExternalForm());
    documentMetadata.setDocumentBaseUri(currentDocumentUri.toURI().toURL().toExternalForm());
    documentMetadata.setCollectionId(currentDocumentUri.toURI().toURL().toExternalForm());
    documentMetadata.setDocumentUri(new File(dir.getAbsolutePath() + "/" + PROJECT_FOLDER + "/" + project.getId() + "/" + DOCUMENT_FOLDER + "/" + aDocument.getId() + "/" + SOURCE_FOLDER + "/" + aFileName).toURI().toURL().toExternalForm());
    // update with the correct tagset name
    List<AnnotationFeature> features = annotationService.listAnnotationFeature(project);
    for (AnnotationFeature feature : features) {
        TagSet tagSet = feature.getTagset();
        if (tagSet == null) {
            continue;
        } else if (!feature.getLayer().getType().equals(WebAnnoConst.CHAIN_TYPE)) {
            updateCasWithTagSet(cas, feature.getLayer().getName(), tagSet.getName());
        }
    }
    File exportTempDir = File.createTempFile("webanno", "export");
    try {
        exportTempDir.delete();
        exportTempDir.mkdirs();
        AnalysisEngineDescription writer;
        if (aWriter.getName().equals("de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv3Writer")) {
            List<AnnotationLayer> layers = annotationService.listAnnotationLayer(aDocument.getProject());
            List<String> slotFeatures = new ArrayList<>();
            List<String> slotTargets = new ArrayList<>();
            List<String> linkTypes = new ArrayList<>();
            Set<String> spanLayers = new HashSet<>();
            Set<String> slotLayers = new HashSet<>();
            for (AnnotationLayer layer : layers) {
                if (layer.getType().contentEquals(WebAnnoConst.SPAN_TYPE)) {
                    // TSV will not use this
                    if (!annotationExists(cas, layer.getName())) {
                        continue;
                    }
                    boolean isslotLayer = false;
                    for (AnnotationFeature f : annotationService.listAnnotationFeature(layer)) {
                        if (MultiValueMode.ARRAY.equals(f.getMultiValueMode()) && LinkMode.WITH_ROLE.equals(f.getLinkMode())) {
                            isslotLayer = true;
                            slotFeatures.add(layer.getName() + ":" + f.getName());
                            slotTargets.add(f.getType());
                            linkTypes.add(f.getLinkTypeName());
                        }
                    }
                    if (isslotLayer) {
                        slotLayers.add(layer.getName());
                    } else {
                        spanLayers.add(layer.getName());
                    }
                }
            }
            spanLayers.addAll(slotLayers);
            List<String> chainLayers = new ArrayList<>();
            for (AnnotationLayer layer : layers) {
                if (layer.getType().contentEquals(WebAnnoConst.CHAIN_TYPE)) {
                    if (!chainAnnotationExists(cas, layer.getName() + "Chain")) {
                        continue;
                    }
                    chainLayers.add(layer.getName());
                }
            }
            List<String> relationLayers = new ArrayList<>();
            for (AnnotationLayer layer : layers) {
                if (layer.getType().contentEquals(WebAnnoConst.RELATION_TYPE)) {
                    // TSV will not use this
                    if (!annotationExists(cas, layer.getName())) {
                        continue;
                    }
                    relationLayers.add(layer.getName());
                }
            }
            writer = createEngineDescription(aWriter, JCasFileWriter_ImplBase.PARAM_TARGET_LOCATION, exportTempDir, JCasFileWriter_ImplBase.PARAM_STRIP_EXTENSION, aStripExtension, "spanLayers", spanLayers, "slotFeatures", slotFeatures, "slotTargets", slotTargets, "linkTypes", linkTypes, "chainLayers", chainLayers, "relationLayers", relationLayers);
        } else {
            writer = createEngineDescription(aWriter, JCasFileWriter_ImplBase.PARAM_TARGET_LOCATION, exportTempDir, JCasFileWriter_ImplBase.PARAM_STRIP_EXTENSION, aStripExtension);
        }
        runPipeline(cas, writer);
        // If the writer produced more than one file, we package it up as a ZIP file
        File exportFile;
        if (exportTempDir.listFiles().length > 1) {
            exportFile = new File(exportTempDir.getAbsolutePath() + ".zip");
            try {
                ZipUtils.zipFolder(exportTempDir, exportFile);
            } catch (Exception e) {
                try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID, String.valueOf(project.getId()))) {
                    log.info("Unable to create zip File");
                }
            }
        } else {
            exportFile = new File(exportTempDir.getParent(), exportTempDir.listFiles()[0].getName());
            FileUtils.copyFile(exportTempDir.listFiles()[0], exportFile);
        }
        return exportFile;
    } finally {
        if (exportTempDir != null) {
            FileUtils.forceDelete(exportTempDir);
        }
    }
}

Example 38 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class CoreferenceLayerInitializer method configure.

@Override
public void configure(Project aProject) throws IOException {
    TagSet corefTypeTagSet = JsonImportUtil.importTagSetFromJson(aProject, new ClassPathResource("/tagsets/de-coref-type-bart.json").getInputStream(), annotationSchemaService);
    TagSet corefRelTagSet = JsonImportUtil.importTagSetFromJson(aProject, new ClassPathResource("/tagsets/de-coref-rel-tuebadz.json").getInputStream(), annotationSchemaService);
    AnnotationLayer base = new AnnotationLayer("de.tudarmstadt.ukp.dkpro.core.api.coref.type.Coreference", "Coreference", CHAIN_TYPE, aProject, true);
    base.setCrossSentence(true);
    base.setAllowStacking(true);
    base.setMultipleTokens(true);
    base.setLockToTokenOffset(false);
    annotationSchemaService.createLayer(base);
    annotationSchemaService.createFeature(new AnnotationFeature(aProject, base, "referenceType", "referenceType", CAS.TYPE_NAME_STRING, "Coreference type", corefTypeTagSet));
    annotationSchemaService.createFeature(new AnnotationFeature(aProject, base, "referenceRelation", "referenceRelation", CAS.TYPE_NAME_STRING, "Coreference relation", corefRelTagSet));
}

Example 39 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class DependencyLayerInitializer method configure.

@Override
public void configure(Project aProject) throws IOException {
    TagSet depTagSet = JsonImportUtil.importTagSetFromJson(aProject, new ClassPathResource("/tagsets/mul-dep-ud.json").getInputStream(), annotationSchemaService);
    // Dependency Layer
    AnnotationLayer depLayer = new AnnotationLayer(Dependency.class.getName(), "Dependency", RELATION_TYPE, aProject, true);
    AnnotationLayer tokenLayer = annotationSchemaService.getLayer(Token.class.getName(), aProject);
    List<AnnotationFeature> tokenFeatures = annotationSchemaService.listAnnotationFeature(tokenLayer);
    AnnotationFeature tokenPosFeature = null;
    for (AnnotationFeature feature : tokenFeatures) {
        if (feature.getName().equals("pos")) {
            tokenPosFeature = feature;
            break;
        }
    }
    depLayer.setAttachType(tokenLayer);
    depLayer.setAttachFeature(tokenPosFeature);
    annotationSchemaService.createLayer(depLayer);
    annotationSchemaService.createFeature(new AnnotationFeature(aProject, depLayer, "DependencyType", "Relation", CAS.TYPE_NAME_STRING, "Dependency relation", depTagSet));
    String[] flavors = { DependencyFlavor.BASIC, DependencyFlavor.ENHANCED };
    String[] flavorDesc = { DependencyFlavor.BASIC, DependencyFlavor.ENHANCED };
    TagSet flavorsTagset = annotationSchemaService.createTagSet("Dependency flavors", "Dependency flavors", "mul", flavors, flavorDesc, aProject);
    annotationSchemaService.createFeature(new AnnotationFeature(aProject, depLayer, "flavor", "Flavor", CAS.TYPE_NAME_STRING, "Dependency relation", flavorsTagset));
}

Example 40 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class MorphologicalFeaturesLayerInitializer method configure.

@Override
public void configure(Project aProject) throws IOException {
    AnnotationLayer tokenLayer = annotationSchemaService.getLayer(Token.class.getName(), aProject);
    AnnotationFeature tokenMorphFeature = new AnnotationFeature(aProject, tokenLayer, "morph", "morph", Lemma.class.getName());
    annotationSchemaService.createFeature(tokenMorphFeature);
    AnnotationLayer morphLayer = new AnnotationLayer(MorphologicalFeatures.class.getName(), "Morphological features", SPAN_TYPE, aProject, true);
    morphLayer.setAttachType(tokenLayer);
    morphLayer.setAttachFeature(tokenMorphFeature);
    annotationSchemaService.createLayer(morphLayer);
    AnnotationFeature valueFeature = new AnnotationFeature();
    valueFeature.setDescription("Morphological features");
    valueFeature.setName("value");
    valueFeature.setType(CAS.TYPE_NAME_STRING);
    valueFeature.setProject(aProject);
    valueFeature.setUiName("Features");
    valueFeature.setLayer(morphLayer);
    valueFeature.setIncludeInHover(true);
    valueFeature.setVisible(false);
    annotationSchemaService.createFeature(valueFeature);
}