envmap added

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

@@ -114,7 +114,7 @@ public class Kubernetes {
     private static void getYamls(CommandOptionsKubernetes commandOptionsKubernetes, Connection connection) throws JargonException, GenQueryBuilderException, JargonQueryException, IOException, ApiException, InterruptedException {
         // List all project turtle files...
         if (commandOptionsKubernetes.project.contains("references")) {
-            String path = "/" + commandOptionsKubernetes.zone + "/references/genomes/bacteria%";
+            String path = "/" + commandOptionsKubernetes.zone + "/references/genomes/bacteria%mycoplasma%";
             if (commandOptionsKubernetes.reset)
                 resetFailures(connection, path);
             Search.getAllUnprocessedReferences(commandOptionsKubernetes, connection, path);
@@ -262,6 +262,16 @@ public class Kubernetes {
         containerItem.name(UUID.randomUUID().toString());
         containerItem.image("docker-registry.wur.nl/unlock/docker");
 
+        // Set path environment through rancher environment variable using the envFrom object
+        // Project (unlock) > Resources > Config > Key / Value environment
+        List<V1EnvFromSource> envFrom = new ArrayList<>();
+        V1EnvFromSource v1EnvFromSource = new V1EnvFromSource();
+        V1ConfigMapEnvSource v1ConfigMapEnvSource = new V1ConfigMapEnvSource();
+        v1ConfigMapEnvSource.setName("path");
+        v1EnvFromSource.setConfigMapRef(v1ConfigMapEnvSource);
+        envFrom.add(v1EnvFromSource);
+        containerItem.setEnvFrom(envFrom);
+
         V1ResourceRequirements resource = new V1ResourceRequirements();
         // Set limits to the job
         Map<String, Quantity> limit = new HashMap<>();
@@ -313,19 +323,19 @@ public class Kubernetes {
         // Unlock mount
         containerItem.addVolumeMountsItem(new V1VolumeMount().name("unlock").mountPath("/unlock"));
 
-        // HashMap TODO make this a secret
-        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");
+//        // HashMap TODO make this a secret
+//        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);
-        }
+//        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);
+//        containerItem.env(env);
 
         // Set the name
         String name = "cwl-" + new File(yamlFile).getParentFile().getName().toLowerCase().replaceAll("[_\\.]", "") + "-" + new File(yamlFile).getName().toLowerCase().replaceAll("[_\\.]", "");