jobmanager removal

src/main/java/nl/munlock/App.java

@@ -20,8 +20,6 @@ public class App {
         } else if (Arrays.asList(args).contains("-kubernetes")) {
             log.info("Executing kubernetes workflows");
             nl.munlock.kubernetes.App.main(args);
-        } else if (Arrays.asList(args).contains("-manager")) {
-            nl.munlock.kubernetes.App.manager();
         }
     }
 }

src/main/java/nl/munlock/kubernetes/App.java

@@ -28,118 +28,4 @@ public class App {
         Connection connection = new Connection(commandOptions);
         Kubernetes.main(commandOptions, connection);
     }
-
-    /**
-     * Method to start the cron job manager basically executes this program on a kubernetes cluster for all projects
-     */
-    public static void manager() throws ApiException, IOException {
-        V1PodTemplateSpec template = new V1PodTemplateSpec();
-
-        // Defines the docker container
-        V1Container containerItem = new V1Container();
-        containerItem.name("jobmanager");
-        containerItem.image("docker-registry.wur.nl/unlock/docker");
-
-        V1ResourceRequirements resource = new V1ResourceRequirements();
-        // Set limits to the job
-        Map<String, Quantity> limit = new HashMap<>();
-        Quantity quantity_cpu = new Quantity(2000 + "m");
-        Quantity quantity_mem = new Quantity(1000 + "Mi");
-        limit.put("cpu", quantity_cpu);
-        limit.put("memory", quantity_mem);
-        resource.limits(limit);
-
-        // Set requests for the job
-        Map<String, Quantity> request = new HashMap<>();
-        quantity_mem = new Quantity(1000 + "Mi");
-        quantity_cpu = new Quantity(2000 + "m");
-        request.put("memory", quantity_mem);
-        request.put("cpu", quantity_cpu);
-        resource.requests(request);
-
-        containerItem.resources(resource);
-
-        // List of arguments for the command during startup
-        List<String> args = new ArrayList<>();
-        // Execute.sh should sync the collection after the run
-        args.add("/scripts/jobManager.sh");
-        containerItem.args(args);
-
-        // Base command
-        List<String> command = new ArrayList<>();
-        command.add("bash");
-        containerItem.command(command);
-
-        // Unlock mount
-        containerItem.addVolumeMountsItem(new V1VolumeMount().name("unlock").mountPath("/unlock"));
-
-        // Environmental path for java etc...
-        HashMap<String, String> envMap = new HashMap<>();
-        envMap.put("PATH", "/root/.sdkman/candidates/maven/current/bin:/root/.sdkman/candidates/java/current/bin:/root/.sdkman/candidates/gradle/current/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin");
-
-        List<V1EnvVar> env = new ArrayList();
-        for (String key : envMap.keySet()) {
-            V1EnvVar v1EnvVar = new V1EnvVar();
-            v1EnvVar.setName(key);
-            v1EnvVar.setValue(envMap.get(key));
-            env.add(v1EnvVar);
-        }
-
-        containerItem.env(env);
-
-        // Set the name
-        containerItem.name("jobmanager");
-
-        // Setting secrets
-        containerItem.addEnvItem(setSecret("irodsHost","unlock-secret", "irodsHost"));
-        containerItem.addEnvItem(setSecret("irodsPort","unlock-secret", "irodsPort"));
-        containerItem.addEnvItem(setSecret("irodsUserName","unlock-secret", "irodsUserName"));
-        containerItem.addEnvItem(setSecret("irodsZone","unlock-secret", "irodsZone"));
-        containerItem.addEnvItem(setSecret("irodsAuthScheme","unlock-secret", "irodsAuthScheme"));
-        containerItem.addEnvItem(setSecret("irodsHome","unlock-secret", "irodsHome"));
-        containerItem.addEnvItem(setSecret("irodsCwd","unlock-secret", "irodsCwd"));
-        containerItem.addEnvItem(setSecret("irodsPassword","unlock-secret", "irodsPassword"));
-        containerItem.addEnvItem(setSecret("irodsSSL","unlock-secret", "irodsSSL"));
-
-        // Job specifications
-        V1JobSpec v1JobSpec = new V1JobSpec();
-        v1JobSpec.ttlSecondsAfterFinished(1000);
-        v1JobSpec.setTtlSecondsAfterFinished(1000);
-        v1JobSpec.setBackoffLimit(1);
-
-        // 60 min runtime, disabled as when queue is large jobs get killed when not even started
-        // specs.activeDeadlineSeconds((long) 3600);
-        v1JobSpec.template(template);
-
-        V1PodSpec v1PodSpec = new V1PodSpec();
-        // https://rancher.com/docs/k3s/latest/en/storage/
-        v1PodSpec.addVolumesItem(new V1Volume().name("unlock").persistentVolumeClaim(new V1PersistentVolumeClaimVolumeSource().claimName("unlock")));
-        v1PodSpec.addContainersItem(containerItem);
-        v1PodSpec.restartPolicy("OnFailure");
-        template.spec(v1PodSpec);
-        // Set priority level
-        // v1PodSpec.setPriority(commandOptions.priority);
-
-        V1ObjectMeta v1ObjectMeta = new V1ObjectMeta();
-        v1ObjectMeta.generateName("jobmanager");
-
-        V1Job v1Job = new V1Job();
-        v1Job.apiVersion("batch/v1");
-        v1Job.kind("Job");
-        v1Job.metadata(v1ObjectMeta);
-        v1Job.spec(v1JobSpec);
-
-        // Load and make connection
-        ApiClient client = Config.defaultClient();
-        client.setDebugging(true);
-        Configuration.setDefaultApiClient(client);
-
-
-        // v1Job.setKind("my-kind");
-        BatchV1Api batchV1Api = new BatchV1Api();
-
-        // Submit the job to nl.wur.ssb.kubernetes
-        batchV1Api.createNamespacedJob("unlock", v1Job, false, null, null);
-        batchV1Api.createNamespacedJobCall("unlock", v1Job, null, null, null, null, null);
-    }
 }