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[Jsbml-svn] SF.net SVN: jsbml:[2397] trunk
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From: <nik...@us...> - 2015-11-10 13:27:10
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Revision: 2397
http://sourceforge.net/p/jsbml/code/2397
Author: niko-rodrigue
Date: 2015-11-10 13:27:08 +0000 (Tue, 10 Nov 2015)
Log Message:
-----------
some more corrections to be able to generate the test jar files. To have all maven tests succesful in core, we need to move/remove/correct few more classes.
Modified Paths:
--------------
trunk/build.xml
trunk/core/pom.xml
trunk/extensions/distrib/pom.xml
trunk/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java
trunk/extensions/pom.xml
trunk/pom.xml
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/build.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -126,6 +126,8 @@
<fileset dir="${simulation.core.dir}/lib/ext-lib/" includes="*.jar"/>
</path>
+ <property name="maven.repo.url" value="file:///homes/maven/public_html/m2repo"/>
+ <!-- local test instance url file:///homes/maven/public_html/m2repo -->
</target>
@@ -735,8 +737,10 @@
<arg value="deploy:deploy-file"/>
<arg value="-DpomFile=./dev/maven/pom.xml"/>
<arg value="-Dfile=./dev/maven/jsbml-pom.jar"/>
+ <arg value="-Durl=${maven.repo.url}"/>
</exec>
+ <!-- mvn test jar:test-jar to generate the test jar files to be able to run the tests in a new project -->
</target>
Modified: trunk/core/pom.xml
===================================================================
--- trunk/core/pom.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/core/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -61,12 +61,6 @@
<testResource>
<directory>test</directory>
</testResource>
- <testResource>
- <directory>resources</directory>
- </testResource>
- <testResource>
- <directory>src</directory>
- </testResource>
</testResources>
<extensions>
@@ -78,7 +72,7 @@
</extensions>
<plugins>
- <plugin>
+ <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
Modified: trunk/extensions/distrib/pom.xml
===================================================================
--- trunk/extensions/distrib/pom.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/extensions/distrib/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -35,4 +35,14 @@
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>jsbml-distrib</artifactId>
<packaging>jar</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.sbml.jsbml.modules</groupId>
+ <artifactId>jsbml-tidy</artifactId>
+ <version>${project.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
</project>
Modified: trunk/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java
===================================================================
--- trunk/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java 2015-11-10 13:27:08 UTC (rev 2397)
@@ -25,6 +25,7 @@
import java.io.File;
import java.io.IOException;
+import java.io.InputStream;
import javax.xml.stream.XMLStreamException;
@@ -46,6 +47,7 @@
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
import org.sbml.jsbml.ext.layout.TextGlyph;
+import org.sbml.jsbml.xml.test.SBML_L2V1Test;
/**
*
@@ -69,16 +71,15 @@
static {
final SBMLReader reader = new SBMLReader();
- final String LAYOUT = System.getProperty("user.dir") + "/extensions/layout/test/org/sbml/jsbml/xml/test/data/layout/Layout_Example_1.xml";
+ final InputStream fileStream = SBML_L2V1Test.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/layout/Layout_Example_1.xml");
final String LAYOUT_NS = "http://www.sbml.org/sbml/level3/version1/layout/version1";
try {
- doc = reader.readSBML(new File(LAYOUT));
+ doc = reader.readSBMLFromStream(fileStream);
} catch (XMLStreamException e) {
e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- }
+ }
+
layoutModel = (LayoutModelPlugin) doc.getModel().getExtension(LAYOUT_NS);
}
Modified: trunk/extensions/pom.xml
===================================================================
--- trunk/extensions/pom.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/extensions/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -36,31 +36,6 @@
<relativePath>../</relativePath>
</parent>
- <build>
- <sourceDirectory>${basedir}/src/</sourceDirectory>
- <!--
- <testSourceDirectory>${basedir}/test/</testSourceDirectory>
- -->
- <resources>
- <resource>
- <directory>${basedir}/resources/</directory>
- </resource>
- </resources>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-surefire-plugin</artifactId>
- <version>2.5</version>
- <configuration>
- <skipTests>true</skipTests>
- <systemPropertyVariables>
- <user.dir>${basedir}/../../</user.dir>
- </systemPropertyVariables>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
<dependencies>
<dependency>
<groupId>org.sbml.jsbml</groupId>
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -24,23 +24,44 @@
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
-
- <groupId>org.sbml.jsbml</groupId>
- <artifactId>jsbml-parent</artifactId>
- <version>1.1-b1</version>
- <packaging>pom</packaging>
-
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
- </properties>
-
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-parent</artifactId>
+ <version>1.1-b1</version>
+ <packaging>pom</packaging>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+ </properties>
+
<build>
+
+ <sourceDirectory>src</sourceDirectory>
+ <testSourceDirectory>test</testSourceDirectory>
+ <resources>
+ <resource>
+ <directory>resources</directory>
+ </resource>
+ </resources>
+ <testResources>
+ <testResource>
+ <directory>test</directory>
+ </testResource>
+ </testResources>
+
+ <extensions>
+ <extension>
+ <groupId>org.apache.maven.wagon</groupId>
+ <artifactId>wagon-ssh</artifactId>
+ <version>2.4</version>
+ </extension>
+ </extensions>
+
<plugins>
-
-<!-- properties file not used at the moment
-
+
+ <!-- properties file not used at the moment
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
@@ -60,8 +81,7 @@
</execution>
</executions>
</plugin>
- </plugins>
--->
+ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@@ -113,12 +133,12 @@
</build>
- <modules>
- <module>core</module>
- <module>extensions</module>
- <module>modules</module>
- </modules>
-
+ <modules>
+ <module>core</module>
+ <module>extensions</module>
+ <module>modules</module>
+ </modules>
+
<repositories>
<repository>
<id>local-repo</id>
@@ -126,21 +146,21 @@
</repository>
</repositories>
- <distributionManagement>
- <repository>
+ <distributionManagement>
+ <repository>
<id>local-repo-deploy</id>
<name>Test Maven2 repository</name>
<url>file:///var/www/html/repo</url>
</repository>
- <snapshotRepository>
+ <snapshotRepository>
+ <id>jsbmlmavenrepotest.sourceforge.net</id>
+ <name>JSBML Maven2 SNAPSHOT repository</name>
+ <url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/snapshotRepository</url>
+ </snapshotRepository>
+ </distributionManagement>
+
+ <!-- <repository>
<id>jsbmlmavenrepotest.sourceforge.net</id>
- <name>JSBML Maven2 SNAPSHOT repository</name>
- <url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/snapshotRepository</url>
- </snapshotRepository>
- </distributionManagement>
-
-<!-- <repository>
- <id>jsbmlmavenrepotest.sourceforge.net</id>
<name>JSBML Maven2 repository</name>
<url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/releaseRepository</url>
</repository>
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