Merge pull request #88 from icgc-argo/RC/2.1.0

Release 2.1.0
icgc-argo · Jul 2, 2020 · 2b5c8ab · 2b5c8ab
2 parents fdf435d + c9dbbc7
commit 2b5c8ab
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Showing 3 changed files with 19 additions and 12 deletions.
diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
     </parent>
     <groupId>org.icgc.argo</groupId>
     <artifactId>workflow-management</artifactId>
-    <version>2.0.0</version>
+    <version>2.1.0</version>
     <name>workflow-management</name>
     <description>ARGO Workflow Management</description>
 

diff --git a/src/main/java/org/icgc/argo/workflow_management/controller/model/WorkflowEngineParams.java b/src/main/java/org/icgc/argo/workflow_management/controller/model/WorkflowEngineParams.java
@@ -7,6 +7,8 @@
 import lombok.Data;
 import lombok.NoArgsConstructor;
 
+import java.util.UUID;
+
 @Data
 @AllArgsConstructor
 @NoArgsConstructor
@@ -15,7 +17,7 @@
 public class WorkflowEngineParams {
   private String defaultContainer;
   private String revision;
-  private String resume;
+  private UUID resume;
   private String launchDir;
   private String projectDir;
   private String workDir;

diff --git a/src/main/java/org/icgc/argo/workflow_management/service/NextflowService.java b/src/main/java/org/icgc/argo/workflow_management/service/NextflowService.java
@@ -141,7 +141,12 @@ private String cancelRun(@NonNull String runId) {
     try (final val client = getClient()) {
       isPodRunning(runId);
       val childPods =
-          client.pods().inNamespace(namespace).withLabel("runName", runId).list().getItems()
+          client
+              .pods()
+              .inNamespace(namespace)
+              .withLabel("runName", runId)
+              .list()
+              .getItems()
               .stream()
               .filter(pod -> pod.getMetadata().getName().startsWith(NEXTFLOW_PREFIX))
               .collect(Collectors.toList());
@@ -242,34 +247,34 @@ private CmdKubeRun createCmd(@NonNull Launcher launcher, @NonNull WESRunParams p
     cmdParams.put("withWebLog", webLogUrl);
 
     // Dynamic engine properties/config
-    val workflowEngineOptions = params.getWorkflowEngineParams();
+    val workflowEngineParams = params.getWorkflowEngineParams();
 
     // Write config file for run using required and optional arguments
     // Use launchDir, projectDir and/or workDir if provided in workflow_engine_options
     val config =
         createNextflowConfigFile(
             runName,
             k8sConfig.getRunAsUser(),
-            workflowEngineOptions.getLaunchDir(),
-            workflowEngineOptions.getProjectDir(),
-            workflowEngineOptions.getWorkDir());
+            workflowEngineParams.getLaunchDir(),
+            workflowEngineParams.getProjectDir(),
+            workflowEngineParams.getWorkDir());
     cmdParams.put("runConfig", List.of(config));
 
     // Resume workflow by name/id
-    cmdParams.put("resume", workflowEngineOptions.getResume());
+    cmdParams.put("resume", workflowEngineParams.getResume().toString());
 
     // Use revision if provided in workflow_engine_options
-    cmdParams.put("revision", workflowEngineOptions.getRevision());
+    cmdParams.put("revision", workflowEngineParams.getRevision());
 
     // should pull latest code before running?
     // does not prevent us running a specific version (revision),
     // does enforce pulling of that branch/hash before running)
-    cmdParams.put("latest", workflowEngineOptions.getLatest(), v -> parseBoolean((String) v));
+    cmdParams.put("latest", workflowEngineParams.getLatest(), v -> parseBoolean((String) v));
 
     // Process options (default docker container to run for process if not specified)
-    if (nonNull(workflowEngineOptions.getDefaultContainer())) {
+    if (nonNull(workflowEngineParams.getDefaultContainer())) {
       val processOptions = new HashMap<String, String>();
-      processOptions.put("container", workflowEngineOptions.getDefaultContainer());
+      processOptions.put("container", workflowEngineParams.getDefaultContainer());
       cmdParams.put("process", processOptions);
     }