iteration with env var for test env[ci skip]

Author: abhi18av

plugins/nf-nomad/src/main/nextflow/nomad/builders/JobBuilder.groovy

@@ -107,11 +107,11 @@ class JobBuilder {
 
     static protected Resources getResources(TaskRun task) {
         final DEFAULT_CPUS = 1
-        final DEFAULT_MEMORY = "500.MB"
+        final DEFAULT_MEMORY = "1.GB"
 
         final taskCfg = task.getConfig()
         final taskCores =  !taskCfg.get("cpus") ? DEFAULT_CPUS :  taskCfg.get("cpus") as Integer
-        final taskMemory = taskCfg.get("memory") ? new MemoryUnit( taskCfg.get("memory") as String ) : new MemoryUnit(DEFAULT_MEMORY)
+        final taskMemory = !taskCfg.get("memory") ?  new MemoryUnit(DEFAULT_MEMORY) : new MemoryUnit( taskCfg.get("memory") as String )
 
         final res = new Resources()
                 .cores(taskCores)
@@ -313,4 +313,4 @@ class JobBuilder {
     }
 
 
-}
+}

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

@@ -136,20 +136,6 @@ class NomadService implements Closeable{
 
 
 
-    String getJobStatus(String jobId){
-        try {
-            Job job = safeExecutor.apply {
-                jobsApi.getJob(jobId, config.jobOpts().region, config.jobOpts().namespace,
-                        null, null, null, null, null, null, null)
-            }
-            log.debug "[NOMAD] getJobStatus jobID=$job.ID; status=$job.status"
-            job.status
-        }catch (Exception e){
-            log.debug("[NOMAD] getJobStatus Failed to get jobState ${jobId} -- Cause: ${e.message ?: e}", e)
-            "unknown"
-        }
-    }
-
     void kill(String jobId) {
         purgeJob(jobId, false)
     }

…/test/nextflow/nomad/NomadDSLSpec.groovy …t/nextflow/nomad/MockNomadDSLSpec.groovyplugins/nf-nomad/src/test/nextflow/nomad/NomadDSLSpec.groovy renamed to plugins/nf-nomad/src/test/nextflow/nomad/MockNomadDSLSpec.groovy plugins/nf-nomad/src/test/nextflow/nomad/NomadDSLSpec.groovy renamed to plugins/nf-nomad/src/test/nextflow/nomad/MockNomadDSLSpec.groovy

@@ -28,6 +28,7 @@ import okhttp3.mockwebserver.MockWebServer
 import okhttp3.mockwebserver.RecordedRequest
 import org.jetbrains.annotations.NotNull
 import org.pf4j.PluginDescriptorFinder
+import spock.lang.Requires
 import spock.lang.Shared
 import spock.lang.Timeout
 import test.Dsl2Spec
@@ -43,7 +44,8 @@ import java.util.jar.Manifest
  * @author : Jorge Aguilera <[email protected]>
  */
 @Timeout(60)
-class NomadDSLSpec  extends Dsl2Spec{
+@Requires({ System.getenv('NF_NOMAD_TEST_ENV') == 'mock' })
+class MockNomadDSLSpec  extends Dsl2Spec{
     @Shared String pluginsMode
 
     MockWebServer mockWebServer

…d/executor/NomadSecretServiceSpec.groovy …ecutor/MockNomadSecretServiceSpec.groovyplugins/nf-nomad/src/test/nextflow/nomad/executor/NomadSecretServiceSpec.groovy renamed to plugins/nf-nomad/src/test/nextflow/nomad/executor/MockNomadSecretServiceSpec.groovy plugins/nf-nomad/src/test/nextflow/nomad/executor/NomadSecretServiceSpec.groovy renamed to plugins/nf-nomad/src/test/nextflow/nomad/executor/MockNomadSecretServiceSpec.groovy

@@ -16,30 +16,23 @@
  */
 package nextflow.nomad.executor
 
-import groovy.json.JsonOutput
-import groovy.json.JsonSlurper
-import nextflow.executor.Executor
+
 import nextflow.nomad.config.NomadConfig
-import nextflow.processor.TaskBean
-import nextflow.processor.TaskConfig
-import nextflow.processor.TaskProcessor
-import nextflow.processor.TaskRun
-import nextflow.script.ProcessConfig
 import okhttp3.mockwebserver.MockResponse
 import okhttp3.mockwebserver.MockWebServer
+import spock.lang.Requires
 import spock.lang.Specification
 
-import java.nio.file.Files
-import java.nio.file.Path
-
 /**
  * Unit test for Nomad Service for Secrets requests
  *
  * Validate requests using a Mock WebServer
  *
  * @author : Jorge Aguilera <[email protected]>
  */
-class NomadSecretServiceSpec extends Specification{
+
+@Requires({ System.getenv('NF_NOMAD_TEST_ENV') == 'mock' })
+class MockNomadSecretServiceSpec extends Specification{
 
     MockWebServer mockWebServer
 
@@ -90,6 +83,7 @@ class NomadSecretServiceSpec extends Specification{
         recordedRequest2.path == "/v1/var/another%2FMySecret"
     }
 
+    @Requires({ System.getenv('NF_NOMAD_TEST_ENV') == 'mock' })
     void "should set a variable"(){
         given:
         def config = new NomadConfig(

…w/nomad/executor/NomadServiceSpec.groovy …mad/executor/MockNomadServiceSpec.groovyplugins/nf-nomad/src/test/nextflow/nomad/executor/NomadServiceSpec.groovy renamed to plugins/nf-nomad/src/test/nextflow/nomad/executor/MockNomadServiceSpec.groovy plugins/nf-nomad/src/test/nextflow/nomad/executor/NomadServiceSpec.groovy renamed to plugins/nf-nomad/src/test/nextflow/nomad/executor/MockNomadServiceSpec.groovy

@@ -27,6 +27,7 @@ import nextflow.processor.TaskRun
 import nextflow.script.ProcessConfig
 import okhttp3.mockwebserver.MockResponse
 import okhttp3.mockwebserver.MockWebServer
+import spock.lang.Requires
 import spock.lang.Specification
 
 import java.nio.file.Files
@@ -39,7 +40,9 @@ import java.nio.file.Path
  *
  * @author : Jorge Aguilera <[email protected]>
  */
-class NomadServiceSpec extends Specification{
+
+@Requires({ System.getenv('NF_NOMAD_TEST_ENV') == 'mock' })
+class MockNomadServiceSpec extends Specification{
 
     MockWebServer mockWebServer
 

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

@@ -32,6 +32,7 @@ import java.nio.file.Path
  *
  * @author : Jorge Aguilera <[email protected]>
  */
+
 class NomadTaskHandlerSpec extends Specification{
 
     void "a task should have a container"(){

…w/nomad/models/JobConstraintsSpec.groovy …mad/models/MockJobConstraintsSpec.groovyplugins/nf-nomad/src/test/nextflow/nomad/models/JobConstraintsSpec.groovy renamed to plugins/nf-nomad/src/test/nextflow/nomad/models/MockJobConstraintsSpec.groovy plugins/nf-nomad/src/test/nextflow/nomad/models/JobConstraintsSpec.groovy renamed to plugins/nf-nomad/src/test/nextflow/nomad/models/MockJobConstraintsSpec.groovy

@@ -29,9 +29,9 @@ import nextflow.processor.TaskRun
 import nextflow.script.ProcessConfig
 import okhttp3.mockwebserver.MockResponse
 import okhttp3.mockwebserver.MockWebServer
+import spock.lang.Requires
 import spock.lang.Specification
 
-import java.nio.file.Files
 import java.nio.file.Path
 
 /**
@@ -41,7 +41,9 @@ import java.nio.file.Path
  *
  * @author : Jorge Aguilera <[email protected]>
  */
-class JobConstraintsSpec extends Specification{
+
+@Requires({ System.getenv('NF_NOMAD_TEST_ENV') == 'mock' })
+class MockJobConstraintsSpec extends Specification{
 
     MockWebServer mockWebServer
 

validation/sun-nomadlab/nextflow.config

@@ -4,6 +4,9 @@ plugins {
 
 process {
     executor = "nomad"
+
+    resourceLimits = [ cpus: 4, memory: 4.GB, time: 1.h ]
+
 }
 
 aws {
@@ -30,6 +33,7 @@ fusion {
     logLevel = 'verbose' // 'info' | 'debug'
 }
 
+
 nomad {
 
     client {
@@ -47,14 +51,14 @@ nomad {
         volume = { type "host" name "scratch" }
 
 //         constraints = {
-// //            attr {
+//             attr {
 // //                unique = [hostname:'nomad03']
 // //                //raw 'platform.aws.instance-type', '=', 'm4.xlarge'
 
 //             node {
 //                 unique = [name: "nomad03"]
+//                 }
 //             }
-
 //         }
     }
 }