/**
* 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();
}
/**
* Method which writes a metadata file for the given DatatypeMetadata. DataMatrix may be null.
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param datatypeMetadata DatatypeMetadata
* @param dataMatrix DataMatrix
* @throws Exception
*/
@Override
public void writeMetadataFile(
PortalMetadata portalMetadata,
CancerStudyMetadata cancerStudyMetadata,
DatatypeMetadata datatypeMetadata,
DataMatrix dataMatrix)
throws Exception {
File metaFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
datatypeMetadata.getMetaFilename());
if (LOG.isInfoEnabled()) {
LOG.info("writeMetadataFile(), meta file: " + metaFile);
}
PrintWriter writer =
new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(metaFile, false));
writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n");
writer.print(
"genetic_alteration_type: " + datatypeMetadata.getMetaGeneticAlterationType() + "\n");
String stableID = datatypeMetadata.getMetaStableID();
stableID =
stableID.replaceAll(DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString());
writer.print("stable_id: " + stableID + "\n");
writer.print(
"show_profile_in_analysis_tab: "
+ datatypeMetadata.getMetaShowProfileInAnalysisTab()
+ "\n");
String profileDescription = datatypeMetadata.getMetaProfileDescription();
if (dataMatrix != null) {
profileDescription =
profileDescription.replaceAll(
DatatypeMetadata.NUM_GENES_TAG, Integer.toString(dataMatrix.getGeneIDs().size()));
profileDescription =
profileDescription.replaceAll(
DatatypeMetadata.NUM_CASES_TAG, Integer.toString(dataMatrix.getCaseIDs().size()));
}
profileDescription =
profileDescription.replaceAll(
DatatypeMetadata.TUMOR_TYPE_TAG, cancerStudyMetadata.getTumorType());
writer.print("profile_description: " + profileDescription + "\n");
writer.print("profile_name: " + datatypeMetadata.getMetaProfileName() + "\n");
writer.flush();
writer.close();
}
