Pipeline assembly input

src/main/java/ca/corefacility/bioinformatics/irida/config/analysis/AnalysisExecutionServiceConfig.java

@@ -12,10 +12,6 @@
 import org.springframework.context.annotation.Profile;
 import org.springframework.scheduling.annotation.EnableAsync;
 
-import com.github.jmchilton.blend4j.galaxy.JobsClient;
-import com.github.jmchilton.blend4j.galaxy.ToolsClient;
-import com.google.common.collect.Lists;
-
 import ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig;
 import ca.corefacility.bioinformatics.irida.pipeline.results.AnalysisSubmissionSampleProcessor;
 import ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl;
@@ -28,6 +24,7 @@
 import ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository;
 import ca.corefacility.bioinformatics.irida.service.AnalysisService;
 import ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService;
+import ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService;
 import ca.corefacility.bioinformatics.irida.service.SequencingObjectService;
 import ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionService;
 import ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionServiceAspect;
@@ -42,21 +39,23 @@
 import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
 import ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService;
 
+import com.github.jmchilton.blend4j.galaxy.JobsClient;
+import com.github.jmchilton.blend4j.galaxy.ToolsClient;
+import com.google.common.collect.Lists;
+
 /**
  * Configuration for an AnalysisExecutionService class.
- * 
- *
  */
 @Configuration
 @EnableAsync(order = AnalysisExecutionServiceConfig.ASYNC_ORDER)
 @Profile({ "dev", "prod", "it", "analysis", "ncbi", "processing", "sync", "web" })
 public class AnalysisExecutionServiceConfig {
-	
+
 	private static final Logger logger = LoggerFactory.getLogger(AnalysisExecutionServiceConfig.class);
 
 	/**
-	 * The order for asynchronous tasks. In particular, defines the order for
-	 * methods in {@link AnalysisExecutionServiceGalaxyAsync}.
+	 * The order for asynchronous tasks. In particular, defines the order for methods in
+	 * {@link AnalysisExecutionServiceGalaxyAsync}.
 	 */
 	public static final int ASYNC_ORDER = AnalysisExecutionServiceAspect.ANALYSIS_EXECUTION_ASPECT_ORDER - 1;
 
@@ -68,28 +67,31 @@ public class AnalysisExecutionServiceConfig {
 
 	@Autowired
 	private IridaWorkflowsService iridaWorkflowsService;
-	
+
 	@Autowired
 	private AnalysisParameterServiceGalaxy analysisParameterServiceGalaxy;
-	
+
 	@Autowired
 	private GalaxyHistoriesService galaxyHistoriesService;
-	
+
 	@Autowired
 	private GalaxyLibrariesService galaxyLibrariesService;
-	
+
 	@Autowired
 	private GalaxyWorkflowService galaxyWorkflowService;
-	
+
 	@Autowired
 	private SequencingObjectService sequencingObjectService;
-
+
+	@Autowired
+	private GenomeAssemblyService genomeAssemblyService;
+
 	@Autowired
 	private ToolsClient toolsClient;
-	
+
 	@Autowired
 	private JobsClient jobsClient;
-	
+
 	@Autowired
 	private IridaPluginConfig.IridaPluginList pipelinePlugins;
 
@@ -131,7 +133,7 @@ public AnalysisSubmissionSampleProcessor analysisSubmissionSampleProcessor() {
 
 		return new AnalysisSubmissionSampleProcessorImpl(sampleRepository, analysisSampleUpdaters);
 	}
-	
+
 	@Lazy
 	@Bean
 	public AnalysisExecutionService analysisExecutionService() {
@@ -143,31 +145,31 @@ public AnalysisExecutionService analysisExecutionService() {
 	@Bean
 	public AnalysisExecutionServiceGalaxyAsync analysisExecutionServiceGalaxyAsync() {
 		return new AnalysisExecutionServiceGalaxyAsync(analysisSubmissionService, analysisService,
-				galaxyWorkflowService, analysisWorkspaceService(), iridaWorkflowsService, analysisSubmissionSampleProcessor());
+				galaxyWorkflowService, analysisWorkspaceService(), iridaWorkflowsService,
+				analysisSubmissionSampleProcessor());
 	}
-	
+
 	@Lazy
 	@Bean
 	public AnalysisExecutionServiceGalaxyCleanupAsync analysisExecutionServiceGalaxyCleanupAsync() {
-		return new AnalysisExecutionServiceGalaxyCleanupAsync(analysisSubmissionService,
-				galaxyWorkflowService, galaxyHistoriesService, galaxyLibrariesService);
+		return new AnalysisExecutionServiceGalaxyCleanupAsync(analysisSubmissionService, galaxyWorkflowService,
+				galaxyHistoriesService, galaxyLibrariesService);
 	}
 
 	@Lazy
 	@Bean
 	public AnalysisWorkspaceServiceGalaxy analysisWorkspaceService() {
-		return new AnalysisWorkspaceServiceGalaxy(galaxyHistoriesService, galaxyWorkflowService,
-				galaxyLibrariesService, iridaWorkflowsService, analysisCollectionServiceGalaxy(),
-				analysisProvenanceService(), analysisParameterServiceGalaxy,
-				sequencingObjectService);
+		return new AnalysisWorkspaceServiceGalaxy(galaxyHistoriesService, galaxyWorkflowService, galaxyLibrariesService,
+				iridaWorkflowsService, analysisCollectionServiceGalaxy(), analysisProvenanceService(),
+				analysisParameterServiceGalaxy, sequencingObjectService, genomeAssemblyService);
 	}
 
 	@Lazy
 	@Bean
 	public AnalysisProvenanceServiceGalaxy analysisProvenanceService() {
 		return new AnalysisProvenanceServiceGalaxy(galaxyHistoriesService, toolsClient, jobsClient);
 	}
-	
+
 	@Lazy
 	@Bean
 	public AnalysisCollectionServiceGalaxy analysisCollectionServiceGalaxy() {

src/main/java/ca/corefacility/bioinformatics/irida/model/assembly/GenomeAssembly.java

@@ -21,6 +21,7 @@
 import ca.corefacility.bioinformatics.irida.model.VersionedFileFields;
 import ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile;
 import ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin;
+import ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.google.common.collect.Lists;
@@ -51,6 +52,9 @@ public abstract class GenomeAssembly extends IridaRepresentationModel
 	@OneToMany(fetch = FetchType.LAZY, mappedBy = "genomeAssembly")
 	private List<SampleGenomeAssemblyJoin> sampleGenomeAssemblies;
 
+	@ManyToMany(fetch = FetchType.LAZY, cascade = CascadeType.DETACH, mappedBy = "inputAssemblies")
+	private List<AnalysisSubmission> analysisSubmissions;
+
 	protected GenomeAssembly() {
 		this.id = null;
 		this.createdDate = null;
@@ -64,8 +68,7 @@ public GenomeAssembly(Date createdDate) {
 
 	@Override
 	public String getLabel() {
-		return getFile().getFileName()
-				.toString();
+		return getFile().getFileName().toString();
 	}
 
 	@Override
@@ -128,8 +131,7 @@ public String getFileSize() {
 
 	@Override
 	public String getFileName() {
-		return getFile().getFileName()
-				.toString();
+		return getFile().getFileName().toString();
 	}
 
 	@Override

src/main/java/ca/corefacility/bioinformatics/irida/model/workflow/description/IridaWorkflowDescription.java

@@ -1,16 +1,8 @@
 package ca.corefacility.bioinformatics.irida.model.workflow.description;
 
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.UUID;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlElementWrapper;
-import javax.xml.bind.annotation.XmlRootElement;
+import java.util.*;
+
+import javax.xml.bind.annotation.*;
 
 import ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis;
 import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType;
@@ -19,13 +11,11 @@
 
 /**
  * Class providing access to generic information about a workflow.
- * 
- *
  */
 @XmlRootElement(name = "iridaWorkflow")
 @XmlAccessorType(XmlAccessType.FIELD)
 public class IridaWorkflowDescription {
-	
+
 	@XmlElement(name = "id")
 	private UUID id;
 
@@ -44,7 +34,7 @@ public class IridaWorkflowDescription {
 	@XmlElementWrapper(name = "outputs")
 	@XmlElement(name = "output")
 	private List<IridaWorkflowOutput> outputs;
-	
+
 	@XmlElementWrapper(name = "parameters")
 	@XmlElement(name = "parameter")
 	private List<IridaWorkflowParameter> parameters;
@@ -57,28 +47,19 @@ public IridaWorkflowDescription() {
 	}
 
 	/**
-	 * Generates a new {@link IridaWorkflowDescription} with the given
-	 * information.
+	 * Generates a new {@link IridaWorkflowDescription} with the given information.
 	 * 
-	 * @param id
-	 *            The {@link UUID} for a workflow.
-	 * @param name
-	 *            The name of the workflow.
-	 * @param version
-	 *            The version of the workflow.
-	 * @param analysisType
-	 *            The class type of the {@link Analysis}.
-	 * @param inputs
-	 *            The inputs to the workflow.
-	 * @param outputs
-	 *            The outputs to the workflow.
-	 * @param toolRepositories
-	 *            The list of tools repositories for this workflow.
-	 * @param parameters
-	 *            The valid parameters that can be modified for this workflow.
+	 * @param id               The {@link UUID} for a workflow.
+	 * @param name             The name of the workflow.
+	 * @param version          The version of the workflow.
+	 * @param analysisType     The class type of the {@link Analysis}.
+	 * @param inputs           The inputs to the workflow.
+	 * @param outputs          The outputs to the workflow.
+	 * @param toolRepositories The list of tools repositories for this workflow.
+	 * @param parameters       The valid parameters that can be modified for this workflow.
 	 */
-	public IridaWorkflowDescription(UUID id, String name, String version,
-			AnalysisType analysisType, IridaWorkflowInput inputs, List<IridaWorkflowOutput> outputs,
+	public IridaWorkflowDescription(UUID id, String name, String version, AnalysisType analysisType,
+			IridaWorkflowInput inputs, List<IridaWorkflowOutput> outputs,
 			List<IridaWorkflowToolRepository> toolRepositories, List<IridaWorkflowParameter> parameters) {
 		this.id = id;
 		this.name = name;
@@ -129,8 +110,7 @@ public boolean requiresDynamicSource() {
 	/**
 	 * Whether or not this workflow accepts single sequence files as input.
 	 * 
-	 * @return True if this workflow accepts single sequence files, false
-	 *         otherwise.
+	 * @return True if this workflow accepts single sequence files, false otherwise.
 	 */
 	public boolean acceptsSingleSequenceFiles() {
 		return inputs.getSequenceReadsSingle().isPresent();
@@ -139,31 +119,38 @@ public boolean acceptsSingleSequenceFiles() {
 	/**
 	 * Whether or not this workflow accepts paired sequence files as input.
 	 * 
-	 * @return True if this workflow accepts paired sequence files, false
-	 *         otherwise.
+	 * @return True if this workflow accepts paired sequence files, false otherwise.
 	 */
 	public boolean acceptsPairedSequenceFiles() {
 		return inputs.getSequenceReadsPaired().isPresent();
 	}
 
+	/**
+	 * Whether or not this workflow accepts genome assemblies as input.
+	 * 
+	 * @return True if this workflow accepts genome assemblies, false otherwise.
+	 */
+	public boolean acceptsGenomeAssemblies() {
+		return inputs.getGenomeAssemblies().isPresent();
+	}
+
 	public IridaWorkflowInput getInputs() {
 		return inputs;
 	}
 
 	public List<IridaWorkflowOutput> getOutputs() {
 		return outputs;
 	}
-	
+
 	public List<IridaWorkflowParameter> getParameters() {
 		return parameters;
 	}
 
 	/**
-	 * Gets a {@link Map} representation of the outputs of a workflow, linking
-	 * the output name to the {@link IridaWorkflowOutput} entry.
+	 * Gets a {@link Map} representation of the outputs of a workflow, linking the output name to the
+	 * {@link IridaWorkflowOutput} entry.
 	 * 
-	 * @return A {@link Map} linking the output name to the
-	 *         {@link IridaWorkflowOutput} entry.
+	 * @return A {@link Map} linking the output name to the {@link IridaWorkflowOutput} entry.
 	 */
 	public Map<String, IridaWorkflowOutput> getOutputsMap() {
 		Map<String, IridaWorkflowOutput> outputsMap = new HashMap<>();
@@ -182,7 +169,7 @@ public List<IridaWorkflowToolRepository> getToolRepositories() {
 	public AnalysisType getAnalysisType() {
 		return analysisType;
 	}
-	
+
 	/**
 	 * Determines if this workflow accepts parameters.
 	 * 
@@ -215,7 +202,7 @@ else if (obj instanceof IridaWorkflowDescription) {
 
 	@Override
 	public String toString() {
-		return "IridaWorkflowDescription [id=" + id + ", name=" + name + ", version=" + version 
-				+ ", analysisType=" + analysisType + "]";
+		return "IridaWorkflowDescription [id=" + id + ", name=" + name + ", version=" + version + ", analysisType="
+				+ analysisType + "]";
 	}
 }