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@ypriverol
ypriverol committed Sep 23, 2015
1 parent 7fc3b4c commit 8befb99
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242 changes: 242 additions & 0 deletions validator/pom.xml
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<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/maven-v4_0_0.xsd">

<modelVersion>4.0.0</modelVersion>

<groupId>psidev.psi.ms</groupId>
<artifactId>mzMLValidator</artifactId>
<packaging>jar</packaging>
<version>1.2-SNAPSHOT</version>

<name>PSI mzML semantic validator</name>
<description>
A semantic validator for PSI mzML XMl files.
</description>

<!-- Additions Florian -->
<properties>
<lib.dir>lib</lib.dir>
</properties>
<!-- Additions Florian -->

<build>
<!-- fix the versions of the plugins used in the build -->
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.5.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.4</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- To compile with JDK5.0 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.5</source>
<target>1.5</target>
</configuration>
</plugin>

<!-- Additions Florian -->
<!-- To copy the dependencies from the maven repository to the lib directory -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${lib.dir}</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
<!-- Additions Florian -->

</plugins>
</build>

<!-- Additions Florian -->
<profiles>
<profile>
<id>gui-app</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<!-- to create a executable jar to start the MzMLValidatorGUI -->
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLValidatorGUI</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>gui-assembly</id>
<activation>
<activeByDefault>false</activeByDefault>
</activation>
<build>
<plugins>
<!-- to create a executable jar to start the MzMLValidatorGUI -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLValidatorGUI</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>schemaValidation</id>
<build>
<plugins>
<!-- to create a executable jar to start the MzMLSchemaValidator -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLSchemaValidator</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>commandlineValidator</id>
<build>
<plugins>
<!-- to create a executable jar to start the command line MzMLValidator -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLValidator</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<!-- Additions Florian -->

<repositories>
<!-- removed java.net repositories, these are now mirrored in maven central -->
<!-- EBI repositories -->
<repository>
<id>ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>ebi-repo-snapshots</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo_snapshots</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>

<dependencies>
<dependency>
<groupId>psidev.psi.tools</groupId>
<artifactId>validator</artifactId>
<version>2.0.3-SNAPSHOT</version>
</dependency>

<dependency>
<groupId>uk.ac.ebi.jmzml</groupId>
<artifactId>jmzml</artifactId>
<version>1.6.8-SNAPSHOT</version>
</dependency>

<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.9</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>net.java.dev.swing-layout</groupId>
<artifactId>swing-layout</artifactId>
<version>1.0.2</version>
</dependency>
</dependencies>

<distributionManagement>
</distributionManagement>

</project>
44 changes: 44 additions & 0 deletions validator/src/main/java/psidev/psi/ms/ClusteredContext.java
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package psidev.psi.ms;

import java.util.ArrayList;
import java.util.List;

import psidev.psi.tools.validator.Context;

/**
* A context which cluster the different contexts for a same error message
*
*/
public class ClusteredContext extends Context {

List<Context> contexts = new ArrayList<Context>();

public ClusteredContext(String context) {
super(context);
}

public ClusteredContext() {
super(null);
}

public List<Context> getContexts() {
return contexts;
}

public int getNumberOfContexts() {
return contexts.size();
}

@Override
public String toString() {
StringBuilder sb = new StringBuilder(128);

if (!contexts.isEmpty()) {
sb.append(contexts.iterator().next());
if (contexts.size() > 1)
sb.append(" in " + getNumberOfContexts() + " locations");
}

return sb.toString();
}
}

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