/**
* Method which writes the cancer study metadata file.
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param numCases int
* @throws Exception
*/
@Override
public void writeCancerStudyMetadataFile(
PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, int numCases)
throws Exception {
File metaFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
cancerStudyMetadata.getCancerStudyMetadataFilename());
if (LOG.isInfoEnabled()) {
LOG.info("writeMetadataFile(), meta file: " + metaFile);
}
PrintWriter writer =
new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(metaFile, false));
writer.print("type_of_cancer: " + cancerStudyMetadata.getTumorType() + "\n");
writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n");
String name =
(cancerStudyMetadata.getName().length() > 0)
? cancerStudyMetadata.getName()
: cancerStudyMetadata.getTumorTypeMetadata().getName();
name =
name.replaceAll(
CancerStudyMetadata.TUMOR_TYPE_NAME_TAG,
cancerStudyMetadata.getTumorTypeMetadata().getName());
writer.print("name: " + name + "\n");
String description = cancerStudyMetadata.getDescription();
description =
description.replaceAll(CancerStudyMetadata.NUM_CASES_TAG, Integer.toString(numCases));
description =
description.replaceAll(
CancerStudyMetadata.TUMOR_TYPE_TAG,
cancerStudyMetadata.getTumorTypeMetadata().getType());
description =
description.replaceAll(
CancerStudyMetadata.TUMOR_TYPE_NAME_TAG,
cancerStudyMetadata.getTumorTypeMetadata().getName());
writer.print("description: " + description + "\n");
if (cancerStudyMetadata.getCitation().length() > 0) {
writer.print("citation: " + cancerStudyMetadata.getCitation() + "\n");
}
if (cancerStudyMetadata.getPMID().length() > 0) {
writer.print("pmid: " + cancerStudyMetadata.getPMID() + "\n");
}
writer.flush();
writer.close();
}
