From db06363455ce6a91ce225ec49073020f1b69eee0 Mon Sep 17 00:00:00 2001 From: Richard Eckart de Castilho Date: Wed, 25 Sep 2024 20:19:41 +0200 Subject: [PATCH] #5064 - Project template for PHI annotation - Added the project template --- inception/inception-app-webapp/pom.xml | 5 + inception/inception-bom/pom.xml | 5 + .../OpenNlpRecommenderAutoConfiguration.java | 2 +- ...ot.autoconfigure.AutoConfiguration.imports | 2 +- .../LICENSE.txt | 202 + .../marker-wicket-module | 1 + .../pom.xml | 122 + .../phi/PhiProjectInitializer.java | 184 + .../phi/PhiProjectInitializer.svg | 665 + .../phi/PhiSpanLayerInitializer.java | 139 + .../phi/PhiSpanLayerInitializer.svg | 938 ++ ...iSpanOpenNlpNerRecommenderInitializer.java | 96 + ...nStringMatchingRecommenderInitializer.java | 96 + .../phi/PhiSpanTagSetInitializer.java | 86 + ...iProjectInitializersAutoConfiguration.java | 91 + .../phi/wicket-package.properties | 28 + ...ot.autoconfigure.AutoConfiguration.imports | 1 + .../initializers/phi/data/Albers.txt_phi.json | 11210 ++++++++++++++++ .../phi/data/Amanda_Alzheimer.txt_phi.json | 8891 ++++++++++++ .../phi/data/Baastrup.txt_phi.json | 1880 +++ .../project/initializers/phi/phi.json | 108 + ...iversalDependenciesProjectInitializer.java | 3 +- .../EntityAnnotationProjectInitializer.java | 5 +- ...gProjectInitializersAutoConfiguration.java | 6 +- .../DefaultAnnotationEditorStatePanel.java | 12 +- .../DefaultAnnotationSidebarStatePanel.java | 20 +- inception/pom.xml | 1 + 27 files changed, 24770 insertions(+), 29 deletions(-) rename inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/{doccat => }/config/OpenNlpRecommenderAutoConfiguration.java (99%) create mode 100644 inception/inception-project-initializers-phi/LICENSE.txt create mode 100644 inception/inception-project-initializers-phi/marker-wicket-module create mode 100644 inception/inception-project-initializers-phi/pom.xml create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiProjectInitializer.java create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiProjectInitializer.svg create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanLayerInitializer.java create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanLayerInitializer.svg create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanOpenNlpNerRecommenderInitializer.java create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanStringMatchingRecommenderInitializer.java create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanTagSetInitializer.java create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/config/InceptionPhiProjectInitializersAutoConfiguration.java create mode 100644 inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/wicket-package.properties create mode 100644 inception/inception-project-initializers-phi/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports create mode 100644 inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/data/Albers.txt_phi.json create mode 100644 inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/data/Amanda_Alzheimer.txt_phi.json create mode 100644 inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/data/Baastrup.txt_phi.json create mode 100644 inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/phi.json diff --git a/inception/inception-app-webapp/pom.xml b/inception/inception-app-webapp/pom.xml index bc00874cdaa..0eeacdc3d83 100644 --- a/inception/inception-app-webapp/pom.xml +++ b/inception/inception-app-webapp/pom.xml @@ -128,6 +128,10 @@ de.tudarmstadt.ukp.inception.app inception-project-initializers-doclabeling + + de.tudarmstadt.ukp.inception.app + inception-project-initializers-phi + de.tudarmstadt.ukp.inception.app inception-project-initializers-sentencelabeling @@ -1031,6 +1035,7 @@ de.tudarmstadt.ukp.inception.app:inception-processing de.tudarmstadt.ukp.inception.app:inception-project-initializers-basic de.tudarmstadt.ukp.inception.app:inception-project-initializers-doclabeling + de.tudarmstadt.ukp.inception.app:inception-project-initializers-phi de.tudarmstadt.ukp.inception.app:inception-project-initializers-sentencelabeling de.tudarmstadt.ukp.inception.app:inception-project-initializers-ud de.tudarmstadt.ukp.inception.app:inception-project-initializers-wikidatalinking diff --git a/inception/inception-bom/pom.xml b/inception/inception-bom/pom.xml index 9f773e3457c..416d3353b07 100644 --- a/inception/inception-bom/pom.xml +++ b/inception/inception-bom/pom.xml @@ -574,6 +574,11 @@ inception-project-initializers-doclabeling 34.0-SNAPSHOT + + de.tudarmstadt.ukp.inception.app + inception-project-initializers-phi + 34.0-SNAPSHOT + de.tudarmstadt.ukp.inception.app inception-project-initializers-sentencelabeling diff --git a/inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/doccat/config/OpenNlpRecommenderAutoConfiguration.java b/inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/config/OpenNlpRecommenderAutoConfiguration.java similarity index 99% rename from inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/doccat/config/OpenNlpRecommenderAutoConfiguration.java rename to inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/config/OpenNlpRecommenderAutoConfiguration.java index b63304480e7..00431cd01b4 100644 --- a/inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/doccat/config/OpenNlpRecommenderAutoConfiguration.java +++ b/inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/config/OpenNlpRecommenderAutoConfiguration.java @@ -15,7 +15,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.doccat.config; +package de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.config; import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; import org.springframework.context.annotation.Bean; diff --git a/inception/inception-imls-opennlp/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports b/inception/inception-imls-opennlp/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports index 9fcdb3576de..95539e8c944 100644 --- a/inception/inception-imls-opennlp/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports +++ b/inception/inception-imls-opennlp/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports @@ -1 +1 @@ -de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.doccat.config.OpenNlpRecommenderAutoConfiguration +de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.config.OpenNlpRecommenderAutoConfiguration diff --git a/inception/inception-project-initializers-phi/LICENSE.txt b/inception/inception-project-initializers-phi/LICENSE.txt new file mode 100644 index 00000000000..d6456956733 --- /dev/null +++ b/inception/inception-project-initializers-phi/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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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/inception/inception-project-initializers-phi/marker-wicket-module b/inception/inception-project-initializers-phi/marker-wicket-module new file mode 100644 index 00000000000..44dcaf8bea4 --- /dev/null +++ b/inception/inception-project-initializers-phi/marker-wicket-module @@ -0,0 +1 @@ +Marker file which activates the profile "wicket-module" from the parent POM. diff --git a/inception/inception-project-initializers-phi/pom.xml b/inception/inception-project-initializers-phi/pom.xml new file mode 100644 index 00000000000..01fde629074 --- /dev/null +++ b/inception/inception-project-initializers-phi/pom.xml @@ -0,0 +1,122 @@ + + + 4.0.0 + + de.tudarmstadt.ukp.inception.app + inception-app + 34.0-SNAPSHOT + + inception-project-initializers-phi + INCEpTION - Core - Project initializers - PHI + + + de.tudarmstadt.ukp.inception.app + inception-model + + + de.tudarmstadt.ukp.inception.app + inception-project-api + + + de.tudarmstadt.ukp.inception.app + inception-schema-api + + + de.tudarmstadt.ukp.inception.app + inception-api-annotation + + + de.tudarmstadt.ukp.inception.app + inception-support + + + de.tudarmstadt.ukp.inception.app + inception-recommendation-api + + + de.tudarmstadt.ukp.inception.app + inception-recommendation + + + de.tudarmstadt.ukp.inception.app + inception-imls-stringmatch + + + de.tudarmstadt.ukp.inception.app + inception-imls-opennlp + + + de.tudarmstadt.ukp.inception.app + inception-project-initializers + + + de.tudarmstadt.ukp.inception.app + inception-io-json + + + de.tudarmstadt.ukp.inception.app + inception-brat-editor + + + de.tudarmstadt.ukp.inception.app + inception-documents-api + + + de.tudarmstadt.ukp.inception.app + inception-security + + + de.tudarmstadt.ukp.inception.app + inception-preferences + + + de.tudarmstadt.ukp.inception.app + inception-export + + + + org.apache.wicket + wicket-core + + + + + org.springframework + spring-core + + + org.springframework + spring-context + + + org.springframework + spring-beans + + + org.springframework.boot + spring-boot-autoconfigure + + + + + org.apache.uima + uimaj-core + + + diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiProjectInitializer.java b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiProjectInitializer.java new file mode 100644 index 00000000000..d1692e5ff8c --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiProjectInitializer.java @@ -0,0 +1,184 @@ +/* + * Licensed to the Technische Universität Darmstadt under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The Technische Universität Darmstadt + * licenses this file to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. + * + * 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. + */ +package de.tudarmstadt.ukp.inception.project.initializers.phi; + +import static de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationEditorState.KEY_EDITOR_STATE; + +import java.io.IOException; +import java.lang.invoke.MethodHandles; +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; + +import org.apache.uima.UIMAException; +import org.apache.wicket.request.resource.PackageResourceReference; +import org.apache.wicket.request.resource.ResourceReference; +import org.springframework.context.ApplicationContext; +import org.springframework.core.annotation.Order; + +import de.tudarmstadt.ukp.clarin.webanno.brat.annotation.BratTokenWrappingAnnotationEditorFactory; +import de.tudarmstadt.ukp.clarin.webanno.model.Project; +import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument; +import de.tudarmstadt.ukp.clarin.webanno.project.initializers.QuickProjectInitializer; +import de.tudarmstadt.ukp.clarin.webanno.security.UserDao; +import de.tudarmstadt.ukp.inception.documents.api.DocumentService; +import de.tudarmstadt.ukp.inception.io.jsoncas.UimaJsonCasFormatSupport; +import de.tudarmstadt.ukp.inception.preferences.PreferencesService; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.config.InceptionPhiProjectInitializersAutoConfiguration; +import de.tudarmstadt.ukp.inception.support.wicket.resource.Strings; + +/** + *

+ * This class is exposed as a Spring Component via + * {@link InceptionPhiProjectInitializersAutoConfiguration#phiProjectInitializer}. + *

+ */ +@Order(3000) +public class PhiProjectInitializer + implements QuickProjectInitializer +{ + private static final PackageResourceReference THUMBNAIL = new PackageResourceReference( + MethodHandles.lookup().lookupClass(), "PhiProjectInitializer.svg"); + + private final ApplicationContext context; + + private final DocumentService documentService; + private final UserDao userService; + private final PreferencesService preferencesService; + + public PhiProjectInitializer(ApplicationContext aContext, DocumentService aDocumentService, + UserDao aUserService, PreferencesService aPreferencesService) + { + context = aContext; + documentService = aDocumentService; + userService = aUserService; + preferencesService = aPreferencesService; + } + + @Override + public String getName() + { + return "PHI annotation"; + } + + @Override + public Optional getDescription() + { + return Optional.of("Annotate personal health information (PHI)."); + } + + @Override + public Optional getThumbnail() + { + return Optional.of(THUMBNAIL); + } + + @Override + public boolean alreadyApplied(Project aProject) + { + return false; + } + + @Override + public List> getDependencies() + { + var dependencies = new ArrayList>(); + dependencies.add(PhiSpanLayerInitializer.class); + + if (context.getBeanNamesForType( + PhiSpanStringMatchingRecommenderInitializer.class).length > 0) { + dependencies.add(PhiSpanStringMatchingRecommenderInitializer.class); + } + + if (context.getBeanNamesForType(PhiSpanOpenNlpNerRecommenderInitializer.class).length > 0) { + dependencies.add(PhiSpanOpenNlpNerRecommenderInitializer.class); + } + + return dependencies; + } + + @Override + public void configure(ProjectInitializationRequest aRequest) throws IOException + { + var project = aRequest.getProject(); + project.setName(userService.getCurrentUsername() + " - New PHI annotation project"); + + var description = // + """ + This project comes pre-configured for **Personal Health Information (PHI)**. + + To annotate a PHI information, mark the text with the mouse, then assign a category in annotation detail + panel on the right. + + The tagset used in this project template was derived from the PHI tagset used by the GeMTeX project. + It was originally published as part of the [`GraSCCo_PHI` dataset](https://zenodo.org/records/11502329). + """; + + if (isStringRecommenderAvailable()) { + description += // + """ + + The project includes recommenders that will learn from the annotations you make and suggest further + entities to annotate in the text. These suggestions will appear in gray. You can accept a + suggestion by a single click. A double-click will instead reject the suggestion. + """; + } + + if (aRequest.isIncludeSampleData()) { + importExampleDocument(project, "Albers.txt_phi.json"); + importExampleDocument(project, "Amanda_Alzheimer.txt_phi.json"); + importExampleDocument(project, "Baastrup.txt_phi.json"); + + description += Strings.getString("phi-span-layer.example-data"); + ; + } + + project.setDescription(description); + + var bratEditorFactory = context.getBean(BratTokenWrappingAnnotationEditorFactory.class); + if (bratEditorFactory != null) { + var editorState = preferencesService.loadDefaultTraitsForProject(KEY_EDITOR_STATE, + project); + editorState.setDefaultEditor(bratEditorFactory.getBeanName()); + preferencesService.saveDefaultTraitsForProject(KEY_EDITOR_STATE, project, editorState); + } + } + + private boolean isStringRecommenderAvailable() + { + return context + .getBeanNamesForType(PhiSpanStringMatchingRecommenderInitializer.class).length > 0; + } + + private void importExampleDocument(Project aProject, String docName) throws IOException + { + var doc = SourceDocument.builder() // + .withProject(aProject) // + .withName(docName) // + .withFormat(UimaJsonCasFormatSupport.ID) // + .build(); + try (var is = getClass().getResourceAsStream("data/" + docName)) { + documentService.uploadSourceDocument(is, doc); + } + catch (UIMAException e) { + throw new IOException(e); + } + } +} diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiProjectInitializer.svg b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiProjectInitializer.svg new file mode 100644 index 00000000000..b62d7cc20b7 --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiProjectInitializer.svg @@ -0,0 +1,665 @@ + + + + + +IActorTargetINCEpTIONlike diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanLayerInitializer.java b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanLayerInitializer.java new file mode 100644 index 00000000000..b3a49a3ed5b --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanLayerInitializer.java @@ -0,0 +1,139 @@ +/* + * Licensed to the Technische Universität Darmstadt under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The Technische Universität Darmstadt + * licenses this file to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. + * + * 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. + */ +package de.tudarmstadt.ukp.inception.project.initializers.phi; + +import static de.tudarmstadt.ukp.clarin.webanno.model.AnchoringMode.TOKENS; +import static de.tudarmstadt.ukp.clarin.webanno.model.OverlapMode.OVERLAP_ONLY; +import static de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanTagSetInitializer.PHI_SPAN_TAG_SET_NAME; +import static java.util.Arrays.asList; +import static org.apache.uima.cas.CAS.TYPE_NAME_STRING; + +import java.io.IOException; +import java.lang.invoke.MethodHandles; +import java.util.List; +import java.util.Optional; + +import org.apache.wicket.request.resource.PackageResourceReference; +import org.apache.wicket.request.resource.ResourceReference; +import org.springframework.beans.factory.annotation.Autowired; + +import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature; +import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer; +import de.tudarmstadt.ukp.clarin.webanno.model.Project; +import de.tudarmstadt.ukp.clarin.webanno.project.initializers.LayerInitializer; +import de.tudarmstadt.ukp.clarin.webanno.project.initializers.TokenLayerInitializer; +import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanLayerSupport; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.config.InceptionPhiProjectInitializersAutoConfiguration; +import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService; +import de.tudarmstadt.ukp.inception.support.wicket.resource.Strings; + +/** + *

+ * This class is exposed as a Spring Component via + * {@link InceptionPhiProjectInitializersAutoConfiguration#phiSpanLayerInitializer}. + *

+ */ +public class PhiSpanLayerInitializer + implements LayerInitializer +{ + private static final PackageResourceReference THUMBNAIL = new PackageResourceReference( + MethodHandles.lookup().lookupClass(), "PhiSpanLayerInitializer.svg"); + + public static final String PHI_SPAN_LAYER_NAME = "custom.PHI"; + public static final String PHI_SPAN_LABEL_FEATURE_NAME = "kind"; + + private final AnnotationSchemaService annotationSchemaService; + + @Autowired + public PhiSpanLayerInitializer(AnnotationSchemaService aAnnotationSchemaService) + { + annotationSchemaService = aAnnotationSchemaService; + } + + @Override + public String getName() + { + return "PHI span annotation"; + } + + @Override + public Optional getDescription() + { + return Optional.of(Strings.getString("phi-span-layer.description")); + } + + @Override + public Optional getThumbnail() + { + return Optional.of(THUMBNAIL); + } + + @Override + public boolean applyByDefault() + { + return false; + } + + @Override + public boolean alreadyApplied(Project aProject) + { + return annotationSchemaService.existsLayer(PHI_SPAN_LAYER_NAME, aProject); + } + + @Override + public List> getDependencies() + { + return asList( + // Because locks to token boundaries + TokenLayerInitializer.class, // + // Tagsets + PhiSpanTagSetInitializer.class); + } + + @Override + public void configure(ProjectInitializationRequest aRequest) throws IOException + { + var spanLayer = AnnotationLayer.builder() // + .withName(PHI_SPAN_LAYER_NAME) // + .withUiName("PHI") // + .withType(SpanLayerSupport.TYPE) // + .withProject(aRequest.getProject()) // + .withAnchoringMode(TOKENS) // + .withOverlapMode(OVERLAP_ONLY) // + .withCrossSentence(true) // + .build(); + + annotationSchemaService.createOrUpdateLayer(spanLayer); + + var spanTagSet = annotationSchemaService.getTagSet(PHI_SPAN_TAG_SET_NAME, + aRequest.getProject()); + + var labelFeature = AnnotationFeature.builder() // + .withName(PHI_SPAN_LABEL_FEATURE_NAME) // + .withUiName("Kind") // + .withDescription("PHI kind") // + .withType(TYPE_NAME_STRING) // + .withLayer(spanLayer) // + .withTagset(spanTagSet) // + .build(); + + annotationSchemaService.createFeature(labelFeature); + } +} diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanLayerInitializer.svg b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanLayerInitializer.svg new file mode 100644 index 00000000000..27edc3a8175 --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanLayerInitializer.svg @@ -0,0 +1,938 @@ + + + + + + diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanOpenNlpNerRecommenderInitializer.java b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanOpenNlpNerRecommenderInitializer.java new file mode 100644 index 00000000000..08c595b67b3 --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanOpenNlpNerRecommenderInitializer.java @@ -0,0 +1,96 @@ +/* + * Licensed to the Technische Universität Darmstadt under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The Technische Universität Darmstadt + * licenses this file to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. + * + * 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. + */ +package de.tudarmstadt.ukp.inception.project.initializers.phi; + +import static de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanLayerInitializer.PHI_SPAN_LABEL_FEATURE_NAME; +import static de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanLayerInitializer.PHI_SPAN_LAYER_NAME; +import static java.util.Arrays.asList; + +import java.io.IOException; +import java.util.List; + +import de.tudarmstadt.ukp.clarin.webanno.model.Project; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.config.InceptionPhiProjectInitializersAutoConfiguration; +import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService; +import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender; +import de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.ner.OpenNlpNerRecommenderFactory; +import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService; + +/** + *

+ * This class is exposed as a Spring Component via + * {@link InceptionPhiProjectInitializersAutoConfiguration#phiSpanOpenNlpNerRecommenderInitializer}. + *

+ */ +public class PhiSpanOpenNlpNerRecommenderInitializer + implements ProjectInitializer +{ + private final AnnotationSchemaService annotationService; + private final RecommendationService recommendationService; + private final OpenNlpNerRecommenderFactory recommenderFactory; + + public PhiSpanOpenNlpNerRecommenderInitializer(RecommendationService aRecommenderService, + AnnotationSchemaService aAnnotationService, + OpenNlpNerRecommenderFactory aRecommenderFactory) + { + recommendationService = aRecommenderService; + annotationService = aAnnotationService; + recommenderFactory = aRecommenderFactory; + } + + @Override + public String getName() + { + return "PHI sequence recommender"; + } + + @Override + public boolean applyByDefault() + { + return false; + } + + @Override + public boolean alreadyApplied(Project aProject) + { + return recommendationService.existsRecommender(aProject, getName()); + } + + @Override + public List> getDependencies() + { + return asList(PhiSpanLayerInitializer.class); + } + + @Override + public void configure(ProjectInitializationRequest aRequest) throws IOException + { + var spanLayer = annotationService.findLayer(aRequest.getProject(), PHI_SPAN_LAYER_NAME); + var labelFeature = annotationService.getFeature(PHI_SPAN_LABEL_FEATURE_NAME, spanLayer); + + var recommender = new Recommender(getName(), spanLayer); + recommender.setFeature(labelFeature); + recommender.setMaxRecommendations(3); + recommender.setThreshold(0.0d); + recommender.setTool(recommenderFactory.getId()); + + recommendationService.createOrUpdateRecommender(recommender); + } +} diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanStringMatchingRecommenderInitializer.java b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanStringMatchingRecommenderInitializer.java new file mode 100644 index 00000000000..a4dd6a1e974 --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanStringMatchingRecommenderInitializer.java @@ -0,0 +1,96 @@ +/* + * Licensed to the Technische Universität Darmstadt under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The Technische Universität Darmstadt + * licenses this file to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. + * + * 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. + */ +package de.tudarmstadt.ukp.inception.project.initializers.phi; + +import static de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanLayerInitializer.PHI_SPAN_LABEL_FEATURE_NAME; +import static de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanLayerInitializer.PHI_SPAN_LAYER_NAME; +import static java.util.Arrays.asList; + +import java.io.IOException; +import java.util.List; + +import de.tudarmstadt.ukp.clarin.webanno.model.Project; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.config.InceptionPhiProjectInitializersAutoConfiguration; +import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService; +import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender; +import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.span.StringMatchingRecommenderFactory; +import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService; + +/** + *

+ * This class is exposed as a Spring Component via + * {@link InceptionPhiProjectInitializersAutoConfiguration#phiSpanStringMatchingRecommenderInitializer}. + *

+ */ +public class PhiSpanStringMatchingRecommenderInitializer + implements ProjectInitializer +{ + private final AnnotationSchemaService annotationService; + private final RecommendationService recommendationService; + private final StringMatchingRecommenderFactory recommenderFactory; + + public PhiSpanStringMatchingRecommenderInitializer(RecommendationService aRecommenderService, + AnnotationSchemaService aAnnotationService, + StringMatchingRecommenderFactory aRecommenderFactory) + { + recommendationService = aRecommenderService; + annotationService = aAnnotationService; + recommenderFactory = aRecommenderFactory; + } + + @Override + public String getName() + { + return "PHI string matching recommender"; + } + + @Override + public boolean applyByDefault() + { + return false; + } + + @Override + public boolean alreadyApplied(Project aProject) + { + return recommendationService.existsRecommender(aProject, getName()); + } + + @Override + public List> getDependencies() + { + return asList(PhiSpanLayerInitializer.class); + } + + @Override + public void configure(ProjectInitializationRequest aRequest) throws IOException + { + var spanLayer = annotationService.findLayer(aRequest.getProject(), PHI_SPAN_LAYER_NAME); + var labelFeature = annotationService.getFeature(PHI_SPAN_LABEL_FEATURE_NAME, spanLayer); + + var recommender = new Recommender(getName(), spanLayer); + recommender.setFeature(labelFeature); + recommender.setMaxRecommendations(3); + recommender.setThreshold(0.0d); + recommender.setTool(recommenderFactory.getId()); + + recommendationService.createOrUpdateRecommender(recommender); + } +} diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanTagSetInitializer.java b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanTagSetInitializer.java new file mode 100644 index 00000000000..c13aaa6787b --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/PhiSpanTagSetInitializer.java @@ -0,0 +1,86 @@ +/* + * Licensed to the Technische Universität Darmstadt under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The Technische Universität Darmstadt + * licenses this file to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. + * + * 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. + */ +package de.tudarmstadt.ukp.inception.project.initializers.phi; + +import static de.tudarmstadt.ukp.inception.export.JsonImportUtil.importTagSetFromJson; +import static java.util.Collections.emptyList; + +import java.io.IOException; +import java.util.List; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.core.io.ClassPathResource; + +import de.tudarmstadt.ukp.clarin.webanno.model.Project; +import de.tudarmstadt.ukp.clarin.webanno.project.initializers.TagSetInitializer; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.config.InceptionPhiProjectInitializersAutoConfiguration; +import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService; + +/** + *

+ * This class is exposed as a Spring Component via + * {@link InceptionPhiProjectInitializersAutoConfiguration#phiSpanTagSetInitializer}. + *

+ */ +public class PhiSpanTagSetInitializer + implements TagSetInitializer +{ + public static final String PHI_SPAN_TAG_SET_NAME = "PHI kinds"; + + private final AnnotationSchemaService annotationSchemaService; + + @Autowired + public PhiSpanTagSetInitializer(AnnotationSchemaService aAnnotationSchemaService) + { + annotationSchemaService = aAnnotationSchemaService; + } + + @Override + public String getName() + { + return PHI_SPAN_TAG_SET_NAME; + } + + @Override + public List> getDependencies() + { + return emptyList(); + } + + @Override + public boolean applyByDefault() + { + return false; + } + + @Override + public boolean alreadyApplied(Project aProject) + { + return annotationSchemaService.existsTagSet(getName(), aProject); + } + + @Override + public void configure(ProjectInitializationRequest aRequest) throws IOException + { + importTagSetFromJson(aRequest.getProject(), + new ClassPathResource("phi.json", getClass()).getInputStream(), + annotationSchemaService); + } +} diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/config/InceptionPhiProjectInitializersAutoConfiguration.java b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/config/InceptionPhiProjectInitializersAutoConfiguration.java new file mode 100644 index 00000000000..168f51dc19c --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/config/InceptionPhiProjectInitializersAutoConfiguration.java @@ -0,0 +1,91 @@ +/* + * Licensed to the Technische Universität Darmstadt under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The Technische Universität Darmstadt + * licenses this file to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. + * + * 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. + */ +package de.tudarmstadt.ukp.inception.project.initializers.phi.config; + +import org.springframework.boot.autoconfigure.AutoConfigureAfter; +import org.springframework.boot.autoconfigure.condition.ConditionalOnBean; +import org.springframework.context.ApplicationContext; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import de.tudarmstadt.ukp.clarin.webanno.security.UserDao; +import de.tudarmstadt.ukp.inception.documents.api.DocumentService; +import de.tudarmstadt.ukp.inception.preferences.PreferencesService; +import de.tudarmstadt.ukp.inception.project.initializers.phi.PhiProjectInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanLayerInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanOpenNlpNerRecommenderInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanStringMatchingRecommenderInitializer; +import de.tudarmstadt.ukp.inception.project.initializers.phi.PhiSpanTagSetInitializer; +import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService; +import de.tudarmstadt.ukp.inception.recommendation.config.RecommenderServiceAutoConfiguration; +import de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.config.OpenNlpRecommenderAutoConfiguration; +import de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.ner.OpenNlpNerRecommenderFactory; +import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.config.StringMatchingRecommenderAutoConfiguration; +import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.span.StringMatchingRecommenderFactory; +import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService; + +@AutoConfigureAfter({ // + RecommenderServiceAutoConfiguration.class, // + OpenNlpRecommenderAutoConfiguration.class, // + StringMatchingRecommenderAutoConfiguration.class }) +@Configuration +public class InceptionPhiProjectInitializersAutoConfiguration +{ + @Bean + public PhiProjectInitializer phiProjectInitializer(ApplicationContext aContext, + DocumentService aDocumentService, UserDao aUserService, + PreferencesService aPreferencesService) + { + return new PhiProjectInitializer(aContext, aDocumentService, aUserService, + aPreferencesService); + } + + @Bean + public PhiSpanLayerInitializer phiSpanLayerInitializer( + AnnotationSchemaService aAnnotationSchemaService) + { + return new PhiSpanLayerInitializer(aAnnotationSchemaService); + } + + @ConditionalOnBean({ RecommendationService.class, StringMatchingRecommenderFactory.class }) + @Bean + public PhiSpanStringMatchingRecommenderInitializer phiSpanStringMatchingRecommenderInitializer( + RecommendationService aRecommenderService, AnnotationSchemaService aAnnotationService, + StringMatchingRecommenderFactory aRecommenderFactory) + { + return new PhiSpanStringMatchingRecommenderInitializer(aRecommenderService, + aAnnotationService, aRecommenderFactory); + } + + @ConditionalOnBean({ RecommendationService.class, OpenNlpNerRecommenderFactory.class }) + @Bean + public PhiSpanOpenNlpNerRecommenderInitializer phiSpanOpenNlpNerRecommenderInitializer( + RecommendationService aRecommenderService, AnnotationSchemaService aAnnotationService, + OpenNlpNerRecommenderFactory aRecommenderFactory) + { + return new PhiSpanOpenNlpNerRecommenderInitializer(aRecommenderService, aAnnotationService, + aRecommenderFactory); + } + + @Bean + public PhiSpanTagSetInitializer phiSpanTagSetInitializer( + AnnotationSchemaService aAnnotationSchemaService) + { + return new PhiSpanTagSetInitializer(aAnnotationSchemaService); + } +} diff --git a/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/wicket-package.properties b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/wicket-package.properties new file mode 100644 index 00000000000..673ded4c4cd --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/phi/wicket-package.properties @@ -0,0 +1,28 @@ +# Licensed to the Technische Universität Darmstadt under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The Technische Universität Darmstadt +# licenses this file to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. +# +# 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. +phi-span-layer.description=Annotate any information that can be used to identify a patient or individual and is \ + in documents such as healthcare records, clinical notes, or other medical documentation as PHI (Protected Health \ + Information). + +phi-span-layer.example-data= \n\ + The project includes example documents. \n\ + \n\ + Open the **Annotation** page from the left sidbar menu to dive right in.\n\ + \n\ + The example documents used in this project template was also derived the \n\ + [`GraSCCo_PHI` dataset](https://zenodo.org/records/11502329) and provided under \n\ + the [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/legalcode) \n\ + license.\n diff --git a/inception/inception-project-initializers-phi/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports b/inception/inception-project-initializers-phi/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports new file mode 100644 index 00000000000..6e5d0f41cbf --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports @@ -0,0 +1 @@ +de.tudarmstadt.ukp.inception.project.initializers.phi.config.InceptionPhiProjectInitializersAutoConfiguration diff --git a/inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/data/Albers.txt_phi.json b/inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/data/Albers.txt_phi.json new file mode 100644 index 00000000000..fef55c14483 --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/data/Albers.txt_phi.json @@ -0,0 +1,11210 @@ +{ + "%TYPES" : { + "custom.PHI" : { + "%NAME" : "custom.PHI", + "%SUPER_TYPE" : "uima.tcas.Annotation", + "kind" : { + "%NAME" : "kind", + "%RANGE" : "uima.cas.String" + } + } + }, + "%FEATURE_STRUCTURES" : [ { + "%ID" : 6, + "%TYPE" : "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence", + "@sofa" : 4, + "begin" : 4, + "end" : 54 + }, { + "%ID" : 7, + "%TYPE" : "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence", + "@sofa" : 4, + "begin" : 55, + 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"de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token", + "@sofa" : 4, + "begin" : 9957, + "end" : 9965, + "order" : 0 + }, { + "%ID" : 1576, + "%TYPE" : "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token", + "@sofa" : 4, + "begin" : 9966, + "end" : 9973, + "order" : 0 + }, { + "%ID" : 4, + "%TYPE" : "uima.cas.Sofa", + "sofaNum" : 1, + "sofaID" : "_InitialView", + "mimeType" : "text", + "sofaString" : " \n\nWerte Frau Kollegin, werter geehrter Herr Kollege!\nWir berichten über lhre Patientin Beate Albers (* 4.4.1997), die sich vom 19.3. bis zum 7.5.2029 in unserer stat. Behandlung befand.\n \nVorgeschichte Befund\n \n•\tVerbrennung 1. – 3. Grades, Kopf I Hals,5% v KOF \n•\tHandamputation LI\n•\tAkute Psychose aus dem schizophrenen Formenkreis \n•\tSelbstschädigung \n•\tBlutungsanamie \n•\tHypokaliämie \n•\tArterieller Hypertonus\n•\tSymptomatisches Anfallsleiden seit 2007\n•\tSt.p. Aneurysmablutung \n•\tPassagerer Diabetes mellitus \n\n19.03.2029: Handreplantaticm\n25.03.2029: Revision \n27.03.2029: Nekrosektomie Kopf / Hals\n30.03.2029: Jet-Lavage, Debridement und VAG Wechsel linken Hand \n01.04.2029: Jet-Lavage, Debridement und VAG-Wechsel linke Hand \n6.04.2029: Nachdebridement am Kopf, VAG-Wechsel linke Hand\n07.04.2029: Weicliteildeckung mit Spalthautsheet und Keratinozytensprühsuspension\n15.04.2029: Debridement, Jet Lavage Lind VAC Wechsel linke Hand\n23.04.2029 Restdefektdeckung Kopf u. Hals (Sheets), Defektdeckung Handrücken\n06.05.2029 K-Draht-Entfernung Ii. Handgelenk\n\nBei Frau Albers ist psychiatrischerseits eine Wahnvorstellung bekannt. Sie hatte sich zuhause die Ii. Hand selbst amputiert und sich das Haupthaar angezündet. Sie informierte telefonfach eine Freundin, die direkt den Rettungsdienst alarmierte. Lt. Protokoll öffnete die Patientin selbst die Tür und hielt die abgetrennte Hand. Sie wurde darauf umgehend in die Rettungsstelle unseres Zentrums verbracht. Bei Aufnahme zeigte sich klinisch und radiologisch eine komplette Amputation der linken Hand. Beide Ohren sowie insbesondere die re. Hals-/Nackenregion waren ll bis Ill gradig verbrannt. Das Kopf-CT zeigte keinen Nachweis frischer intrakranieller Traumafolgen bei Zustand nach osteoplastischer Trepanation der hinteren Schädelgrube links sowie rechts frontotemporal und nachweisbare Gefa-Clips links infratentoriell im Bereich der linken A. vertebralis sowie im Bereich der A . cerebri media rechts.\n\nVerlauf\nFrau Albers wurde durch die Kollegen der Hand- u. Mikrochirurgischen Abteilung umgehend operativ versorgt. Die Hand konnte in einem die ganze Nacht dauerndem Eingriff replantiert werden. Ein streckseitiger WT-Defekt wurde temporär mit Vacuseal gedeckt. Die verbrannten Areale wurden zunächst antiseptisch mit Lavaseptgelverbänden versorgt. Anschließend wurde Frau Albers intuobiert und beatmet auf die lntensivstation des Brandverletztenzentrums aufgenommen.\nAm 25.03.2029 erfolgte eine Wundrevision mil Vacusealwechsel. Das Verbandsregime am Kopf wurde auf ein enzymatisches Debridement mit lruxolsalbe umgestellt. Ein erster debridierender Eingriff erfolgte am 27.03.2029.\nEin erneutes Debridement erfolgte bei weitgehend sauberen Wunden am Kopf am 06.04.2029. Daraufhin konnte am 08.04.2029 die Defektdeckung am Kopf mit Keratinozytensprühsuspension und Spalthautsheets vorn linken Ãœberschenkel erfolgen. Insgesamt sahen wir eine problemlose Einheilung der Transplantate. Lediglich am rechten retroauriculären Hals und an kleineren Arealen am Kopf musste im Verlauf am 23.04 2029 nochmals nachtransplantiert werden. Der Kopf mit Gesicht zeigt sich gegenwärtig bis auf kleinere Defekte abgeheilt. Die Entnahmestellen sind gänzlich reepithelisert. Im beharrten Teil des Kopfes sind multiple alopezische Areale verblieben, bei initial drittgradiger Verbrennungstiefe.\n\nAm 23.04.2029 erfolgte ebenfalls die Defektdeckung des mittlerweile sauber granulierenden Defektes am II. Handrücken mittels Spalthautsheet\nDie temporare Arthrodese im Handgelenk wurde am 06.05.2029 entfernt. Physio- bzw. ergotherapeutische Behandlung wurde begleitend durchgeführt.\n\nIntensivmedizinischer Krankheitsverlauf:\nDie Patientin wurde vom 20.3.2029 bis zum 27.3.2029 zunächst kontrolliert und im weiteren Verlauf unter reduzierter Analgosedierung augmentiert maschinell beatmet. Bei FIüssigkeitseinlagerungen pulmonal und peripher unter der FIüssigkeitstherapie nach Baxter-Parkland Formel induzierten wir eine forcierte Diurese mit Furosemid. Hierunter war die Oxygenierung im Verlauf suffizient. Die Entwöhnung vom Respirator gelang problemlos. Frau Albers konnte am 27.3.2029 bei intakten Schutzreflexen extubiert werden . Seitdem imponiert eine suffiziente Spontanatmung mit einer peripheren Sauerstoffsättgung von 98% unter Raumluft.\nNach Beendigung der Analgosedierung imponierte ein mildes Entzugsdelir. das suffizient mit Clonidin behandlet werden konnte. Eine intermittierende psychotische Symptomatik therapierten wir zunächst mit Lorazepam (Tavor®) und Haloperidol (Haldol®). Im weiteren Verlauf wurde diese Medikation einschleichend durch Risperidon (Risperdal®) ersetzt. Die vorbestehende antiepileptische Medikation mit Levothiracetam (Keppra®) führten wir fort. Näheres bitten wir dem psychiatrischen Verlauf zu entnehmen.\nNach Aufnahme strebten wir zunächst eine positive FIüssigkeitsbilanz an Die Diurese war unter FIüssigkeitstherapie unter Anlehnung an die Baxter-Parklandformel qualitativ und quantitativ suffizient. Im weiteren stationären Verlauf wurde eine antiödematöse Therapie mit Furosemid notwendig. Die Retentionsparameter lagen allzeit im Normbereich.\nUnter adäquater Volumentherapie zeigte sich die Patientin initial und im Weiteren hämodynamisch stabil. Nach Beendigung der Analgosedierung wurde bei arteriellem Hypertonus eine antihypertensive Therapie mit Metoprolol (Beloc zok mite®) und Ramipril (Delix®) begonnen. Hiermit gelang eine zufriedenstellende Blutdruckeinstellung.\nUnter Analgosedierung begannen wir die enterale Ernährung über die einliegende Magensonde. Nach Stimulation führte Frau Albers am 26.3.2029 zum ersten Mal ab. Nach Extubation gelang der orale Kostaufbau problemlos Die Patientin nimmt Wunschkost zu sich.\n\nPsychiatrischer Verlauf\nFremdanamnestisch war von der Freundin und der ambulant behandelnden Ärztin für Psychiatrie und Psychotherapie zu erfahren, dass die Patientin bereits seit Anfang des Jahres akut psychotisch gewesen sei. Sie hatte die letzte antipsychotische Erhaltungsmedikation von 2 mg abgesetzt, die ambulant behandelnde Psychiaterin Frau Dr. Siewert wusste davon. Trotz häufiger telefonischer Kontakte mit der behandelnden Ärztin ließ sie sich nicht zu einer weiteren medikamentösen Therapie motivieren. Noch am Tag der Selbstverletzung war die besorgte Freundin mit ihr beim Sozialpsychiatrischen Dienst vorstellig gewesen. Da Frau Albers zu einer freiwilligen stationären Aufnahme nicht bereit war und keine Unterbringungsgründe vorlagen, war eine Vorstellung bei der ambulanten Psychiaterin vorgesehen. Auf dem Weg dorthin sei Frau Albers aus dem Taxi gesprungen und hatte sich zuhause o.g. Verletzungen zugefügt. Sie teilte dies telefonisch der Freundin mit, die daraufhin die Feuerwehr alarmierte.\nInitial fanden sich erhebliche Denkstörungen. lnhaltlich klang Wahnerleben an, Gott zu sein. Sie erinnerte sich daran, sich die linke Hand mit dem Brotmesser abgeschnitten zu haben. Dies sei geschehen um das Böse in der Welt zu Sühnen. Sie war zunächst noch erheblich inadäquat, spuckte permanent, geordnete Gespräche mit ihr waren nur schwer möglich. Unter einer Sedierung mit Tavor und nach Umstellung auf Haloperidol sistierte diese Symptomatik zunehmend, so dass wir die antipsychotische Medikation in Absprache mit ihr auf eine Dosis von 6 mg Risperdal umstellten. Das Tavor bat sie auszuschleichen.\nDarunter war sie im Verlauf weitgehend distanziert von psychotischem Erleben, ruhig, gut im Kontakt und bedauerte, was sie sich da angetan hatte und nachdem sie zunächst eine stationäre psychiatrische Verlegung ablehnte, willigte sie nach einem motivierenden Gespräch schließlich ein, sich freiwillig in lhre Abteilung verlegen zu lassen. Sie war sehr interessiert an der Therapie, verfügte hier auch aus der Vorgeschichte über gute Kenntnisse z.B. über die Rezeptorwirkung der Medikamente. Im Affekt blieb sie insgesamt eher distanziert zur Dramatik ihrer Selbstverletzung.\nZiel der Verlegung soll die weitere Belastungserprobung unter zunehmender Konfrontation milder Außenwelt im Anschluss an die stationäre intensivmedizinische Behandlung sein. Darüber hinaus ist eine sozialpsychiatrische Einbettung in ein ambulantes Setting nach dieser schweren Selbstverletzung angestrebt sowie die therapeutische Begleitung bei der Bewältigung der Folgeschaden im Alltag.\nProcedere: Wir verlegen Frau Albers, die in Ihrem Hause vorbekannt ist, am 14.05.2029 in lhre weitere stationäre fachpsychiatrische Behandlung.\nDurch die Orthopädiemechanik unseres Hauses wurde eine teils flexible Orthese angefertigt. Diese muss bis auf Weiteres getragen werden. Wir bitten bei per Patientin 1 x tgl. eine ergo- und physiotherapeutische Beübung der Iinken Hand durchzuführen. Hierbei sollten die Fingergelenke und das Handgelenk belastungsfrei in allen Ebenen therapiert werden. Die Ãœbungen sollten aktiv und passiv aus der Orthese heraus erfolgen. \nDie Transplantat· und Entnahmeareale sollten tgl. mehrfach mit fettenden Salben (z.B. Panthenol) gepflegt werden. Restdefekte, die ggf. etwas nässen können mit Betaisodona – Lsg. behandelt werden. \nAus plastisch- u. handchirurgischer Sicht werden mittel- bis langfristig noch mehrere korrigierende Eingriffe 1otwendig sein. Hierzu zählen beispielsweise operative Sehnen- und Gelenklösungen zur Verbesserung der Beweglichkeit der Hand sowie Korrektureingriffe im Bereich der Narben insbesondere im Kopf-/Halsbereich und der haarlosen Kopfareale. Wir werden Frau Albers hierzu in Kooperation mit den Handchirurgen an unsere Sprechstunde anbinden.\nMedikamente bei Entlassunq:\n Enoxaparin (Clexane®) 0,4 ml \nPantoprazol (Pantozol®) 40 mg \nRamipril (Detix®) 2.5 mg\nMetoprolol (Beloc zok mite®) 47,5 mg\nLevothir c.etarn (Keppra®) 1500mg \nRisperidon {Risperdaf®) 2 mg\nIbuprofen .600mg\nThiamin (Vil. B1) 100 mg + Pyridoxin (Vit. 8) 100 mg (Neurorathiopharrn®) \nEs konnen bioaquivalente Generika (weiter-) verordnet werden.\n\nMit freundlichen kollegialen Grüßen\n \nDr.med. 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"de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token", + "@sofa" : 4, + "begin" : 6363, + "end" : 6376, + "order" : 0 + }, { + "%ID" : 4, + "%TYPE" : "uima.cas.Sofa", + "sofaNum" : 1, + "sofaID" : "_InitialView", + "mimeType" : "text", + "sofaString" : "Sehr geehrter Herr Kollege, sehr geehrte Frau Kollegin,\n\nwir berichten Ihnen abschließend über unsere gemeinsame Patientin Amanda Alzheimer, die sich vom 24.01.2028 bis zum 06.02.2028 in unserer intensivmedizinischen Behandlung befand.\n\nDiagnosen:\n1. Resp. Insuffizienz bei Pleuraergüssen bds. \n2. Komb. Aortenklappenvitium mit Aortenstenose KÖF 0,7\n3. Komb. Mitralvitium mit mittel- bis hochgradiger Stenose (KÖF 0.8-1.3) \n4. normale LV-F 5. cerebrale Ischämie im Bereich der Stammganglien li mit diffusen älteren ischämischen Veränderungen \n5. V.a. Pneumonie 15.12.2027 \n6. Z.n. Apoplex 2002 (Hemiparese re) keine Residuen \n7. Hypothyreose bei Autoimmunthyreoiditis \n8. Diabetes mellitus mit diab. Nephropathie \n9. Gramnegative Sepsis (Fokus pulmonal oder Harnwege) \n10. Akutes Nierenversagen \n\nTherapie: \n23.01.28: Klappenersatz MKE bio, AKE 23er bio, Klemmzeit 2h30 min, SM Schwelle Ventrikel 1,3, Vorhof 13. 6 EK, 800 ml HLM-Blut, 2 TK. \n25.01.28: TEE, unauffällig 27.01.28: HIT-Schnelltest unauff., Sono Pleura \n28.01.28: HIT negativ 31.01.28: Angio-CCT 29.01.28: Beginn CVVH \n05.02.28: CCT und GK-CT Anamnese: Ãœbernahme von der 3 Süd. Pt mit Kombiniertem Aortenvitium und führender Stenose. Jetzt seit heute Anend zunehmend eingetrübt und Dyspnö. \nJetzt 24.01.28 bei OP-Indikation und nach entsprechender Vorbereitung: OP Vormedikation \n\nVerlauf: \n24.12.2027 Echokardiographie: \n1. Normal großer, konzentrsich hypertrophierter linker Ventrikel mit noch guter LV-Funktion \n2. Kombiniertes Mitralklappenvitium (MI II°, MS II°), kombiniertes Aortenklappenvitium, turbulenter Fluß über die Aortenkalppe, mittl. Gradient 20 mmHg (bei schlechter SB am ehesten unterschätzt) TI I° \n3. Erhöhte Druckwerte im kleinen Kreislauf. Punktionswürdige Pleuraergüße bds. \n\n24.12.2027 Konsil OA Prof. Brinkmann: Normotone RR-Werte, Sinusrhythmus; --> Therapieziel deutliche Minusbilanz mittels konservativer Maßnahmen - Beginn mit Toremperfusor unter Beachtung des Kreatininwertes - möglichst keine Pleuradrainagenanlage, sondern Einmalpunktion \n24.12.2027 Rechter Pleuraerguss wurde unter sterilen Bedingungen erfolgreich Punktiert und 1,2 Liter PE abgelassen. Hierunter atmet die Patientin deutlich entspannter, die periphere Sättigung ist unter 60% O2 jetzt >90%. Torem-Perfusor läuft auf 2.1, hierunter bisher knapp 700ml ausgeschieden. \nN: Pupillen isokor, lichtreagibel \nP: bds. basal abgeschwächtes AG li>re, keine feuchten RGs C: 5/6 Systolikum \nA: weich, DG vorhanden \nE: geringe US Ödeme bds \n\nProcedere: \n- weiterhin Bilanz, Ziel -500 - -1000ml \n- auf Retentionsparameter achten \n- bei erneuter verschlechterung erneute Pleurapunktion \n- Beginn mit Voll-Heparinisierung, Ziel PTT 50-70sec; \n\nPTT Kontrolle 24.12.2027 17:06 Pat. somnolent, erweckbar, antwortet mit ja und nein auf gestelte Fragen.\nAtmet mit OptiFlow hierunter periph. \nsp02 >90% BGA nach Pleurapunktion unverändert \np02 55, pC02 46 bei subjektiv zunehmender Atemnot erhöhung der 02-Gabe auf 80% \nKein Fieber, gute Ausscheidung, Pat. mit Torem-Perf. negativ bilanziert \nN: Pupillen isocor bds lichtreagibel C: HT rhythmisch 3/6 syst II ICR re. \nP: bds belüftet, endexpiratorisches Knistern re. basal, Dämpfung li. basal \nA: weich, kein DS, D++ \nE: minimale Ödeme Unterschenkel bds Procedere: BGA Kontrolle bei Verschlechterung der resp. Situation - Punktion links - ggf. CPAP \n\n03.02.2028 Änderung der ABx: \n* im TS vom 01.02.2028 Klebsiellen, die auf Piperacillin resistent sind, nicht jedoch auf Tazobac. \n* Da Infektparameter steigend, Umsetzen auf Meronem 2x1 g/die (Hämofiltration). \n04.02.2028 Sono Pleura / Abdomen: Magen ragt bis vor die Leber nach re, daher T. coeliacus nicht beurteilbar. \nPulsation in den Lebervenen, daher V.a. Rechtsherzinsuffizienz. \nLeberparenchym echoarm. \nIntrahepatische Cholestase, GB gefüllt + Sludge, keine Wandverdickung. \nPfortaderfluß: 18 cm/s, A.hepatica RI-Wert: 0,86. Reduziertes Flußsignal in VCI. \nNiere re kein Harnstau, Niere links+Milz nicht einsehbar. \nRetroperitoneum nicht einsehbar. PE re ca 800 ml, Pleura li nicht darstellbar. \n\n04.02.2028 \nHTG über PE 800ml informiert \n05.02.2028 CCT und GK-CT: Befunde folgen nach Vergleich mit VU (Drs. Seiler und Wantzer melden sich bei Xxxxx). Pat. während Transport und Untersuchung kardiopulmonal stabil. 05.02.2028 GKCT-Befund (Dr. Bechterew): Keine Thrombosen, keine Ischämien, viel freie FF im Abdomen, im Bereich des Pylorus und proximalen Duodenum ödematöse Wandverdickung -> könnte auf ein Ulcus hinweisen. Pleuraergüsse: re (ca. 800 ml) > li. (deutlich weniger) Tubus liegt tief über Carinawinkel -> kann 2 cm zurückgezogen werden. \n05.02.2028 HIT-Test negativ \n05.02.2028 CCT-Befund: \nViele alte postischämische Läsionen, keine frische Ischämien, keine Blutungen. \n06.02.2028 Durchsicht des Abdominal-CT durch Fr. Dr. Müller (ACH): kein Handlungsbedarf. \nEmpfehlungen: Mikrobiologie: Die Mikrobiologiedaten entnehmen Sie bitte dem Anhang. \nLabor:Labor-Resultate (Zeitraum je 3 Tage) \n\nAktuelle Medikation:\nMedikamente (letzte Gabe in 24 Stunden): \nDiflucan - 400mg Bolus in 200ml fertig gelöst \nDigimerck - 0,2mg Bolus - 12:09 Laxoberal Trpf. - 20gtt p.o. in 1ml fertig gelöst p.o. \nL-Thyroxin - 150μg p.o. in 10ml Wasser p.o. \nMeronem - 1g Bolus in 100ml NaCl 0,9% \nPantozol - 40mg KI in 100ml NaCl 0,9% \nRefludan - 1mg - 11:30 SDD-Suspension - 5ml p.o. in 5ml fertig gelöst p.o. \nInfusionen (letzte 24 Stunden, ohne Spülungen): \nIntraflow - 9,0ml/h (500ml ) \nNaCl 0,9% - 9,0ml/h (500ml ) \nNaCl 0,9% - 11,0ml/h (250ml , 1000mg Vancomycin ) \nTropf-Infusionen: Actrapid HM - 0,122E/kg/h , 10,0ml/h (50E in 50ml NaCl 0,9% ) \nArterenol - 0,122μg/kg/min , 6,0ml/h (5mg in 50ml NaCl 0,9% ) \nHydrocortison - 0,098mg/kg/h , 2,0ml/h (200mg in 50ml NaCl 0,9% ) \nKaliumchlorid 7,45% - 10mEqhr , 10,0ml/h (60mval in 60ml fertig gelöst ) \nSuprarenin - 0,081μg/kg/min , 4,0ml/h (5mg in 50ml fertig gelöst ) \n\n\nWir danken für die prompte Ãœbernahme von Frau Alzheimer und stehen für Rückfragen gerne unter der o.g. Telefon-Nr. zur Verfügung. Die Angehörigen von Frau Alzheimer haben wir über die Verlegung zu Ihnen unterrichtet. (Telefon: Sohn Alois Alzheimer 08991/23354 Handy 0699-15099887) \n\nMit freundlichen kollegialen Grüßen \n\nProf. Dr. Norbert Breuer Klaus Pfeiffer Priv.-Doz. Dr. med. 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MED. H. BLASENSTEIN\n\nHerrn\nHelge Klabauter\nUrologe\nFriesische Str. 21 a\n24937 Flensburg\n \n\nFlensburg, 27. März 2025\nRote Str. 3 \nTelefon (0461) 708 - 223\n\n\nBetr.: Asger Baastrup, geb. 5.7.54, Schleswiger Str. 95a, 24941 Flensburg \n\n\nSehr geehrte Herr Kollege Klabauter!\n\nHr. Baastrup Asger war vom 8.3. - 22.3.2025 bei uns in stationärer Behandlung.\n\nDiagnosen: Narbige Blasanhalsstenose. nach Prostata-Adenom-Enukleatio 2006.\nBekannte Blindheit nach Maculadeg. bds.\nHerzinsuffizienz\n\nKleines Prostata-Ca Stadium pT1a,· G1.\n\n1 Tag vor der stationären Aufnahme war eine Sachse­Spaltung der narbigen Stenose durchgeführt worden. Der Katheter war herausgefallen. Nach nochmaliger vorübergehender Kathetervers6rgung betrug der Resturin·aber immer noch 150 ml., so daß wir uns zur·Elektro-Resektion entschlossen haben.\n\nDie präoperativen Blutwerte: PSA 0,7 ng/ml, Kreatinin\n1,5, Harnstoff 51 mg%, Elektrolyte ausgeglichen. Gerinnungsverhalten unauffällig.\n\nTherapie und Verlauf:\n\nResektion des Blasenhalses am 15.3.95. Histologisch zeigte sich außer Narbengewebe ein winziges, gut differenziertes Carcinom. Diesen Befund haben wir dem Patienten vorenthalten, da eine Therapie aufgrund des fortgeschrittenen Alters sicher nicht erforderlich ist.\n\nNach Katheter-Entfernung restharnfreie Blasenentleerung. Die Medikation von Adalat und Lanitop sowie Augentropfen \nwurde hier weitergeführt.\n\nMit freundlichen Grüßen bin ich\nIhr\n\nDr. Blasenstein\nChefarzt\n" + } ], + "%VIEWS" : { + "_InitialView" : { + "%SOFA" : 4, + "%MEMBERS" : [ 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274 ] + } + } +} \ No newline at end of file diff --git a/inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/phi.json b/inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/phi.json new file mode 100644 index 00000000000..a0d617a0fd6 --- /dev/null +++ b/inception/inception-project-initializers-phi/src/main/resources/de/tudarmstadt/ukp/inception/project/initializers/phi/phi.json @@ -0,0 +1,108 @@ +{ + "name": "PHI kinds", + "typeUiName": null, + "description": "Kinds of Personal Health Information (PHI)", + "language": "en", + "type": null, + "type_name": null, + "type_description": null, + "tags": [ + { + "tag_name": "AGE", + "tag_description": "Specific age details (not in date format)" + }, + { + "tag_name": "CONTACT_EMAIL", + "tag_description": "Email address" + }, + { + "tag_name": "NAME_EXT", + "tag_description": "Mention of individuals in connection with offices, insurance, etc." + }, + { + "tag_name": "NAME_OTHER", + "tag_description": "Mention of additional names" + }, + { + "tag_name": "NAME_RELATIVE", + "tag_description": "Relatives of the patient" + }, + { + "tag_name": "NAME_TITLE", + "tag_description": "Title designations" + }, + { + "tag_name": "PROFESSION", + "tag_description": "Designations of professions related to the patient, without mentioning a status (e.g., unemployed, retired, part-time)" + }, + { + "tag_name": "OTHER", + "tag_description": "Other features to be de-identified that cannot be covered by other categories" + }, + { + "tag_name": "CONTACT_FAX", + "tag_description": "Fax number" + }, + { + "tag_name": "CONTACT_PHONE", + "tag_description": "Phone number" + }, + { + "tag_name": "CONTACT_URL", + "tag_description": "URL of a website" + }, + { + "tag_name": "DATE", + "tag_description": "All date information (e.g., birth date, death date)" + }, + { + "tag_name": "ID", + "tag_description": "Number for identifying a patient, number for identifying a medical case, other identification numbers" + }, + { + "tag_name": "LOCATION_CITY", + "tag_description": "Name of a city" + }, + { + "tag_name": "LOCATION_COUNTRY", + "tag_description": "Name of a country" + }, + { + "tag_name": "LOCATION_HOSPITAL", + "tag_description": "Mention of a medical facility" + }, + { + "tag_name": "LOCATION_ORGANIZATION", + "tag_description": "Name of a (medical) organization" + }, + { + "tag_name": "LOCATION_OTHER", + "tag_description": "Other addresses" + }, + { + "tag_name": "LOCATION_STATE", + "tag_description": "Name of a state" + }, + { + "tag_name": "LOCATION_STREET", + "tag_description": "Street name + house number" + }, + { + "tag_name": "LOCATION_ZIP", + "tag_description": "Postal code" + }, + { + "tag_name": "NAME_DOCTOR", + "tag_description": "First and last name of a doctor or medical personnel" + }, + { + "tag_name": "NAME_USERNAME", + "tag_description": "Username, secretarial initials" + }, + { + "tag_name": "NAME_PATIENT", + "tag_description": "First and last name of a patient or relatives" + } + ], + "create_tag": false +} diff --git a/inception/inception-project-initializers-ud/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/ud/UniversalDependenciesProjectInitializer.java b/inception/inception-project-initializers-ud/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/ud/UniversalDependenciesProjectInitializer.java index d4193f9058d..39ed640add1 100644 --- a/inception/inception-project-initializers-ud/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/ud/UniversalDependenciesProjectInitializer.java +++ b/inception/inception-project-initializers-ud/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/ud/UniversalDependenciesProjectInitializer.java @@ -37,6 +37,7 @@ import de.tudarmstadt.ukp.clarin.webanno.project.initializers.SurfaceFormLayerInitializer; import de.tudarmstadt.ukp.clarin.webanno.project.initializers.TokenLayerInitializer; import de.tudarmstadt.ukp.clarin.webanno.project.initializers.config.ProjectInitializersAutoConfiguration; +import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest; import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer; import de.tudarmstadt.ukp.inception.support.wicket.resource.Strings; @@ -91,7 +92,7 @@ public List> getDependencies() } @Override - public void configure(Project aProject) throws IOException + public void configure(ProjectInitializationRequest aRequest) throws IOException { // Nothing to do - all initialization is already done by the dependencies } diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/neannotation/EntityAnnotationProjectInitializer.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/neannotation/EntityAnnotationProjectInitializer.java index 4a6b12c92f6..28ef09a40ab 100644 --- a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/neannotation/EntityAnnotationProjectInitializer.java +++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/neannotation/EntityAnnotationProjectInitializer.java @@ -29,7 +29,6 @@ import org.springframework.context.ApplicationContext; import org.springframework.core.annotation.Order; -import de.tudarmstadt.ukp.clarin.webanno.api.export.DocumentImportExportService; import de.tudarmstadt.ukp.clarin.webanno.model.Project; import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument; import de.tudarmstadt.ukp.clarin.webanno.project.initializers.NamedEntityLayerInitializer; @@ -59,18 +58,16 @@ public class EntityAnnotationProjectInitializer private final AnnotationSchemaService annotationService; private final ApplicationContext context; - private final DocumentImportExportService documentImportExportService; private final DocumentService documentService; private final UserDao userService; public EntityAnnotationProjectInitializer(ApplicationContext aContext, AnnotationSchemaService aAnnotationService, DocumentService aDocumentService, - DocumentImportExportService aDocumentImportExportService, UserDao aUserService) + UserDao aUserService) { context = aContext; annotationService = aAnnotationService; documentService = aDocumentService; - documentImportExportService = aDocumentImportExportService; userService = aUserService; } diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/config/WikiDataLinkingProjectInitializersAutoConfiguration.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/config/WikiDataLinkingProjectInitializersAutoConfiguration.java index acef38223ca..1eb3a20fa91 100644 --- a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/config/WikiDataLinkingProjectInitializersAutoConfiguration.java +++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/config/WikiDataLinkingProjectInitializersAutoConfiguration.java @@ -23,7 +23,6 @@ import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; -import de.tudarmstadt.ukp.clarin.webanno.api.export.DocumentImportExportService; import de.tudarmstadt.ukp.clarin.webanno.security.UserDao; import de.tudarmstadt.ukp.inception.documents.api.DocumentService; import de.tudarmstadt.ukp.inception.kb.KnowledgeBaseService; @@ -78,11 +77,10 @@ public EntityLinkingProjectInitializer entityLinkingProjectInitializer( @Bean public EntityAnnotationProjectInitializer entityAnnotationProjectInitializer( ApplicationContext aContext, AnnotationSchemaService aAnnotationService, - DocumentService aDocumentService, - DocumentImportExportService aDocumentImportExportService, UserDao aUserService) + DocumentService aDocumentService, UserDao aUserService) { return new EntityAnnotationProjectInitializer(aContext, aAnnotationService, - aDocumentService, aDocumentImportExportService, aUserService); + aDocumentService, aUserService); } @ConditionalOnBean(RecommendationService.class) diff --git a/inception/inception-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/dashboard/settings/annotation/DefaultAnnotationEditorStatePanel.java b/inception/inception-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/dashboard/settings/annotation/DefaultAnnotationEditorStatePanel.java index 6b4b7158da3..edd256b5869 100644 --- a/inception/inception-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/dashboard/settings/annotation/DefaultAnnotationEditorStatePanel.java +++ b/inception/inception-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/dashboard/settings/annotation/DefaultAnnotationEditorStatePanel.java @@ -22,7 +22,6 @@ import java.util.List; import java.util.Objects; -import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import org.apache.wicket.ajax.AjaxRequestTarget; @@ -38,7 +37,6 @@ import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationEditorState; import de.tudarmstadt.ukp.clarin.webanno.model.Project; -import de.tudarmstadt.ukp.inception.editor.AnnotationEditorFactory; import de.tudarmstadt.ukp.inception.editor.AnnotationEditorRegistry; import de.tudarmstadt.ukp.inception.preferences.PreferencesService; import de.tudarmstadt.ukp.inception.support.lambda.LambdaForm; @@ -83,10 +81,9 @@ public DefaultAnnotationEditorStatePanel(String aId, IModel aProjectMod private List> listAvailableEditors() { - List> editorChoices = annotationEditorRegistry.getEditorFactories() - .stream().map(f -> Pair.of(f.getBeanName(), f.getDisplayName())) - .collect(Collectors.toList()); - return editorChoices; + return annotationEditorRegistry.getEditorFactories().stream() // + .map(f -> Pair.of(f.getBeanName(), f.getDisplayName())) // + .toList(); } @SuppressWarnings("unchecked") @@ -101,8 +98,7 @@ private void actionLoad() getModel().getObject())); var defaultEditorId = state.getObject().getDefaultEditor(); - AnnotationEditorFactory factory = annotationEditorRegistry - .getEditorFactory(defaultEditorId); + var factory = annotationEditorRegistry.getEditorFactory(defaultEditorId); if (factory != null) { defaultEditor.setObject(listAvailableEditors().stream() // diff --git a/inception/inception-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/dashboard/settings/annotation/DefaultAnnotationSidebarStatePanel.java b/inception/inception-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/dashboard/settings/annotation/DefaultAnnotationSidebarStatePanel.java index 37d52c385a3..dcd0d22fdd8 100644 --- a/inception/inception-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/dashboard/settings/annotation/DefaultAnnotationSidebarStatePanel.java +++ b/inception/inception-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/dashboard/settings/annotation/DefaultAnnotationSidebarStatePanel.java @@ -17,6 +17,7 @@ */ package de.tudarmstadt.ukp.inception.ui.core.dashboard.settings.annotation; +import static de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.SidebarTabbedPanel.KEY_SIDEBAR_STATE; import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.visibleWhen; import static java.util.stream.Collectors.toList; @@ -37,7 +38,6 @@ import de.tudarmstadt.ukp.clarin.webanno.model.Project; import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.AnnotationSidebarFactory; import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.AnnotationSidebarRegistry; -import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.SidebarTabbedPanel; import de.tudarmstadt.ukp.inception.preferences.PreferencesService; import de.tudarmstadt.ukp.inception.support.lambda.LambdaAjaxFormComponentUpdatingBehavior; import de.tudarmstadt.ukp.inception.support.lambda.LambdaForm; @@ -61,13 +61,13 @@ public DefaultAnnotationSidebarStatePanel(String aId, IModel aProjectMo LambdaForm form = new LambdaForm<>("form"); - Label description = new Label("description", defaultTab.map(SidebarHandle::getDescription)); + var description = new Label("description", defaultTab.map(SidebarHandle::getDescription)); description.setOutputMarkupPlaceholderTag(true); description.add(visibleWhen(defaultTab.isPresent())); form.add(description); - DropDownChoice defaultTabSelect = new DropDownChoice<>("defaultTab", - defaultTab, LoadableDetachableModel.of(this::listAvailableSidebars), + var defaultTabSelect = new DropDownChoice("defaultTab", defaultTab, + LoadableDetachableModel.of(this::listAvailableSidebars), new ChoiceRenderer<>("displayName", "id")); defaultTabSelect.setNullValid(true); defaultTabSelect.add(new LambdaAjaxFormComponentUpdatingBehavior("change", @@ -89,8 +89,8 @@ public IModel getModel() private void actionLoad() { - var state = preferencesService.loadDefaultTraitsForProject( - SidebarTabbedPanel.KEY_SIDEBAR_STATE, getModel().getObject()); + var state = preferencesService.loadDefaultTraitsForProject(KEY_SIDEBAR_STATE, + getModel().getObject()); var factory = annotationSidebarRegistry.getExtension(state.getSelectedTab()); defaultTab.setObject(factory.map(SidebarHandle::new).orElse(null)); @@ -98,14 +98,14 @@ private void actionLoad() private void actionSave(AjaxRequestTarget aTarget, Form aDummy) { - var state = preferencesService.loadDefaultTraitsForProject( - SidebarTabbedPanel.KEY_SIDEBAR_STATE, getModel().getObject()); + var state = preferencesService.loadDefaultTraitsForProject(KEY_SIDEBAR_STATE, + getModel().getObject()); state.setSelectedTab(defaultTab.map(SidebarHandle::getId).orElse(null).getObject()); state.setExpanded(defaultTab.isPresent().getObject()); - preferencesService.saveDefaultTraitsForProject(SidebarTabbedPanel.KEY_SIDEBAR_STATE, - getModel().getObject(), state); + preferencesService.saveDefaultTraitsForProject(KEY_SIDEBAR_STATE, getModel().getObject(), + state); } private List listAvailableSidebars() diff --git a/inception/pom.xml b/inception/pom.xml index 52ca1ef95d6..e384fed8dbc 100644 --- a/inception/pom.xml +++ b/inception/pom.xml @@ -178,6 +178,7 @@ inception-project-initializers inception-project-initializers-basic inception-project-initializers-doclabeling + inception-project-initializers-phi inception-project-initializers-sentencelabeling inception-project-initializers-ud inception-project-initializers-wikidatalinking