Commit aa530ac5 authored by Koehorst, Jasper's avatar Koehorst, Jasper
Browse files

envmap added

parent c4f49f63
Pipeline #23260 passed with stage
in 1 minute and 19 seconds
...@@ -114,7 +114,7 @@ public class Kubernetes { ...@@ -114,7 +114,7 @@ public class Kubernetes {
private static void getYamls(CommandOptionsKubernetes commandOptionsKubernetes, Connection connection) throws JargonException, GenQueryBuilderException, JargonQueryException, IOException, ApiException, InterruptedException { private static void getYamls(CommandOptionsKubernetes commandOptionsKubernetes, Connection connection) throws JargonException, GenQueryBuilderException, JargonQueryException, IOException, ApiException, InterruptedException {
// List all project turtle files... // List all project turtle files...
if (commandOptionsKubernetes.project.contains("references")) { if (commandOptionsKubernetes.project.contains("references")) {
String path = "/" + commandOptionsKubernetes.zone + "/references/genomes/bacteria%"; String path = "/" + commandOptionsKubernetes.zone + "/references/genomes/bacteria%mycoplasma%";
if (commandOptionsKubernetes.reset) if (commandOptionsKubernetes.reset)
resetFailures(connection, path); resetFailures(connection, path);
Search.getAllUnprocessedReferences(commandOptionsKubernetes, connection, path); Search.getAllUnprocessedReferences(commandOptionsKubernetes, connection, path);
...@@ -262,6 +262,16 @@ public class Kubernetes { ...@@ -262,6 +262,16 @@ public class Kubernetes {
containerItem.name(UUID.randomUUID().toString()); containerItem.name(UUID.randomUUID().toString());
containerItem.image("docker-registry.wur.nl/unlock/docker"); 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(); V1ResourceRequirements resource = new V1ResourceRequirements();
// Set limits to the job // Set limits to the job
Map<String, Quantity> limit = new HashMap<>(); Map<String, Quantity> limit = new HashMap<>();
...@@ -313,19 +323,19 @@ public class Kubernetes { ...@@ -313,19 +323,19 @@ public class Kubernetes {
// Unlock mount // Unlock mount
containerItem.addVolumeMountsItem(new V1VolumeMount().name("unlock").mountPath("/unlock")); containerItem.addVolumeMountsItem(new V1VolumeMount().name("unlock").mountPath("/unlock"));
// HashMap TODO make this a secret // // HashMap TODO make this a secret
HashMap<String, String> envMap = new HashMap<>(); // 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"); // 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(); // List<V1EnvVar> env = new ArrayList();
for (String key : envMap.keySet()) { // for (String key : envMap.keySet()) {
V1EnvVar v1EnvVar = new V1EnvVar(); // V1EnvVar v1EnvVar = new V1EnvVar();
v1EnvVar.setName(key); // v1EnvVar.setName(key);
v1EnvVar.setValue(envMap.get(key)); // v1EnvVar.setValue(envMap.get(key));
env.add(v1EnvVar); // env.add(v1EnvVar);
} // }
containerItem.env(env); // containerItem.env(env);
// Set the name // Set the name
String name = "cwl-" + new File(yamlFile).getParentFile().getName().toLowerCase().replaceAll("[_\\.]", "") + "-" + new File(yamlFile).getName().toLowerCase().replaceAll("[_\\.]", ""); String name = "cwl-" + new File(yamlFile).getParentFile().getName().toLowerCase().replaceAll("[_\\.]", "") + "-" + new File(yamlFile).getName().toLowerCase().replaceAll("[_\\.]", "");
......
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