diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index b19a2e4180..7e03bbfd48 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -14,6 +14,9 @@ on: pull_request: branches: [ "main", "release/**" ] +permissions: + contents: read + jobs: build: strategy: diff --git a/dkpro-core-api-datasets-asl/src/main/java/org/dkpro/core/api/datasets/DatasetLoader.java b/dkpro-core-api-datasets-asl/src/main/java/org/dkpro/core/api/datasets/DatasetLoader.java index e94de6c148..5efdd677d6 100644 --- a/dkpro-core-api-datasets-asl/src/main/java/org/dkpro/core/api/datasets/DatasetLoader.java +++ b/dkpro-core-api-datasets-asl/src/main/java/org/dkpro/core/api/datasets/DatasetLoader.java @@ -250,8 +250,8 @@ private void extract(File aArchive, ArchiveInputStream aArchiveStream, File aTar throw new IllegalStateException("Filename must not contain line break"); } - Path base = aTarget.toPath().toAbsolutePath(); - Path out = base.resolve(name).toAbsolutePath(); + Path base = aTarget.toPath().toAbsolutePath().normalize(); + Path out = base.resolve(name).toAbsolutePath().normalize(); if (!out.startsWith(base)) { // Ignore attempts to write outside the base diff --git a/dkpro-core-api-datasets-asl/src/main/java/org/dkpro/core/api/datasets/internal/actions/Explode.java b/dkpro-core-api-datasets-asl/src/main/java/org/dkpro/core/api/datasets/internal/actions/Explode.java index f6e9c0d5f2..5f65c1cefd 100644 --- a/dkpro-core-api-datasets-asl/src/main/java/org/dkpro/core/api/datasets/internal/actions/Explode.java +++ b/dkpro-core-api-datasets-asl/src/main/java/org/dkpro/core/api/datasets/internal/actions/Explode.java @@ -109,7 +109,8 @@ private void extract7z(ActionDescription aAction, Path aArchive, Path aTarget) throws IOException, RarException { // We always extract archives into a subfolder. Figure out the name of the folder. - Path base = aTarget.resolve(getPathWithoutFileExtension(aArchive)).toAbsolutePath(); + Path base = aTarget.resolve(getPathWithoutFileExtension(aArchive)).toAbsolutePath() + .normalize(); Map cfg = aAction.getConfiguration(); int strip = cfg.containsKey("strip") ? (int) cfg.get("strip") : 0; @@ -131,7 +132,7 @@ private void extract7z(ActionDescription aAction, Path aArchive, Path aTarget) } if (filter.accept(name)) { - Path out = base.resolve(name).toAbsolutePath(); + Path out = base.resolve(name).toAbsolutePath().normalize(); if (!out.startsWith(base)) { throw new IOException( "Archive tries to generate file outside target folder: [" + name @@ -159,7 +160,8 @@ private void extractRar(ActionDescription aAction, Path aArchive, Path aTarget) throws IOException, RarException { // We always extract archives into a subfolder. Figure out the name of the folder. - Path base = aTarget.resolve(getPathWithoutFileExtension(aArchive)).toAbsolutePath(); + Path base = aTarget.resolve(getPathWithoutFileExtension(aArchive)).toAbsolutePath() + .normalize(); Map cfg = aAction.getConfiguration(); int strip = cfg.containsKey("strip") ? (int) cfg.get("strip") : 0; @@ -181,7 +183,7 @@ private void extractRar(ActionDescription aAction, Path aArchive, Path aTarget) } if (filter.accept(name)) { - Path out = base.resolve(name).toAbsolutePath(); + Path out = base.resolve(name).toAbsolutePath().normalize(); if (!out.startsWith(base)) { throw new IOException( "Archive tries to generate file outside target folder: [" + name @@ -209,7 +211,8 @@ private void extract(ActionDescription aAction, Path aArchive, ArchiveInputStrea throws IOException { // We always extract archives into a subfolder. Figure out the name of the folder. - Path base = aTarget.resolve(getPathWithoutFileExtension(aArchive)).toAbsolutePath(); + Path base = aTarget.resolve(getPathWithoutFileExtension(aArchive)).toAbsolutePath() + .normalize(); Map cfg = aAction.getConfiguration(); int strip = cfg.containsKey("strip") ? (int) cfg.get("strip") : 0; @@ -230,7 +233,7 @@ private void extract(ActionDescription aAction, Path aArchive, ArchiveInputStrea } if (filter.accept(name)) { - Path out = base.resolve(name).toAbsolutePath(); + Path out = base.resolve(name).toAbsolutePath().normalize(); if (!out.startsWith(base)) { throw new IOException( "Archive tries to generate file outside target folder: [" + name + "]"); diff --git a/dkpro-core-api-frequency-asl/src/main/java/org/dkpro/core/api/frequency/util/FrequencyDistribution.java b/dkpro-core-api-frequency-asl/src/main/java/org/dkpro/core/api/frequency/util/FrequencyDistribution.java index d5b599bce1..f6bf38be96 100644 --- a/dkpro-core-api-frequency-asl/src/main/java/org/dkpro/core/api/frequency/util/FrequencyDistribution.java +++ b/dkpro-core-api-frequency-asl/src/main/java/org/dkpro/core/api/frequency/util/FrequencyDistribution.java @@ -255,7 +255,7 @@ public void load(File file) throws IOException, ClassNotFoundException freqDist = (Object2LongOpenHashMap) in.readObject(); in.close(); - int samples = 0; + long samples = 0; LongIterator sampleIter = freqDist.values().iterator(); diff --git a/dkpro-core-api-io-asl/src/main/java/org/dkpro/core/api/io/JCasFileWriter_ImplBase.java b/dkpro-core-api-io-asl/src/main/java/org/dkpro/core/api/io/JCasFileWriter_ImplBase.java index d8e4a401ff..3ed63f196a 100644 --- a/dkpro-core-api-io-asl/src/main/java/org/dkpro/core/api/io/JCasFileWriter_ImplBase.java +++ b/dkpro-core-api-io-asl/src/main/java/org/dkpro/core/api/io/JCasFileWriter_ImplBase.java @@ -27,6 +27,7 @@ import java.net.URI; import java.net.URLDecoder; import java.net.URLEncoder; +import java.nio.file.Paths; import java.util.zip.ZipEntry; import java.util.zip.ZipOutputStream; @@ -217,8 +218,13 @@ else if (targetLocation.startsWith(JAR_PREFIX)) { } // Begin new entry - ZipEntry entry = new ZipEntry( - zipEntryPrefix + aRelativePath + aExtension + compression.getExtension()); + String entryName = zipEntryPrefix + aRelativePath + aExtension + + compression.getExtension(); + if (Paths.get(entryName).normalize().startsWith("..")) { + throw new IOException( + "ZIP entry name [" + entryName + "] would escape archive root"); + } + ZipEntry entry = new ZipEntry(entryName); zipOutputStream.putNextEntry(entry); // We return an OutputStream for an individual entry. When this is closed by the diff --git a/dkpro-core-api-parameter-asl/src/main/java/org/dkpro/core/api/parameter/MimeTypes.java b/dkpro-core-api-parameter-asl/src/main/java/org/dkpro/core/api/parameter/MimeTypes.java index abc1c11a67..799c24e6dc 100644 --- a/dkpro-core-api-parameter-asl/src/main/java/org/dkpro/core/api/parameter/MimeTypes.java +++ b/dkpro-core-api-parameter-asl/src/main/java/org/dkpro/core/api/parameter/MimeTypes.java @@ -100,9 +100,6 @@ public final class MimeTypes public final static String APPLICATION_X_STANFORDNLP_NER = "application/x.org.dkpro.core.stanfordnlp.ner"; public final static String APPLICATION_X_STANFORDNLP_TAGGER = "application/x.org.dkpro.core.stanfordnlp.tagger"; - // LingPipe model types - public final static String APPLICATION_X_LINGPIPE_NER = "application/x.org.dkpro.core.lingpipe.ner"; - // ArkTweet model types public final static String APPLICATION_X_ARKTWEET_TAGGER = "application/x.org.dkpro.core.arktweet.tagger"; diff --git a/dkpro-core-api-parameter-asl/src/main/resources/META-INF/eu.openminted.share/mimeTypeMapping.map b/dkpro-core-api-parameter-asl/src/main/resources/META-INF/eu.openminted.share/mimeTypeMapping.map index c98a230fb4..e0ce742edb 100644 --- a/dkpro-core-api-parameter-asl/src/main/resources/META-INF/eu.openminted.share/mimeTypeMapping.map +++ b/dkpro-core-api-parameter-asl/src/main/resources/META-INF/eu.openminted.share/mimeTypeMapping.map @@ -5,7 +5,6 @@ application/vnd.xmi+xml=http://w3id.org/meta-share/omtd-share/Xmi #application/x.org.dkpro.ancora+xml application/x.org.dkpro.bnc+xml=http://w3id.org/meta-share/omtd-share/BncFormat application/x.org.dkpro.brat=http://w3id.org/meta-share/omtd-share/Brat -#application/x.org.dkpro.core.lingpipe.ner #application/x.org.dkpro.core.opennlp.chunk #application/x.org.dkpro.core.opennlp.lemma #application/x.org.dkpro.core.opennlp.ner diff --git a/dkpro-core-decompounding-asl/src/main/java/org/dkpro/core/decompounding/ranking/CompoundProbabilityRanker.java b/dkpro-core-decompounding-asl/src/main/java/org/dkpro/core/decompounding/ranking/CompoundProbabilityRanker.java index b3b1a55f9c..bc970f88f3 100644 --- a/dkpro-core-decompounding-asl/src/main/java/org/dkpro/core/decompounding/ranking/CompoundProbabilityRanker.java +++ b/dkpro-core-decompounding-asl/src/main/java/org/dkpro/core/decompounding/ranking/CompoundProbabilityRanker.java @@ -76,9 +76,9 @@ public List rank(List aSplits) /** * Calculates the weight for a split */ - private float calcRank(DecompoundedWord aSplit) + private double calcRank(DecompoundedWord aSplit) { - float result = 0; + double result = 0; for (Fragment elem : aSplit.getSplits()) { result += -1 * Math diff --git a/dkpro-core-gpl/pom.xml b/dkpro-core-gpl/pom.xml index 5a0a748d16..a363bac889 100644 --- a/dkpro-core-gpl/pom.xml +++ b/dkpro-core-gpl/pom.xml @@ -42,7 +42,6 @@ ../dkpro-core-corenlp-gpl - ../dkpro-core-lingpipe-gpl ../dkpro-core-sfst-gpl ../dkpro-core-io-tgrep-gpl diff --git a/dkpro-core-lingpipe-gpl/.license-header.txt b/dkpro-core-lingpipe-gpl/.license-header.txt deleted file mode 100644 index bbaf6e0e56..0000000000 --- a/dkpro-core-lingpipe-gpl/.license-header.txt +++ /dev/null @@ -1,16 +0,0 @@ -Copyright ${inceptionYear}-${currentYear} -Ubiquitous Knowledge Processing (UKP) Lab -Technische Universität Darmstadt - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see http://www.gnu.org/licenses/. diff --git a/dkpro-core-lingpipe-gpl/LICENSE.txt b/dkpro-core-lingpipe-gpl/LICENSE.txt deleted file mode 100644 index 99ace43661..0000000000 --- a/dkpro-core-lingpipe-gpl/LICENSE.txt +++ /dev/null @@ -1,888 +0,0 @@ -The code in this repository is licensed under the Apache License 2.0. Some parts may depend on -libraries licensed under the GPL. These parts should be considered under GPL for the -purpose of use. For the purpose of refactoring, the respective code may be used under the ASL -2.0 as long as all references to the GPLed libraries are removed. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. - diff --git a/dkpro-core-lingpipe-gpl/pom.xml b/dkpro-core-lingpipe-gpl/pom.xml deleted file mode 100644 index ac0d8c41e8..0000000000 --- a/dkpro-core-lingpipe-gpl/pom.xml +++ /dev/null @@ -1,189 +0,0 @@ - - - 4.0.0 - - - org.dkpro.core - dkpro-core-gpl - 3.0.0-SNAPSHOT - ../dkpro-core-gpl - - - dkpro-core-lingpipe-gpl - jar - DKPro Core GPL - LingPipe (v ${lingpipe.version}) - https://dkpro.github.io/dkpro-core/ - - - 4.1.2-JL1.0 - - - - - org.apache.uima - uimaj-core - - - org.apache.uima - uimafit-core - - - commons-io - commons-io - - - org.apache.commons - commons-lang3 - - - de.julielab - aliasi-lingpipe - ${lingpipe.version} - - - org.dkpro.core - dkpro-core-api-metadata-asl - ${project.version} - - - org.dkpro.core - dkpro-core-api-resources-asl - ${project.version} - - - org.dkpro.core - dkpro-core-api-segmentation-asl - ${project.version} - - - org.dkpro.core - dkpro-core-api-lexmorph-asl - ${project.version} - - - org.dkpro.core - dkpro-core-api-ner-asl - ${project.version} - - - org.dkpro.core - dkpro-core-api-parameter-asl - ${project.version} - - - eu.openminted.share.annotations - omtd-share-annotations-api - - - org.dkpro.core - dkpro-core-testing-asl - ${project.version} - test - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-bio-genia - test - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-bio-medpost - test - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-general-brown - test - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-news-muc6 - test - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-bio-genia - test - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-bio-genetag - test - - - - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-bio-genia - 20110623.1 - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-bio-medpost - 20110623.1 - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-general-brown - 20110623.1 - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-news-muc6 - 20110623.1 - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-bio-genia - 20110623.1 - - - de.tudarmstadt.ukp.dkpro.core - de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-bio-genetag - 20110623.1 - - - - - - - - - org.apache.maven.plugins - maven-dependency-plugin - - - - de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-bio-genia - de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-bio-medpost - de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.lingpipe-model-tagger-en-general-brown - de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-news-muc6 - de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-bio-genia - de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.lingpipe-model-ner-en-bio-genetag - - - - - - - diff --git a/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizer.java b/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizer.java deleted file mode 100644 index 84b18074b3..0000000000 --- a/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizer.java +++ /dev/null @@ -1,239 +0,0 @@ -/* - * Copyright 2007-2024 - * Ubiquitous Knowledge Processing (UKP) Lab - * Technische Universität Darmstadt - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see http://www.gnu.org/licenses/. - */ -package org.dkpro.core.lingpipe; - -import static java.util.Arrays.asList; -import static org.apache.uima.fit.util.JCasUtil.select; -import static org.apache.uima.fit.util.JCasUtil.toText; -import static org.apache.uima.util.Level.INFO; -import static org.dkpro.core.api.resources.MappingProviderFactory.createNerMappingProvider; - -import java.io.InputStream; -import java.io.ObjectInputStream; -import java.util.ArrayList; -import java.util.List; -import java.util.Map; - -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.lang3.reflect.FieldUtils; -import org.apache.uima.UimaContext; -import org.apache.uima.analysis_engine.AnalysisEngineProcessException; -import org.apache.uima.cas.CAS; -import org.apache.uima.cas.Type; -import org.apache.uima.fit.component.JCasAnnotator_ImplBase; -import org.apache.uima.fit.descriptor.ConfigurationParameter; -import org.apache.uima.fit.descriptor.ResourceMetaData; -import org.apache.uima.fit.descriptor.TypeCapability; -import org.apache.uima.jcas.JCas; -import org.apache.uima.resource.ResourceInitializationException; -import org.dkpro.core.api.metadata.SingletonTagset; -import org.dkpro.core.api.parameter.ComponentParameters; -import org.dkpro.core.api.parameter.MimeTypes; -import org.dkpro.core.api.parameter.ResourceParameter; -import org.dkpro.core.api.resources.MappingProvider; -import org.dkpro.core.api.resources.ModelProviderBase; - -import com.aliasi.chunk.AbstractCharLmRescoringChunker; -import com.aliasi.chunk.Chunk; -import com.aliasi.chunk.Chunker; -import com.aliasi.chunk.Chunking; -import com.aliasi.chunk.HmmChunker; -import com.aliasi.chunk.TokenShapeChunker; -import com.aliasi.hmm.HiddenMarkovModel; -import com.aliasi.symbol.SymbolTable; - -import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity; -import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token; -import eu.openminted.share.annotations.api.Component; -import eu.openminted.share.annotations.api.constants.OperationType; - -/** - * LingPipe named entity recognizer. - */ -@Component(OperationType.NAMED_ENTITITY_RECOGNIZER) -@ResourceMetaData(name = "LingPipe Named Entity Recognizer") -@TypeCapability(inputs = { - "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token" }, outputs = { - "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity" }) -public class LingPipeNamedEntityRecognizer - extends JCasAnnotator_ImplBase -{ - /** - * Log the tag set(s) when a model is loaded. - */ - public static final String PARAM_PRINT_TAGSET = ComponentParameters.PARAM_PRINT_TAGSET; - @ConfigurationParameter(name = PARAM_PRINT_TAGSET, mandatory = true, defaultValue = "false") - protected boolean printTagSet; - - /** - * Use this language instead of the document language to resolve the model. - */ - public static final String PARAM_LANGUAGE = ComponentParameters.PARAM_LANGUAGE; - @ConfigurationParameter(name = PARAM_LANGUAGE, mandatory = false) - protected String language; - - /** - * Variant of a model the model. Used to address a specific model if here are multiple models - * for one language. - */ - public static final String PARAM_VARIANT = ComponentParameters.PARAM_VARIANT; - @ConfigurationParameter(name = PARAM_VARIANT, mandatory = false) - protected String variant; - - /** - * URI of the model artifact. This can be used to override the default model resolving mechanism - * and directly address a particular model. - * - *

- * The URI format is {@code mvn:${groupId}:${artifactId}:${version}}. Remember to set the - * variant parameter to match the artifact. If the artifact contains the model in a non-default - * location, you also have to specify the model location parameter, e.g. - * {@code classpath:/model/path/in/artifact/model.bin}. - *

- */ - public static final String PARAM_MODEL_ARTIFACT_URI = ComponentParameters.PARAM_MODEL_ARTIFACT_URI; - @ConfigurationParameter(name = PARAM_MODEL_ARTIFACT_URI, mandatory = false) - protected String modelArtifactUri; - - /** - * Location from which the model is read. - */ - public static final String PARAM_MODEL_LOCATION = ComponentParameters.PARAM_MODEL_LOCATION; - @ConfigurationParameter(name = PARAM_MODEL_LOCATION, mandatory = false) - @ResourceParameter(MimeTypes.APPLICATION_X_LINGPIPE_NER) - protected String modelLocation; - - /** - * Location of the mapping file for named entity tags to UIMA types. - */ - public static final String PARAM_NAMED_ENTITY_MAPPING_LOCATION = // - ComponentParameters.PARAM_NAMED_ENTITY_MAPPING_LOCATION; - @ConfigurationParameter(name = PARAM_NAMED_ENTITY_MAPPING_LOCATION, mandatory = false) - protected String mappingLocation; - - private ModelProviderBase modelProvider; - private MappingProvider mappingProvider; - - @Override - public void initialize(UimaContext aContext) throws ResourceInitializationException - { - super.initialize(aContext); - - modelProvider = new ModelProviderBase(this, "lingpipe", "ner") - { - { - setDefault(GROUP_ID, "de.tudarmstadt.ukp.dkpro.core"); - setDefault(LOCATION, - "classpath:/de/tudarmstadt/ukp/dkpro/core/lingpipe/lib/ner-${language}-${variant}.properties"); - } - - @Override - protected Chunker produceResource(InputStream aStream) throws Exception - { - ObjectInputStream ois = new ObjectInputStream(aStream); - Chunker chunker = (Chunker) ois.readObject(); - - System.out.println(chunker.getClass()); - - SingletonTagset tags = new SingletonTagset(NamedEntity.class, null); - if (chunker instanceof HmmChunker) { - HiddenMarkovModel hmm = ((HmmChunker) chunker).getDecoder().getHmm(); - - List prefixes = asList("B_", "M_", "E_", "W_", "BB_O_", "EE_O_", - "WW_O_"); - - for (int n = 0; n < hmm.stateSymbolTable().numSymbols(); n++) { - String tag = hmm.stateSymbolTable().idToSymbol(n); - - if (prefixes.contains(StringUtils.substring(tag, 0, 5))) { - tag = tag.substring(5); - } - else if (prefixes.contains(StringUtils.substring(tag, 0, 2))) { - tag = tag.substring(2); - } - if ("BOS".equals(tag) || "MM_O".equals(tag)) { - // BOS is reserved by the system - continue; - } - - tags.add(tag); - } - } - else if (chunker instanceof TokenShapeChunker) { - Object decoder = FieldUtils.readField(chunker, "mDecoder", true); - Object estimator = FieldUtils.readField(decoder, "mEstimator", true); - SymbolTable tagTable = (SymbolTable) FieldUtils.readField(estimator, - "mTagSymbolTable", true); - for (int n = 0; n < tagTable.numSymbols(); n++) { - String tag = tagTable.idToSymbol(n); - // Handle BIO encoding - if (tag.startsWith("B-") || tag.startsWith("I-")) { - tag = tag.substring(2); - } - if ("O".equals(tag)) { - continue; - } - tags.add(tag); - } - } - else if (chunker instanceof AbstractCharLmRescoringChunker) { - @SuppressWarnings("unchecked") - Map typeToChar = (Map) FieldUtils - .readField(chunker, "mTypeToChar", true); - for (String tag : typeToChar.keySet()) { - tags.add(tag); - } - } - addTagset(tags); - - if (printTagSet) { - getContext().getLogger().log(INFO, tags.toString()); - } - - return chunker; - } - }; - - mappingProvider = createNerMappingProvider(this, mappingLocation, language, variant, - modelProvider); - } - - @Override - public void process(JCas aJCas) throws AnalysisEngineProcessException - { - CAS cas = aJCas.getCas(); - modelProvider.configure(cas); - mappingProvider.configure(cas); - - // get the document text - List tokenList = new ArrayList(select(aJCas, Token.class)); - String[] tokens = toText(tokenList).toArray(new String[tokenList.size()]); - - Chunking chunking = modelProvider.getResource().chunk(cas.getDocumentText()); - - // get the named entities and their character offsets - for (Chunk namedEntity : chunking.chunkSet()) { - Type type = mappingProvider.getTagType(namedEntity.type()); - NamedEntity neAnno = (NamedEntity) cas.createAnnotation(type, namedEntity.start(), - namedEntity.end()); - neAnno.setValue(namedEntity.type()); - neAnno.addToIndexes(); - } - } -} diff --git a/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizerTrainer.java b/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizerTrainer.java deleted file mode 100644 index ad82ffbe95..0000000000 --- a/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizerTrainer.java +++ /dev/null @@ -1,268 +0,0 @@ -/* - * Copyright 2007-2024 - * Ubiquitous Knowledge Processing (UKP) Lab - * Technische Universität Darmstadt - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see http://www.gnu.org/licenses/. - */ -package org.dkpro.core.lingpipe; - -import static org.apache.uima.fit.util.JCasUtil.indexCovered; -import static org.apache.uima.fit.util.JCasUtil.select; - -import java.io.File; -import java.io.FileInputStream; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.PrintWriter; -import java.nio.charset.StandardCharsets; -import java.util.ArrayList; -import java.util.Collection; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.regex.Pattern; - -import org.apache.commons.io.IOUtils; -import org.apache.uima.analysis_engine.AnalysisEngineProcessException; -import org.apache.uima.fit.component.JCasConsumer_ImplBase; -import org.apache.uima.fit.descriptor.ConfigurationParameter; -import org.apache.uima.fit.descriptor.MimeTypeCapability; -import org.apache.uima.fit.descriptor.ResourceMetaData; -import org.apache.uima.jcas.JCas; -import org.dkpro.core.api.parameter.ComponentParameters; -import org.dkpro.core.api.parameter.MimeTypes; -import org.xml.sax.InputSource; - -import com.aliasi.chunk.BioTagChunkCodec; -import com.aliasi.chunk.CharLmRescoringChunker; -import com.aliasi.chunk.Chunking; -import com.aliasi.chunk.TagChunkCodec; -import com.aliasi.chunk.TagChunkCodecAdapters; -import com.aliasi.corpus.ObjectHandler; -import com.aliasi.corpus.StringParser; -import com.aliasi.tag.LineTaggingParser; -import com.aliasi.tag.Tagging; -import com.aliasi.tokenizer.IndoEuropeanTokenizerFactory; -import com.aliasi.tokenizer.TokenizerFactory; -import com.aliasi.util.AbstractExternalizable; - -import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity; -import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence; -import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token; -import eu.openminted.share.annotations.api.Component; -import eu.openminted.share.annotations.api.Parameters; -import eu.openminted.share.annotations.api.constants.OperationType; - -/** - * LingPipe named entity recognizer trainer. - */ -@Component(OperationType.TRAINER_OF_MACHINE_LEARNING_MODELS) -@MimeTypeCapability(MimeTypes.APPLICATION_X_LINGPIPE_NER) -@Parameters(exclude = { LingPipeNamedEntityRecognizerTrainer.PARAM_TARGET_LOCATION }) -@ResourceMetaData(name = "LingPipe Named Entity Recognizer Trainer") -public class LingPipeNamedEntityRecognizerTrainer - extends JCasConsumer_ImplBase -{ - /** - * Location to which the output is written. - */ - public static final String PARAM_TARGET_LOCATION = ComponentParameters.PARAM_TARGET_LOCATION; - @ConfigurationParameter(name = PARAM_TARGET_LOCATION, mandatory = true) - private File targetLocation; - - /** - * Regex to filter the {@link de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity#getValue() - * named entity} by type. - */ - public static final String PARAM_ACCEPTED_TAGS_REGEX = ComponentParameters.PARAM_ACCEPTED_TAGS_REGEX; - @ConfigurationParameter(name = PARAM_ACCEPTED_TAGS_REGEX, mandatory = false) - protected String acceptedTagsRegex; - - private static final int NUM_CHUNKINGS_RESCORED = 64; - - private static final int NUM_CHARS = 256; - - private int nGram = 12; - - private File tempData; - private PrintWriter out; - - @Override - public void process(JCas aJCas) throws AnalysisEngineProcessException - { - if (tempData == null) { - try { - tempData = File.createTempFile("dkpro-lingpipe-ner-trainer", ".tsv"); - out = new PrintWriter(new OutputStreamWriter(new FileOutputStream(tempData), - StandardCharsets.UTF_8)); - } - catch (IOException e) { - throw new AnalysisEngineProcessException(e); - } - } - - Map> index = indexCovered(aJCas, Sentence.class, Token.class); - Map> neIndex = getNamedEntityIndex(aJCas); - - for (Sentence sentence : select(aJCas, Sentence.class)) { - Collection tokens = index.get(sentence); - - NamedEntity ne = null; - for (Token token : tokens) { - out.print(token.getText()); - - Collection coveredNEs = neIndex.get(token); - if (coveredNEs != null && !coveredNEs.isEmpty()) { - NamedEntity next = coveredNEs.iterator().next(); - if (next != ne) { - out.print(" B"); - } - else { - out.print(" I"); - } - - out.print("-"); - out.print(next.getValue()); - - ne = next; - } - else { - out.print(" O"); - } - out.println(); - } - - out.println(); - } - } - - private Map> getNamedEntityIndex(JCas aJCas) - { - Map> idx = indexCovered(aJCas, Token.class, NamedEntity.class); - - if (acceptedTagsRegex != null) { - Pattern pattern = Pattern.compile(acceptedTagsRegex); - - Map> filteredIdx = new HashMap<>(); - for (Token token : idx.keySet()) { - List nes = new ArrayList<>(); - - for (NamedEntity ne : idx.get(token)) { - if (pattern.matcher(ne.getValue()).matches()) { - nes.add(ne); - } - } - - filteredIdx.put(token, nes); - } - - return filteredIdx; - } - - return idx; - } - - @Override - public void collectionProcessComplete() throws AnalysisEngineProcessException - { - if (out != null) { - IOUtils.closeQuietly(out); - } - - // Setting up Chunker Estimator - TokenizerFactory factory = IndoEuropeanTokenizerFactory.INSTANCE; - CharLmRescoringChunker chunkerEstimator = new CharLmRescoringChunker(factory, - NUM_CHUNKINGS_RESCORED, nGram, NUM_CHARS, nGram); - - Conll2002ChunkTagParser parser = new Conll2002ChunkTagParser(); - parser.setHandler(chunkerEstimator); - - try (FileInputStream fis = new FileInputStream(tempData)) { - InputSource in = new InputSource(fis); - parser.parse(in); - - AbstractExternalizable.compileTo(chunkerEstimator, targetLocation); - } - catch (IOException e) { - throw new AnalysisEngineProcessException(e); - } - - } - - private static class Conll2002ChunkTagParser - extends StringParser> - { - - /** - * token ?posTag entityTag - */ - private static final String TOKEN_TAG_LINE_REGEX = "(\\S+)\\s(\\S+\\s)?(O|[B|I]-\\S+)"; - - /** - * token - */ - private static final int TOKEN_GROUP = 1; - - /** - * entityTag - */ - private static final int TAG_GROUP = 3; - - /** - * lines that start with "-DOCSTART" - */ - private static final String IGNORE_LINE_REGEX = "-DOCSTART(.*)"; - - /** - * empty lines - */ - private static final String EOS_REGEX = "\\A\\Z"; - - private static final String BEGIN_TAG_PREFIX = "B-"; - private static final String IN_TAG_PREFIX = "I-"; - private static final String OUT_TAG = "O"; - - private final LineTaggingParser mParser = new LineTaggingParser(TOKEN_TAG_LINE_REGEX, - TOKEN_GROUP, TAG_GROUP, IGNORE_LINE_REGEX, EOS_REGEX); - - private final TagChunkCodec mCodec = new BioTagChunkCodec( - // no tokenizer - null, - // don't enforce consistency - false, - // custom BIO tag coding matches regex - BEGIN_TAG_PREFIX, IN_TAG_PREFIX, OUT_TAG); - - @Override - public void parseString(char[] cs, int start, int end) - { - mParser.parseString(cs, start, end); - } - - /** - * @param handler - */ - @Override - public void setHandler(ObjectHandler handler) - { - ObjectHandler> taggingHandler = TagChunkCodecAdapters - .chunkingToTagging(mCodec, handler); - mParser.setHandler(taggingHandler); - } - - } - -} diff --git a/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipePosTagger.java b/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipePosTagger.java deleted file mode 100644 index 722200cfec..0000000000 --- a/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipePosTagger.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - * Copyright 2007-2024 - * Ubiquitous Knowledge Processing (UKP) Lab - * Technische Universität Darmstadt - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see http://www.gnu.org/licenses/. - */ -package org.dkpro.core.lingpipe; - -import static java.util.Arrays.asList; -import static org.apache.uima.fit.util.JCasUtil.select; -import static org.apache.uima.fit.util.JCasUtil.selectCovered; -import static org.apache.uima.fit.util.JCasUtil.toText; -import static org.apache.uima.util.Level.INFO; -import static org.dkpro.core.api.resources.MappingProviderFactory.createPosMappingProvider; - -import java.io.InputStream; -import java.io.ObjectInputStream; -import java.util.List; -import java.util.Locale; - -import org.apache.uima.UimaContext; -import org.apache.uima.analysis_engine.AnalysisEngineProcessException; -import org.apache.uima.cas.CAS; -import org.apache.uima.cas.Type; -import org.apache.uima.fit.component.JCasAnnotator_ImplBase; -import org.apache.uima.fit.descriptor.ConfigurationParameter; -import org.apache.uima.fit.descriptor.ResourceMetaData; -import org.apache.uima.fit.descriptor.TypeCapability; -import org.apache.uima.jcas.JCas; -import org.apache.uima.resource.ResourceInitializationException; -import org.dkpro.core.api.lexmorph.pos.POSUtils; -import org.dkpro.core.api.metadata.SingletonTagset; -import org.dkpro.core.api.parameter.ComponentParameters; -import org.dkpro.core.api.resources.CasConfigurableProviderBase; -import org.dkpro.core.api.resources.MappingProvider; -import org.dkpro.core.api.resources.ModelProviderBase; - -import com.aliasi.hmm.HiddenMarkovModel; -import com.aliasi.hmm.HmmDecoder; -import com.aliasi.tag.Tagging; - -import de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS; -import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence; -import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token; -import eu.openminted.share.annotations.api.Component; -import eu.openminted.share.annotations.api.DocumentationResource; -import eu.openminted.share.annotations.api.constants.OperationType; - -/** - * LingPipe part-of-speech tagger. - */ -@Component(OperationType.PART_OF_SPEECH_TAGGER) -@ResourceMetaData(name = "LingPipe POS-Tagger") -@DocumentationResource("${docbase}/component-reference.html#engine-${shortClassName}") -@TypeCapability(inputs = { "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token", - "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence" }, outputs = { - "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS" }) -public class LingPipePosTagger - extends JCasAnnotator_ImplBase -{ - /** - * Use this language instead of the document language to resolve the model. - */ - public static final String PARAM_LANGUAGE = ComponentParameters.PARAM_LANGUAGE; - @ConfigurationParameter(name = PARAM_LANGUAGE, mandatory = false) - protected String language; - - /** - * Override the default variant used to locate the model. - */ - public static final String PARAM_VARIANT = ComponentParameters.PARAM_VARIANT; - @ConfigurationParameter(name = PARAM_VARIANT, mandatory = false) - protected String variant; - - /** - * URI of the model artifact. This can be used to override the default model resolving mechanism - * and directly address a particular model. - * - *

- * The URI format is {@code mvn:${groupId}:${artifactId}:${version}}. Remember to set the - * variant parameter to match the artifact. If the artifact contains the model in a non-default - * location, you also have to specify the model location parameter, e.g. - * {@code classpath:/model/path/in/artifact/model.bin}. - *

- */ - public static final String PARAM_MODEL_ARTIFACT_URI = ComponentParameters.PARAM_MODEL_ARTIFACT_URI; - @ConfigurationParameter(name = PARAM_MODEL_ARTIFACT_URI, mandatory = false) - protected String modelArtifactUri; - - /** - * Load the model from this location instead of locating the model automatically. - */ - public static final String PARAM_MODEL_LOCATION = ComponentParameters.PARAM_MODEL_LOCATION; - @ConfigurationParameter(name = PARAM_MODEL_LOCATION, mandatory = false) - protected String modelLocation; - - /** - * Enable/disable type mapping. - */ - public static final String PARAM_MAPPING_ENABLED = ComponentParameters.PARAM_MAPPING_ENABLED; - @ConfigurationParameter(name = PARAM_MAPPING_ENABLED, defaultValue = ComponentParameters.DEFAULT_MAPPING_ENABLED) - protected boolean mappingEnabled; - - /** - * Load the part-of-speech tag to UIMA type mapping from this location instead of locating the - * mapping automatically. - */ - public static final String PARAM_POS_MAPPING_LOCATION = ComponentParameters.PARAM_POS_MAPPING_LOCATION; - @ConfigurationParameter(name = PARAM_POS_MAPPING_LOCATION, mandatory = false) - protected String posMappingLocation; - - /** - * Log the tag set(s) when a model is loaded. - */ - public static final String PARAM_PRINT_TAGSET = ComponentParameters.PARAM_PRINT_TAGSET; - @ConfigurationParameter(name = PARAM_PRINT_TAGSET, defaultValue = "false") - protected boolean printTagSet; - - /** - * Lingpipe models tend to be trained on lower-case tags, but our POS mappings use uppercase. - */ - public static final String PARAM_UPPERCASE_TAGS = "uppercaseTags"; - @ConfigurationParameter(name = PARAM_UPPERCASE_TAGS, defaultValue = "true") - protected boolean uppercaseTags; - - private CasConfigurableProviderBase modelProvider; - private MappingProvider mappingProvider; - - @Override - public void initialize(UimaContext aContext) throws ResourceInitializationException - { - super.initialize(aContext); - - modelProvider = new ModelProviderBase(this, "lingpipe", "tagger") - { - { - setDefault(GROUP_ID, "de.tudarmstadt.ukp.dkpro.core"); - setDefault(LOCATION, - "classpath:/de/tudarmstadt/ukp/dkpro/core/lingpipe/lib/tagger-${language}-${variant}.properties"); - } - - @Override - protected HmmDecoder produceResource(InputStream aStream) throws Exception - { - ObjectInputStream ois = new ObjectInputStream(aStream); - HiddenMarkovModel hmm = (HiddenMarkovModel) ois.readObject(); - - SingletonTagset tags = new SingletonTagset(POS.class, - getResourceMetaData().getProperty(("pos.tagset"))); - for (int n = 0; n < hmm.stateSymbolTable().numSymbols(); n++) { - String tag = hmm.stateSymbolTable().idToSymbol(n); - if (uppercaseTags) { - tag = tag.toUpperCase(Locale.US); - } - tags.add(tag); - } - addTagset(tags); - - if (printTagSet) { - getContext().getLogger().log(INFO, getTagset().toString()); - } - - return new HmmDecoder(hmm); - } - }; - - mappingProvider = createPosMappingProvider(this, posMappingLocation, language, - modelProvider); - } - - @Override - public void process(JCas aJCas) throws AnalysisEngineProcessException - { - CAS cas = aJCas.getCas(); - - modelProvider.configure(cas); - mappingProvider.configure(cas); - - for (Sentence sentence : select(aJCas, Sentence.class)) { - List tokens = selectCovered(aJCas, Token.class, sentence); - String[] tokenTexts = toText(tokens).toArray(new String[tokens.size()]); - - Tagging tagging = modelProvider.getResource().tag(asList(tokenTexts)); - - for (int n = 0; n < tagging.size(); n++) { - Token t = tokens.get(n); - String tag = tagging.tag(n); - if (uppercaseTags) { - tag = tag.toUpperCase(Locale.US); - } - Type posTag = mappingProvider.getTagType(tag); - POS posAnno = (POS) cas.createAnnotation(posTag, t.getBegin(), t.getEnd()); - posAnno.setPosValue(tag != null ? tag.intern() : null); - POSUtils.assignCoarseValue(posAnno); - posAnno.addToIndexes(); - t.setPos(posAnno); - } - } - } -} diff --git a/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeSegmenter.java b/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeSegmenter.java deleted file mode 100644 index b39cdc1d65..0000000000 --- a/dkpro-core-lingpipe-gpl/src/main/java/org/dkpro/core/lingpipe/LingPipeSegmenter.java +++ /dev/null @@ -1,92 +0,0 @@ -/* - * Copyright 2007-2024 - * Ubiquitous Knowledge Processing (UKP) Lab - * Technische Universität Darmstadt - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see http://www.gnu.org/licenses/. - */ -package org.dkpro.core.lingpipe; - -import org.apache.uima.UimaContext; -import org.apache.uima.analysis_engine.AnalysisEngineProcessException; -import org.apache.uima.fit.descriptor.ResourceMetaData; -import org.apache.uima.fit.descriptor.TypeCapability; -import org.apache.uima.jcas.JCas; -import org.apache.uima.resource.ResourceInitializationException; -import org.dkpro.core.api.segmentation.SegmenterBase; - -import com.aliasi.sentences.IndoEuropeanSentenceModel; -import com.aliasi.sentences.SentenceModel; -import com.aliasi.tokenizer.IndoEuropeanTokenizerFactory; -import com.aliasi.tokenizer.Tokenization; -import com.aliasi.tokenizer.TokenizerFactory; - -import eu.openminted.share.annotations.api.DocumentationResource; - -/** - * LingPipe segmenter. - */ -@ResourceMetaData(name = "LingPipe Segmenter") -@DocumentationResource("${docbase}/component-reference.html#engine-${shortClassName}") -@TypeCapability(outputs = { "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token", - "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence" }) -public class LingPipeSegmenter - extends SegmenterBase -{ - private SentenceModel sentenceModel; - private TokenizerFactory tokenizerFactory; - - @Override - public void initialize(UimaContext aContext) throws ResourceInitializationException - { - super.initialize(aContext); - - sentenceModel = new IndoEuropeanSentenceModel(); - tokenizerFactory = IndoEuropeanTokenizerFactory.INSTANCE; - } - - @Override - protected void process(JCas aJCas, String aText, int aZoneBegin) - throws AnalysisEngineProcessException - { - String text = aJCas.getDocumentText(); - - // Generate tokens - Tokenization toks = new Tokenization(text, tokenizerFactory); - for (int n = 0; n < toks.numTokens(); n++) { - createToken(aJCas, toks.tokenStart(n), toks.tokenEnd(n)); - } - - // Generate sentences - int[] sentenceBoundaries = sentenceModel.boundaryIndices(toks.tokens(), toks.whitespaces()); - if (sentenceBoundaries.length == 0) { - if (toks.numTokens() > 0) { - createSentence(aJCas, toks.tokenStart(0), toks.tokenEnd(toks.numTokens() - 1)); - } - } - else { - int startToken = 0; - for (int i = 0; i < sentenceBoundaries.length; ++i) { - int endToken = sentenceBoundaries[i]; - createSentence(aJCas, toks.tokenStart(startToken), toks.tokenEnd(endToken)); - startToken = endToken + 1; - } - // If there are trailing tokens after the last sentence, turn them into a final sentence - if (startToken < toks.numTokens()) { - createSentence(aJCas, toks.tokenStart(startToken), - toks.tokenEnd(toks.numTokens() - 1)); - } - } - } -} diff --git a/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/ner-default-variants.map b/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/ner-default-variants.map deleted file mode 100644 index 3f505c4cbf..0000000000 --- a/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/ner-default-variants.map +++ /dev/null @@ -1 +0,0 @@ -en=news-muc6 diff --git a/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/ner-en-news-muc6.map b/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/ner-en-news-muc6.map deleted file mode 100644 index 8b4319b929..0000000000 --- a/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/ner-en-news-muc6.map +++ /dev/null @@ -1,4 +0,0 @@ -ORGANIZATION=de.tudarmstadt.ukp.dkpro.core.api.ner.type.Organization -PERSON=de.tudarmstadt.ukp.dkpro.core.api.ner.type.Person -LOCATION=de.tudarmstadt.ukp.dkpro.core.api.ner.type.Location -*=de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity \ No newline at end of file diff --git a/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/tagger-default-variants.map b/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/tagger-default-variants.map deleted file mode 100644 index 404ee63aa4..0000000000 --- a/dkpro-core-lingpipe-gpl/src/main/resources/org/dkpro/core/lingpipe/lib/tagger-default-variants.map +++ /dev/null @@ -1 +0,0 @@ -en=general-brown diff --git a/dkpro-core-lingpipe-gpl/src/scripts/build.xml b/dkpro-core-lingpipe-gpl/src/scripts/build.xml deleted file mode 100644 index cf01271503..0000000000 --- a/dkpro-core-lingpipe-gpl/src/scripts/build.xml +++ /dev/null @@ -1,186 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizerTest.java b/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizerTest.java deleted file mode 100644 index cd5fc070b6..0000000000 --- a/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipeNamedEntityRecognizerTest.java +++ /dev/null @@ -1,99 +0,0 @@ -/* - * Copyright 2007-2024 - * Ubiquitous Knowledge Processing (UKP) Lab - * Technische Universität Darmstadt - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see http://www.gnu.org/licenses/. - */ -package org.dkpro.core.lingpipe; - -import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine; -import static org.apache.uima.fit.util.JCasUtil.select; - -import org.apache.uima.analysis_engine.AnalysisEngine; -import org.apache.uima.jcas.JCas; -import org.dkpro.core.testing.AssertAnnotations; -import org.dkpro.core.testing.TestRunner; -import org.junit.jupiter.api.Test; - -import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity; - -public class LingPipeNamedEntityRecognizerTest -{ - @Test - public void testEnglish() throws Exception - { - JCas jcas = runTest("en", null, "IBM where John works is in Germany ."); - - String[] ne = { "[ 0, 3]Organization(ORGANIZATION) (IBM)", - "[ 10, 14]Person(PERSON) (John)", "[ 27, 34]Location(LOCATION) (Germany)" }; - - String[] tags = { "LOCATION", "ORGANIZATION", "PERSON" }; - - AssertAnnotations.assertTagset(NamedEntity.class, null, tags, jcas); - // AssertAnnotations.assertTagsetMapping(NamedEntity.class, null, unmapped, jcas); - - AssertAnnotations.assertNamedEntity(ne, select(jcas, NamedEntity.class)); - } - - @Test - public void testEnglishGenia() throws Exception - { - JCas jcas = runTest("en", "bio-genia", "IBM where John works is in Germany ."); - - String[] ne = { "[ 0, 3]NamedEntity(other_name) (IBM)" }; - - String[] tags = { "DNA_N", "DNA_domain_or_region", "DNA_family_or_group", "DNA_molecule", - "DNA_substructure", "RNA_N", "RNA_domain_or_region", "RNA_family_or_group", - "RNA_molecule", "RNA_substructure", "amino_acid_monomer", "atom", "body_part", - "carbohydrate", "cell_component", "cell_line", "cell_type", "inorganic", "lipid", - "mono_cell", "multi_cell", "nucleotide", "other_artificial_source", "other_name", - "other_organic_compound", "peptide", "polynucleotide", "protein_N", - "protein_complex", "protein_domain_or_region", "protein_family_or_group", - "protein_molecule", "protein_substructure", "protein_subunit", "tissue", "virus" }; - - AssertAnnotations.assertTagset(NamedEntity.class, null, tags, jcas); - - AssertAnnotations.assertNamedEntity(ne, select(jcas, NamedEntity.class)); - } - - @Test - public void testEnglishGenetag() throws Exception - { - JCas jcas = runTest("en", "bio-genetag", "IBM where John works is in Germany ."); - - String[] ne = { "[ 0, 3]NamedEntity(GENE) (IBM)" }; - - String[] tags = { "GENE" }; - - AssertAnnotations.assertTagset(NamedEntity.class, null, tags, jcas); - - AssertAnnotations.assertNamedEntity(ne, select(jcas, NamedEntity.class)); - } - - // @Test(expected = AnalysisEngineProcessException.class) - // public void testMissingModel() throws Exception - // { - // runTest("xx", null, "Xec xena Xeo ."); - // } - - private JCas runTest(String language, String variant, String testDocument) throws Exception - { - AnalysisEngine engine = createEngine(LingPipeNamedEntityRecognizer.class, - LingPipeNamedEntityRecognizer.PARAM_VARIANT, variant, - LingPipeNamedEntityRecognizer.PARAM_PRINT_TAGSET, true); - - return TestRunner.runTest(engine, language, testDocument); - } -} diff --git a/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipePosTaggerTest.java b/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipePosTaggerTest.java deleted file mode 100644 index 50fe979099..0000000000 --- a/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipePosTaggerTest.java +++ /dev/null @@ -1,115 +0,0 @@ -/* - * Copyright 2007-2024 - * Ubiquitous Knowledge Processing (UKP) Lab - * Technische Universität Darmstadt - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see http://www.gnu.org/licenses/. - */ -package org.dkpro.core.lingpipe; - -import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine; -import static org.apache.uima.fit.util.JCasUtil.select; - -import org.apache.uima.analysis_engine.AnalysisEngine; -import org.apache.uima.jcas.JCas; -import org.dkpro.core.testing.AssertAnnotations; -import org.dkpro.core.testing.TestRunner; -import org.junit.jupiter.api.Test; - -import de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS; - -public class LingPipePosTaggerTest -{ - @Test - public void testEnglish() throws Exception - { - runTest("en", null, "This is a test .", new String[] { "DT", "BEZ", "AT", "NN", "." }, - new String[] { "POS_DET", "POS_VERB", "POS_DET", "POS_NOUN", "POS_PUNCT" }); - - runTest("en", null, "A neural net .", new String[] { "AT", "JJ", "NN", "." }, - new String[] { "POS_DET", "POS_ADJ", "POS_NOUN", "POS_PUNCT" }); - - runTest("en", null, "John is purchasing oranges .", - new String[] { "NP", "BEZ", "VBG", "NNS", "." }, - new String[] { "POS_PROPN", "POS_VERB", "POS_VERB", "POS_NOUN", "POS_PUNCT" }); - - // This is WRONG tagging. "jumps" is tagged as "NNS" - JCas jcas = runTest("en", "general-brown", - "The quick brown fox jumps over the lazy dog . \n", - new String[] { "AT", "JJ", "JJ", "NN", "NNS", "IN", "AT", "JJ", "NN", "." }, - new String[] { "POS_DET", "POS_ADJ", "POS_ADJ", "POS_NOUN", "POS_NOUN", "POS_ADP", - "POS_DET", "POS_ADJ", "POS_NOUN", "POS_PUNCT" }); - - String[] brownTags = { "'", "''", "(", ")", "*", ",", "--", ".", ":", "ABL", "ABN", "ABX", - "AP", "AP$", "AT", "BE", "BED", "BEDZ", "BEG", "BEM", "BEN", "BER", "BEZ", "CC", - "CD", "CD$", "CS", "DO", "DOD", "DOZ", "DT", "DT$", "DTI", "DTS", "DTX", "EX", "HV", - "HVD", "HVG", "HVN", "HVZ", "IN", "JJ", "JJ$", "JJR", "JJS", "JJT", "MD", "NIL", - "NN", "NN$", "NNS", "NNS$", "NP", "NP$", "NPS", "NPS$", "NR", "NR$", "NRS", "OD", - "PN", "PN$", "PP$", "PP$$", "PPL", "PPLS", "PPO", "PPS", "PPSS", "QL", "QLP", "RB", - "RB$", "RBR", "RBT", "RN", "RP", "TL", "TO", "UH", "VB", "VBD", "VBG", "VBN", "VBZ", - "WDT", "WP$", "WPO", "WPS", "WQL", "WRB", "``" }; - - String[] unmappedBrown = { "'", "''", "*", "--", "AP$", "DT$", "JJ$", "NIL", "``" }; - - AssertAnnotations.assertTagset(POS.class, "brown", brownTags, jcas); - AssertAnnotations.assertTagsetMapping(POS.class, "brown", unmappedBrown, jcas); - - jcas = runTest("en", "bio-genia", "The quick brown fox jumps over the lazy dog . \n", - new String[] { "DT", "RB", "VBN", "NN", "NNS", "IN", "DT", "NN", "NN", "." }, - new String[] { "POS_DET", "POS_ADV", "POS_VERB", "POS_NOUN", "POS_NOUN", "POS_ADP", - "POS_DET", "POS_NOUN", "POS_NOUN", "POS_PUNCT" }); - - String[] ptbTags = { "", "''", "(", ")", ",", "-", ".", ":", "CC", "CD", "CT", "DT", "EX", - "FW", "IN", "JJ", "JJR", "JJS", "LS", "MD", "N", "NN", "NNP", "NNPS", "NNS", "PDT", - "POS", "PP", "PRP", "PRP$", "RB", "RBR", "RBS", "RP", "SYM", "TO", "VB", "VBD", - "VBG", "VBN", "VBP", "VBZ", "WDT", "WP", "WP$", "WRB", "XT", "``" }; - - String[] unmappedPtb = { "", "CT", "N", "XT" }; - - AssertAnnotations.assertTagset(POS.class, "ptb", ptbTags, jcas); - AssertAnnotations.assertTagsetMapping(POS.class, "ptb", unmappedPtb, jcas); - - jcas = runTest("en", "bio-medpost", "The quick brown fox jumps over the lazy dog . \n", - new String[] { "DD", "NN", "JJ", "NN", "NNS", "II", "DD", "NN", "NN", "." }, - new String[] { "POS_DET", "POS_NOUN", "POS_ADJ", "POS_NOUN", "POS_NOUN", "POS_ADP", - "POS_DET", "POS_NOUN", "POS_NOUN", "POS_PUNCT" }); - - String[] medpostTags = { "''", "(", ")", ",", ".", ":", "CC", "CC+", "CS", "CS+", "CSN", - "CST", "DB", "DD", "EX", "GE", "II", "II+", "JJ", "JJ+", "JJR", "JJT", "MC", "NN", - "NN+", "NNP", "NNS", "PN", "PND", "PNG", "PNR", "RR", "RR+", "RRR", "RRT", "SYM", - "TO", "VBB", "VBD", "VBG", "VBI", "VBN", "VBZ", "VDB", "VDD", "VDN", "VDZ", "VHB", - "VHD", "VHG", "VHI", "VHZ", "VM", "VVB", "VVD", "VVG", "VVGJ", "VVGN", "VVI", "VVN", - "VVNJ", "VVZ", "``" }; - - String[] unmappedMedpost = { "CC+", "CS+", "II+", "JJ+", "NN+", "RR+" }; - - AssertAnnotations.assertTagset(POS.class, "medpost", medpostTags, jcas); - AssertAnnotations.assertTagsetMapping(POS.class, "medpost", unmappedMedpost, jcas); - } - - private JCas runTest(String language, String variant, String testDocument, String[] tags, - String[] tagClasses) - throws Exception - { - AnalysisEngine engine = createEngine(LingPipePosTagger.class, - LingPipePosTagger.PARAM_VARIANT, variant, LingPipePosTagger.PARAM_PRINT_TAGSET, - true); - - JCas jcas = TestRunner.runTest(engine, language, testDocument); - - AssertAnnotations.assertPOS(tagClasses, tags, select(jcas, POS.class)); - - return jcas; - } -} diff --git a/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipeSegmenterTest.java b/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipeSegmenterTest.java deleted file mode 100644 index b06af631e4..0000000000 --- a/dkpro-core-lingpipe-gpl/src/test/java/org/dkpro/core/lingpipe/LingPipeSegmenterTest.java +++ /dev/null @@ -1,37 +0,0 @@ -/* - * Copyright 2007-2024 - * Ubiquitous Knowledge Processing (UKP) Lab - * Technische Universität Darmstadt - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see http://www.gnu.org/licenses/. - */ -package org.dkpro.core.lingpipe; - -import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription; - -import org.apache.uima.analysis_engine.AnalysisEngineDescription; -import org.dkpro.core.testing.harness.SegmenterHarness; -import org.junit.jupiter.api.Test; - -public class LingPipeSegmenterTest -{ - @Test - public void runHarness() throws Throwable - { - AnalysisEngineDescription aed = createEngineDescription(LingPipeSegmenter.class); - - SegmenterHarness.run(aed, "de.1", "de.4", "en.1", "en.3", "en.5", "en.6", "en.9", "ar.1", - "zh.1", "zh.2"); - } -} diff --git a/dkpro-core-lingpipe-gpl/src/test/resources/log4j2.xml b/dkpro-core-lingpipe-gpl/src/test/resources/log4j2.xml deleted file mode 100644 index 31c71b9dc4..0000000000 --- a/dkpro-core-lingpipe-gpl/src/test/resources/log4j2.xml +++ /dev/null @@ -1,16 +0,0 @@ - - - - - - - - - - - - - - - - diff --git a/dkpro-core-maltparser-asl/src/main/java/org/dkpro/core/maltparser/MaltParser.java b/dkpro-core-maltparser-asl/src/main/java/org/dkpro/core/maltparser/MaltParser.java index f07c1845d5..eb1431eb12 100644 --- a/dkpro-core-maltparser-asl/src/main/java/org/dkpro/core/maltparser/MaltParser.java +++ b/dkpro-core-maltparser-asl/src/main/java/org/dkpro/core/maltparser/MaltParser.java @@ -237,7 +237,13 @@ protected MaltParserService produceResource(URL aUrl) throws IOException // However, Maltparser is not happy at all if the model file does not have the // right name, so we are forced to create a temporary directory and place the // file there. - File modelFile = new File(workingDir, getRealName(aUrl)); + String realName = getRealName(aUrl); + File modelFile = new File(workingDir, realName); + if (!modelFile.toPath().toAbsolutePath().normalize() + .startsWith(workingDir.toPath().toAbsolutePath().normalize())) { + throw new IOException("Model name [" + realName + + "] would escape working directory [" + workingDir + "]"); + } if (!modelFile.exists()) { InputStream is = null; OutputStream os = null;