From 178813585171315f36742f9d7c4af803aed38f7a Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Wed, 23 Aug 2023 12:41:53 +0200 Subject: [PATCH] Refactor workspace classes --- .../cloudgene/mapred/jobs/AbstractJob.java | 13 ++++---- .../cloudgene/mapred/jobs/CloudgeneJob.java | 19 +++++------- ...ExternalWorkspace.java => IWorkspace.java} | 2 +- .../mapred/jobs/workspace/LocalWorkspace.java | 2 +- .../mapred/jobs/workspace/S3Workspace.java | 2 +- ...paceFactory.java => WorkspaceFactory.java} | 8 ++--- .../jobs/workspace/WorkspaceWrapper.java | 4 +-- .../mapred/plugins/nextflow/NextflowStep.java | 8 ++--- .../server/controller/DownloadController.java | 3 +- .../server/services/DownloadService.java | 12 +++---- .../server/services/JobCleanUpService.java | 8 ++--- .../mapred/server/services/JobService.java | 31 +++++++++---------- .../jobs/PriorityThreadPoolExecutorTest.java | 6 ++-- .../mapred/jobs/WorkflowEngineTest.java | 6 ++-- .../mapred/jobs/WrongWorkspaceTest.java | 6 ++-- .../cloudgene/mapred/steps/TestCommand.java | 6 ++-- 16 files changed, 64 insertions(+), 72 deletions(-) rename src/main/java/cloudgene/mapred/jobs/workspace/{IExternalWorkspace.java => IWorkspace.java} (95%) rename src/main/java/cloudgene/mapred/jobs/workspace/{ExternalWorkspaceFactory.java => WorkspaceFactory.java} (85%) diff --git a/src/main/java/cloudgene/mapred/jobs/AbstractJob.java b/src/main/java/cloudgene/mapred/jobs/AbstractJob.java index 88eceba1..e5279087 100644 --- a/src/main/java/cloudgene/mapred/jobs/AbstractJob.java +++ b/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) { diff --git a/src/main/java/cloudgene/mapred/jobs/CloudgeneJob.java b/src/main/java/cloudgene/mapred/jobs/CloudgeneJob.java index 8cc61ed5..1b7404b4 100644 --- a/src/main/java/cloudgene/mapred/jobs/CloudgeneJob.java +++ b/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 downloads = externalWorkspace.getDownloads(out.getValue()); + List 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; - } - } diff --git a/src/main/java/cloudgene/mapred/jobs/workspace/IExternalWorkspace.java b/src/main/java/cloudgene/mapred/jobs/workspace/IWorkspace.java similarity index 95% rename from src/main/java/cloudgene/mapred/jobs/workspace/IExternalWorkspace.java rename to src/main/java/cloudgene/mapred/jobs/workspace/IWorkspace.java index b7cf0cd6..51745501 100644 --- a/src/main/java/cloudgene/mapred/jobs/workspace/IExternalWorkspace.java +++ b/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; diff --git a/src/main/java/cloudgene/mapred/jobs/workspace/LocalWorkspace.java b/src/main/java/cloudgene/mapred/jobs/workspace/LocalWorkspace.java index 31de2b81..18575aed 100644 --- a/src/main/java/cloudgene/mapred/jobs/workspace/LocalWorkspace.java +++ b/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"; diff --git a/src/main/java/cloudgene/mapred/jobs/workspace/S3Workspace.java b/src/main/java/cloudgene/mapred/jobs/workspace/S3Workspace.java index 9059a988..8c48e345 100644 --- a/src/main/java/cloudgene/mapred/jobs/workspace/S3Workspace.java +++ b/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"; diff --git a/src/main/java/cloudgene/mapred/jobs/workspace/ExternalWorkspaceFactory.java b/src/main/java/cloudgene/mapred/jobs/workspace/WorkspaceFactory.java similarity index 85% rename from src/main/java/cloudgene/mapred/jobs/workspace/ExternalWorkspaceFactory.java rename to src/main/java/cloudgene/mapred/jobs/workspace/WorkspaceFactory.java index 58342468..561d7a58 100644 --- a/src/main/java/cloudgene/mapred/jobs/workspace/ExternalWorkspaceFactory.java +++ b/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(); } diff --git a/src/main/java/cloudgene/mapred/jobs/workspace/WorkspaceWrapper.java b/src/main/java/cloudgene/mapred/jobs/workspace/WorkspaceWrapper.java index 1d5f84c8..12826cd3 100644 --- a/src/main/java/cloudgene/mapred/jobs/workspace/WorkspaceWrapper.java +++ b/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; } diff --git a/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowStep.java b/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowStep.java index 70ea0ea7..0a6b0935 100644 --- a/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowStep.java +++ b/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); diff --git a/src/main/java/cloudgene/mapred/server/controller/DownloadController.java b/src/main/java/cloudgene/mapred/server/controller/DownloadController.java index 9f76d9dd..5c10147d 100644 --- a/src/main/java/cloudgene/mapred/server/controller/DownloadController.java +++ b/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 downloadExternalResults(String jobId, St @Get("/share/results/{hash}/{filename:.+}") @Secured(SecurityRule.IS_ANONYMOUS) public MutableHttpResponse downloadPublicLink(String hash, String filename) throws URISyntaxException, IOException { -System.out.println("------> " + filename); + DownloadDao dao = new DownloadDao(application.getDatabase()); Download download = dao.findByHash(hash); diff --git a/src/main/java/cloudgene/mapred/server/services/DownloadService.java b/src/main/java/cloudgene/mapred/server/services/DownloadService.java index 60a6d1b9..ae3f877c 100644 --- a/src/main/java/cloudgene/mapred/server/services/DownloadService.java +++ b/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 download(Download download) throws URISyntaxException, IOException { @@ -42,15 +42,15 @@ public MutableHttpResponse 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())); } } diff --git a/src/main/java/cloudgene/mapred/server/services/JobCleanUpService.java b/src/main/java/cloudgene/mapred/server/services/JobCleanUpService.java index 9443b7ae..6f0a322a 100644 --- a/src/main/java/cloudgene/mapred/server/services/JobCleanUpService.java +++ b/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()); diff --git a/src/main/java/cloudgene/mapred/server/services/JobService.java b/src/main/java/cloudgene/mapred/server/services/JobService.java index 2a3d3af2..3c138cf0 100644 --- a/src/main/java/cloudgene/mapred/server/services/JobService.java +++ b/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 form, User user) { Map 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 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 parseAndUpdateInputParams(List form, WdlApp app, - IExternalWorkspace externalWorkspace) throws Exception { + private Map parseAndUpdateInputParams(List form, WdlApp app, IWorkspace workspace) + throws Exception { Map props = new HashMap(); Map params = new HashMap(); @@ -402,10 +401,10 @@ private Map parseAndUpdateInputParams(List 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); diff --git a/src/test/java/cloudgene/mapred/jobs/PriorityThreadPoolExecutorTest.java b/src/test/java/cloudgene/mapred/jobs/PriorityThreadPoolExecutorTest.java index 0dd2a525..101f23ef 100644 --- a/src/test/java/cloudgene/mapred/jobs/PriorityThreadPoolExecutorTest.java +++ b/src/test/java/cloudgene/mapred/jobs/PriorityThreadPoolExecutorTest.java @@ -12,7 +12,7 @@ import cloudgene.mapred.TestApplication; import cloudgene.mapred.core.User; import cloudgene.mapred.database.UserDao; -import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory; +import cloudgene.mapred.jobs.workspace.WorkspaceFactory; import cloudgene.mapred.util.Settings; import cloudgene.mapred.wdl.WdlApp; import cloudgene.mapred.wdl.WdlReader; @@ -29,7 +29,7 @@ public class PriorityThreadPoolExecutorTest { TestApplication application; @Inject - ExternalWorkspaceFactory workspaceFactory; + WorkspaceFactory workspaceFactory; @Test public void testCancelRunningJob() throws Exception { @@ -479,7 +479,7 @@ public CloudgeneJob createJobFromWdl(WdlApp app, String id, Map CloudgeneJob job = new CloudgeneJob(user, id,app, inputs); job.setId(id); job.setName(id); - job.setExternalWorkspace(workspaceFactory.getDefault()); + job.setWorkspace(workspaceFactory.getDefault()); job.setLocalWorkspace(localWorkspace); job.setSettings(settings); job.setApplication(app.getName() + " " + app.getVersion()); diff --git a/src/test/java/cloudgene/mapred/jobs/WorkflowEngineTest.java b/src/test/java/cloudgene/mapred/jobs/WorkflowEngineTest.java index df5420d1..ef366c4e 100644 --- a/src/test/java/cloudgene/mapred/jobs/WorkflowEngineTest.java +++ b/src/test/java/cloudgene/mapred/jobs/WorkflowEngineTest.java @@ -13,7 +13,7 @@ import cloudgene.mapred.TestApplication; import cloudgene.mapred.core.User; import cloudgene.mapred.database.UserDao; -import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory; +import cloudgene.mapred.jobs.workspace.WorkspaceFactory; import cloudgene.mapred.util.Settings; import cloudgene.mapred.wdl.WdlApp; import cloudgene.mapred.wdl.WdlReader; @@ -29,7 +29,7 @@ public class WorkflowEngineTest { TestApplication application; @Inject - ExternalWorkspaceFactory workspaceFactory; + WorkspaceFactory workspaceFactory; @Test @@ -753,7 +753,7 @@ public CloudgeneJob createJobFromWdl(WdlApp app, Map inputs, Use CloudgeneJob job = new CloudgeneJob(user, id, app, inputs); job.setId(id); job.setName(id); - job.setExternalWorkspace(workspaceFactory.getDefault()); + job.setWorkspace(workspaceFactory.getDefault()); job.setLocalWorkspace(localWorkspace); job.setSettings(settings); job.setApplication(app.getName() + " " + app.getVersion()); diff --git a/src/test/java/cloudgene/mapred/jobs/WrongWorkspaceTest.java b/src/test/java/cloudgene/mapred/jobs/WrongWorkspaceTest.java index 73dfe0b1..4f73f6e7 100644 --- a/src/test/java/cloudgene/mapred/jobs/WrongWorkspaceTest.java +++ b/src/test/java/cloudgene/mapred/jobs/WrongWorkspaceTest.java @@ -11,7 +11,7 @@ import cloudgene.mapred.core.User; import cloudgene.mapred.database.JobDao; import cloudgene.mapred.database.UserDao; -import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory; +import cloudgene.mapred.jobs.workspace.WorkspaceFactory; import cloudgene.mapred.util.Settings; import cloudgene.mapred.wdl.WdlApp; import cloudgene.mapred.wdl.WdlReader; @@ -26,7 +26,7 @@ public class WrongWorkspaceTest { TestApplication application; @Inject - ExternalWorkspaceFactory workspaceFactory; + WorkspaceFactory workspaceFactory; @Test public void testReturnTrueStep() throws Exception { @@ -69,7 +69,7 @@ public CloudgeneJob createJobFromWdl(WdlApp app, Map inputs) thr CloudgeneJob job = new CloudgeneJob(user, id, app, inputs); job.setId(id); job.setName(id); - job.setExternalWorkspace(workspaceFactory.getDefault()); + job.setWorkspace(workspaceFactory.getDefault()); job.setLocalWorkspace(localWorkspace); job.setSettings(settings); job.setApplication(app.getName() + " " + app.getVersion()); diff --git a/src/test/java/cloudgene/mapred/steps/TestCommand.java b/src/test/java/cloudgene/mapred/steps/TestCommand.java index 93714ea7..d426e82f 100644 --- a/src/test/java/cloudgene/mapred/steps/TestCommand.java +++ b/src/test/java/cloudgene/mapred/steps/TestCommand.java @@ -16,7 +16,7 @@ import cloudgene.mapred.jobs.CloudgeneJob; import cloudgene.mapred.jobs.Message; import cloudgene.mapred.jobs.WorkflowEngine; -import cloudgene.mapred.jobs.workspace.ExternalWorkspaceFactory; +import cloudgene.mapred.jobs.workspace.WorkspaceFactory; import cloudgene.mapred.util.Settings; import cloudgene.mapred.wdl.WdlApp; import cloudgene.mapred.wdl.WdlReader; @@ -33,7 +33,7 @@ public class TestCommand { TestApplication application; @Inject - ExternalWorkspaceFactory workspaceFactory; + WorkspaceFactory workspaceFactory; @Test public void testValidCommand() throws Exception { @@ -145,7 +145,7 @@ public CloudgeneJob createJobFromWdl(WdlApp app, Map inputs) thr CloudgeneJob job = new CloudgeneJob(user, id, app, inputs); job.setId(id); - job.setExternalWorkspace(workspaceFactory.getDefault()); + job.setWorkspace(workspaceFactory.getDefault()); job.setName(id); job.setLocalWorkspace(localWorkspace); job.setSettings(settings);