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Updating example workflow
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@apetkau
apetkau committed Aug 31, 2018
1 parent 16e6787 commit 1a4c92c
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Showing 8 changed files with 378 additions and 121 deletions.
4 changes: 4 additions & 0 deletions .gitignore
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.idea
target
*.iml
/.classpath
/.project
/.settings
/bin
138 changes: 76 additions & 62 deletions pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<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>
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>ca.tom</groupId>
<artifactId>testPlugin</artifactId>
<version>1.0-SNAPSHOT</version>
<groupId>ca.tom</groupId>
<artifactId>example-plugin</artifactId>
<version>1.0-SNAPSHOT</version>

<dependencies>
<dependency>
<groupId>ca.corefacility.bioinformatics</groupId>
<artifactId>irida</artifactId>
<version>0.23.0-SNAPSHOT</version>
<classifier>classes</classifier>
</dependency>
<!-- Please fill out these properties with information about your particular plugin -->
<properties>
<plugin.id>example-plugin</plugin.id>
<plugin.class>ca.corefacility.bioinformatics.irida.plugins.ExamplePlugin</plugin.class>
<plugin.version>0.1.0</plugin.version>
<plugin.provider>Aaron Petkau</plugin.provider>
<plugin.dependencies></plugin.dependencies>
<plugin.requires>1.0.0</plugin.requires>

<dependency>
<groupId>org.pf4j</groupId>
<artifactId>pf4j</artifactId>
<version>2.3.0</version>
<scope>provided</scope>
</dependency>
</dependencies>
<!-- The version of IRIDA your plugin must be compiled against. -->
<irida.version>0.23.0-SNAPSHOT</irida.version>

<!-- Version of the pf4j dependency -->
<pf4j.version>2.4.0</pf4j.version>

<build>
<plugins>
<!-- Maven compiler plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<forceJavacCompilerUse>true</forceJavacCompilerUse>
</configuration>
</plugin>
<!-- Version of Java to target for this plugin -->
<java.version>1.8</java.version>
</properties>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<dependencies>
<dependency>
<groupId>ca.corefacility.bioinformatics</groupId>
<artifactId>irida</artifactId>
<version>${irida.version}</version>
<classifier>classes</classifier>
</dependency>

<configuration>
<archive>
<manifestEntries>
<Plugin-Class>ca.corefacility.bioinformatics.irida.ExamplePlugin</Plugin-Class>
<Plugin-Dependencies></Plugin-Dependencies>
<Plugin-Id>plugin-example</Plugin-Id>
<Plugin-Provider>Tom Matthews</Plugin-Provider>
<Plugin-Version>0.0.1</Plugin-Version>
</manifestEntries>
</archive>
</configuration>
</plugin>
<dependency>
<groupId>org.pf4j</groupId>
<artifactId>pf4j</artifactId>
<version>${pf4j.version}</version>
<scope>provided</scope>
</dependency>
</dependencies>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
<forceJavacCompilerUse>true</forceJavacCompilerUse>
</configuration>
</plugin>

</plugins>


</build>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>

<configuration>
<archive>
<manifestEntries>
<Plugin-Class>${plugin.class}</Plugin-Class>
<Plugin-Dependencies>${plugin.dependencies}</Plugin-Dependencies>
<Plugin-Id>${plugin.id}</Plugin-Id>
<Plugin-Provider>${plugin.provider}</Plugin-Provider>
<Plugin-Version>${plugin.version}</Plugin-Version>
<Plugin-Requires>${plugin.requires}</Plugin-Requires>
</manifestEntries>
</archive>
</configuration>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>
</project>
58 changes: 0 additions & 58 deletions src/main/java/ca/corefacility/bioinformatics/irida/ExamplePlugin.java
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76 changes: 76 additions & 0 deletions src/main/java/ca/corefacility/bioinformatics/irida/plugins/ExamplePlugin.java
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package ca.corefacility.bioinformatics.irida.plugins;

import java.awt.Color;
import java.util.Optional;
import java.util.UUID;

import org.pf4j.Extension;
import org.pf4j.Plugin;
import org.pf4j.PluginWrapper;

import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType;
import ca.corefacility.bioinformatics.irida.plugins.IridaPlugin;

/**
* An example {@link IridaPlugin} implementation
*/
public class ExamplePlugin extends Plugin {

public ExamplePlugin(PluginWrapper wrapper) {
super(wrapper);
}

@Extension
public static class PluginInfo implements IridaPlugin {

/***************************************************************************************
* Required methods
*
* These methods are required to be overridden when implementing a pipeline as a plugin.
***************************************************************************************/

/**
* Gets the particular {@link AnalysisType} object for this workflow.
* This should correspond to the <strong>analysisType</strong> entry in the <strong>irida_workflow.xml</strong> file.
*
* <pre>{@code <analysisType>FIRST_LINES</analysisType>}</pre>
*/
@Override
public AnalysisType getAnalysisType() {
return new AnalysisType("FIRST_LINES");
}

/**
* Gets the particular workflow id.
* This should correspond to the <strong>id</strong> entry in the <strong>irida_workflow.xml</strong> file.
*
* <pre>{@code <id>c07a0d4c-fb53-4183-8ded-298f8a4decca</id>}</pre>
*/
@Override
public UUID getDefaultWorkflowUUID() {
return UUID.fromString("c07a0d4c-fb53-4183-8ded-298f8a4decca");
}

/*********************************************************************************************************************
* Optional methods.
*
* These methods are not required to be overridden but can be used to adjust the appearance/behaviour of the pipeline.
*********************************************************************************************************************/

/**
* Defines the background color in the IRIDA UI corresponding to this pipeline.
*/
@Override
public Optional<Color> getBackgroundColor() {
return Optional.of(Color.decode("#7fcdbb"));
}

/**
* Defines the text color in the IRIDA UI corresponding to this pipeline.
*/
@Override
public Optional<Color> getTextColor() {
return Optional.of(Color.BLACK);
}
}
}
1 change: 0 additions & 1 deletion src/main/resources/messages/messages_en.properties
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20 changes: 20 additions & 0 deletions src/main/resources/workflows/0.1.0/irida_workflow.xml
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<?xml version="1.0" encoding="UTF-8"?>
<iridaWorkflow>
<id>c07a0d4c-fb53-4183-8ded-298f8a4decca</id>
<name>FirstLines</name>
<version>0.1.0</version>
<analysisType>FIRST_LINES</analysisType>
<inputs>
<sequenceReadsPaired>fastq_paired</sequenceReadsPaired>
<requiresSingleSample>true</requiresSingleSample>
</inputs>
<parameters>
<parameter name="show-beginning1-1-lineNum" defaultValue="4">
<toolParameter toolId="Show beginning1" parameterName="lineNum"/>
</parameter>
</parameters>
<outputs>
<output name="first-lines.txt" fileName="first-lines.txt"/>
</outputs>
<toolRepositories/>
</iridaWorkflow>
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