[ctakes] branch main updated: BackwardsTimeAnnotator log init, process start ConstituencyParser log init, process start DegreeOfRelationExtractorAnnotator log init, process start DeterministicMarkable

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[ctakes] branch main updated: Some touch ups on the examples Added [set] creator to IdentifiedAnnotationBuilder for non-umls group IA

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[ctakes] branch main updated: Extracted PausableFileLoggerAE from CommandRunner and CtakesRunner Comments in StartFinishLogger and XmiCollectionReaderCtakes

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[ctakes] branch main updated: Added some deprecations

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[ctakes] branch main updated: Use IdentifiedAnnotationBuilder

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[ctakes] branch main updated: Add deprecation message and stub reminder for assertion. ListAnnotator Add catch for exception from TimSort

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[ctakes] branch main updated: CTAKES-72 Remove eclipse launch configurations.

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[ctakes] branch main updated: CTAKES-532 CTAKES-531

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[ctakes] branch main updated: PropertyAeFactory : much faster AE Description creation Added "initializing" and "processing" log messages to AEs, switched addLogged to add in their pipers Changed comme

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[ctakes] branch main updated: Add a profile to just package module jars. Use no-build-zips to avoid the long wait for zip and tar.gz

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svn commit: r1906189 - in /ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources: eventDict.txt org/apache/ctakes/temporal/eventDict.txt

Author: seanfinan Date: Fri Dec 23 17:08:38 2022 New Revision: 1906189 URL: http://svn.apache.org/viewvc?rev=1906189&view=rev Log: Move file Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/eventDict.txt - copied unchanged

[ctakes] branch main updated: Cleared compile wanrings in bin.xml and the 4 java classes pom switched from user resources copy in package phase to prepare-package phase

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[ctakes] branch main updated: updated some pom files, moved example notes, still working on getting web-rest and user-resources happy

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[ctakes] branch main updated: ctakes-web-rest docker uses actual ctakes pom, not a local copy. Git instead of svn, mv not copy, RUN && Renamed profiles moved web-rest profile declaration to main pom

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[ctakes] branch main updated: A bunch of comments for ctakes-web-rest regarding possible future development. Moved pom versions from dependencies to properties. Refactored CuiResponse to use newer uti

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[ctakes] branch main updated: Deprecation message in old dictionary ae. Removed imports of deprecated classes in Assertino classes.

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[ctakes] branch main updated: Some more refactoring - I am not sure what started this class implementation, but here it is.

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[ctakes] branch main updated: CTAKES-503, patch from Sean Mullane

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[ctakes] branch main updated (6b760d2 -> 677d6ad)

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[ctakes] branch main updated: CTAKES-564 All engines now implement uimafit JCasAnnotator_ImplBase We still need to refactor them to use @ConfigurationParameter RecordResolutionCasConsumer is fully ref

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[ctakes] branch main updated (fafd849 -> c43c029)

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[ctakes] branch main updated: Got rid of compile warnings. The only reamining warnings are for types (unchecked, etc.) in modules that use older untyped 3rd party code. Updating dependencies in the

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[ctakes] branch main updated: PiperFileRunEngine cleans enclosing quotes. CTAKES-453 CTAKES-490 Moved runCVD runCPE profiles to ctakes-examples

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[ctakes] branch main updated: ctakes-web-rest removed copies of standard ctakes piper files. ctakes-ytex-web added ctakes-user-resources dependency. TypeSystem.xml Add Episode and Regimen types.

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[ctakes] branch main updated: missed the piper/ references in this file. Really, there should only be 1 Default.piper, either in docker or resources, but not both.

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[ctakes] branch main updated: Create .asf.yaml

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[ctakes] branch main updated: Syntax Error

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[ctakes] branch main updated: Label changes

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[ctakes] branch main updated: Label Resolution?

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[ctakes] branch main updated: Starting with Maven 3.8.1 http:// dependencies are frowned upon. The ctakes-models actually exist with https:// but it wasn't actually checked. Specified that apache.sn

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[ctakes] branch main updated: Added SuppressWarnings unchecked for older code Copied TemplateFillerAnnotator to ctakes-core, deprecated in ctakes-template-filler since that module is otherwise empty c

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[ctakes] branch main updated: Check for null log parent directory before trying to create it.

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[ctakes] branch main updated (e4767d1 -> 9018bcf)

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[ctakes] branch main updated: type system moved

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[ctakes] branch main updated: Added parameter SetJavaHome that can be set to "no" should the user wish external processes to not use jdk8.

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[ctakes] branch main updated: Artemis should never need a javahome override.

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[ctakes] branch main updated: Refactored PBJ, moved python from src/main to src/user, some renaming Added pbj cnlpt negation example to ctakes-examples, need to add more of the cnlpt examples Added Py

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[ctakes] branch main updated: Revert change of ${basedir} to ${project.basedir}. change commit: d998331c1cfef48d792c78a8d3c1670498a8b925 aka d998331

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[ctakes] branch main updated: Removed Regimen from type system. Added generic attributes and modifiers. Added generic attributes and modifiers to Medication and Procedure types. Removed outdated pbj t

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[ctakes] branch main updated: Added get/set AnatomicalSite to Procedure Types. AnatomicalSite has slots for body side and laterality. So, this actually will replace 3 slots with 1, and the whole "circ

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svn commit: r1907472 - /ctakes/site/trunk/content/downloads.mdtext

Author: seanfinan Date: Mon Feb 6 17:00:44 2023 New Revision: 1907472 URL: http://svn.apache.org/viewvc?rev=1907472&view=rev Log: Java required: removed Oracle, remove "or higher" Modified: ctakes/site/trunk/content/downloads.mdtext Modified: ctakes/site/trunk/content/downlo

svn commit: r1907475 - /ctakes/site/trunk/content/downloads.mdtext

Author: seanfinan Date: Mon Feb 6 18:24:12 2023 New Revision: 1907475 URL: http://svn.apache.org/viewvc?rev=1907475&view=rev Log: Java required: removed Oracle, remove "or higher" Modified: ctakes/site/trunk/content/downloads.mdtext Modified: ctakes/site/trunk/content/downlo

[ctakes] branch main updated: API improvements, better interface with cnlpt negation.

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[ctakes] branch main updated: Improved comments

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[ctakes] branch main updated: Improved comments

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[ctakes] branch main updated: Improved readme. Still a work in progress.

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[ctakes] branch main updated: helper_functions added get_document_id. Added Queue size placeholders - not yet used. Added 3 second wait before exiting ctakes. Changed python stomp heartbeats to 10 sec

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[ctakes] branch main updated: Add a Skeleton TinyRestPipeline.piper that loads Default.piper Dockerfile copies a TinyRestPipeline.piper

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[ctakes] branch main updated: -l, -s no longer reserved for lookupXml and SubDirectory. If wanted, they should be declared such as in DictionarySubPipe which has cli LookupXml=l

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[ctakes] branch main updated: event_creator.py Replaced missing type EventMention helper_functions.py Fixed Procedure != EventMention, removed unnecessary i=0 reset negation_delegator.py Made caller

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[ctakes] branch main updated: Update issue templates

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[ctakes] branch main updated: Create BUG_REPORT.YML

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[ctakes] branch main updated: Replaced with yaml

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[ctakes] branch main updated: Attempting to enable the bug report yaml template

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[ctakes] branch main updated: File writer that saves Events and Times in an Anafora format.

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[ctakes] branch main updated: Fix for possible null Events.

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[ctakes] branch main updated: Corrected path to sentence detector

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[ctakes] branch main updated: Add PipeBitInfo to EventTimeAnaforaWriter Add simple token text and span writers: - example extending AbstractJCasFileWriter - core extending AbstractTableFileWriter Add

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[ctakes] branch main updated: DictionaryCuiCounter utility to count number of cuis in rare word dictionary. SemanticTableComparator utility to compare cuis (etc.) discovered in one pipeline vs. anothe

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[ctakes] branch main updated: Dictionary creator without poor man wsd DictionaryComparator util

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[ctakes] branch main updated: Added Collection Reader instead of generic annotator Added parameter declaration by reader and annotators

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[ctakes] branch main updated: Annotation Engine wrapper for the PbjReceiver collection reader. Example piper that has all of the ctakes steps in 1 pipeline

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[ctakes] branch main updated: PbjReceiverAE will disconnect on collectionProcessComplete() PythonRunner adds -u to command for unbuffered output

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[ctakes] branch main updated: Remove nashorn @Immutable. Required for jenkins build.

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[ctakes] branch main updated (afe638a -> def3dea)

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[ctakes-website] branch main updated: Create jekyll.yml

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[ctakes-website] branch main updated (d8aeda1 -> cc22663)

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[ctakes-website] 01/01: Merge pull request #1 from apache/dependabot/bundler/commonmarker-0.23.10

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(ctakes) branch main updated: Upgraded dependency version of fast-classpath-scanner to 3.1.6 (latest) to get rid of crash while scanning classpath in the piper creator gui (Simple Pipeline Fabricator)

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(ctakes) branch main updated: Removing unfinished classes, per author's permission.

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(ctakes) branch main updated: Require command line parameter name specification for names of send and receive queues. Refactoring of variable names. Better help messages.

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(ctakes) branch main updated: Maven plugin updates. As maven preps for a 4.x release it is validating some plugins as past freshness. 5.0.0 should be prepared.

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(ctakes) branch main updated: Bug fix in cnlpt negation example. code cleanup.

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(ctakes) branch main updated: Added parameter "ForceExit" to ExitForcer. Default is yes. Set to "no" and the ExitForcer will not force ctakes to exit when the run is complete.

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svn commit: r1914893 - in /ctakes/ctakes-models/trunk: KEYS pom.xml

Author: seanfinan Date: Sat Dec 23 18:40:52 2023 New Revision: 1914893 URL: http://svn.apache.org/viewvc?rev=1914893&view=rev Log: Prep for release Modified: ctakes/ctakes-models/trunk/KEYS ctakes/ctakes-models/trunk/pom.xml Modified: ctakes/ctakes-models/trunk/KEYS URL:

(ctakes) branch main updated: Gave README .md extension. Updated readme to have a bit more information - resembles the wiki landing page. Should sync the two when ready.

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(ctakes) branch main updated: Changed reference for README to README.md Might as well add fhir to BigPipeline.piper

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svn commit: r1914908 - /ctakes/ctakes-models/trunk/pom.xml

Author: seanfinan Date: Sun Dec 24 15:50:43 2023 New Revision: 1914908 URL: http://svn.apache.org/viewvc?rev=1914908&view=rev Log: Wrong gpg version? Was ok yesterday? Modified: ctakes/ctakes-models/trunk/pom.xml Modified: ctakes/ctakes-models/trunk/pom.xml URL: http://svn.apache

(ctakes) branch main updated: For goodness sake ...

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svn commit: r1914910 - /ctakes/ctakes-models/tags/ctakes-models-5.0.0/

Author: seanfinan Date: Sun Dec 24 17:10:21 2023 New Revision: 1914910 URL: http://svn.apache.org/viewvc?rev=1914910&view=rev Log: [maven-release-plugin] copy for tag ctakes-models-5.0.0 Added: ctakes/ctakes-models/tags/ctakes-models-5.0.0/ - copied from r1914909, ctakes/ctakes-mo

svn commit: r1914909 - in /ctakes/ctakes-models/trunk: ./ ctakes-assertion-models/ ctakes-chunker-models/ ctakes-constituency-parser-models/ ctakes-core-models/ ctakes-coreference-models/ ctakes-depen

Author: seanfinan Date: Sun Dec 24 17:10:20 2023 New Revision: 1914909 URL: http://svn.apache.org/viewvc?rev=1914909&view=rev Log: [maven-release-plugin] prepare release ctakes-models-5.0.0 Modified: ctakes/ctakes-models/trunk/ctakes-assertion-models/pom.xml ctakes/ctakes-models/t

svn commit: r1914911 - in /ctakes/ctakes-models/trunk: ./ ctakes-assertion-models/ ctakes-chunker-models/ ctakes-constituency-parser-models/ ctakes-core-models/ ctakes-coreference-models/ ctakes-depen

Author: seanfinan Date: Sun Dec 24 17:10:22 2023 New Revision: 1914911 URL: http://svn.apache.org/viewvc?rev=1914911&view=rev Log: [maven-release-plugin] prepare for next development iteration Modified: ctakes/ctakes-models/trunk/ctakes-assertion-models/pom.xml ctakes/ctakes-models/t

(ctakes) branch main updated: Update pom.xml

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(ctakes) branch main updated: switched from using ctakes.models.version to just project.version for all ctakes model dependencies

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(ctakes) annotated tag ctakes-5.0.0 updated (4031d3d -> 656cf21)

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(ctakes) branch main updated: Outdated test

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(ctakes) annotated tag ctakes-5.0.0 deleted (was 656cf21)

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(ctakes) annotated tag ctakes-5.0.0 updated (cab42de -> 76ddfe2)

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(ctakes) branch main updated: Removed resources/ from the src builds.

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(ctakes) annotated tag ctakes-5.0.0 updated (e8c98ae -> 3a1dc24)

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(ctakes) annotated tag ctakes-5.0.0 deleted (was 3a1dc24)

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(ctakes) annotated tag ctakes-5.0.0 updated (3cafa6c -> 0f5a498)

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(ctakes) branch main updated: Update model resources for 5.0.0 upcoming code release

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(ctakes) tag cTAKES-5.0.0 created (now ecdf4b2)

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(ctakes) tag cTAKES-5.0.0 created (now ecdf4b2)

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(ctakes) branch main updated: -Silent- 5.0.0 code freeze undone. Fix div by 0 in FinishedLogger Add detect null in HsqlWriter Replace local hardcoded input directory path in ZonerRunner with error, in

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(ctakes) annotated tag ctakes-5.0.0 updated (ecdf4b2 -> a9bd642)

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