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seanfinan pushed a commit to branch main
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The following commit(s) were added to refs/heads/main by this push:
new 3cbc199 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.
3cbc199 is described below
commit 3cbc199e6c4bf6e27ef01bf6192697a01129ccfb
Author: Sean Finan <[email protected]>
AuthorDate: Tue Jan 10 09:16:41 2023 -0500
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.
---
.../apache/ctakes/typesystem/types/TypeSystem.xml | 102 ++++++++++++++++++++-
.../pipers/AdvancedTokenizerPipeline.piper | 24 -----
.../resources/pipers/AttributeCleartkSubPipe.piper | 19 ----
.../src/main/resources/pipers/ChunkerSubPipe.piper | 5 -
.../src/main/resources/pipers/CorefSubPipe.piper | 10 --
.../src/main/resources/pipers/Default.piper | 8 +-
.../main/resources/pipers/DictionarySubPipe.piper | 10 --
.../src/main/resources/pipers/Full.piper | 12 +--
.../main/resources/pipers/TemporalSubPipe.piper | 19 ----
.../pipers/TsAttributeCleartkSubPipe.piper | 19 ----
.../main/resources/pipers/TsChunkerSubPipe.piper | 5 -
.../pipers/TsDefaultTokenizerPipeline.piper | 5 -
.../resources/pipers/TsDictionarySubPipe.piper | 10 --
ctakes-ytex-web/pom.xml | 7 ++
pom.xml | 6 --
15 files changed, 118 insertions(+), 143 deletions(-)
diff --git
a/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
b/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
index c2c440b..829764e 100644
---
a/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
+++
b/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
@@ -1788,7 +1788,7 @@ This instantiates a manages/treats relation which should
be marked as conditiona
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.textsem.MedicationEventMention</name>
- <description>As of cTAKEs 3.1, see
org.apache.ctakes.typesystem.type.textsem.MedicationMention.</description>
+ <description>Deprecated. As of cTAKEs 3.1, see
org.apache.ctakes.typesystem.type.textsem.MedicationMention.</description>
<supertypeName>org.apache.ctakes.typesystem.type.textsem.EventMention</supertypeName>
<features>
<featureDescription>
@@ -2511,5 +2511,105 @@ More qualifying information on how the procedure was
done.</description>
</featureDescription>
</features>
</typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.typesystem.type.textspan.Episode</name>
+ <description>An annotation within a text span for an
Episode.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>episodeType</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.typesystem.type.refsem.Regimen</name>
+ <description>A Therapeutic or Preventive Procedure that consists of
individual notable events. No Text Span.</description>
+
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Event</supertypeName>
+ <features>
+ <featureDescription>
+ <name>startTime</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.refsem.Time</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>endTime</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.refsem.Time</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>duration</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.TemporalRelation</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>relativeTemporalContext</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.TemporalRelation</rangeTypeName>
+ </featureDescription>
+ <!-- Arrays for Procedures (e.g. RadioTherapy) and Medications
(e.g. ChemoTherapy) -->
+ <featureDescription>
+ <name>procedures</name>
+ <description/>
+ <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+
<elementType>org.apache.ctakes.typesystem.type.refsem.Procedure</elementType>
+ </featureDescription>
+ <featureDescription>
+ <name>medications</name>
+ <description/>
+ <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+
<elementType>org.apache.ctakes.typesystem.type.refsem.Medication</elementType>
+ </featureDescription>
+ </features>
+ </typeDescription>
+
+ <typeDescription>
+ <name>org.apache.ctakes.typesystem.type.textsem.RegimenMention</name>
+ <description>A Therapeutic or Preventive Procedure that consists of
individual notable events. Text Span.</description>
+
<supertypeName>org.apache.ctakes.typesystem.type.textsem.EventMention</supertypeName>
+ <features>
+ <!-- Temporal information common to all Regimen types -->
+ <featureDescription>
+ <name>startDate</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.textsem.TimeMention</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>endDate</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.textsem.TimeMention</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>duration</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.TemporalTextRelation</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequency</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.TemporalTextRelation</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>relativeTemporalContext</name>
+ <description/>
+
<rangeTypeName>org.apache.ctakes.typesystem.type.relation.TemporalTextRelation</rangeTypeName>
+ </featureDescription>
+ <!-- Arrays for Procedures (e.g. RadioTherapy) and Medications
(e.g. ChemoTherapy) -->
+ <featureDescription>
+ <name>procedures</name>
+ <description/>
+ <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+
<elementType>org.apache.ctakes.typesystem.type.textsem.ProcedureMention</elementType>
+ </featureDescription>
+ <featureDescription>
+ <name>medications</name>
+ <description/>
+ <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+
<elementType>org.apache.ctakes.typesystem.type.textsem.MedicationMention</elementType>
+ </featureDescription>
+ </features>
+ </typeDescription>
+
</types>
</typeSystemDescription>
diff --git
a/ctakes-web-rest/src/main/resources/pipers/AdvancedTokenizerPipeline.piper
b/ctakes-web-rest/src/main/resources/pipers/AdvancedTokenizerPipeline.piper
deleted file mode 100644
index 3fe9315..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/AdvancedTokenizerPipeline.piper
+++ /dev/null
@@ -1,24 +0,0 @@
-// Commands and parameters to create a token processing pipeline with
sections, paragraphs and lists
-
-// Annotate sections by known regex
-add BsvRegexSectionizer
-
-// The sentence detector needs our custom model path, otherwise default values
are used.
-addLogged SentenceDetectorAnnotatorBIO
classifierJarPath=/org/apache/ctakes/core/models/sentdetect/model.jar
-
-// The SentenceDetectorAnnotatorBIO is a "lumper" that works well for notes in
which end of line does not indicate a sentence.
-// If that is not your case, then you may get better results using the more
standard SentenceDetector
-// add SentenceDetector
-
-// By default, paragraphs are parsed using empty lines as separators and Part
#:
-add ParagraphAnnotator
-// Fix sentences so that no sentence spans across two or more paragraphs.
-add ParagraphSentenceFixer
-
-// Use regular expressions created for the Pitt notes to discover formatted
lists and tables.
-add ListAnnotator
-// Fix sentences so that no sentence spans across two or more list entries.
-add ListSentenceFixer
-
-// Now we can finally tokenize, tag parts of speech and chunk using adjusted
sentences.
-add TokenizerAnnotatorPTB
diff --git
a/ctakes-web-rest/src/main/resources/pipers/AttributeCleartkSubPipe.piper
b/ctakes-web-rest/src/main/resources/pipers/AttributeCleartkSubPipe.piper
deleted file mode 100644
index 5e87225..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/AttributeCleartkSubPipe.piper
+++ /dev/null
@@ -1,19 +0,0 @@
-// Commands and parameters to create a default entity attributes processing
sub-pipeline. This is not a full pipeline.
-
-// Add the Dependency parser for use by cleartk
-addDescription ClearNLPDependencyParserAE
-// Add the Semantic Role Labeler parser for use by cleartk
-addLogged ClearNLPSemanticRoleLabelerAE
-
-// Add the cleartk package for cleartk class lookups
-package org.apache.ctakes.assertion.medfacts.cleartk
-
-// Add the cleartk attribute engines, logging for them as a block
-add StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning
Attributes" IS_START=true
-addDescription PolarityCleartkAnalysisEngine
-addDescription UncertaintyCleartkAnalysisEngine
-addDescription HistoryCleartkAnalysisEngine
-addDescription ConditionalCleartkAnalysisEngine
-addDescription GenericCleartkAnalysisEngine
-addDescription SubjectCleartkAnalysisEngine
-add StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning
Attributes"
diff --git a/ctakes-web-rest/src/main/resources/pipers/ChunkerSubPipe.piper
b/ctakes-web-rest/src/main/resources/pipers/ChunkerSubPipe.piper
deleted file mode 100644
index 523bd4d..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/ChunkerSubPipe.piper
+++ /dev/null
@@ -1,5 +0,0 @@
-// Commands and parameters to create a default chunker processing
sub-pipeline. This is not a full pipeline.
-
-add Chunker
-addDescription adjuster.ChunkAdjuster NP,NP 1
-addDescription adjuster.ChunkAdjuster NP,PP,NP 2
diff --git a/ctakes-web-rest/src/main/resources/pipers/CorefSubPipe.piper
b/ctakes-web-rest/src/main/resources/pipers/CorefSubPipe.piper
deleted file mode 100644
index d06f5d1..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/CorefSubPipe.piper
+++ /dev/null
@@ -1,10 +0,0 @@
-// Commands and parameters to create a default coreference processing
sub-pipeline. This is not a full pipeline.
-
-// A Dependency Parser is necessary, but is usually added for assertion so
don't add one here
-
-// Constituency Parser adds Terminal Treebank Nodes, needed to create Markables
-add ConstituencyParser
-
-add DeterministicMarkableAnnotator
-addDescription MarkableSalienceAnnotator
/org/apache/ctakes/temporal/models/salience/model.jar
-addDescription MentionClusterCoreferenceAnnotator
/org/apache/ctakes/coreference/models/mention-cluster/model.jar
diff --git a/ctakes-web-rest/src/main/resources/pipers/Default.piper
b/ctakes-web-rest/src/main/resources/pipers/Default.piper
index 07f3826..a18153d 100644
--- a/ctakes-web-rest/src/main/resources/pipers/Default.piper
+++ b/ctakes-web-rest/src/main/resources/pipers/Default.piper
@@ -4,17 +4,17 @@
threads 3
// Load a simple token processing pipeline from another pipeline file
-load pipers/TsDefaultTokenizerPipeline
+load TsDefaultTokenizerPipeline
// Add non-core annotators
add ContextDependentTokenizerAnnotator
addDescription POSTagger
// Add Chunkers
-load pipers/TsChunkerSubPipe
+load TsChunkerSubPipe
// Default fast dictionary lookup
-load pipers/TsDictionarySubPipe
+load TsDictionarySubPipe
// Add Cleartk Entity Attribute annotators
-load pipers/TsAttributeCleartkSubPipe
+load TsAttributeCleartkSubPipe
diff --git a/ctakes-web-rest/src/main/resources/pipers/DictionarySubPipe.piper
b/ctakes-web-rest/src/main/resources/pipers/DictionarySubPipe.piper
deleted file mode 100644
index 16baa3c..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/DictionarySubPipe.piper
+++ /dev/null
@@ -1,10 +0,0 @@
-// Commands and parameters to create a default dictionary lookup
sub-pipeline. This is not a full pipeline.
-
-// path to the xml file containing information for dictionary lookup
configuration.
-cli LookupXml=org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml
-// umls credentials
-cli umlsUser=user
-cli umlsPass=pass
-
-// Default fast dictionary lookup
-add DefaultJCasTermAnnotator
LookupXml=org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml
diff --git a/ctakes-web-rest/src/main/resources/pipers/Full.piper
b/ctakes-web-rest/src/main/resources/pipers/Full.piper
index 611210b..b1413e5 100644
--- a/ctakes-web-rest/src/main/resources/pipers/Full.piper
+++ b/ctakes-web-rest/src/main/resources/pipers/Full.piper
@@ -1,17 +1,17 @@
// Advanced Tokenization: Regex sectionization, BIO Sentence Detector(lumper),
Paragraphs,Lists
-load pipers/AdvancedTokenizerPipeline.piper
+load AdvancedTokenizerPipeline.piper
add ContextDependentTokenizerAnnotator
add POSTagger
// Chunkers
-load pipers/ChunkerSubPipe.piper
+load ChunkerSubPipe.piper
// Default fast dictionary lookup
-load pipers/DictionarySubPipe.piper
+load DictionarySubPipe.piper
add org.apache.ctakes.drugner.ae.DrugMentionAnnotator
// Cleartk Entity Attributes
-load pipers/AttributeCleartkSubPipe.piper
+load AttributeCleartkSubPipe.piper
// Temporal
-load pipers/TemporalSubPipe.piper
+load TemporalSubPipe.piper
// Coreferences
-load pipers/CorefSubPipe.piper
+load CorefSubPipe.piper
add ContextAnnotator
add LabValueFinder
\ No newline at end of file
diff --git a/ctakes-web-rest/src/main/resources/pipers/TemporalSubPipe.piper
b/ctakes-web-rest/src/main/resources/pipers/TemporalSubPipe.piper
deleted file mode 100644
index 83f0f69..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/TemporalSubPipe.piper
+++ /dev/null
@@ -1,19 +0,0 @@
-// Commands and parameters to create a default temporal processing
sub-pipeline. This is not a full pipeline.
-
-// 'Generic' Events. Use addDescription and let the EventAnnotator set itself
up with defaults.
-addDescription EventAnnotator
-
-// Times. Use addLogged to log start and finish of processing. There aren't
default models, so set specifically
-addLogged BackwardsTimeAnnotator
classifierJarPath=/org/apache/ctakes/temporal/models/timeannotator/model.jar
-
-// DocTimeRel: the relation bin for Events to the Document Creation Time.
-addLogged DocTimeRelAnnotator
classifierJarPath=/org/apache/ctakes/temporal/models/doctimerel/model.jar
-
-// Event - Time binary relations.
-addLogged EventTimeRelationAnnotator
classifierJarPath=/org/apache/ctakes/temporal/models/eventtime/model.jar
-
-// Event - Event binary relations.
-addLogged EventEventRelationAnnotator
classifierJarPath=/org/apache/ctakes/temporal/models/eventevent/model.jar
-
-// Need to improve. Generic Events (head words) should be replaced by
overlapping subclasses with relations adjusted.
-//add FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
diff --git
a/ctakes-web-rest/src/main/resources/pipers/TsAttributeCleartkSubPipe.piper
b/ctakes-web-rest/src/main/resources/pipers/TsAttributeCleartkSubPipe.piper
deleted file mode 100644
index a1f4c80..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/TsAttributeCleartkSubPipe.piper
+++ /dev/null
@@ -1,19 +0,0 @@
-// Commands and parameters to create a default entity attributes processing
sub-pipeline. This is not a full pipeline.
-
-// Add the Dependency parser for use by cleartk
-addDescription concurrent.ThreadSafeClearNlpDepParser
-// Add the Semantic Role Labeler parser for use by cleartk
-addDescription concurrent.ThreadSafeClearNlpSemRoleLabeler
-
-// Add the cleartk package for cleartk class lookups
-package org.apache.ctakes.assertion.medfacts.cleartk
-
-// Add the cleartk attribute engines, logging for them as a block
-add StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning
Attributes" IS_START=true
-addDescription PolarityCleartkAnalysisEngine
-addDescription UncertaintyCleartkAnalysisEngine
-addDescription HistoryCleartkAnalysisEngine
-addDescription ConditionalCleartkAnalysisEngine
-addDescription GenericCleartkAnalysisEngine
-addDescription SubjectCleartkAnalysisEngine
-add StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning
Attributes"
diff --git a/ctakes-web-rest/src/main/resources/pipers/TsChunkerSubPipe.piper
b/ctakes-web-rest/src/main/resources/pipers/TsChunkerSubPipe.piper
deleted file mode 100644
index 9f81bdc..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/TsChunkerSubPipe.piper
+++ /dev/null
@@ -1,5 +0,0 @@
-// Commands and parameters to create a default chunker processing
sub-pipeline. This is not a full pipeline.
-
-add concurrent.ThreadSafeChunker
-addDescription adjuster.ChunkAdjuster NP,NP 1
-addDescription adjuster.ChunkAdjuster NP,PP,NP 2
diff --git
a/ctakes-web-rest/src/main/resources/pipers/TsDefaultTokenizerPipeline.piper
b/ctakes-web-rest/src/main/resources/pipers/TsDefaultTokenizerPipeline.piper
deleted file mode 100644
index 4c3225c..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/TsDefaultTokenizerPipeline.piper
+++ /dev/null
@@ -1,5 +0,0 @@
-// Commands and parameters to create a default token processing pipeline
-
-add SimpleSegmentAnnotator
-add concurrent.ThreadSafeSentenceDetector
-add TokenizerAnnotatorPTB
diff --git
a/ctakes-web-rest/src/main/resources/pipers/TsDictionarySubPipe.piper
b/ctakes-web-rest/src/main/resources/pipers/TsDictionarySubPipe.piper
deleted file mode 100644
index 3fc703d..0000000
--- a/ctakes-web-rest/src/main/resources/pipers/TsDictionarySubPipe.piper
+++ /dev/null
@@ -1,10 +0,0 @@
-// Commands and parameters to create a default dictionary lookup
sub-pipeline. This is not a full pipeline.
-
-// path to the xml file containing information for dictionary lookup
configuration.
-cli LookupXml=l
-// umls credentials
-cli umlsUser=user
-cli umlsPass=pass
-
-// Default fast dictionary lookup
-add concurrent.ThreadSafeFastLookup
LookupXml=org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml
diff --git a/ctakes-ytex-web/pom.xml b/ctakes-ytex-web/pom.xml
index 9d278d9..8ddc91b 100644
--- a/ctakes-ytex-web/pom.xml
+++ b/ctakes-ytex-web/pom.xml
@@ -15,6 +15,7 @@
<url>http://ctakes.apache.org</url>
<inceptionYear>2012</inceptionYear>
<properties>
+ <ctakes.version>5.0.0-SNAPSHOT</ctakes.version>
<jetty.useTestScope>false</jetty.useTestScope>
</properties>
<dependencies>
@@ -26,6 +27,12 @@
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
</dependency>
+ <!-- ctakes-user-resources exists specifically for standalone
products like ctakes-ytex-web -->
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-user-resources</artifactId>
+ <version>${ctakes.version}</version>
+ </dependency>
<dependency>
<groupId>com.sun.faces</groupId>
<artifactId>jsf-api</artifactId>
diff --git a/pom.xml b/pom.xml
index 2c8b7f6..b9c7977 100644
--- a/pom.xml
+++ b/pom.xml
@@ -877,12 +877,6 @@
<artifactId>maven-deploy-plugin</artifactId>
<version>${maven-deploy-plugin.version}</version>
</plugin>
- <!-- The maven
eclipse plugin is retired and no longer supported.-->
- <!--
https://maven.apache.org/plugins/maven-eclipse-plugin/ -->
- <!-- <plugin>-->
- <!--
<artifactId>maven-eclipse-plugin</artifactId>-->
- <!--
<version>2.9</version>-->
- <!-- </plugin>-->
<plugin>
<artifactId>maven-gpg-plugin</artifactId>
<version>${maven-gpg-plugin.version}</version>
