Merge branch 'update-example' into 'master'

Update example

See merge request irida/irida-plugin-example!1

.gitignore

@@ -1,3 +1,7 @@
 .idea
 target
 *.iml
+/.classpath
+/.project
+/.settings
+/bin

pom.xml

@@ -1,75 +1,92 @@
 <?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.corefacility.bioinformatics.irida.plugins</groupId>
+	<artifactId>example-plugin</artifactId>
+	<version>0.1.0-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>
+		<!-- Information used to define properties about a plugin. Please see the PF4J docs for more details https://pf4j.org/doc/getting-started.html -->
+		<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.runtime>1.0.0</plugin.requires.runtime>
 
-        <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.compiletime>0.23.0-SNAPSHOT</irida.version.compiletime>
+
+		<!-- 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 used to build this plugin package -->
+	<dependencies>
+		<dependency>
+			<groupId>ca.corefacility.bioinformatics</groupId>
+			<artifactId>irida</artifactId>
+			<version>${irida.version.compiletime}</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>
+	<!-- You should normally not have to modify any of the below information -->
+	<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.runtime}</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>

src/main/java/ca/corefacility/bioinformatics/irida/plugins/ExamplePlugin.java

@@ -0,0 +1,129 @@
+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.pipeline.results.updater.AnalysisSampleUpdater;
+import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
+import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
+import ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService;
+
+/**
+ * An example {@link IridaPlugin} implementation which will extract some
+ * information from the sequencing reads.
+ */
+public class ExamplePlugin extends Plugin {
+
+	/**
+	 * The {@link AnalysisType} used by this plugin. This wraps around a string and
+	 * is used to store the type of the analysis pipeline (which should be unique
+	 * for each pipeline).
+	 */
+	public static final AnalysisType READ_INFO = new AnalysisType("READ_INFO");
+
+	public ExamplePlugin(PluginWrapper wrapper) {
+		super(wrapper);
+	}
+
+	/**
+	 * This class defines information about this particular plugin. On start-up,
+	 * IRIDA will make use of the information provided by this class to integrate
+	 * the plugin pipeline.
+	 */
+	@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>READ_INFO</analysisType>}
+		 * </pre>
+		 * 
+		 * @return The particular {@link AnalysisType} for this pipeline.
+		 */
+		@Override
+		public AnalysisType getAnalysisType() {
+			return READ_INFO;
+		}
+
+		/**
+		 * 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>79d90ca8-00ae-441b-b5c7-193c9e85a968</id>}
+		 * </pre>
+		 * 
+		 * @return A {@link UUID} defining the id of this pipeline.
+		 */
+		@Override
+		public UUID getDefaultWorkflowUUID() {
+			return UUID.fromString("79d90ca8-00ae-441b-b5c7-193c9e85a968");
+		}
+
+		/*******************************************************************************
+		 * Optional methods
+		 * 
+		 * These methods are not required to be overridden but can be used to adjust the
+		 * appearance/behavior of the pipeline.
+		 *******************************************************************************/
+
+		/**
+		 * Defines the background color in the IRIDA UI corresponding to this pipeline.
+		 * 
+		 * @return An {@link Optional} color for the background of the IRIDA UI for this
+		 *         pipeline.
+		 */
+		@Override
+		public Optional<Color> getBackgroundColor() {
+			return Optional.of(Color.decode("#dd1c77"));
+		}
+
+		/**
+		 * Defines the text color in the IRIDA UI corresponding to this pipeline.
+		 * 
+		 * @return An {@link Optional} color for the text of the IRIDA UI for this
+		 *         pipeline.
+		 */
+		@Override
+		public Optional<Color> getTextColor() {
+			return Optional.of(Color.BLACK);
+		}
+
+		/**
+		 * Builds a {@link Optional} {@link AnalysisSampleUpdater} used to update
+		 * metadata from the pipeline results.
+		 * 
+		 * @param metadataTemplateService An IRIDA service to manipulate and save
+		 *                                metadata templates.
+		 * @param sampleService           An IRIDA service to manipulate and save
+		 *                                information associated with a {@link Sample}.
+		 * @param iridaWorkflowsService   An IRIDA service for getting information about
+		 *                                the workflow.
+		 * 
+		 * @return An {@link Optional} {@link AnalysisSampleUpdater} used to update
+		 *         metadata from the pipeline results.
+		 */
+		@Override
+		public Optional<AnalysisSampleUpdater> getUpdater(MetadataTemplateService metadataTemplateService,
+				SampleService sampleService, IridaWorkflowsService iridaWorkflowsService) throws IridaPluginException {
+			return Optional.of(new ExamplePluginUpdater(metadataTemplateService, sampleService, iridaWorkflowsService));
+		}
+	}
+}