#3611 - Upgrade to Spring 6, Boot 3, Wicket 10, etc. #3612
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- Java 11 -> 17 - spring 5.3.24 -> 6.0.2 - spring-boot 2.7.5 -> 3.0.0 - spring-security 5.7.5 -> 6.0.0 - log4j 2.18.0 -> 2.19.0 - tomcat 9.0.69 -> 10.1.1 - servlet-api 4.0.1 -> 6.0.0 - hibernate 5.6.14 -> 6.1.5 - hibernate-validator 6.2.5 -> 8.0.0 - wicket 9.11.0 -> 10.0.0-M1-SNAPSHOT - UIMA 3.3.1 -> 3.4.0-SNAPSHOT - uimaFIT 3.3.0 -> 3.4.0-SNAPSHOT - Use Jakarta dependencies instead of old javax dependencies
* main: (212 commits) No issue. Pull CSS out of HTML file and into a separate CSS file. #3831 - Better support a direct-access workflow #3831 - Better support a direct-access workflow #3831 - Better support a direct-access workflow No issue: Avoid hard crash if selection points to a non-existing feature structure. No issue: Formatting No issue: Fix endless recursion. No issue. Make some constants accessible. #3571 - Update dependencies #3571 - Update dependencies #3826 - Update dependencies #3783 - Ability to sort projects by created date #3826 - Update dependencies [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-27.0-beta-4 #3822 - Order of matches found in knowledge base search is not correct #3822 - Order of matches found in knowledge base search is not correct #3822 - Order of matches found in knowledge base search is not correct No issue. Reduce memory usage of test and display memory usage while test is running. #3793 - Ability to trigger sidebar curation mode via URL parameter ... % Conflicts: % inception/inception-app-webapp/src/main/java/de/tudarmstadt/ukp/inception/app/config/InceptionSecurityWebUIBuiltInAutoConfiguration.java % inception/inception-app-webapp/src/main/java/de/tudarmstadt/ukp/inception/app/config/InceptionSecurityWebUIPreAuthenticatedAutoConfiguration.java % inception/inception-app-webapp/src/main/java/de/tudarmstadt/ukp/inception/app/config/InceptionServletContextInitializer.java % inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/experimental/editor/diamdebugeditor/DiamDebugEditorComponent.java % inception/inception-html-editor/pom.xml % inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/config/SecurityAutoConfiguration.java % inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/preauth/ShibbolethRequestHeaderAuthenticationFilter.java % inception/inception-support/src/main/java/de/tudarmstadt/ukp/inception/support/vue/VueBehavior.java % inception/inception-tutorial/src/main/java/de/tudarmstadt/ukp/inception/tutorial/TutorialFooterPanel.java % inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/config/AnnotationUIAutoConfiguration.java % inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/login/LoginPage.java % inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/page/ProjectPageBase.java % inception/inception-ui-curation/src/main/java/de/tudarmstadt/ukp/inception/ui/curation/sidebar/config/CurationSidebarAutoConfiguration.java % inception/inception-websocket/pom.xml % inception/inception-websocket/src/main/java/de/tudarmstadt/ukp/inception/websocket/footer/LoggedEventFooterPanel.java % inception/pom.xml
- spring 6.0.2 -> 6.0.5 - spring boot 3.0.0 -> 3.0.3 - spring data 3.0.0 -> 3.0.2 - spring security 6.0.0 -> 6.0.2 - wicket jquery 9.11.0 -> 10.0.0-SNAPSHOT - jetty -> 10.0.13 - added jakarta jaxb runtime - fixed auto-configuration for Spring Boot 3 - fixed calls to changed spring security api - MVC controllers now need a `@Controller` annotation and can no longer be auto-configured
- get Hibernate to validate existing MariaDB DB schema
- Fix login by accessing session directly instead of through Wicket - the Wicket session wrapper now adds an attribute prefix and with that Spring Security won't find the security context of course
- Fix filters and listeners
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* main: (189 commits) No issue. Minor additions to BioC format description #4062 - ViewportTracker should focus on block-like elements #4032 - Allow using externalized strings from backend code #4060 - Clean up redundant code in annotation handlers #4026: Support for error tracking with Sentry #3673 - Update dependencies update dead link to the new file #4055 - Editor scrolls up when left sidebar is opened/closed [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-28.2 #4052 - Admins no longer see all projects in the project overview #3673 - Update dependencies #4048 - Document navigation options not visible to manager when viewing other users document #3673 - Update dependencies #3673 - Update dependencies #1496 - Some spans are missing begin offset field #1511 - External recommender fails when CAS contains control characters #1496 - Some spans are missing begin offset field #4040 - Ability to store preferences from client-side code #1066 - Recommender status info ... % Conflicts: % inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/page/AnnotationPageBase.java % inception/inception-brat-editor/src/main/java/de/tudarmstadt/ukp/clarin/webanno/brat/annotation/BratAnnotationEditor.java % inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/service/DiamWebsocketController.java % inception/inception-documents/src/test/java/de/tudarmstadt/ukp/inception/documents/DocumentServiceImplConcurrencyTest.java % inception/inception-external-search-solr/pom.xml % inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentViewControllerImpl.java % inception/inception-html-editor/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports % inception/inception-preferences/src/main/java/de/tudarmstadt/ukp/inception/preferences/config/PreferencesServiceAutoConfig.java % inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/service/LearningRecordServiceImpl.java % inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImpl.java % inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/TrainingTask.java % inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/footer/RecommendationEventWebsocketControllerImplTest.java % inception/inception-support/pom.xml % inception/inception-ui-core/pom.xml % inception/inception-websocket/pom.xml % inception/pom.xml
- Fix compatibility of knowledge base type column with Hibernate 6
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- Remove some deprecated and unused APIs - Move a DB query to the criteria API as the string-based query no longer worked with Hibernate 6 - Fixed bug in hibernate integer enum type - Use SnakeYAML 1.33 for some tests because DKPro Core Dataset doesn't work with SnakeYAML 2.0 atm
- spring 6.0.9 -> 6.0.10 - spring-boot 3.1.0 -> 3.1.1 - spring-data 3.1.0 -> 3.1.1 - spring-security 6.1.0 -> 6.1.1 - tomcat 10.1.1 -> 10.1.11 - wicketstuff 10.0.0-SNAPSHOT 10.0.0-M1 - wicket-jquery-selectors 3.0.4 -> 3.0.6 - wicket-webjars 3.0.6 -> 4.0.0 - Remove outdated JavaDoc
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* main: (94 commits) #4150 - Upgrade dependencies #4155 - Better annotation suggestion IDs #4155 - Better annotation suggestion IDs #4150 - Upgrade dependencies #4150 - Upgrade dependencies #1861 - Add viewport offsets to external recommender #4155 - Better annotation suggestion IDs #4155 - Better annotation suggestion IDs #4139 - Reusable popover component for annotation editors #4139 - Reusable popover component for annotation editors #4139 - Reusable popover component for annotation editors Issue #4148: Switch PDF editor to compact model v2 #4139 - Reusable popover component for annotation editors [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-29.0 #3673 - Update dependencies Issue #4139: Reusable popover component for annotation editors #4140 - Simplify lazy detail lookup Issue #4139: Reusable popover component for annotation editors No issue. Set version to 30.0-SNAPSHOT ... % Conflicts: % inception/inception-diam/pom.xml % inception/inception-docker/src/main/docker/Dockerfile % inception/inception-io-xmi/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports % inception/inception-project-export/src/test/java/de/tudarmstadt/ukp/inception/project/export/controller/ExportServiceControllerImplTest.java % inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/footer/RecommendationEventWebsocketControllerImplTest.java % inception/inception-remote/pom.xml % inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/page/ApplicationPageBase.java % inception/pom.xml
* main: (42 commits) #4221 - Upgrade dependencies #4219 - Improve speed of importing a large KB #4217 - Speed up properties list loading on KB page #4209 - Improve query speed for large KBs when using RDF4J Lucene FTS #4212 - Unable to mark local KB as read-only [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-29.3 No issue. Fix PubMed test. #4192 - Upgrade dependencies No issue. Fix PubMed test. #4205 - Ability to refresh document to load pending suggestions #4158 - Exception when annotating something after a longer pause #4158 - Exception when annotating something after a longer pause No issue: Enable parallel builds #4158 - Exception when annotating something after a longer pause #4158 - Exception when annotating something after a longer pause #4192 - Upgrade dependencies #4201 - Layer export as JSON does not include coloring rules #4199 - Jumping to the end of a long annotation sometimes does not work #4198 - Show layer name instead of no-label ... % Conflicts: % inception/inception-workload-dynamic/src/main/java/de/tudarmstadt/ukp/inception/workload/dynamic/annotation/DynamicAnnotatorWorkflowActionBarItemGroup.java % pom.xml
* main: #4232 - Drop evaluation page #4230 - Upgrade dependencies No issue: Update system requirements and improve pointers to Docker-based deployment No issue: Call out to admins to look at the admin guide when reaching the installation section in the users guide. #4215 - Ability to specify GID and UID for the user used inside the Docker image [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-29.4 #4226 - Display logout button on annotation page if dashboard access is disabled #4215 - Ability to specify GID and UID for the user used inside the Docker image #4226 - Display logout button on annotation page if dashboard access is disabled #4150 - Upgrade dependencies #4223 - Covered text should show in popover #4215 - Ability to specify GID and UID for the user used inside the Docker image % Conflicts: % inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/logout/LogoutPanel.java
* main: [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-29.5 #4230 - Upgrade dependencies #4230 - Upgrade dependencies #4235 - Direct access-by-URL to sidebar curation mode sometimes does not work #4229 - Better project template selection #4229 - Better project template selection #4229 - Better project template selection #4229 - Better project template selection % Conflicts: % pom.xml
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* main: (39 commits) No issue: Try to get build work on Windows No issue: Added gitattributes file #4618 - Resizing a span does not update annotations on disk #4616 - Option to disable displaying suggestions in sidebar curation mode #4554 - Allow displaying comments from annotators on hover when curating using curation sidebar on the annotation page No issue: Try to get build work on Windows #4610 - Annotations are misaligned when PDF pages vary in dimensions #4611 - Run the three SPARQL queries in the concept linker in parallel No issue: Added gitattributes file No issue: Enable matrix build #4557 - Bulk process page should not show processes from other projects #4596 - Ability to temporarily suspend recommenders #4603 - Bulk actions in search sidebar should not be greyed-out when in sidebar curation mode #4602 - Project-specific user preferences may be saved without a user #4603 - Bulk actions in search sidebar should not be greyed-out when in sidebar curation mode #4602 - Project-specific user preferences may be saved without a user #4600 - Error when exporting project during preference phase No issue: Fix example CSS file for custom XML format which was actually an SCSS file #4583 - Ability to configure layer visibility via a sidebar Remove <Proxy> directive as it shouldn't be necessary ... % Conflicts: % inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/service/DiamWebsocketController.java % inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/FullTextIndexUpgradeTest.java % inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/config/RecommenderServiceAutoConfiguration.java % inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/footer/RecommendationEventFooterPanel.java % inception/inception-ui-scheduling/src/main/java/de/tudarmstadt/ukp/inception/ui/scheduling/TaskMonitorPanel.java % inception/inception-websocket/pom.xml
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- Wicket 10.0.0-M2 -> 10.0.0
* main: #1321 - Importing .ann files from BRAT #4614 - Display suggestions from Named Entity Linker immediately #4638 - Ability to filter annotation sidebar by covered text #4636 - Ability to collapse groups in annotation sidebar #4634 - Pull document file storage code out of document service into a new service #4550 - Clean up code #4625 - Azure AI Open AI recommender #4628 - Better results when using unlabelled annotations for few-shot learning #4550 - Clean up code #4625 - Azure AI Open AI recommender #1321 - Importing .ann files from BRAT [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-31.3 #1321 - Importing .ann files from BRAT #4622 - No helpful error message when recommender is not called due to feature being disabled No issue: Better logging #4550 - Clean up code
- jakarta.xml.bind-api 4.0.1 -> 4.0.2 - woodstox-core 6.6.0 -> 6.6.1 - json-schema-validator 1.3.3 -> 1.4.0 - oauth2-oidc-sdk 9.43.3 -> 9.43.4 - commons-compress 1.26.0 -> 1.26.1 - groovy 4.0.18 -> 4.0.20 - mockito 5.10.0 -> 5.11.0 - testcontainers 1.19.6 -> 1.19.7 - awaitility 4.2.0 -> 4.2.1 - spring 6.1.4 -> 6.1.5 - spring-data 3.2.4 -> 3.2.4 - springdoc 1.7.0 -> 1.8.0 - log4j 2.23.0 -> 2.23.1 - postgres-driver 42.7.2 -> 42.7.3 - wicket-bootstrap 7.0.1 -> 7.0.3 - wicket-jquery-selectors 4.0.2 -> 4.0.4 - wicket-webjars 4.0.1 -> 4.0.3 - wicketstuff 10.0.0-M2 -> 10.0.0
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* main: (110 commits) #4787 - When re-merging a document CASMetadata is not retained #4785 - Upgrade dependencies [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-33.0-beta-1 #4768 - Bulk curation [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-33.0-beta-1 [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-32.1 #4782 - Avoid duplicate key error when importing documents very rapidly #4780 - Optionally include example documents in project templates #4778 - Links and other active elements in PDFs interfere with annotation and should be disabled #4739 - Auto-merge on open document in curation mode #4774 - Ability to not reset curation when performing a manual merge (sidebar curation) #4772 - Repair to trim whitespace off annotations #4769 - Cannot export CAS RDF #4768 - Bulk curation #4766 - Add ID column to documents table in dev mode #4764 - No longer force-enable server-side timings when dev mode is disabled #4762 - Re-merging via the curation sidebar always uses the project settings instead of the dialog settings ... % Conflicts: % inception/inception-dependencies/pom.xml % inception/inception-diam-editor/pom.xml % inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/DiamAnnotationBrowser.java % inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorBase.java % inception/inception-remote/src/main/java/de/tudarmstadt/ukp/clarin/webanno/webapp/remoteapi/config/RemoteApiAutoConfiguration.java % inception/inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchServiceImpl.java % inception/inception-sharing/src/main/java/de/tudarmstadt/ukp/inception/sharing/config/InviteServiceAutoConfiguration.java % inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/detail/AnnotationDetailEditorPanel.java % inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/login/LoginPage.java % inception/inception-ui-curation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/curation/config/CurationUIAutoConfiguration.java % inception/inception-ui-curation/src/main/java/de/tudarmstadt/ukp/inception/ui/curation/sidebar/config/CurationSidebarAutoConfiguration.java % inception/inception-ui-dashboard-activity/pom.xml % inception/inception-ui-kb/pom.xml % inception/inception-workload-dynamic/src/main/java/de/tudarmstadt/ukp/inception/workload/dynamic/annotation/DynamicWorkflowDocumentNavigationActionBarExtension.java % pom.xml
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* main: #4791 - BOM not removed when importing plain text files #4791 - BOM not removed when importing plain text files No issue: Formatting No issue: Split chart example into a separate cell No issue: Example notebook dealing for dealing with JSON CAS data No issue: Show on screen that disable export also applies to curation docs/Update installation_kubernetes.adoc guide
* main: (47 commits) #4854 - Upgrade dependencies #1959 - Curation mode does not render cross-sentence relations #4846 - Control JUL bridge using a dedicated property #4745 - Upgrade dependencies #4745 - Upgrade dependencies #4835 - Error when trying to open certain documents with stacked annotations for curation #4839 - Scrolling to selection does sometimes not work in Apache Annotator Editor #4809 - Connecting annotation and entity with arc over different pages #4809 - Connecting annotation and entity with arc over different pages #4809 - Connecting annotation and entity with arc over different pages [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-33.0-beta-3 [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-32.3 #4832 - Improve self-help for reverse proxies #4832 - Improve self-help for reverse proxies #4832 - Improve self-help for reverse proxies #4830 - Cannot enable logging for JUL-based libraries #4809 - Connecting annotation and entity with arc over different pages #4809 - Connecting annotation and entity with arc over different pages ... % Conflicts: % inception/inception-app-webapp/pom.xml % inception/inception-constraints/src/main/java/de/tudarmstadt/ukp/clarin/webanno/constraints/ConstraintsServiceImpl.java % inception/inception-recommendation/pom.xml % inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/service/AnnotationSchemaServiceImpl.java % inception/inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchServiceImpl.java % pom.xml
- wicket 10.0.0 -> 10.1.0 - wicketstuff 10.0.0-M1 -> 10.2.0-SNAPSHOT
* main: #1319 - Cross-Layer Relations #4064 - Support for agreement calculation on document-level annotations #4860 - Knowledge base items should be matched even if query contains terms out of order #4858 - Option to not finish bulk-processed documents if no annotations were accepted #4064 - Support for agreement calculation on document-level annotations #4844 - Write project export directly to ZIP file #4853 - Detail popover on curation suggestions does not show lazy details when using sidebar curation mode #4844 - Write project export directly to ZIP file #4844 - Write project export directly to ZIP file #4844 - Write project export directly to ZIP file % Conflicts: % inception/inception-concept-linking/src/test/java/de/tudarmstadt/ukp/inception/conceptlinking/service/ConceptLinkingServiceImplTest.java
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- Added workaround for Wicket JQuery not yet properly initializing its themes - Removed redundant dependencies
- spring 6.1.5 -> 6.1.8 - spring-boot 3.2.3 -> 3.3.0 - spring-data 3.2.3 -> 3.3.0 - spring-security 6.2.2 -> 6.3.0 - tomcat 10.1.19 -> 10.1.24 - hibernate 6.4.4 -> 6.5.2 - wicket-bootstrap 7.0.3 -> 7.0.5 - wicket-jquery-selectors 4.0.4 -> 4.0.5 - wicket-webjars 4.0.3 -> 4.0.4 - wicket-spring-boot 4.0.0-M1 -> 4.0.0
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* main: [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-33.0 #4860 - Knowledge base items should be matched even if query contains terms out of order #4869 - Cannot re-merge curation document #4867 - Cannot re-open document for curation if it contains an invalid feature value No issue: Warn about slow queries when using a scope No issue: Set version to 34.0-SNAPSHOT
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What's in the PR
Problems
@LobString need to be set to@Column(length = 16_777_216)to make current MySQL scheme validation pass because Hibernate now uses the length to determine the best column type (before@Lobwas alwaysLONGTEXT) - that is maybe not the best idea. Might need to migrate the DB to use other types. Need to check embedded DB as well.How to test manually
Automatic testing
Documentation