implement datacenters directive

closes #42 Signed-off-by: Jorge Aguilera <[email protected]>
nextflow-io · Jun 16, 2024 · a2f9f30 · a2f9f30
1 parent 7ed26c2
commit a2f9f30
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Showing 8 changed files with 5 additions and 37 deletions.
diff --git a/plugins/nf-nomad/src/main/nextflow/nomad/config/VolumeSpec.groovy b/plugins/nf-nomad/src/main/nextflow/nomad/config/VolumeSpec.groovy
@@ -1,7 +1,5 @@
 package nextflow.nomad.config
 
-import nextflow.nomad.NomadConfig
-
 class VolumeSpec {
 
     final static public String VOLUME_DOCKER_TYPE = "docker"

diff --git a/plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadScriptLauncher.groovy b/plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadScriptLauncher.groovy
@@ -17,11 +17,8 @@
 
 package nextflow.nomad.executor
 
-
 import nextflow.executor.BashWrapperBuilder
-import nextflow.executor.SimpleFileCopyStrategy
 import nextflow.processor.TaskBean
-import nextflow.util.Escape
 
 /**
  * Custom bash wrapper builder for Nomad jobs/tasks

diff --git a/plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadService.groovy b/plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadService.groovy
@@ -21,19 +21,7 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import io.nomadproject.client.ApiClient
 import io.nomadproject.client.api.JobsApi
-import io.nomadproject.client.model.Affinity
-import io.nomadproject.client.model.AllocationListStub
-import io.nomadproject.client.model.Constraint
-import io.nomadproject.client.model.Job
-import io.nomadproject.client.model.JobRegisterRequest
-import io.nomadproject.client.model.JobRegisterResponse
-import io.nomadproject.client.model.ReschedulePolicy
-import io.nomadproject.client.model.Resources
-import io.nomadproject.client.model.RestartPolicy
-import io.nomadproject.client.model.Task
-import io.nomadproject.client.model.TaskGroup
-import io.nomadproject.client.model.VolumeMount
-import io.nomadproject.client.model.VolumeRequest
+import io.nomadproject.client.model.*
 import nextflow.nomad.NomadConfig
 import nextflow.nomad.config.VolumeSpec
 import nextflow.processor.TaskRun
@@ -236,7 +224,7 @@ class NomadService implements Closeable{
     }
 
     protected Job assignDatacenters(TaskRun task, Job job){
-        def datacenters = task.processor.config.get("datacenters")
+        def datacenters = task.processor?.config?.get("datacenters")
         if( datacenters ){
             if( datacenters instanceof List<String>) {
                 job.datacenters( datacenters as List<String>)

diff --git a/plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadTaskHandler.groovy b/plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadTaskHandler.groovy
@@ -16,11 +16,8 @@
  */
 package nextflow.nomad.executor
 
-
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import io.nomadproject.client.model.Resources
-import io.nomadproject.client.model.TaskGroupSummary
 import nextflow.exception.ProcessSubmitException
 import nextflow.exception.ProcessUnrecoverableException
 import nextflow.executor.BashWrapperBuilder
@@ -31,7 +28,6 @@ import nextflow.processor.TaskHandler
 import nextflow.processor.TaskRun
 import nextflow.processor.TaskStatus
 import nextflow.util.Escape
-import nextflow.util.MemoryUnit
 
 import java.nio.file.Path
 

diff --git a/plugins/nf-nomad/src/test/nextflow/nomad/MockScriptRunner.groovy b/plugins/nf-nomad/src/test/nextflow/nomad/MockScriptRunner.groovy
@@ -15,23 +15,19 @@
  */
 package nextflow.nomad
 
-import groovy.util.logging.Slf4j
+
 import groovyx.gpars.dataflow.DataflowBroadcast
 import nextflow.Session
 import nextflow.executor.Executor
 import nextflow.executor.ExecutorFactory
 import nextflow.nomad.executor.NomadExecutor
 import nextflow.processor.TaskHandler
 import nextflow.processor.TaskMonitor
-import nextflow.processor.TaskRun
-import nextflow.processor.TaskStatus
 import nextflow.script.BaseScript
 import nextflow.script.ChannelOut
 import nextflow.script.ScriptRunner
 import nextflow.script.ScriptType
 
-import java.nio.file.Paths
-
 /**
  * Mock runner for test
  *

diff --git a/plugins/nf-nomad/src/test/nextflow/nomad/executor/NomadServiceSpec.groovy b/plugins/nf-nomad/src/test/nextflow/nomad/executor/NomadServiceSpec.groovy
@@ -18,15 +18,13 @@ package nextflow.nomad.executor
 
 import groovy.json.JsonOutput
 import groovy.json.JsonSlurper
-import io.nomadproject.client.model.Resources
 import nextflow.executor.Executor
 import nextflow.nomad.NomadConfig
 import nextflow.processor.TaskBean
 import nextflow.processor.TaskConfig
 import nextflow.processor.TaskProcessor
 import nextflow.processor.TaskRun
 import nextflow.script.ProcessConfig
-import nextflow.util.MemoryUnit
 import okhttp3.mockwebserver.MockResponse
 import okhttp3.mockwebserver.MockWebServer
 import spock.lang.Specification

diff --git a/plugins/nf-nomad/src/test/nextflow/nomad/executor/NomadTaskHandlerSpec.groovy b/plugins/nf-nomad/src/test/nextflow/nomad/executor/NomadTaskHandlerSpec.groovy
@@ -20,12 +20,7 @@ package nextflow.nomad.executor
 import nextflow.exception.ProcessSubmitException
 import nextflow.executor.Executor
 import nextflow.nomad.NomadConfig
-import nextflow.processor.TaskBean
-import nextflow.processor.TaskConfig
-import nextflow.processor.TaskProcessor
-import nextflow.processor.TaskRun
-import nextflow.processor.TaskStatus
-import nextflow.script.ProcessConfig
+import nextflow.processor.*
 import spock.lang.Specification
 
 import java.nio.file.Files

diff --git a/src/docs/asciidoc/parts/directives.adoc b/src/docs/asciidoc/parts/directives.adoc
@@ -2,7 +2,7 @@
 
 You can tag your processes with following directives:
 
-- datacenters (a strings list)
+- datacenters (a strings list or a closure returning a String)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,7 +2,7 @@

		You can tag your processes with following directives:

		- datacenters (a strings list)
		- datacenters (a strings list or a closure returning a String)