Extended the API, updated dependencies, bumped to v2.0.0-SNAPSHOT.

PathwayCommons · Sep 10, 2023 · d907c14 · d907c14
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commit d907c14
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diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -14,13 +14,13 @@ jobs:
   build-with-jdk17:
     runs-on: ubuntu-latest
     env:
-      _JAVA_OPTIONS: "--add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED"
+      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: 17
+          java-version: 20
           distribution: 'temurin'
           cache: maven
-      - name: Build with Maven and JDK-17
+      - name: Build with Maven and JDK-20
         run: mvn --batch-mode --update-snapshots package
diff --git a/README.md b/README.md
@@ -1,9 +1,8 @@
 # reconx-to-biopax
-Originated from Arman's https://bitbucket.org/armish/gsoc14 and will continue here (ToDo).
+Originated from Arman's https://bitbucket.org/armish/gsoc14
 
 [![Java CI with Maven](https://github.com/PathwayCommons/reconx-to-biopax/actions/workflows/maven.yml/badge.svg)](https://github.com/PathwayCommons/reconx-to-biopax/actions/workflows/maven.yml)
 
-
 ## SBML to BioPAX Level3 converter, specific to the Recon2 data/model.
 Although there already existed an 
 [SBML-to-BioPAX converter](https://sourceforge.net/apps/mediawiki/sbfc/index.php?title=Main_Page#SBML_to_BioPax), 
@@ -38,12 +37,8 @@ The main class of this project, `ReconxToBiopax`, serves as an
 example to show how to use this API:
 
 	//java
-	// ...
-	SBMLDocument sbmlDocument = SBMLReader.read(new File(sbmlFile));
 	SbmlToBiopaxConverter converter = new SbmlToBiopaxConverter();
-	Model bpModel = converter.convert(sbmlDocument);
-	// where bpModel is the BioPAX model
-	// ...
+	Model bpModel = converter.convert(new File(sbmlFile)); //can also be an InputStream
 
 During implementation, we separated utility methods and main flow as 
 much as possible, so that we have all main conversion logic in the 

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>pathwaycommons</groupId>
     <artifactId>reconx-to-biopax</artifactId>
-    <version>1.2.0-SNAPSHOT</version>
+    <version>2.0.0-SNAPSHOT</version>
     <name>reconx-to-biopax</name>
 
     <description>
@@ -50,7 +50,7 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <paxtools.version>5.3.0-SNAPSHOT</paxtools.version>
+        <paxtools.version>6.0.0-SNAPSHOT</paxtools.version>
         <github.global.server>github</github.global.server>
     </properties>
 
@@ -59,9 +59,9 @@
             <plugins>
                 <plugin>
                     <artifactId>maven-compiler-plugin</artifactId>
-                    <version>3.8.1</version>
+                    <version>3.11.0</version>
                     <configuration>
-                        <release>8</release>
+                        <release>17</release>
                     </configuration>
                 </plugin>
             </plugins>
@@ -70,19 +70,19 @@
             <extension>
                 <groupId>org.apache.maven.wagon</groupId>
                 <artifactId>wagon-ssh</artifactId>
-                <version>2.8</version>
+                <version>3.5.3</version>
             </extension>
             <extension>
                 <groupId>org.apache.maven.wagon</groupId>
                 <artifactId>wagon-scm</artifactId>
-                <version>2.8</version>
+                <version>3.5.3</version>
             </extension>
         </extensions>
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-shade-plugin</artifactId>
-                <version>3.3.0</version>
+                <version>3.5.0</version>
                 <executions>
                     <execution>
                         <phase>package</phase>
@@ -113,14 +113,15 @@
                     <plugin>
                         <groupId>org.sonatype.plugins</groupId>
                         <artifactId>nexus-staging-maven-plugin</artifactId>
-                        <version>1.6.8</version>
+                        <version>1.6.13</version>
                         <extensions>true</extensions>
                         <configuration>
                             <serverId>ossrh</serverId>
                             <nexusUrl>https://oss.sonatype.org/</nexusUrl>
                         </configuration>
                     </plugin>
                     <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-source-plugin</artifactId>
                         <version>3.2.1</version>
                         <executions>
@@ -133,8 +134,9 @@
                         </executions>
                     </plugin>
                     <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-javadoc-plugin</artifactId>
-                        <version>3.0.1</version>
+                        <version>3.5.0</version>
                         <executions>
                             <execution>
                                 <id>attach-javadocs</id>
@@ -145,6 +147,7 @@
                         </executions>
                     </plugin>
                     <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-gpg-plugin</artifactId>
                         <version>1.6</version>
                         <executions>
@@ -194,7 +197,7 @@
         <dependency>
             <groupId>org.sbml.jsbml</groupId>
             <artifactId>jsbml-core</artifactId>
-            <version>1.3.1</version>
+            <version>1.6.1</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>
@@ -204,24 +207,32 @@
                     <groupId>junit</groupId>
                     <artifactId>junit</artifactId>
                 </exclusion>
+                <exclusion>
+                    <groupId>com.fasterxml.woodstox</groupId>
+                    <artifactId>woodstox-core</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.thoughtworks.xstream</groupId>
+                    <artifactId>xstream</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
-            <version>1.7.25</version>
+            <version>2.0.7</version>
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>log4j-over-slf4j</artifactId>
-            <version>1.7.25</version>
+            <version>2.0.7</version>
             <scope>runtime</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
-            <version>1.1.11</version>
+            <version>1.4.11</version>
             <scope>runtime</scope>
             <optional>true</optional>
         </dependency>

diff --git a/src/main/java/org/humanmetabolism/ReconxToBiopax.java b/src/main/java/org/humanmetabolism/ReconxToBiopax.java
@@ -4,7 +4,6 @@
 import org.biopax.paxtools.io.SimpleIOHandler;
 import org.biopax.paxtools.model.BioPAXLevel;
 import org.biopax.paxtools.model.Model;
-import org.sbml.jsbml.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -28,17 +27,14 @@ public static void main(String[] args) throws IOException, XMLStreamException {
 
         String sbmlFile = args[0];
         String bpFile = args[1];
-        if(args.length > 2 && args[2].equals("--pathway"))
+        if(args.length > 2 && args[2].equals("--pathway")) {
             makePathway = true;
-
-        log.info("Reading SBML file: " + sbmlFile);
-        SBMLDocument sbmlDocument = SBMLReader.read(new File(sbmlFile));
-        log.info("SBML model loaded: " + sbmlDocument.getModel().getNumReactions() + " reactions in it.");
+        }
 
         log.info("Converting SBML model to BioPAX...");
         SbmlToBiopaxConverter sbmlToBiopaxConverter = new SbmlToBiopaxConverter();
         sbmlToBiopaxConverter.setMakePathway(makePathway);
-        Model bpModel = sbmlToBiopaxConverter.convert(sbmlDocument);
+        Model bpModel = sbmlToBiopaxConverter.convert(new File(sbmlFile));
 
         log.info("Saving BioPAX model to " + bpFile);
         SimpleIOHandler bpHandler = new SimpleIOHandler(BioPAXLevel.L3);

diff --git a/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxConverter.java b/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxConverter.java
@@ -6,6 +6,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.xml.stream.XMLStreamException;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+
 public class SbmlToBiopaxConverter {
     private static Logger log = LoggerFactory.getLogger(SbmlToBiopaxConverter.class);
     private final SbmlToBiopaxUtils sbmlToBiopaxUtils = new SbmlToBiopaxUtils();
@@ -23,6 +28,14 @@ public void setMakePathway(boolean makePathway) {
         this.makePathway = makePathway;
     }
 
+    public Model convert(InputStream sbmlInputStream) throws XMLStreamException {
+        return convert(SBMLReader.read(sbmlInputStream));
+    }
+
+    public Model convert(File sbmlFile) throws XMLStreamException, IOException {
+        return convert(SBMLReader.read(sbmlFile));
+    }
+
     public Model convert(SBMLDocument sbmlDocument) {
         return convert(sbmlDocument.getModel());
     }

diff --git a/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxUtils.java b/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxUtils.java
@@ -1,6 +1,5 @@
 package org.humanmetabolism.converter;
 
-import org.biopax.paxtools.model.BioPAXElement;
 import org.biopax.paxtools.model.BioPAXFactory;
 import org.biopax.paxtools.model.BioPAXLevel;
 import org.biopax.paxtools.model.Model;