/** * 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 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(); }
/** * 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); } }
/** * 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(); }
/** * Create a case list file from the given case list metadata file. * * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param caseListMetadata CaseListMetadata * @param caseList String[] * @throws Exception */ @Override public void writeCaseListFile( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, CaseListMetadata caseListMetadata, String[] caseList) throws Exception { File caseListFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), "case_lists", caseListMetadata.getCaseListFilename()); if (LOG.isInfoEnabled()) { LOG.info("writeCaseListFile(), case list file: " + caseListFile.getCanonicalPath()); } PrintWriter writer = new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(caseListFile, false)); writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n"); String stableID = caseListMetadata.getMetaStableID(); stableID = stableID.replaceAll(DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString()); writer.print("stable_id: " + stableID + "\n"); writer.print("case_list_name: " + caseListMetadata.getMetaCaseListName() + "\n"); String caseListDescription = caseListMetadata.getMetaCaseListDescription(); caseListDescription = caseListDescription.replaceAll( DatatypeMetadata.NUM_CASES_TAG, Integer.toString(caseList.length)); writer.print("case_list_description: " + caseListDescription + "\n"); writer.print("case_list_category: " + caseListMetadata.getMetaCaseListCategory() + "\n"); writer.print("case_list_ids: "); for (String caseID : caseList) { writer.print(caseID + Converter.VALUE_DELIMITER); } writer.println(); writer.flush(); writer.close(); }
/** * If it exists, moves an override file into the proper location in the given portals staging area * * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param overrideFilename String * @param stagingFilename String * @throws Exception */ @Override public void applyOverride( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, String overrideFilename, String stagingFilename) throws Exception { // check for override file File overrideFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getOverrideDirectory(), cancerStudyMetadata.getStudyPath(), overrideFilename); if (overrideFile.exists()) { File stagingFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), stagingFilename); if (LOG.isInfoEnabled()) { LOG.info( "applyOverride(), override file exists for " + stagingFile.getCanonicalPath() + ": " + overrideFile.getCanonicalPath()); } // copy override file to staging area if (overrideFile.isFile()) { org.apache.commons.io.FileUtils.copyFile(overrideFile, stagingFile); } else { org.apache.commons.io.FileUtils.copyDirectory(overrideFile, stagingFile); } } }
/** * Creates a z-score staging file from the given dependencies. It assumes that the dependency - * staging files have already been created. This code also assumes that the dependencies are * ordered by cna, then expression. * * @param portalMetadata PortalMetadata * @param cancerStudy CancerStudyMetadata * @param datatypeMetadata DatatypeMetadata * @param dependencies DatatypeMetadata[] * @throws Exception */ @Override public void writeZScoresStagingFile( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, DatatypeMetadata datatypeMetadata, DatatypeMetadata[] dependencies) throws Exception { // sanity check if (dependencies.length != 2) { throw new IllegalArgumentException( "writeZScoresStagingFile(), datatypeMetadatas.length != 2, aborting..."); } // check for existence of dependencies if (LOG.isInfoEnabled()) { LOG.info( "writeZScoresStagingFile(), checking for existence of dependencies: " + Arrays.asList(dependencies)); } File cnaFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), dependencies[0].getStagingFilename()); if (!cnaFile.exists()) { if (LOG.isInfoEnabled()) { LOG.info( "writeZScoresStagingFile(), cannot find cna file dependency: " + cnaFile.getCanonicalPath()); } return; } File expressionFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), dependencies[1].getStagingFilename()); if (!expressionFile.exists()) { if (LOG.isInfoEnabled()) { LOG.info( "writeZScoresStagingFile(), cannot find expression file dependency: " + expressionFile.getCanonicalPath()); } return; } // we need a zscore file File zScoresFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), datatypeMetadata.getStagingFilename()); // call NormalizeExpressionLevels String[] args = { cnaFile.getCanonicalPath(), expressionFile.getCanonicalPath(), zScoresFile.getCanonicalPath() }; if (LOG.isInfoEnabled()) { LOG.info( "writingZScoresStagingFlie(), calling NormalizeExpressionLevels: " + Arrays.toString(args)); } try { NormalizeExpressionLevels.driver(args); } catch (RuntimeException e) { // houston we have a problem... if (LOG.isInfoEnabled()) { LOG.info( "writingZScoresStagingFlie(), exception thrown by NormalizeExpressionLevels: " + e.getMessage() + ", aborting..."); } if (zScoresFile.exists()) { org.apache.commons.io.FileUtils.forceDelete(zScoresFile); } return; } // meta file if (datatypeMetadata.requiresMetafile()) { if (LOG.isInfoEnabled()) { LOG.info( "writingZScoresStagingFile(), creating metadata file for staging file: " + zScoresFile.getCanonicalPath()); } writeMetadataFile(portalMetadata, cancerStudyMetadata, datatypeMetadata, null); } }
/** * Get the case list from the staging file. * * @param caseIDs CaseIDs; * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param stagingFilename String * @return List<String> * @throws Exception */ @Override public List<String> getCaseListFromStagingFile( CaseIDs caseIDs, PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, String stagingFilename) throws Exception { if (LOG.isInfoEnabled()) { LOG.info("getCaseListFromStagingFile(): " + stagingFilename); } // we use set here HashSet<String> caseSet = new HashSet<String>(); // staging file File stagingFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), stagingFilename); // sanity check if (!stagingFile.exists()) { return new ArrayList<String>(); } // iterate over all rows in file org.apache.commons.io.LineIterator it = org.apache.commons.io.FileUtils.lineIterator(stagingFile); try { int mafCaseIDColumnIndex = 0; boolean processHeader = true; while (it.hasNext()) { // create a string list from row in file List<String> thisRow = Arrays.asList(it.nextLine().split(Converter.VALUE_DELIMITER)); // is this the header file? if (processHeader) { // look for MAF file case id column header mafCaseIDColumnIndex = thisRow.indexOf(Converter.MUTATION_CASE_ID_COLUMN_HEADER); // this is not a MAF file, header contains the case ids, return here if (mafCaseIDColumnIndex == -1) { for (String potentialCaseID : thisRow) { if (caseIDs.isTumorCaseID(potentialCaseID)) { caseSet.add(caseIDs.convertCaseID(potentialCaseID)); } } break; } processHeader = false; continue; } // we want to add the value at mafCaseIDColumnIndex into return set - this is a case ID String potentialCaseID = thisRow.get(mafCaseIDColumnIndex); if (caseIDs.isTumorCaseID(potentialCaseID)) { caseSet.add(caseIDs.convertCaseID(potentialCaseID)); } } } finally { it.close(); } // outta here return new ArrayList<String>(caseSet); }