Updated dependencies, workflow, logging, compiler, min. java version …

…(11); removed "trove" dep.
PathwayCommons · Feb 4, 2024 · b60443a · b60443a
1 parent 3d315ba
commit b60443a
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Showing 7 changed files with 101 additions and 54 deletions.
diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -0,0 +1,26 @@
+# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+name: Java CI with Maven
+
+on:
+  push:
+    branches: 
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build-maven-jdk20:
+    runs-on: ubuntu-latest
+    env:
+      JDK_JAVA_OPTIONS: "--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-java@v3
+        with:
+          java-version: 20
+          distribution: 'temurin'
+          cache: maven
+      - name: Build with Maven and JDK-20
+        run: mvn --batch-mode --update-snapshots package
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>pathwaycommons</groupId>
     <artifactId>ctd-to-biopax</artifactId>
-    <version>1.0.1-SNAPSHOT</version>
+    <version>1.0.2-SNAPSHOT</version>
     <name>ctd-to-biopax</name>
 
     <description>
@@ -46,26 +46,36 @@
     </issueManagement>
 
     <ciManagement>
-        <system>Travis CI</system>
-        <url>https://travis-ci.org/PathwayCommons/${project.name}</url>
+        <system>GitHub</system>
+        <url>https://github.com/PathwayCommons/${project.name}/actions/workflows/maven.yml</url>
     </ciManagement>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <paxtools.version>5.1.0-SNAPSHOT</paxtools.version>
-        <slf4j.version>1.7.7</slf4j.version>
+        <paxtools.version>5.3.0</paxtools.version>
+        <slf4j.version>2.0.11</slf4j.version>
         <github.global.server>github</github.global.server>
+        <jvm.options>--add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED</jvm.options>
     </properties>
 
     <build>
         <pluginManagement>
             <plugins>
                 <plugin>
                     <artifactId>maven-compiler-plugin</artifactId>
-                    <version>3.5.1</version>
+                    <version>3.11.0</version>
                     <configuration>
-                        <source>1.8</source>
-                        <target>1.8</target>
+                        <source>11</source>
+                        <target>11</target>
+                    </configuration>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-surefire-plugin</artifactId>
+                    <version>3.1.2</version>
+                    <configuration>
+                        <argLine>${jvm.options}</argLine>
+                        <runOrder>alphabetical</runOrder>
                     </configuration>
                 </plugin>
             </plugins>
@@ -117,7 +127,7 @@
                     <plugin>
                         <groupId>org.sonatype.plugins</groupId>
                         <artifactId>nexus-staging-maven-plugin</artifactId>
-                        <version>1.6.7</version>
+                        <version>1.6.13</version>
                         <extensions>true</extensions>
                         <configuration>
                             <serverId>ossrh</serverId>
@@ -126,7 +136,7 @@
                     </plugin>
                     <plugin>
                         <artifactId>maven-source-plugin</artifactId>
-                        <version>3.0.1</version>
+                        <version>3.3.0</version>
                         <executions>
                             <execution>
                                 <id>attach-sources</id>
@@ -138,7 +148,7 @@
                     </plugin>
                     <plugin>
                         <artifactId>maven-javadoc-plugin</artifactId>
-                        <version>2.10.4</version>
+                        <version>3.5.0</version>
                         <executions>
                             <execution>
                                 <id>attach-javadocs</id>
@@ -180,30 +190,18 @@
         <downloadUrl>http://www.pathwaycommons.org/archives/</downloadUrl>
     </distributionManagement>
 
-    <!--<repositories>-->
-        <!--<repository>-->
-            <!--<id>ossrh</id>-->
-            <!--<name>OSSRH Repository</name>-->
-            <!--<url>https://oss.sonatype.org/content/groups/public/</url>-->
-        <!--</repository>-->
-    <!--</repositories>-->
-
     <dependencies>
         <dependency>
             <groupId>org.biopax.paxtools</groupId>
             <artifactId>paxtools-core</artifactId>
             <version>${paxtools.version}</version>
         </dependency>
         <dependency>
-            <groupId>org.biopax.paxtools</groupId>
-            <artifactId>paxtools-trove</artifactId>
-            <version>${paxtools.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-            <version>1.2.16</version>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+            <version>1.4.12</version>
             <scope>runtime</scope>
+            <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
@@ -212,9 +210,8 @@
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-log4j12</artifactId>
+            <artifactId>log4j-over-slf4j</artifactId>
             <version>${slf4j.version}</version>
-            <scope>runtime</scope>
         </dependency>
         <dependency>
             <groupId>commons-cli</groupId>
@@ -229,11 +226,11 @@
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
-            <version>4.12</version>
+            <version>4.13.2</version>
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>javax.xml</groupId>
+            <groupId>javax.xml.bind</groupId>
             <artifactId>jaxb-api</artifactId>
             <version>2.1</version>
         </dependency>

diff --git a/src/main/java/org/ctdbase/CtdToBiopax.java b/src/main/java/org/ctdbase/CtdToBiopax.java
@@ -4,21 +4,17 @@
 import org.ctdbase.converter.CTDGeneConverter;
 import org.ctdbase.converter.CTDInteractionConverter;
 import org.ctdbase.converter.Converter;
-import org.ctdbase.util.CtdUtil;
 import org.apache.commons.cli.*;
 import org.biopax.paxtools.controller.Merger;
 import org.biopax.paxtools.controller.ModelUtils;
 import org.biopax.paxtools.io.SimpleIOHandler;
 import org.biopax.paxtools.model.BioPAXElement;
 import org.biopax.paxtools.model.Model;
 import org.biopax.paxtools.model.level3.EntityReference;
-import org.biopax.paxtools.trove.TProvider;
-import org.biopax.paxtools.util.BPCollections;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.Set;
@@ -49,9 +45,6 @@ public static void main( String[] args ) {
                 System.exit(-1);
             }
 
-            // Memory efficiency fix for huge BioPAX models
-            BPCollections.I.setProvider(new TProvider());
-
             SimpleIOHandler simpleIOHandler = new SimpleIOHandler();
             Merger merger = new Merger(simpleIOHandler.getEditorMap());
             Model finalModel = simpleIOHandler.getFactory().createModel();

diff --git a/src/main/resources/log4j.properties b/src/main/resources/log4j.properties
diff --git a/src/main/resources/logback.xml b/src/main/resources/logback.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration>
+
+    <contextListener class="ch.qos.logback.classic.jul.LevelChangePropagator">
+        <resetJUL>true</resetJUL>
+    </contextListener>
+
+    <!-- To enable JMX Management (also prints additional logback initializing info)-->
+    <jmxConfigurator/>
+
+    <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>
+            <outputPatternAsHeader>true</outputPatternAsHeader>
+        </encoder>
+    </appender>
+
+    <logger name="org.ctdbase" level="info"/>
+    <logger name="org.biopax.paxtools" level="info"/>
+    <root level="warn">
+        <appender-ref ref="console"/>
+    </root>
+
+</configuration>
diff --git a/src/test/java/org/ctdbase/converter/CTDInteractionConverterTest.java b/src/test/java/org/ctdbase/converter/CTDInteractionConverterTest.java
@@ -2,8 +2,6 @@
 
 import org.biopax.paxtools.model.Model;
 import org.biopax.paxtools.model.level3.*;
-import org.biopax.paxtools.trove.TProvider;
-import org.biopax.paxtools.util.BPCollections;
 import org.junit.Test;
 
 import static org.junit.Assert.*;
@@ -14,13 +12,9 @@
 public class CTDInteractionConverterTest {
 
     @Test
-    public void convert() throws Exception {
-        // Memory efficiency fix for huge BioPAX models
-        BPCollections.I.setProvider(new TProvider());
-
+    public void convert() {
         CTDInteractionConverter converter = new CTDInteractionConverter(null);
         Model m = converter.convert(getClass().getResourceAsStream("/chem_gene_ixns_struct.xml"));
-//        (new SimpleIOHandler()).convertToOWL(m, System.out);
 
         TemplateReactionRegulation trr = (TemplateReactionRegulation) m.getByID(m.getXmlBase()+"EXP_4963086");
         assertNotNull(trr);
@@ -102,7 +96,6 @@ public void convert() throws Exception {
     // test filtering by a taxonomy id which is not present in the data
     @Test
     public void convertYest() {
-        BPCollections.I.setProvider(new TProvider());
         CTDInteractionConverter converter = new CTDInteractionConverter("559292");
         Model m = converter.convert(getClass().getResourceAsStream("/chem_gene_ixns_struct.xml"));
         assertTrue(m.getObjects(Control.class).isEmpty());

diff --git a/src/test/resources/logback-test.xml b/src/test/resources/logback-test.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration>
+
+    <contextListener class="ch.qos.logback.classic.jul.LevelChangePropagator">
+        <resetJUL>true</resetJUL>
+    </contextListener>
+
+    <!-- To enable JMX Management (also prints additional logback initializing info)-->
+    <jmxConfigurator/>
+
+    <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>
+            <outputPatternAsHeader>true</outputPatternAsHeader>
+        </encoder>
+    </appender>
+
+    <root level="info">
+        <appender-ref ref="console"/>
+    </root>
+
+</configuration>