Add clientoken

gradle.properties

@@ -1 +1 @@
-version=0.0.2-rc1
+version=0.0.2

plugins/build.gradle

@@ -1,8 +1,7 @@
 /*
+ * Copyright 2023-, Stellenbosch University, South Africa
  * Copyright 2024, Evaluacion y Desarrollo de Negocios, Spain
- * 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

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

@@ -1,6 +1,6 @@
 /*
- * Copyright 2023, Stellenbosch University, South Africa
- * Copyright 2022, Center for Medical Genetics, Ghent
+ * Copyright 2023-, Stellenbosch University, South Africa
+ * Copyright 2024, Evaluacion y Desarrollo de Negocios, Spain
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

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

@@ -1,4 +1,19 @@
-
+/*
+ * Copyright 2023-, Stellenbosch University, South Africa
+ * Copyright 2024, Evaluacion y Desarrollo de Negocios, Spain
+ *
+ * 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.executor
 
 import groovy.transform.CompileStatic

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

@@ -1,3 +1,20 @@
+/*
+ * Copyright 2023-, Stellenbosch University, South Africa
+ * Copyright 2024, Evaluacion y Desarrollo de Negocios, Spain
+ *
+ * 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.executor
 
 

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

@@ -1,7 +1,6 @@
 /*
+ * Copyright 2023-, Stellenbosch University, South Africa
  * Copyright 2024, Evaluacion y Desarrollo de Negocios, Spain
- * 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.
@@ -51,6 +50,10 @@ class NomadService implements Closeable{
         this.config = config
         ApiClient apiClient = new ApiClient()
         apiClient.basePath = config.clientOpts.address
+        if( config.clientOpts.token ){
+            log.debug "[NOMAD BATCH] Creating Nomad connection using token: ${config.clientOpts.token?.substring(0,5)}.."
+            apiClient.apiKey = config.clientOpts.token
+        }
         this.jobsApi = new JobsApi(apiClient);
     }
 

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

@@ -1,4 +1,19 @@
-
+/*
+ * Copyright 2023-, Stellenbosch University, South Africa
+ * Copyright 2024, Evaluacion y Desarrollo de Negocios, Spain
+ *
+ * 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.executor
 
 

plugins/nf-nomad/src/test/nextflow/nomad/NomadDSLSpec.groovy

@@ -1,4 +1,6 @@
 /*
+ * Copyright 2023-, Stellenbosch University, South Africa
+ * Copyright 2024, Evaluacion y Desarrollo de Negocios, Spain*
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

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

@@ -245,4 +245,42 @@ class NomadServiceSpec extends Specification{
         body.Job.TaskGroups[0].Tasks[0].VolumeMounts[0] == [Destination:"a", Volume:"test"]
 
     }
+
+        void "should send the token"(){
+        given:
+        def config = new NomadConfig(
+                client:[
+                        address : "http://${mockWebServer.hostName}:${mockWebServer.port}",
+                        token: "1234"
+                ],
+                jobs:[
+                        dockerVolume:'test'
+                ]
+        )
+        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"]
+
+        mockWebServer.enqueue(new MockResponse()
+                .setBody(JsonOutput.toJson(["EvalID":"test"]).toString())
+                .addHeader("Content-Type", "application/json"));
+        when:
+
+        def idJob = service.submitTask(id, name, image, args, workingDir,env)
+        def recordedRequest = mockWebServer.takeRequest();
+        def body = new JsonSlurper().parseText(recordedRequest.body.readUtf8())
+
+        then:
+        idJob
+
+        and:
+        recordedRequest.method == "POST"
+        recordedRequest.path == "/v1/jobs"
+        recordedRequest.headers.values('X-Nomad-Token').first()=='1234'
+    }
 }