Jamia system upgrades no timenorm

Dockerfile

@@ -32,16 +32,16 @@ disable_system_repos=0\n'\
 # Clean all yum cache
 RUN yum update -y && \
     yum install -y yum-utils && \
-    yum install -y which java-1.8.0-openjdk java-1.8.0-openjdk-devel unzip && \
+    yum install -y which java-17-openjdk java-17-openjdk-devel unzip && \
     curl -fsSL https://archive.apache.org/dist/maven/maven-3/$MAVEN_VERSION/binaries/apache-maven-$MAVEN_VERSION-bin.tar.gz | tar xzf - -C /usr/share && \
     mv /usr/share/apache-maven-$MAVEN_VERSION /usr/share/maven && \
     ln -s /usr/share/maven/bin/mvn /usr/bin/mvn && \
     yum install -y gcc git python39 python39-devel && \
     alternatives --set python /usr/bin/python3.9 && \
     pip3 install --upgrade pip && \
-    curl -LO https://archive.apache.org/dist/activemq/activemq-artemis/2.19.1/apache-artemis-2.19.1-bin.zip && \
-    unzip apache-artemis-2.19.1-bin.zip && \
-    apache-artemis-2.19.1/bin/artemis create mybroker --user deepphe --password deepphe --allow-anonymous && \
+    curl -LO https://archive.apache.org/dist/activemq/activemq-artemis/2.36.0/apache-artemis-2.36.0-bin.zip && \
+    unzip apache-artemis-2.36.0-bin.zip && \
+    apache-artemis-2.36.0/bin/artemis create mybroker --user deepphe --password deepphe --allow-anonymous && \
     yum clean all
 
 # Set environment variables for Java and Maven
@@ -61,7 +61,7 @@ RUN mvn -U clean package
 
 # Execute the parser jar
 CMD ["java", "-cp", \
-"instance-generator/target/instance-generator-5.0.0-SNAPSHOT-jar-with-dependencies.jar", \
+"instance-generator/target/instance-generator-7.0.0-SNAPSHOT-jar-with-dependencies.jar", \
 "org.apache.ctakes.core.pipeline.PiperFileRunner", \
 "-p", "org/apache/ctakes/timelines/pipeline/Timelines", \
 "-i", "/usr/src/app/input", \

README.md

@@ -83,14 +83,14 @@ Due to a current issue in the inter process communication, the process will fini
 ## Running the system outside of a Docker image
 
 This is for the most part actually how we have ran the system during development, and can be resorted to in the event of issues with creating or running a Docker image.  Use the following steps for setup:
-- Make sure you have Java JDK 8  (we use OpenJDK) and the latest version of maven installed and that Java 8 is set as your default system Java
+- Make sure you have Java JDK 11  (we use OpenJDK) and the latest version of maven installed and that Java 11 is set as your default system Java
 - Create a conda 3.9 environment with `conda create -n timelines python=3.9`
 - Change directory into `timelines` under the project root
 - Create an ActiveMQ broker named `mybroker` in your current directory via:
 ```
-curl -LO https://archive.apache.org/dist/activemq/activemq-artemis/2.19.1/apache-artemis-2.19.1-bin.zip && \
-unzip apache-artemis-2.19.1-bin.zip && \
-apache-artemis-2.19.1/bin/artemis create mybroker --user deepphe --password deepphe --allow-anonymous
+curl -LO https://archive.apache.org/dist/activemq/activemq-artemis/2.32.0/apache-artemis-2.32.0-bin.zip && \
+unzip apache-artemis-2.32.0-bin.zip && \
+apache-artemis-2.32.0/bin/artemis create mybroker --user deepphe --password deepphe --allow-anonymous
 ```
 - (temporary fix until we fix the PBJ and timelines dependencies issue) Install the system's Python dependencies via:
 ```

timelines/gold_debug_just_run.sh

@@ -1,9 +1,9 @@
-java -cp instance-generator/target/instance-generator-5.0.0-SNAPSHOT-jar-with-dependencies.jar \
+java -cp instance-generator/target/instance-generator-7.0.0-SNAPSHOT-jar-with-dependencies.jar \
      org.apache.ctakes.core.pipeline.PiperFileRunner \
      -p org/apache/ctakes/timelines/pipeline/Timelines \
-     -a  mybroker \
-     -v /usr/local/miniconda3/envs/timelines-docker \
-     -i ../input/ \
-     -o ../output \
+     -a  C:\Users\ch229935\Documents\apache-artemis-2.39.0-bin\mybroker \
+     -v  C:\Users\ch229935\.conda\envs\ctakes-chemotime \
+     -i  C:\Users\ch229935\Desktop\cTakes\chemoTimelinesBaselineSystem\input\breast_dev_restrictions\ \
+     -o . \
      -l org/apache/ctakes/dictionary/lookup/fast/bsv/Unified_Gold_Dev.xml \
      --pipPbj yes \

timelines/instance-generator/pom.xml

@@ -5,17 +5,17 @@
   <parent>
     <artifactId>txtimelines-lookup</artifactId>
     <groupId>org.healthnlp</groupId>
-    <version>5.0.0-SNAPSHOT</version>
+    <version>7.0.0-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 
   <artifactId>instance-generator</artifactId>
 
   <packaging>jar</packaging>
   <properties>
-    <maven.compiler.source>8</maven.compiler.source>
-    <maven.compiler.target>8</maven.compiler.target>
-    <ctakes.version>5.0.0-SNAPSHOT</ctakes.version>
+    <maven.compiler.source>17</maven.compiler.source>
+    <maven.compiler.target>17</maven.compiler.target>
+    <ctakes.version>7.0.0-SNAPSHOT</ctakes.version>
     <skip.assembly>false</skip.assembly>
   </properties>
   <dependencies>
@@ -25,6 +25,16 @@
       <version>${ctakes.version}</version>
     </dependency>
 
+    <dependency>
+      <groupId>org.apache.ctakes</groupId>
+      <artifactId>ctakes-examples</artifactId>
+      <version>${ctakes.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.ctakes</groupId>
+      <artifactId>ctakes-user-resources</artifactId>
+      <version>${ctakes.version}</version>
+    </dependency>
     <dependency>
       <groupId>com.google.guava</groupId>
       <artifactId>guava</artifactId>
@@ -65,11 +75,11 @@
       <version>${ctakes.version}</version>
 
     </dependency>
-    <dependency>
-      <groupId>org.healthnlp</groupId>
-      <artifactId>tweaked-timenorm</artifactId>
-      <version>${project.parent.version}</version>
-    </dependency>
+    <!--    <dependency>-->
+    <!--      <groupId>org.healthnlp</groupId>-->
+    <!--      <artifactId>tweaked-timenorm</artifactId>-->
+    <!--      <version>${project.parent.version}</version>-->
+    <!--    </dependency>-->
   </dependencies>
 
   <build>

timelines/instance-generator/src/main/java/org/apache/ctakes/temporal/ae/DCTAnnotator.java

@@ -5,7 +5,8 @@
 import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
 import org.apache.ctakes.typesystem.type.structured.DocumentPath;
 import org.apache.ctakes.typesystem.type.structured.SourceData;
-import org.apache.log4j.Logger;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.fit.util.JCasUtil;
@@ -21,7 +22,7 @@
 )
 
 public class DCTAnnotator extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
-    final static private Logger LOGGER = Logger.getLogger( "DCTAnnotator" );
+    final static private Logger LOGGER = LoggerFactory.getLogger( "DCTAnnotator" );
     final static private DocTimeApproximator _approximator = new DocTimeApproximator();
     @Override
     public void initialize( UimaContext context ) throws ResourceInitializationException {
@@ -41,7 +42,7 @@ public void process( JCas jCas ) throws AnalysisEngineProcessException {
         if ( fileNameElements.length >= 3 ){
 
             String[] possibleDate =
-                fileNameElements[2].split("-");
+                    fileNameElements[2].split("-");
 
             if ( possibleDate.length == 3 ){