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Commit 1ee32167 authored by Koehorst, Jasper's avatar Koehorst, Jasper
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uuid only for container name and changed logging for metagenomics.java

parent e5441a28
Pipeline #22685 passed with stage
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src/main/java/nl/munlock/kubernetes/Kubernetes.java
View file @ 1ee32167
......@@ -253,13 +253,13 @@ public class Kubernetes {
log.info("CWL: " + cwlFile);
String uuid = UUID.randomUUID().toString();
String yamlName = new File(yamlFile).getName();
// String uuid = UUID.randomUUID().toString();
// String yamlName = new File(yamlFile).getName();
V1PodTemplateSpec template = new V1PodTemplateSpec();
// Defines the docker container
V1Container containerItem = new V1Container();
containerItem.name(uuid + "_" + yamlName);
containerItem.name(UUID.randomUUID().toString());
containerItem.image("docker-registry.wur.nl/unlock/docker");
V1ResourceRequirements resource = new V1ResourceRequirements();
......
src/main/java/nl/munlock/yaml/MetaGenomics.java
View file @ 1ee32167
......@@ -45,8 +45,8 @@ public class MetaGenomics {
HashSet<String> filePaths = new HashSet<>();
if (assay.getClassTypeIri().endsWith("DNASeqAssay")) {
log.info("==============================================");
log.info(assay.getResource().getURI());
log.debug("==============================================");
log.debug(assay.getResource().getURI());
// Fill object
WorkflowMetagenomics workflow = new WorkflowMetagenomics();
......@@ -58,14 +58,14 @@ public class MetaGenomics {
String destination = assay.getLogicalPath().replaceAll("/Unprocessed.*", "/processed/") + "/" + commandOptions.wid;
for (Data_sample data_sample : assay.getAllFile()) {
log.error(data_sample.getResource().getURI());
log.debug(data_sample.getResource().getURI());
// Parse each sequence dataset, as we might have overlapping identifiers in the future...
SequenceDataSet sequenceDataSet = (SequenceDataSet) data_sample;
// If file already processed skip...
if (filePaths.contains(new URL(sequenceDataSet.getContentUrl()).getPath())) continue;
if (sequenceDataSet.getSeqPlatform().getIRI().endsWith("Illumina")) {
log.info("illumina sequence data detected");
log.debug("illumina sequence data detected");
PairedSequenceDataSet pairedSequenceDataSet = (PairedSequenceDataSet) data_sample;
workflow.addForward_reads(new URL(pairedSequenceDataSet.getContentUrl()).getPath());
workflow.addReverse_reads(new URL(pairedSequenceDataSet.getPaired().getContentUrl()).getPath());
......@@ -110,8 +110,6 @@ public class MetaGenomics {
// Fix Clazz > Class
Workflow.fixClazz(yamlName);
log.info("NOT FINISHED YET");
// Save to iRODS
IRODSFile destFile = connection.fileFactory.instanceIRODSFile(assay.getLogicalPath() + "/" + yamlName);
......@@ -135,8 +133,8 @@ public class MetaGenomics {
// OU level
for (String observationUnitURL : observationUnitsList) {
log.info("==============================================");
log.info(observationUnitURL);
log.debug("==============================================");
log.debug(observationUnitURL);
// Fill object
WorkflowMetagenomics workflow = new WorkflowMetagenomics();
......@@ -167,7 +165,7 @@ public class MetaGenomics {
continue;
if (sequenceDataSet.getSeqPlatform().getIRI().endsWith("Illumina")) {
log.info("illumina sequence data detected");
log.debug("illumina sequence data detected");
PairedSequenceDataSet pairedSequenceDataSet = (PairedSequenceDataSet) data_sample;
workflow.addForward_reads(new URL(pairedSequenceDataSet.getContentUrl()).getPath());
workflow.addReverse_reads(new URL(pairedSequenceDataSet.getPaired().getContentUrl()).getPath());
......@@ -214,8 +212,6 @@ public class MetaGenomics {
// Fix Clazz > Class
Workflow.fixClazz(yamlName);
log.info("NOT FINISHED YET");
// Save to iRODS
IRODSFile destFile = connection.fileFactory.instanceIRODSFile(observationUnit.getLogicalPath() + "/" + yamlName);
......
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