Merge pull request #44 from nextflow-io/dump-job

dump job definition if nomad.debug.json = true

plugins/nf-nomad/src/main/nextflow/nomad/NomadConfig.groovy

@@ -35,10 +35,12 @@ class NomadConfig {
 
     final NomadClientOpts clientOpts
     final NomadJobOpts jobOpts
+    final NomadDebug debug
 
     NomadConfig(Map nomadConfigMap) {
         clientOpts = new NomadClientOpts((nomadConfigMap?.client ?: Collections.emptyMap()) as Map)
         jobOpts = new NomadJobOpts((nomadConfigMap?.jobs ?: Collections.emptyMap()) as Map)
+        debug = new NomadDebug((nomadConfigMap?.debug ?:  Collections.emptyMap()) as Map)
     }
 
     class NomadClientOpts{
@@ -129,4 +131,15 @@ class NomadConfig {
         }
     }
 
+    static class NomadDebug {
+
+        @Delegate
+        Map<String,Object> target
+
+        NomadDebug(Map<String,Object> debug) {
+            this.target = debug ?: Collections.<String,Object>emptyMap()
+        }
+
+        boolean getJson() { Boolean.valueOf( target.json as String ) }
+    }
 }

plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadService.groovy

@@ -38,6 +38,9 @@ import nextflow.nomad.NomadConfig
 import nextflow.nomad.config.VolumeSpec
 import nextflow.processor.TaskRun
 import nextflow.util.MemoryUnit
+import org.yaml.snakeyaml.Yaml
+
+import java.nio.file.Path
 
 /**
  * Nomad Service
@@ -90,7 +93,7 @@ class NomadService implements Closeable{
     void close() throws IOException {
     }
 
-    String submitTask(String id, TaskRun task, List<String> args, Map<String, String>env){
+    String submitTask(String id, TaskRun task, List<String> args, Map<String, String>env, Path saveJsonPath=null){
         Job job = new Job();
         job.ID = id
         job.name = task.name
@@ -102,6 +105,14 @@ class NomadService implements Closeable{
 
         JobRegisterRequest jobRegisterRequest = new JobRegisterRequest();
         jobRegisterRequest.setJob(job);
+
+        if( saveJsonPath ) try {
+            saveJsonPath.text = job.toString()
+        }
+        catch( Exception e ) {
+            log.debug "WARN: unable to save request json -- cause: ${e.message ?: e}"
+        }
+
         JobRegisterResponse jobRegisterResponse = jobsApi.registerJob(jobRegisterRequest, config.jobOpts.region, config.jobOpts.namespace, null, null)
         jobRegisterResponse.evalID
     }

plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadTaskHandler.groovy

@@ -16,7 +16,7 @@
  */
 package nextflow.nomad.executor
 
-
+import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import io.nomadproject.client.model.Resources
@@ -131,14 +131,19 @@ class NomadTaskHandler extends TaskHandler implements FusionAwareTask {
 
         final taskLauncher = getSubmitCommand(task)
         final taskEnv = getEnv(task)
-        nomadService.submitTask(this.jobName, task, taskLauncher, taskEnv)
+        nomadService.submitTask(this.jobName, task, taskLauncher, taskEnv, debugPath())
 
         // submit the task execution
         log.debug "[NOMAD] Submitted task ${task.name} with taskId=${this.jobName}"
         // update the status
         this.status = TaskStatus.SUBMITTED
     }
 
+    protected Path debugPath() {
+        boolean debug = config.debug?.getJson()
+        return debug ? task.workDir.resolve('.job.json') : null
+    }
+
     protected List<String> getSubmitCommand(TaskRun task) {
         return fusionEnabled()
                 ? fusionSubmitCli()

plugins/nf-nomad/src/test/nextflow/nomad/executor/NomadServiceSpec.groovy

@@ -30,6 +30,7 @@ import okhttp3.mockwebserver.MockResponse
 import okhttp3.mockwebserver.MockWebServer
 import spock.lang.Specification
 
+import java.nio.file.Files
 import java.nio.file.Path
 
 /**
@@ -504,4 +505,60 @@ class NomadServiceSpec extends Specification{
         body.Job.TaskGroups[0].Tasks[0].Constraints[0].LTarget == '${meta.my_custom_value}'
     }
 
+    void "save the job spec if requested"(){
+        given:
+        def config = new NomadConfig(
+                client:[
+                        address : "http://${mockWebServer.hostName}:${mockWebServer.port}"
+                ],
+                debug:[
+                        json: true
+                ]
+        )
+        def service = new NomadService(config)
+
+        String id = "theId"
+        String name = "theName"
+        String image = "theImage"
+        List<String> args = ["theCommand", "theArgs"]
+        String workingDir = "/a/b/c"
+        Map<String, String>env = [test:"test"]
+
+        def mockTask = Mock(TaskRun){
+            getName() >> name
+            getContainer() >> image
+            getConfig() >> Mock(TaskConfig)
+            getWorkDirStr() >> workingDir
+            getContainer() >> "ubuntu"
+            getProcessor() >> Mock(TaskProcessor){
+                getExecutor() >> Mock(Executor){
+                    isFusionEnabled() >> false
+                }
+            }
+            getWorkDir() >> Path.of(workingDir)
+            toTaskBean() >> Mock(TaskBean){
+                getWorkDir() >> Path.of(workingDir)
+                getScript() >> "theScript"
+                getShell() >> ["bash"]
+                getInputFiles() >> [:]
+            }
+        }
+
+        mockWebServer.enqueue(new MockResponse()
+                .setBody(JsonOutput.toJson(["EvalID":"test"]).toString())
+                .addHeader("Content-Type", "application/json"));
+
+        def outputJson = Files.createTempFile("nomad",".json")
+        when:
+
+        def idJob = service.submitTask(id, mockTask, args, env, outputJson)
+
+        then:
+        idJob
+
+        and:
+        outputJson.text.indexOf(" Job {") != -1
+    }
+
+
 }