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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 fa72585 A bunch of comments for ctakes-web-rest regarding possible
future development. Moved pom versions from dependencies to properties.
Refactored CuiResponse to use newer utility code.
fa72585 is described below
commit fa725852f97c86645e1e89ab7f74c5807c74604b
Author: Sean Finan <[email protected]>
AuthorDate: Wed Dec 28 11:38:01 2022 -0500
A bunch of comments for ctakes-web-rest regarding possible future
development.
Moved pom versions from dependencies to properties.
Refactored CuiResponse to use newer utility code.
---
ctakes-web-rest/docker/Dockerfile | 10 ++++++-
ctakes-web-rest/pom.xml | 23 ++++++++++------
.../apache/ctakes/rest/service/CuiResponse.java | 32 ++++++++++++----------
3 files changed, 42 insertions(+), 23 deletions(-)
diff --git a/ctakes-web-rest/docker/Dockerfile
b/ctakes-web-rest/docker/Dockerfile
index 2525bb4..6c82ff5 100644
--- a/ctakes-web-rest/docker/Dockerfile
+++ b/ctakes-web-rest/docker/Dockerfile
@@ -1,5 +1,13 @@
FROM openjdk:8-alpine
-
+
+## This Dockerfile checks out and builds all of ctakes. Is there a reason for
this?
+## If you just checked in some fresh code and can't wait for a jenkins build
then ok.
+## Otherwise you can just check out the ctakes-web-rest directory and build it
for the war.
+## You can also add ctakes-web-rest as a dependency in a -dummy- pom with an
output directory for the war.
+## If you do have brand new code then another tactic is a copy of local source
into the container, then building.
+## That is more useful for developers who are not ctakes committers.
+## Consider offering multiple dockerfiles.
+
RUN apk update && \
apk add --no-cache git openssh ca-certificates openssl wget unzip
subversion maven
diff --git a/ctakes-web-rest/pom.xml b/ctakes-web-rest/pom.xml
index 73f8bc2..bafb54a 100644
--- a/ctakes-web-rest/pom.xml
+++ b/ctakes-web-rest/pom.xml
@@ -14,13 +14,20 @@
<ctakes.version>5.0.0-SNAPSHOT</ctakes.version>
<springframework.version>4.3.12.RELEASE</springframework.version>
<jackson.version>2.9.7</jackson.version>
+ <maven.compiler.plugin.version>3.10.1</maven.compiler.plugin.version>
+ <maven.war.plugin.version>3.2.3</maven.war.plugin.version>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<jettyVersion>9.2.6.v20141205</jettyVersion>
+ <spring.version>4.3.12.RELEASE</spring.version>
+ <uimafit.version>2.4.0</uimafit.version>
+ <uimaj.version>2.10.2</uimaj.version>
+ <servlet.version>2.5</servlet.version>
+ <mysql.connect.version>6.0.6</mysql.connect.version>
</properties>
<dependencies>
-<!-- TODO Exclusions. See the pom files in dockhand goal/rest/pom/ -->
+<!-- TODO Any Exclusions? See the pom files in dockhand goal/rest/pom/
-->
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
@@ -141,28 +148,28 @@
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
- <version>2.10.2</version>
+ <version>${uimaj.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-json</artifactId>
- <version>2.10.2</version>
+ <version>${uimaj.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimafit-core</artifactId>
- <version>2.4.0</version>
+ <version>${uimafit.version}</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
- <version>6.0.6</version>
+ <version>${mysql.connect.version}</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
- <version>2.5</version>
+ <version>${servlet.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
@@ -227,7 +234,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
- <version>3.2.3</version>
+ <version>${maven.war.plugin.version}</version>
<configuration>
<warName>ctakes-web-rest</warName>
<outputDirectory>${project.build.directory}</outputDirectory>
@@ -236,7 +243,7 @@
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
- <version>2.4</version>
+
<version>${maven.compiler.plugin.version}</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
diff --git
a/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java
b/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java
index 5786933..8def380 100644
---
a/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java
+++
b/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java
@@ -18,20 +18,22 @@
*/
package org.apache.ctakes.rest.service;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.tcas.Annotation;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
/**
* Created by tmill on 12/20/18.
*/
public class CuiResponse {
+ // TODO - We don't seem to be returning relations (etc.) anywhere, so why
does the war contain so many modules?
+ // TODO - consider having multiple return types available. see
ctakes-tiny-rest service/response/* and
+ // service/TinyController.
+ // TODO - consider an additional json such as UmlsJsonFormatter.
final private String _type;
public int begin;
public int end;
@@ -46,17 +48,19 @@ public class CuiResponse {
text = annotation.getCoveredText();
if(annotation instanceof IdentifiedAnnotation) {
- IdentifiedAnnotation ia = (IdentifiedAnnotation) annotation;
+ final IdentifiedAnnotation ia = (IdentifiedAnnotation) annotation;
polarity = ia.getPolarity();
- if(ia.getOntologyConceptArr() != null) {
- for (UmlsConcept concept :
JCasUtil.select(ia.getOntologyConceptArr(), UmlsConcept.class)) {
- Map<String, String> atts = new HashMap<>();
- atts.put("codingScheme", concept.getCodingScheme());
- atts.put("cui", concept.getCui());
- atts.put("code", concept.getCode() == null ? "n/a" :
concept.getCode());
- atts.put("tui", concept.getTui());
- conceptAttributes.add(atts);
+ final Collection<OntologyConcept> concepts
+ = OntologyConceptUtil.getOntologyConcepts( ia );
+ for ( OntologyConcept concept : concepts ) {
+ final Map<String,String> attributes = new HashMap<>();
+ attributes.put( "codingScheme", concept.getCodingScheme() );
+ attributes.put( "code", concept.getCode() == null ? "n/a" :
concept.getCode() );
+ if ( concept instanceof UmlsConcept ) {
+ attributes.put( "cui", ( (UmlsConcept) concept ).getCui()
);
+ attributes.put("tui", ( (UmlsConcept) concept ).getTui() );
}
+ conceptAttributes.add( attributes );
}
}
}
