private List<String> getPatientIds(DataMatrix dataMatrix) {
List<LinkedList<String>> patientIds = dataMatrix.getColumnData(PATIENT_ID);
if (patientIds.isEmpty()) {
patientIds = dataMatrix.getColumnData(FOLLOW_UP_PATIENT_ID);
}
return (patientIds.isEmpty())
? Collections.<String>emptyList()
: convertFollowupPatientIds(patientIds.get(0));
}
/**
* Creates a staging file with contents from the given DataMatrix.
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param datatypeMetadata DatatypeMetadata
* @param dataMatrix DataMatrix
* @throws Exception
*/
@Override
public void writeStagingFile(
PortalMetadata portalMetadata,
CancerStudyMetadata cancerStudyMetadata,
DatatypeMetadata datatypeMetadata,
DataMatrix dataMatrix)
throws Exception {
// staging file
String stagingFilename = datatypeMetadata.getStagingFilename();
stagingFilename =
stagingFilename.replaceAll(
DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString());
File stagingFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
stagingFilename);
if (LOG.isInfoEnabled()) {
LOG.info("writingStagingFile(), staging file: " + stagingFile);
}
FileOutputStream out = org.apache.commons.io.FileUtils.openOutputStream(stagingFile, false);
dataMatrix.write(out);
IOUtils.closeQuietly(out);
// meta file
if (datatypeMetadata.requiresMetafile()) {
if (LOG.isInfoEnabled()) {
LOG.info("writingStagingFile(), creating metadata file for staging file: " + stagingFile);
}
writeMetadataFile(portalMetadata, cancerStudyMetadata, datatypeMetadata, dataMatrix);
}
}
/**
* 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();
}
private String getValue(int index, String columnName, DataMatrix dataMatrix) {
List<LinkedList<String>> columnData = dataMatrix.getColumnData(columnName);
String value = MissingAttributeValues.getNotAvailable();
if (!columnData.isEmpty()) {
value = columnData.get(0).get(index);
}
return (value.isEmpty()) ? MissingAttributeValues.getNotAvailable() : value;
}
/**
* Creates a staging file for mutation data (and meta file) with contents from the given
* DataMatrix. This is called when the mutation file needs to be run through the Oncotator and
* Mutation Assessor Tools.
*
* @param portalMetadata PortalMetadata
* @param cancerStudy CancerStudyMetadata
* @param datatypeMetadata DatatypeMetadata
* @param dataMatrix DataMatrix
* @throws Exception
*/
@Override
public void writeMutationStagingFile(
PortalMetadata portalMetadata,
CancerStudyMetadata cancerStudyMetadata,
DatatypeMetadata datatypeMetadata,
DataMatrix dataMatrix)
throws Exception {
// we only have data matrix at this point, we need to create a temp with its contents
File oncotatorInputFile =
org.apache.commons.io.FileUtils.getFile(
org.apache.commons.io.FileUtils.getTempDirectory(), "oncotatorInputFile");
FileOutputStream out = org.apache.commons.io.FileUtils.openOutputStream(oncotatorInputFile);
dataMatrix.write(out);
IOUtils.closeQuietly(out);
// output should be the path/name of staging file
String stagingFilename = datatypeMetadata.getStagingFilename();
stagingFilename =
stagingFilename.replaceAll(
DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString());
File stagingFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
stagingFilename);
// call oncotateAF
oncotateMAF(
FileUtils.FILE_URL_PREFIX + oncotatorInputFile.getCanonicalPath(),
FileUtils.FILE_URL_PREFIX + stagingFile.getCanonicalPath());
// clean up
if (oncotatorInputFile.exists()) {
org.apache.commons.io.FileUtils.forceDelete(oncotatorInputFile);
}
// meta file
if (datatypeMetadata.requiresMetafile()) {
if (LOG.isInfoEnabled()) {
LOG.info(
"writingMutationStagingFile(), creating metadata file for staging file: "
+ stagingFile);
}
writeMetadataFile(portalMetadata, cancerStudyMetadata, datatypeMetadata, dataMatrix);
}
}
