Commit 908042dd authored by Koehorst, Jasper's avatar Koehorst, Jasper
Browse files

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parent dfa7fb2e
Pipeline #15401 passed with stage
in 53 seconds
...@@ -262,7 +262,7 @@ public class Search { ...@@ -262,7 +262,7 @@ public class Search {
// } // }
break; break;
} }
if (Kubernetes.yamls.size() == 10) { if (Kubernetes.yamls.size() > 0) {
log.info("Starting kubernetes"); log.info("Starting kubernetes");
Kubernetes.createJobs(commandOptionsKubernetes, connection); Kubernetes.createJobs(commandOptionsKubernetes, connection);
// Reset references... // Reset references...
...@@ -318,7 +318,7 @@ public class Search { ...@@ -318,7 +318,7 @@ public class Search {
String path = irodsQueryResultSetResult.getColumn(0) + "/" + irodsQueryResultSetResult.getColumn(1); String path = irodsQueryResultSetResult.getColumn(0) + "/" + irodsQueryResultSetResult.getColumn(1);
log.info("Processing " + line); log.info("Processing " + line);
Kubernetes.yamls.add(path); Kubernetes.yamls.add(path);
if (Kubernetes.yamls.size() > 10) { if (Kubernetes.yamls.size() > 0) {
log.info("Starting kubernetes"); log.info("Starting kubernetes");
Kubernetes.createJobs(commandOptionsKubernetes, connection); Kubernetes.createJobs(commandOptionsKubernetes, connection);
// Reset references... // Reset references...
......
...@@ -277,6 +277,7 @@ public class Kubernetes { ...@@ -277,6 +277,7 @@ public class Kubernetes {
// Set the name // Set the name
containerItem.name("cwl-" + new File(yamlFile).getName().toLowerCase().replaceAll("[_\\.]", "")); containerItem.name("cwl-" + new File(yamlFile).getName().toLowerCase().replaceAll("[_\\.]", ""));
// Setting secrets
containerItem.addEnvItem(setSecret("irodsHost","unlock-secret", "irodsHost")); containerItem.addEnvItem(setSecret("irodsHost","unlock-secret", "irodsHost"));
containerItem.addEnvItem(setSecret("irodsPort","unlock-secret", "irodsPort")); containerItem.addEnvItem(setSecret("irodsPort","unlock-secret", "irodsPort"));
containerItem.addEnvItem(setSecret("irodsUserName","unlock-secret", "irodsUserName")); containerItem.addEnvItem(setSecret("irodsUserName","unlock-secret", "irodsUserName"));
......
...@@ -27,7 +27,6 @@ public class RNASeq { ...@@ -27,7 +27,6 @@ public class RNASeq {
log.info("Processing: " + assays.size()); log.info("Processing: " + assays.size());
for (Assay assay : assays) { for (Assay assay : assays) {
String yamlFileName;
// Only rnaseq types allowed // Only rnaseq types allowed
if (!assay.getClassTypeIri().endsWith("/RNASeqAssay")) { if (!assay.getClassTypeIri().endsWith("/RNASeqAssay")) {
......
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