Refactor workspace classes

src/main/java/cloudgene/mapred/jobs/AbstractJob.java

@@ -21,9 +21,8 @@
 import cloudgene.mapred.apps.ApplicationRepository;
 import cloudgene.mapred.core.User;
 import cloudgene.mapred.jobs.queue.PriorityRunnable;
-import cloudgene.mapred.jobs.workspace.IExternalWorkspace;
+import cloudgene.mapred.jobs.workspace.IWorkspace;
 import cloudgene.mapred.util.Settings;
-import cloudgene.mapred.wdl.WdlApp;
 import cloudgene.mapred.wdl.WdlParameterInputType;
 import genepi.io.FileUtil;
 
@@ -119,7 +118,7 @@ abstract public class AbstractJob extends PriorityRunnable {
 
 	private boolean canceld = false;
 
-	protected IExternalWorkspace externalWorkspace;
+	protected IWorkspace workspace;
 
 	private String workspaceSize = null;
 
@@ -743,12 +742,12 @@ public void setLocalWorkspace(String localWorkspace) {
 		this.localWorkspace = localWorkspace;
 	}
 
-	public void setExternalWorkspace(IExternalWorkspace externalWorkspace) {
-		this.externalWorkspace = externalWorkspace;
+	public void setWorkspace(IWorkspace workspace) {
+		this.workspace = workspace;
 	}
 
-	public IExternalWorkspace getExternalWorkspace() {
-		return externalWorkspace;
+	public IWorkspace getWorkspace() {
+		return workspace;
 	}
 
 	public void setApplication(String application) {

src/main/java/cloudgene/mapred/jobs/CloudgeneJob.java

@@ -14,7 +14,6 @@
 import cloudgene.mapred.jobs.engine.Planner;
 import cloudgene.mapred.jobs.engine.graph.Graph;
 import cloudgene.mapred.jobs.engine.graph.GraphNode;
-import cloudgene.mapred.jobs.workspace.IExternalWorkspace;
 import cloudgene.mapred.jobs.workspace.WorkspaceWrapper;
 import cloudgene.mapred.wdl.WdlApp;
 import cloudgene.mapred.wdl.WdlParameterInput;
@@ -104,9 +103,9 @@ public boolean setup() {
 		FileUtil.createDirectory(context.getLocalTemp());
 
 		try {
-			context.log("Setup External Workspace on " + externalWorkspace.getName());
-			externalWorkspace.setup(this.getId());
-			context.setExternalWorkspace(new WorkspaceWrapper(externalWorkspace));
+			context.log("Setup External Workspace on " + workspace.getName());
+			workspace.setup(this.getId());
+			context.setExternalWorkspace(new WorkspaceWrapper(workspace));
 		} catch (Exception e) {
 			writeLog(e.toString());
 			log.info("Error setup external workspace", e);
@@ -124,12 +123,12 @@ public boolean setup() {
 				throw new RuntimeException("HDFS support was removed in Cloudgene 3");
 
 			case LOCAL_FILE:
-				String filename = externalWorkspace.createFile(param.getName(), param.getName());
+				String filename = workspace.createFile(param.getName(), param.getName());
 				param.setValue(filename);
 				break;
 
 			case LOCAL_FOLDER:
-				String folder = externalWorkspace.createFolder(param.getName());
+				String folder = workspace.createFolder(param.getName());
 				param.setValue(folder);
 				break;
 			}
@@ -293,7 +292,7 @@ public boolean executeFailureStep(WdlStep failedStep) {
 	public boolean cleanUp() {
 
 		try {
-			externalWorkspace.cleanup(getId());
+			workspace.cleanup(getId());
 		} catch (IOException e) {
 			writeLog("Cleanup failed.");
 			writeLog(e.getMessage());
@@ -333,7 +332,7 @@ public boolean exportParameter(CloudgeneParameterOutput out) {
 
 		out.setJobId(getId());
 
-		List<Download> downloads = externalWorkspace.getDownloads(out.getValue());
+		List<Download> downloads = workspace.getDownloads(out.getValue());
 		for (Download download : downloads) {
 			download.setParameter(out);
 			download.setCount(MAX_DOWNLOAD);
@@ -384,8 +383,4 @@ public void updateProgress() {
 
 	}
 
-	public IExternalWorkspace getExternalWorkspace() {
-		return externalWorkspace;
-	}
-
 }

src/main/java/cloudgene/mapred/jobs/workspace/IExternalWorkspace.java → src/main/java/cloudgene/mapred/jobs/workspace/IWorkspace.java

@@ -7,7 +7,7 @@
 
 import cloudgene.mapred.jobs.Download;
 
-public interface IExternalWorkspace {
+public interface IWorkspace {
 
 	public void setup(String job) throws IOException;
 

src/main/java/cloudgene/mapred/jobs/workspace/LocalWorkspace.java

@@ -17,7 +17,7 @@
 import cloudgene.mapred.util.HashUtil;
 import genepi.io.FileUtil;
 
-public class LocalWorkspace implements IExternalWorkspace {
+public class LocalWorkspace implements IWorkspace {
 
 	private static final String INPUT_DIRECTORY = "input";
 

src/main/java/cloudgene/mapred/jobs/workspace/S3Workspace.java

@@ -24,7 +24,7 @@
 import cloudgene.mapred.util.S3Util;
 import genepi.io.FileUtil;
 
-public class S3Workspace implements IExternalWorkspace {
+public class S3Workspace implements IWorkspace {
 
 	private static final String OUTPUT_DIRECTORY = "outputs";
 

src/main/java/cloudgene/mapred/jobs/workspace/ExternalWorkspaceFactory.java → src/main/java/cloudgene/mapred/jobs/workspace/WorkspaceFactory.java

@@ -7,12 +7,12 @@
 import jakarta.inject.Singleton;
 
 @Singleton
-public class ExternalWorkspaceFactory {
+public class WorkspaceFactory {
 
 	@Inject
 	protected Application application;
 
-	public IExternalWorkspace getDefault() {
+	public IWorkspace getDefault() {
 
 		Settings settings = application.getSettings();
 
@@ -31,7 +31,7 @@ public IExternalWorkspace getDefault() {
 
 	}
 
-	public IExternalWorkspace getByUrl(String url) {
+	public IWorkspace getByUrl(String url) {
 
 		Settings settings = application.getSettings();
 
@@ -48,7 +48,7 @@ public IExternalWorkspace getByUrl(String url) {
 
 	}
 
-	public IExternalWorkspace getByJob(AbstractJob job) {
+	public IWorkspace getByJob(AbstractJob job) {
 		return getDefault();
 	}
 

src/main/java/cloudgene/mapred/jobs/workspace/WorkspaceWrapper.java

@@ -8,9 +8,9 @@
 
 public class WorkspaceWrapper implements IExternalWorkspace {
 
-	private cloudgene.mapred.jobs.workspace.IExternalWorkspace newWorkspace;
+	private cloudgene.mapred.jobs.workspace.IWorkspace newWorkspace;
 
-	public WorkspaceWrapper(cloudgene.mapred.jobs.workspace.IExternalWorkspace newWorkspace) {
+	public WorkspaceWrapper(cloudgene.mapred.jobs.workspace.IWorkspace newWorkspace) {
 		this.newWorkspace = newWorkspace;
 	}
 

src/main/java/cloudgene/mapred/plugins/nextflow/NextflowStep.java

@@ -14,8 +14,8 @@
 import cloudgene.mapred.jobs.CloudgeneJob;
 import cloudgene.mapred.jobs.CloudgeneStep;
 import cloudgene.mapred.jobs.Message;
-import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory;
-import cloudgene.mapred.jobs.workspace.IExternalWorkspace;
+import cloudgene.mapred.jobs.workspace.WorkspaceFactory;
+import cloudgene.mapred.jobs.workspace.IWorkspace;
 import cloudgene.mapred.util.HashUtil;
 import cloudgene.mapred.wdl.WdlStep;
 import genepi.io.FileUtil;
@@ -88,8 +88,8 @@ public boolean run(WdlStep step, CloudgeneContext context) {
 			nextflowCommand.add("-w");
 			nextflowCommand.add(work);
 		} else {
-			IExternalWorkspace externalWorkspace = job.getExternalWorkspace();
-			String workDir = externalWorkspace.createTempFolder("nextflow");
+			IWorkspace workspace = job.getWorkspace();
+			String workDir = workspace.createTempFolder("nextflow");
 			FileUtil.createDirectory(workDir);
 			nextflowCommand.add("-w");
 			nextflowCommand.add(workDir);

src/main/java/cloudgene/mapred/server/controller/DownloadController.java

@@ -22,7 +22,6 @@
 import cloudgene.mapred.server.services.DownloadService;
 import cloudgene.mapred.server.services.JobService;
 import genepi.io.FileUtil;
-import io.micronaut.http.HttpResponse;
 import io.micronaut.http.HttpStatus;
 import io.micronaut.http.MutableHttpResponse;
 import io.micronaut.http.annotation.Controller;
@@ -81,7 +80,7 @@ public MutableHttpResponse<InputStream> downloadExternalResults(String jobId, St
 	@Get("/share/results/{hash}/{filename:.+}")
 	@Secured(SecurityRule.IS_ANONYMOUS)
 	public MutableHttpResponse<InputStream> downloadPublicLink(String hash, String filename) throws URISyntaxException, IOException {
-System.out.println("------> " + filename);
+
 		DownloadDao dao = new DownloadDao(application.getDatabase());
 		Download download = dao.findByHash(hash);
 

src/main/java/cloudgene/mapred/server/services/DownloadService.java

@@ -7,8 +7,8 @@
 
 import cloudgene.mapred.database.DownloadDao;
 import cloudgene.mapred.jobs.Download;
-import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory;
-import cloudgene.mapred.jobs.workspace.IExternalWorkspace;
+import cloudgene.mapred.jobs.workspace.WorkspaceFactory;
+import cloudgene.mapred.jobs.workspace.IWorkspace;
 import cloudgene.mapred.server.Application;
 import cloudgene.mapred.server.exceptions.JsonHttpStatusException;
 import io.micronaut.http.HttpResponse;
@@ -22,7 +22,7 @@ public class DownloadService {
 	protected Application application;
 
 	@Inject
-	protected ExternalWorkspaceFactory workspaceFactory;
+	protected WorkspaceFactory workspaceFactory;
 
 	public MutableHttpResponse<InputStream> download(Download download) throws URISyntaxException, IOException {
 
@@ -42,15 +42,15 @@ public MutableHttpResponse<InputStream> download(Download download) throws URISy
 			dao.update(download);
 		}
 
-		IExternalWorkspace externalWorkspace = workspaceFactory.getByUrl(download.getPath());
+		IWorkspace workspace = workspaceFactory.getByUrl(download.getPath());
 
 		// external workspace found, use link method and create redirect response
-		String publicUrl = externalWorkspace.createPublicLink(download.getPath());
+		String publicUrl = workspace.createPublicLink(download.getPath());
 		if (publicUrl != null) {
 			URI location = new URI(publicUrl);
 			return HttpResponse.redirect(location);
 		} else {
-			return HttpResponse.ok(externalWorkspace.download(download.getPath()));
+			return HttpResponse.ok(workspace.download(download.getPath()));
 		}
 	}
 

src/main/java/cloudgene/mapred/server/services/JobCleanUpService.java

@@ -9,8 +9,8 @@
 import cloudgene.mapred.database.JobDao;
 import cloudgene.mapred.database.util.Database;
 import cloudgene.mapred.jobs.AbstractJob;
-import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory;
-import cloudgene.mapred.jobs.workspace.IExternalWorkspace;
+import cloudgene.mapred.jobs.workspace.WorkspaceFactory;
+import cloudgene.mapred.jobs.workspace.IWorkspace;
 import cloudgene.mapred.server.Application;
 import cloudgene.mapred.util.MailUtil;
 import cloudgene.mapred.util.Settings;
@@ -27,7 +27,7 @@ public class JobCleanUpService {
 	protected Application application;
 
 	@Inject
-	protected ExternalWorkspaceFactory workspaceFactory;
+	protected WorkspaceFactory workspaceFactory;
 
 	public int executeRetire() {
 
@@ -54,7 +54,7 @@ public int executeRetire() {
 				log.info("Job " + job.getId() + " retired.");
 				deleted++;
 
-				IExternalWorkspace externalWorkspace = workspaceFactory.getByJob(job);
+				IWorkspace externalWorkspace = workspaceFactory.getByJob(job);
 
 				try {
 					externalWorkspace.delete(job.getId());

src/main/java/cloudgene/mapred/server/services/JobService.java

@@ -21,9 +21,8 @@
 import cloudgene.mapred.jobs.CloudgeneParameterOutput;
 import cloudgene.mapred.jobs.Download;
 import cloudgene.mapred.jobs.WorkflowEngine;
-import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory;
-import cloudgene.mapred.jobs.workspace.IExternalWorkspace;
-import cloudgene.mapred.jobs.workspace.LocalWorkspace;
+import cloudgene.mapred.jobs.workspace.IWorkspace;
+import cloudgene.mapred.jobs.workspace.WorkspaceFactory;
 import cloudgene.mapred.server.Application;
 import cloudgene.mapred.server.exceptions.JsonHttpStatusException;
 import cloudgene.mapred.util.FormUtil.Parameter;
@@ -46,7 +45,7 @@ public class JobService {
 	protected Application application;
 
 	@Inject
-	protected ExternalWorkspaceFactory workspaceFactory;
+	protected WorkspaceFactory workspaceFactory;
 
 	private static final String PARAM_JOB_NAME = "job-name";
 
@@ -121,15 +120,15 @@ public AbstractJob submitJob(String appId, List<Parameter> form, User user) {
 
 		Map<String, String> inputParams = null;
 
-		IExternalWorkspace externalWorkspace = workspaceFactory.getDefault();
+		IWorkspace workspace = workspaceFactory.getDefault();
 
 		try {
 
 			// setup workspace
-			externalWorkspace.setup(id);
+			workspace.setup(id);
 
 			// parse input params
-			inputParams = parseAndUpdateInputParams(form, app, externalWorkspace);
+			inputParams = parseAndUpdateInputParams(form, app, workspace);
 
 		} catch (Exception e) {
 			throw new JsonHttpStatusException(HttpStatus.BAD_REQUEST, e.getMessage());
@@ -148,7 +147,7 @@ public AbstractJob submitJob(String appId, List<Parameter> form, User user) {
 		job.setId(id);
 		job.setName(name);
 		job.setLocalWorkspace(localWorkspace);
-		job.setExternalWorkspace(externalWorkspace);
+		job.setWorkspace(workspace);
 		job.setSettings(settings);
 		job.setApplication(app.getName() + " " + app.getVersion());
 		job.setApplicationId(appId);
@@ -229,9 +228,9 @@ public AbstractJob delete(AbstractJob job) {
 
 		// delete all results that are stored on external workspaces
 
-		IExternalWorkspace externalWorkspace = workspaceFactory.getByJob(job);
+		IWorkspace workspace = workspaceFactory.getByJob(job);
 		try {
-			externalWorkspace.delete(job.getId());
+			workspace.delete(job.getId());
 		} catch (Exception e) {
 			log.error("Deleteting " + job.getId() + " form workspace failed.", e);
 		}
@@ -319,10 +318,10 @@ public String archive(AbstractJob job) {
 			job.setState(AbstractJob.STATE_RETIRED);
 			dao.update(job);
 
-			IExternalWorkspace externalWorkspace = workspaceFactory.getByJob(job);
+			IWorkspace workspace = workspaceFactory.getByJob(job);
 
 			try {
-				externalWorkspace.delete(job.getId());
+				workspace.delete(job.getId());
 			} catch (Exception e) {
 				log.error("Deleteting " + job.getId() + " from workspace failed.", e);
 			}
@@ -367,8 +366,8 @@ public String createId() {
 
 	// TODO: refactore and combine this method with CommandLineUtil.parseArgs...
 
-	private Map<String, String> parseAndUpdateInputParams(List<Parameter> form, WdlApp app,
-			IExternalWorkspace externalWorkspace) throws Exception {
+	private Map<String, String> parseAndUpdateInputParams(List<Parameter> form, WdlApp app, IWorkspace workspace)
+			throws Exception {
 
 		Map<String, String> props = new HashMap<String, String>();
 		Map<String, String> params = new HashMap<String, String>();
@@ -402,10 +401,10 @@ private Map<String, String> parseAndUpdateInputParams(List<Parameter> form, WdlA
 					}
 
 					// copy to workspace in input directory
-					String target = externalWorkspace.uploadInput(fieldName, inputFile);
+					String target = workspace.uploadInput(fieldName, inputFile);
 
 					if (inputParam.isFolder()) {
-						props.put(fieldName, externalWorkspace.getParent(target));
+						props.put(fieldName, workspace.getParent(target));
 					} else {
 						// file
 						props.put(fieldName, target);