Bumped jena libs to the latest v3 (3.17.0); other minor changes.

BioPAX · May 13, 2024 · 25425a0 · 25425a0
1 parent 393ad83
commit 25425a0
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Showing 5 changed files with 11 additions and 43 deletions.
diff --git a/json-converter/pom.xml b/json-converter/pom.xml
@@ -18,6 +18,7 @@
 	<build>
 		<plugins>
 			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-assembly-plugin</artifactId>
 				<configuration>
 					<descriptorRefs>
@@ -41,34 +42,8 @@
 		<dependency>
 			<groupId>org.apache.jena</groupId>
 			<artifactId>apache-jena-libs</artifactId>
+			<version>3.17.0</version>
 			<type>pom</type>
-			<!-- This is the last Java 6 compatible version -->
-			<!--<version>2.11.2</version>-->
-			<version>3.2.0</version>
-			<exclusions>
-				<exclusion>
-					<groupId>log4j</groupId>
-					<artifactId>log4j</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.slf4j</groupId>
-					<artifactId>slf4j-log4j12</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-		<dependency>
-			<groupId>com.hp.hpl.jena</groupId>
-			<artifactId>jena</artifactId>
-			<exclusions>
-				<exclusion>
-					<groupId>log4j</groupId>
-					<artifactId>log4j</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.slf4j</groupId>
-					<artifactId>slf4j-log4j12</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.biopax.paxtools</groupId>

diff --git a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java
@@ -1,7 +1,5 @@
 package org.biopax.paxtools.io.jsonld;
 
-import static org.junit.Assert.*;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;

diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/Main.java b/paxtools-console/src/main/java/org/biopax/paxtools/Main.java
@@ -105,12 +105,12 @@ enum Command {
 				"\t'--uri-ids' - URI,type,name(s) and standard identifiers (in JSON format) for each physical entity;\n " +
 				"\tthe options' order defines the results output order.")
 		        {public void run(String[] argv) throws IOException{summarize(argv);} },
-		blacklist("<input> <output>\n" +
+				blacklist("<input> <output>\n" +
 		        "\t- creates a blacklist of ubiquitous small molecules, like ATP, \n"
 		        + "\tfrom the BioPAX model and writes it to the output file. The blacklist can be used with\n "
 		        + "\tpaxtools graph queries or when converting from the SAME BioPAX data to the SIF formats.")
 				{public void run(String[] argv) throws IOException{blacklist(argv);} },
-		pattern("\n\t- BioPAX pattern search tool (opens a new dialog window)")
+				pattern("\n\t- BioPAX pattern search tool (opens a new dialog window)")
 				{public void run(String[] argv){pattern(argv);} },
         help("\n\t- prints this screen and exits\n")
 				{public void run(String[] argv){ help();} };

diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java b/paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java
@@ -341,7 +341,7 @@ public static void validate(String[] argv) throws IOException
 			}
 		}
 
-		Collection<File> files = new HashSet<File>();
+		Collection<File> files = new HashSet<>();
 		File fileOrDir = new File(input);
 		if (!fileOrDir.canRead()) {
 			System.out.println("Cannot read " + input);
@@ -373,8 +373,7 @@ public boolean accept(File dir, String name) {
 			}
 		} catch (Exception ex) {
 			// fall-back: not using the remote validator; trying to read files
-			String msg = "Unable to check with the biopax-validator web service: \n " +
-				ex.toString() +
+			String msg = "Unable to check with the biopax-validator web service: \n " + ex +
 				"\n Fall-back: trying to parse the file(s) with paxtools " +
 				"(up to the first syntax error in each file)...\n";
 			log.error(msg, ex);

diff --git a/pom.xml b/pom.xml
@@ -119,8 +119,8 @@
   </issueManagement>
 
   <ciManagement>
-    <system>Travis CI</system>
-    <url>https://travis-ci.org/BioPAX/Paxtools</url>
+    <system>GitHub</system>
+    <url>https://github.com/BioPAX/Paxtools/actions/workflows/maven.yml</url>
   </ciManagement>
 
   <profiles>
@@ -142,6 +142,7 @@
             </configuration>
           </plugin>
           <plugin>
+            <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-source-plugin</artifactId>
             <executions>
               <execution>
@@ -331,8 +332,8 @@
         <configuration>
           <testFailureIgnore>false</testFailureIgnore>
           <argLine>${java.options} -ea</argLine>
-          <!-- if using JDK >11 use the args below (can set _JAVA_OPTIONS instead) -->
-<!--          <argLine>-ea &#45;&#45;add-opens=java.base/java.lang=ALL-UNNAMED &#45;&#45;add-opens=java.base/java.lang.reflect=ALL-UNNAMED</argLine>-->
+          <!-- if using JDK >11 use the args below (can set JDK_JAVA_OPTIONS instead) -->
+          <argLine>-ea --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED</argLine>
         </configuration>
       </plugin>
       <plugin>
@@ -380,11 +381,6 @@
         <artifactId>jackson-mapper-asl</artifactId>
         <version>1.9.12</version>
       </dependency>
-      <dependency>
-        <groupId>com.hp.hpl.jena</groupId>
-        <artifactId>jena</artifactId>
-        <version>2.6.4</version>
-      </dependency>
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>slf4j-api</artifactId>