Big refactor (#12)

* refactor

- use java library
- remove non used code and config

Signed-off-by: Jorge Aguilera <jagedn@gmail.com>

.gitignore

@@ -11,3 +11,7 @@ out
 _resources
 oracle-nomad-cluster
 sun-nomadlab
+
+.project
+.classpath
+.settings

plugins/build.gradle

@@ -77,6 +77,8 @@ subprojects {
      * Creates plugin zip and json meta file in plugin `build/libs` directory
      */
     task makeZip(type: Jar) {
+        group 'nextflow'
+
         into('classes') { with jar }
         into('lib') { from configurations.runtimeClasspath }
         manifest.from file('src/resources/META-INF/MANIFEST.MF')
@@ -105,6 +107,8 @@ subprojects {
      * Copy the plugin dependencies in the subproject `build/target/libs` directory
      */
     task copyPluginLibs(type: Sync) {
+        group 'nextflow'
+
         from configurations.runtimeClasspath
         into 'build/target/libs'
     }
@@ -113,6 +117,8 @@ subprojects {
      * Copy the plugin in the project root build/plugins directory
      */
     task copyPluginZip(type: Copy, dependsOn: project.tasks.findByName('makeZip')) {
+        group 'nextflow'
+
         from makeZip
         into "$rootProject.buildDir/plugins"
         outputs.file("$rootProject.buildDir/plugins/${project.name}-${project.version}.zip")
@@ -130,6 +136,8 @@ subprojects {
     project.parent.tasks.getByName("assemble").dependsOn << copyPluginZip
 
     task uploadPlugin(type: io.nextflow.gradle.tasks.GithubUploader, dependsOn: makeZip) {
+        group 'nextflow'
+
         assets = providers.provider {["$buildDir/libs/${project.name}-${project.version}.zip",
                                       "$buildDir/libs/${project.name}-${project.version}-meta.json" ]}
         release = providers.provider { project.version }
@@ -150,6 +158,8 @@ classes.dependsOn subprojects.copyPluginLibs
  * Merge and publish the plugins index file
  */
 task publishIndex( type: io.nextflow.gradle.tasks.GithubRepositoryPublisher ) {
+    group 'nextflow'
+
     indexUrl = 'https://github.com/nextflow-io/plugins/main/plugins.json'
     repos = allPlugins()
     owner = github_organization

plugins/nf-nomad/build.gradle

@@ -88,6 +88,8 @@ dependencies {
     }
 
     testImplementation 'com.squareup.okhttp3:mockwebserver:4.9.3'
+    testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
+    testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
 }
 
 // use JUnit 5 platform

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

@@ -0,0 +1,67 @@
+/*
+ * Copyright 2023, Stellenbosch University, South Africa
+ * Copyright 2022, Center for Medical Genetics, Ghent
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nextflow.nomad
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+
+/**
+ * Nomad Config
+ *
+ * @author Jorge Aguilera <jagedn@gmail.com>
+ */
+
+@Slf4j
+@CompileStatic
+class NomadConfig {
+
+    final NomadClientOpts clientOpts
+    final NomadJobOpts jobOpts
+
+    NomadConfig(Map nomadConfigMap) {
+        clientOpts = new NomadClientOpts((nomadConfigMap.client ?: Collections.emptyMap()) as Map)
+        jobOpts = new NomadJobOpts((nomadConfigMap.jobs ?: Collections.emptyMap()) as Map)
+    }
+
+    class NomadClientOpts{
+        final String address
+        final String token
+
+        NomadClientOpts(Map nomadClientOpts){
+            address = (nomadClientOpts.address?.toString() ?: "http://127.0.0.1:4646")+"/v1"
+            token = nomadClientOpts.token ?: null
+        }
+    }
+
+    class NomadJobOpts{
+        final boolean deleteOnCompletion
+        final List<String> datacenters
+        final String region
+        final String namespace
+        final String dockerVolume
+
+        NomadJobOpts(Map nomadJobOpts){
+            deleteOnCompletion = nomadJobOpts.containsKey("deleteOnCompletion") ?
+                    nomadJobOpts.deleteOnCompletion : false
+            datacenters = (nomadJobOpts.containsKey("datacenters") ?
+                    nomadJobOpts.datacenters.toString().split(",") : List.of("dc1")) as List<String>
+            region = nomadJobOpts.region ?: null
+            namespace = nomadJobOpts.namespace ?: null
+            dockerVolume = nomadJobOpts.dockerVolume ?: null
+        }
+    }
+}

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

@@ -17,12 +17,6 @@
 
 package nextflow.nomad
 
-import nextflow.nomad.client.NomadResponseJson
-import nextflow.nomad.model.NomadJobBuilder
-
-import nextflow.processor.TaskRun
-import nextflow.processor.TaskStatus
-
 /**
  * Nomad API Helper methods
  *
@@ -39,92 +33,4 @@ class NomadHelper {
         return str.take(60)
     }
 
-    static String filterStatus (NomadResponseJson resp, String taskName) {
-        def statusMap = resp.json.Summary["${taskName}_taskgroup"]
-        def status = statusMap.find{it.value == 1}.key
-        return status
-    }
-
-    static TaskStatus mapJobToTaskStatus(NomadResponseJson resp, String taskName) {
-        def parsedStatus = filterStatus(resp, taskName)
-
-        def Map<String, TaskStatus> TASK_STATUS = [
-            'Queued'           : TaskStatus.SUBMITTED,
-            'Starting'         : TaskStatus.RUNNING,
-            'Running'          : TaskStatus.RUNNING,
-            'Complete'         : TaskStatus.COMPLETED,
-            'Failed'           : TaskStatus.COMPLETED,
-            'Lost'             : TaskStatus.COMPLETED,
-            'Unknown'          : TaskStatus.COMPLETED,
-        ]
-
-        return TASK_STATUS[parsedStatus]
-    }
-
-
-
 }
-
-
-
-//package nextflow.nomad.model
-//
-//import groovy.transform.CompileStatic
-//import groovy.transform.EqualsAndHashCode
-//import groovy.transform.ToString
-//
-//@CompileStatic
-//@ToString(includeNames = true)
-//@EqualsAndHashCode(includeFields = true)
-//class NomadJobConstraints {
-//
-//    private Map spec = [:]
-//
-//    PodNodeSelector(selector) {
-//        if( selector instanceof CharSequence )
-//            createWithString(selector.toString())
-//
-//        else if( selector instanceof Map )
-//            createWithMap(selector)
-//
-//        else if( selector != null )
-//            throw new IllegalArgumentException("K8s invalid pod nodeSelector value: $selector [${selector.getClass().getName()}]")
-//    }
-//
-//    private createWithMap(Map selection ) {
-//        if(selection) {
-//            for( Map.Entry entry : selection.entrySet() ) {
-//                spec.put(entry.key.toString(), entry.value?.toString())
-//            }
-//        }
-//    }
-//
-//    /**
-//     * @param selector
-//     *      A string representing a comma separated list of pairs
-//     *      e.g. foo=1,bar=2
-//     *
-//     */
-//    private createWithString( String selector ) {
-//        if(!selector) return
-//        def entries = selector.tokenize(',')
-//        for( String item : entries ) {
-//            def pair = item.tokenize('=')
-//            spec.put( trim(pair[0]), trim(pair[1]) ?: 'true' )
-//        }
-//    }
-//
-//    private String trim(String v) {
-//        v?.trim()
-//    }
-//
-//    Map<String,String> toSpec() { spec }
-//
-//    String toString() {
-//        "PodNodeSelector[ ${spec?.toString()} ]"
-//    }
-//}
-//
-//
-//class NomadJobMeta {
-//}