diff --git a/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java b/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java index ce5132ec121..c005d7a8d1c 100644 --- a/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java +++ b/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java @@ -32,10 +32,6 @@ package org.mskcc.cbio.maf; -import static org.mskcc.cbio.maf.ValueTypeUtil.isDouble; -import static org.mskcc.cbio.maf.ValueTypeUtil.isFloat; -import static org.mskcc.cbio.maf.ValueTypeUtil.isInt; - import java.util.*; import java.util.regex.Pattern; @@ -49,8 +45,6 @@ */ public class MafUtil { private static final Pattern validNucleotidesPattern = Pattern.compile("^([ATGC]*)$"); - public static final String NAMESPACE_DELIMITER = "."; - public static final String NAMESPACE_DELIMITER_REGEX = "\\."; // standard header column names public static final String HUGO_SYMBOL = "Hugo_Symbol"; public static final String ENTREZ_GENE_ID = "Entrez_Gene_Id"; @@ -215,7 +209,7 @@ public class MafUtil { // mapping for all column names (both standard and custom columns) private HashMap columnIndexMap; - private Map> namespaceIndexMap; + private final NamespaceColumnParser namespaceColumnParser; public MafUtil(String headerLine) { this(headerLine, null); @@ -226,9 +220,9 @@ public MafUtil(String headerLine) { * @param headerLine Header Line. */ public MafUtil(String headerLine, Set namespaces) { + // init column index map this.columnIndexMap = new HashMap(); - this.namespaceIndexMap = new HashMap>(); // split header names String parts[] = headerLine.split("\t"); @@ -374,26 +368,10 @@ public MafUtil(String headerLine, Set namespaces) { driverTiersIndex = i; } else if(header.equalsIgnoreCase(DRIVER_TIERS_FILTER_ANNOTATION)) { driverTiersAnnIndex = i; - } else if (namespaces != null && !namespaces.isEmpty()) { - int columnIndex = i; - namespaces.stream() - // Perform a case-insensitive match of namespace in meta file with the column name. - .filter(namespace -> header.toLowerCase().startsWith(namespace.toLowerCase( - Locale.ROOT) + NAMESPACE_DELIMITER)) - .findFirst() - .ifPresent(namespace -> { - String columnName = header.split(NAMESPACE_DELIMITER_REGEX)[1]; - // For legacy reasons perform lower-case transformation for ASCN column names. - if (namespace.equalsIgnoreCase("ascn")) { - columnName = columnName.toLowerCase(); - } - // Key the namespaces with the format (upper-/lowercase) specified in the meta file. - Map nsKeyIndexMap = this.namespaceIndexMap.getOrDefault(namespace, new HashMap<>()); - nsKeyIndexMap.put(columnName, columnIndex); - this.namespaceIndexMap.put(namespace, nsKeyIndexMap); - }); } } + + this.namespaceColumnParser = new NamespaceColumnParser(namespaces, parts); } public MafRecord parseRecord(String line) { @@ -485,30 +463,15 @@ public MafRecord parseRecord(String line) { fixEndPointForInsertion(record); - // extract namespace key-value pairs for json annotation support - Map> recordNamespaceAnnotationJsonMap = new HashMap<>(); - if (!namespaceIndexMap.isEmpty()) { - for (Map.Entry> nsKeyIndexMap : namespaceIndexMap.entrySet()) { - String namespace = nsKeyIndexMap.getKey(); - // construct map of the key-value pairs from the record - Map namespaceKeyValueMappings = new HashMap<>(); - for (Map.Entry nsKeyIndexPairs : nsKeyIndexMap.getValue().entrySet()) { - String keyName = nsKeyIndexPairs.getKey(); - Integer keyIndex = nsKeyIndexPairs.getValue(); - String stringValue = TabDelimitedFileUtil.getPartStringAllowEmptyAndNA(keyIndex, parts); - namespaceKeyValueMappings.put(keyName, parseNamespaceValue(stringValue)); - } - // update namespace map with the key-value pairs extracted from record - recordNamespaceAnnotationJsonMap.put(namespace, namespaceKeyValueMappings); - } - record.setNamespacesMap(recordNamespaceAnnotationJsonMap); - } + record.setNamespacesMap( + this.namespaceColumnParser.parseCustomNamespaces(parts) + ); return record; } public Map> getNamespaceIndexMap() { - return namespaceIndexMap; + return this.namespaceColumnParser.getNamespaceColumnIndexMap(); } private void fixEndPointForInsertion(MafRecord record) { @@ -845,17 +808,5 @@ public static boolean variantContainsAmbiguousTumorSeqAllele(String referenceAll (validNucleotidesPattern.matcher(tumorSeqAllele1.toUpperCase()).matches() || validNucleotidesPattern.matcher(tumorSeqAllele2.toUpperCase()).matches())); } - private static Object parseNamespaceValue(String stringValue) { - if (stringValue == null || stringValue.isEmpty()) { - return null; - } else if (isInt(stringValue)) { - return Integer.parseInt(stringValue); - } else if (isFloat(stringValue)) { - return Float.parseFloat(stringValue); - } else if (isDouble(stringValue)) { - return Double.parseDouble(stringValue); - } - return stringValue; - } - } + diff --git a/core/src/main/java/org/mskcc/cbio/maf/NamespaceColumnParser.java b/core/src/main/java/org/mskcc/cbio/maf/NamespaceColumnParser.java new file mode 100644 index 00000000000..10446588014 --- /dev/null +++ b/core/src/main/java/org/mskcc/cbio/maf/NamespaceColumnParser.java @@ -0,0 +1,97 @@ +package org.mskcc.cbio.maf; + +import com.fasterxml.jackson.databind.*; +import org.mskcc.cbio.maf.*; + +import java.io.*; +import java.util.*; + +import static org.mskcc.cbio.maf.ValueTypeUtil.isDouble; +import static org.mskcc.cbio.maf.ValueTypeUtil.isFloat; +import static org.mskcc.cbio.maf.ValueTypeUtil.isInt; + +public class NamespaceColumnParser { + + public static final String NAMESPACE_DELIMITER = "."; + public static final String NAMESPACE_DELIMITER_REGEX = "\\."; + + private Map> namespaceIndexMap; + private ObjectMapper mapper; + + public NamespaceColumnParser(Set namespaces, String[] parts) { + this.namespaceIndexMap = new HashMap<>(); + this.mapper = new ObjectMapper(); + findNamespaceHeaders(namespaces, parts); + } + + public Map> getNamespaceColumnIndexMap() { + return namespaceIndexMap; + } + + private void findNamespaceHeaders( + Set namespaces, + String[] parts + ) { + // find required header indices + for (int i = 0; i < parts.length; i++) { + String header = parts[i]; + if (namespaces == null || namespaces.isEmpty()) { + continue; + } + int columnIndex = i; + namespaces + .stream() + // Perform a case-insensitive match of namespace in meta file with the column name. + .filter(namespace -> header.toLowerCase().startsWith(namespace.toLowerCase( + Locale.ROOT) + NAMESPACE_DELIMITER)) + .findFirst() + .ifPresent(namespace -> { + String columnName = header.split(NAMESPACE_DELIMITER_REGEX)[1]; + // For legacy reasons perform lower-case transformation for ASCN column names. + if (namespace.equalsIgnoreCase("ascn")) { + columnName = columnName.toLowerCase(); + } + // Key the namespaces with the format (upper-/lowercase) specified in the meta file. + Map nsKeyIndexMap = this.namespaceIndexMap.getOrDefault(namespace, new HashMap<>()); + nsKeyIndexMap.put(columnName, columnIndex); + this.namespaceIndexMap.put(namespace, nsKeyIndexMap); + }); + } + } + + public Map> parseCustomNamespaces(String[] parts) { + // extract namespace key-value pairs for json annotation support + Map> recordNamespaceAnnotationJsonMap = new HashMap<>(); + if (this.namespaceIndexMap.isEmpty()) { + return recordNamespaceAnnotationJsonMap; + } + for (Map.Entry> nsKeyIndexMap : namespaceIndexMap.entrySet()) { + String namespace = nsKeyIndexMap.getKey(); + // construct map of the key-value pairs from the record + Map namespaceKeyValueMappings = new HashMap<>(); + for (Map.Entry nsKeyIndexPairs : nsKeyIndexMap.getValue().entrySet()) { + String keyName = nsKeyIndexPairs.getKey(); + Integer keyIndex = nsKeyIndexPairs.getValue(); + String stringValue = TabDelimitedFileUtil.getPartStringAllowEmptyAndNA(keyIndex, parts); + namespaceKeyValueMappings.put(keyName, parseNamespaceValue(stringValue)); + } + // update namespace map with the key-value pairs extracted from record + recordNamespaceAnnotationJsonMap.put(namespace, namespaceKeyValueMappings); + } + return recordNamespaceAnnotationJsonMap; + } + + public static Object parseNamespaceValue(String stringValue) { + if (stringValue == null || stringValue.isEmpty()) { + return null; + } else if (isInt(stringValue)) { + return Integer.parseInt(stringValue); + } else if (isFloat(stringValue)) { + return Float.parseFloat(stringValue); + } else if (isDouble(stringValue)) { + return Double.parseDouble(stringValue); + } + return stringValue; + } + +} diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCnaEvent.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCnaEvent.java index 6a7ab06ae9c..e7785d4f6c6 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCnaEvent.java +++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCnaEvent.java @@ -61,8 +61,9 @@ public static void addCaseCnaEvent(CnaEvent cnaEvent, boolean newCnaEvent) throw MySQLbulkLoader.getMySQLbulkLoader("sample_cna_event").insertRecord( Long.toString(eventId), Integer.toString(cnaEvent.getSampleId()), - Integer.toString(cnaEvent.getCnaProfileId()) - ); + Integer.toString(cnaEvent.getCnaProfileId()), + cnaEvent.getAnnotationJson() + ); if ((cnaEvent.getDriverFilter() != null && !cnaEvent.getDriverFilter().isEmpty() @@ -72,17 +73,17 @@ public static void addCaseCnaEvent(CnaEvent cnaEvent, boolean newCnaEvent) throw && !cnaEvent.getDriverTiersFilter().isEmpty() && !cnaEvent.getDriverTiersFilter().toLowerCase().equals("na")) ) { - MySQLbulkLoader - .getMySQLbulkLoader("alteration_driver_annotation") - .insertRecord( - Long.toString(eventId), - Integer.toString(cnaEvent.getCnaProfileId()), - Integer.toString(cnaEvent.getSampleId()), - cnaEvent.getDriverFilter(), - cnaEvent.getDriverFilterAnnotation(), - cnaEvent.getDriverTiersFilter(), - cnaEvent.getDriverTiersFilterAnnotation() - ); + MySQLbulkLoader + .getMySQLbulkLoader("alteration_driver_annotation") + .insertRecord( + Long.toString(eventId), + Integer.toString(cnaEvent.getCnaProfileId()), + Integer.toString(cnaEvent.getSampleId()), + cnaEvent.getDriverFilter(), + cnaEvent.getDriverFilterAnnotation(), + cnaEvent.getDriverTiersFilter(), + cnaEvent.getDriverTiersFilterAnnotation() + ); } } } diff --git a/core/src/main/java/org/mskcc/cbio/portal/model/CnaEvent.java b/core/src/main/java/org/mskcc/cbio/portal/model/CnaEvent.java index 2dc35b96335..5192d031982 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/model/CnaEvent.java +++ b/core/src/main/java/org/mskcc/cbio/portal/model/CnaEvent.java @@ -47,7 +47,8 @@ public class CnaEvent { private String driverFilterAnnotation; private String driverTiersFilter; private String driverTiersFilterAnnotation; - + private String annotationJson; + public static class Event { private long eventId; private CanonicalGene gene; @@ -221,6 +222,14 @@ public String getDriverTiersFilterAnnotation() { public void setDriverTiersFilterAnnotation(String driverTiersFilterAnnotation) { this.driverTiersFilterAnnotation = driverTiersFilterAnnotation; } + + public String getAnnotationJson() { + return annotationJson; + } + + public void setAnnotationJson(String annotationJson) { + this.annotationJson = annotationJson; + } @Override public int hashCode() { diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java index 7f3483c661a..005d071ad67 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java @@ -47,7 +47,8 @@ public class ImportCnaDiscreteLongData { private CnaUtil cnaUtil; private Set existingCnaEvents = new HashSet<>(); private int samplesSkipped = 0; - + private Set namespaces; + private final ArrayList sampleIdGeneticProfileIds = new ArrayList<>(); public ImportCnaDiscreteLongData( @@ -55,8 +56,10 @@ public ImportCnaDiscreteLongData( int geneticProfileId, String genePanel, DaoGeneOptimized daoGene, - DaoGeneticAlteration daoGeneticAlteration + DaoGeneticAlteration daoGeneticAlteration, + Set namespaces ) { + this.namespaces = namespaces; this.cnaFile = cnaFile; this.geneticProfileId = geneticProfileId; this.genePanel = genePanel; @@ -71,7 +74,8 @@ public void importData() throws Exception { // Pass first line with headers to util: String line = buf.readLine(); int lineIndex = 1; - this.cnaUtil = new CnaUtil(line); + String[] headerParts = line.split("\t", -1); + this.cnaUtil = new CnaUtil(headerParts, this.namespaces); GeneticProfile geneticProfile = DaoGeneticProfile.getGeneticProfileById(geneticProfileId); @@ -147,6 +151,8 @@ public void extractDataToImport( long entrezId = gene.getEntrezGeneId(); int sampleId = sample.getInternalId(); CnaEventImportData eventContainer = new CnaEventImportData(); + eventContainer.cnaEvent = cnaUtil.createEvent(geneticProfile, sample.getInternalId(), lineParts); + Table geneBySampleEventTable = importContainer.eventsTable; if (!geneBySampleEventTable.contains(entrezId, sample.getInternalId())) { @@ -155,7 +161,6 @@ public void extractDataToImport( ProgressMonitor.logWarning(format("Skipping line %d with duplicate gene %d and sample %d", lineIndex, entrezId, sampleId)); } - eventContainer.geneticEvent = cnaUtil.createEvent(geneticProfile, sample.getInternalId(), lineParts); } /** @@ -166,8 +171,8 @@ private void storeCnaEvents(CnaImportData toImport, Long entrezId) throws DaoExc .row(entrezId) .values() .stream() - .filter(v -> v.geneticEvent != null) - .map(v -> v.geneticEvent) + .filter(v -> v.cnaEvent != null) + .map(v -> v.cnaEvent) .collect(Collectors.toList()); CnaUtil.storeCnaEvents(existingCnaEvents, events); } @@ -180,9 +185,9 @@ private boolean storeGeneticAlterations(CnaImportData toImport, Long entrezId) t .row(entrezId) .values() .stream() - .filter(v -> v.geneticEvent != null) + .filter(v -> v.cnaEvent != null) .map(v -> "" + v - .geneticEvent + .cnaEvent .getAlteration() .getCode() ) @@ -324,7 +329,7 @@ private class CnaImportData { private class CnaEventImportData { public int line; - public CnaEvent geneticEvent; + public CnaEvent cnaEvent; public String geneSymbol; } diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java index 0fb58ee380a..c9208e7500b 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java @@ -133,12 +133,14 @@ public void run() { geneticProfile.getGeneticAlterationType() == GeneticAlterationType.COPY_NUMBER_ALTERATION && DISCRETE_LONG.name().equals(geneticProfile.getDatatype()) ) { + Set namespaces = GeneticProfileReader.getNamespaces(descriptorFile); ImportCnaDiscreteLongData importer = new ImportCnaDiscreteLongData( dataFile, geneticProfile.getGeneticProfileId(), genePanel, daoGene, - daoGeneticAlteration + daoGeneticAlteration, + namespaces ); importer.importData(); } else { diff --git a/core/src/main/java/org/mskcc/cbio/portal/util/CnaUtil.java b/core/src/main/java/org/mskcc/cbio/portal/util/CnaUtil.java index f69178e304c..5114772d646 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/util/CnaUtil.java +++ b/core/src/main/java/org/mskcc/cbio/portal/util/CnaUtil.java @@ -1,11 +1,15 @@ package org.mskcc.cbio.portal.util; +import com.fasterxml.jackson.core.*; import org.cbioportal.model.*; +import org.mskcc.cbio.maf.NamespaceColumnParser; import org.mskcc.cbio.maf.TabDelimitedFileUtil; import org.mskcc.cbio.portal.dao.*; import org.mskcc.cbio.portal.model.CnaEvent; import org.mskcc.cbio.portal.model.GeneticProfile; +import com.fasterxml.jackson.databind.ObjectMapper; +import java.io.*; import java.util.*; import static org.mskcc.cbio.portal.scripts.ImportTabDelimData.*; @@ -22,6 +26,25 @@ public class CnaUtil { public static final String CBP_DRIVER_ANNOTATION = "cbp_driver_annotation"; public static final String CBP_DRIVER_TIERS = "cbp_driver_tiers"; + public static final String CBP_DRIVER_TIERS_ANNOTATION = "cbp_driver_tiers_annotation"; + private NamespaceColumnParser namespaceColumnParser; + private ObjectMapper objectMapper = new ObjectMapper(); + + public CnaUtil(String[] headerParts, Set namespaces) { + this.columnIndexMap = new HashMap<>(); + + // Find header indices + for (int i = 0; i < headerParts.length; i++) { + // Put the index in the map + this.columnIndexMap.put(headerParts[i].toLowerCase(), i); + } + + if (getColumnIndex(HUGO_SYMBOL) == -1 && getColumnIndex(ENTREZ_GENE_ID) == -1) { + throw new RuntimeException("Error: at least one of the following columns should be present: Hugo_Symbol or Entrez_Gene_Id"); + } + this.namespaceColumnParser = new NamespaceColumnParser(namespaces, headerParts); + } + public static void storeCnaEvents( Set existingCnaEvents, List cnaEventsToAdd @@ -44,24 +67,11 @@ public static void storeCnaEvents( } } - public static final String CBP_DRIVER_TIERS_ANNOTATION = "cbp_driver_tiers_annotation"; - - public CnaUtil(String headerRow) { - this.columnIndexMap = new HashMap<>(); - String[] headerParts = headerRow.trim().split("\t"); - - // Find header indices - for (int i = 0; i < headerParts.length; i++) { - // Put the index in the map - this.columnIndexMap.put(headerParts[i].toLowerCase(), i); - } - - if (getColumnIndex(HUGO_SYMBOL) == -1 && getColumnIndex(ENTREZ_GENE_ID) == -1) { - throw new RuntimeException("Error: at least one of the following columns should be present: Hugo_Symbol or Entrez_Gene_Id"); - } - } - - public CnaEvent createEvent(GeneticProfile geneticProfile, int sampleId, String[] parts) { + public CnaEvent createEvent( + GeneticProfile geneticProfile, + int sampleId, + String[] parts + ) throws IOException { int cnaProfileId = geneticProfile.getGeneticProfileId(); long entrezGeneId = getEntrezSymbol(parts); short alteration = createAlteration(parts); @@ -70,9 +80,18 @@ public CnaEvent createEvent(GeneticProfile geneticProfile, int sampleId, String[ cna.setDriverFilterAnnotation(TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.CBP_DRIVER_ANNOTATION), parts)); cna.setDriverTiersFilter(TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.CBP_DRIVER_TIERS), parts)); cna.setDriverTiersFilterAnnotation(TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.CBP_DRIVER_TIERS_ANNOTATION), parts)); + cna.setAnnotationJson( + convertMapToJsonString( + this.namespaceColumnParser.parseCustomNamespaces(parts) + ) + ); return cna; } - + + private String convertMapToJsonString(Map> map) throws JsonProcessingException { + return this.objectMapper.writeValueAsString(map); + } + public long getEntrezSymbol(String[] parts) { String entrezAsString = TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.ENTREZ_GENE_ID), parts); if (entrezAsString.isEmpty()) { @@ -98,12 +117,14 @@ private short createAlteration(String[] parts) { return Integer.valueOf(result).shortValue(); } + /** + * @return column index, or -1 when not found + */ public int getColumnIndex(String colName) { - Integer index = this.columnIndexMap.get(colName.toLowerCase()); - if (index == null) { - index = -1; - } - return index; + return this.columnIndexMap.getOrDefault( + colName.toLowerCase(), + -1 + ); } public String getSampleIdStr(String[] parts) { diff --git a/core/src/main/scripts/importer/cbioportalImporter.py b/core/src/main/scripts/importer/cbioportalImporter.py index 4a7c4cd2a47..a40e9dc4525 100755 --- a/core/src/main/scripts/importer/cbioportalImporter.py +++ b/core/src/main/scripts/importer/cbioportalImporter.py @@ -102,7 +102,7 @@ def remove_study_id(jvm_args, study_id): run_java(*args) -def import_study_data(jvm_args, meta_filename, data_filename, update_generic_assay_entity, meta_file_dictionary = None): +def import_study_data(jvm_args, meta_filename, data_filename, update_generic_assay_entity = None, meta_file_dictionary = None): args = jvm_args.split(' ') # In case the meta file is already parsed in a previous function, it is not @@ -238,6 +238,7 @@ def process_directory(jvm_args, study_directory, update_generic_assay_entity = N gsva_score_filepair = None gsva_pvalue_filepair = None structural_variant_filepair = None + cna_long_filepair = None # Determine meta filenames in study directory meta_filenames = ( @@ -327,6 +328,9 @@ def process_directory(jvm_args, study_directory, update_generic_assay_entity = N elif meta_file_type == MetaFileTypes.STRUCTURAL_VARIANT: structural_variant_filepair = ( (meta_filename, os.path.join(study_directory, meta_dictionary['data_filename']))) + elif meta_file_type == MetaFileTypes.CNA_DISCRETE_LONG: + cna_long_filepair = ( + (meta_filename, os.path.join(study_directory, meta_dictionary['data_filename']))) # Add all other types of data else: regular_filepairs.append( @@ -372,6 +376,12 @@ def process_directory(jvm_args, study_directory, update_generic_assay_entity = N meta_filename, data_filename = structural_variant_filepair import_study_data(jvm_args, meta_filename, data_filename, update_generic_assay_entity, study_meta_dictionary[meta_filename]) + # Import cna data + if cna_long_filepair is not None: + meta_filename, data_filename = cna_long_filepair + import_study_data(jvm_args=jvm_args, meta_filename=meta_filename, data_filename=data_filename, + meta_file_dictionary=study_meta_dictionary[meta_filename]) + # Import expression z-score (after expression) for meta_filename, data_filename in zscore_filepairs: import_study_data(jvm_args, meta_filename, data_filename, update_generic_assay_entity, study_meta_dictionary[meta_filename]) diff --git a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java index d9ff9d49bef..3776787c645 100644 --- a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java +++ b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java @@ -27,10 +27,10 @@ package org.mskcc.cbio.portal.scripts; +import org.codehaus.jackson.map.*; import org.junit.After; import org.junit.Assert; import org.junit.Before; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; import org.mskcc.cbio.portal.dao.*; @@ -48,10 +48,10 @@ import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.ArrayList; -import java.util.List; +import java.util.*; import static com.google.common.collect.Lists.newArrayList; +import static com.google.common.collect.Sets.newHashSet; import static java.util.stream.Collectors.joining; import static java.util.stream.Collectors.toList; import static org.cbioportal.model.MolecularProfile.DataType.DISCRETE; @@ -67,6 +67,7 @@ public class TestImportCnaDiscreteLongData { int studyId; GeneticProfile geneticProfile; String genePanel = "TESTPANEL_CNA_DISCRETE_LONG_FORMAT"; + Set noNamespaces = new HashSet<>(); @Before public void setUp() throws DaoException { @@ -93,8 +94,8 @@ public void testImportCnaDiscreteLongDataAddsSamples() throws Exception { geneticProfile.getGeneticProfileId(), genePanel, DaoGeneOptimized.getInstance(), - DaoGeneticAlteration.getInstance() - ).importData(); + DaoGeneticAlteration.getInstance(), + noNamespaces).importData(); // Test new samples are added: List expectedSampleIds = newArrayList("TCGA-A1-A0SB-11", "TCGA-A2-A04U-11"); @@ -119,7 +120,8 @@ public void testImportCnaDiscreteLongDataAddsCnaEvents() throws Exception { geneticProfile.getGeneticProfileId(), genePanel, DaoGeneOptimized.getInstance(), - DaoGeneticAlteration.getInstance() + DaoGeneticAlteration.getInstance(), + noNamespaces ).importData(); List resultCnaEvents = DaoCnaEvent.getAllCnaEvents(); @@ -172,8 +174,8 @@ public void testImportCnaDiscreteLongDataAddsGeneticAlterations() throws Excepti geneticProfile.getGeneticProfileId(), genePanel, DaoGeneOptimized.getInstance(), - DaoGeneticAlteration.getInstance() - ).importData(); + DaoGeneticAlteration.getInstance(), + noNamespaces).importData(); // Test genetic alterations are added for all genes: List resultGeneticAlterations = getAllGeneticAlterations(); @@ -195,8 +197,8 @@ public void testImportCnaDiscreteLongDataAddsGeneticAlterationsAndProfileSamples geneticProfile.getGeneticProfileId(), genePanel, DaoGeneOptimized.getInstance(), - DaoGeneticAlteration.getInstance() - ).importData(); + DaoGeneticAlteration.getInstance(), + noNamespaces).importData(); // Test order of genetic alteration values: TestGeneticAlteration geneticAlteration = getGeneticAlterationBy(2115L); @@ -222,8 +224,8 @@ public void testImportCnaDiscreteLongDataAddsGeneticAlterationsFromNonCnaEvents( geneticProfile.getGeneticProfileId(), genePanel, DaoGeneOptimized.getInstance(), - DaoGeneticAlteration.getInstance() - ).importData(); + DaoGeneticAlteration.getInstance(), + noNamespaces).importData(); // Test genetic alteration are added of non-cna event: TestGeneticAlteration geneticAlteration = getGeneticAlterationBy(56914); @@ -247,8 +249,8 @@ public void testImportCnaDiscreteLongDataIgnoresLineWithDuplicateGene() throws E geneticProfile.getGeneticProfileId(), genePanel, DaoGeneOptimized.getInstance(), - DaoGeneticAlteration.getInstance() - ).importData(); + DaoGeneticAlteration.getInstance(), + noNamespaces).importData(); // Test genetic alteration are deduplicated: TestGeneticAlteration geneticAlteration = getGeneticAlterationBy(57670); @@ -269,7 +271,8 @@ public void testImportCnaDiscreteLongDataAddsPdAnnotations() throws Exception { geneticProfile.getGeneticProfileId(), genePanel, DaoGeneOptimized.getInstance(), - DaoGeneticAlteration.getInstance() + DaoGeneticAlteration.getInstance(), + noNamespaces ).importData(); List genes = newArrayList(3983L, 27334L, 2115L); List resultCnaEvents = DaoCnaEvent.getAllCnaEvents() @@ -298,13 +301,148 @@ public void testImportCnaDiscreteLongData_changesProfileDatatypeFromDiscreteLong geneticProfile.getGeneticProfileId(), genePanel, DaoGeneOptimized.getInstance(), - DaoGeneticAlteration.getInstance() + DaoGeneticAlteration.getInstance(), + noNamespaces ).importData(); String resultDatatype = getGeneticProfileDatatype(this.geneticProfile.getGeneticProfileId()); assertEquals(DISCRETE.name(), resultDatatype); } + + /** + * Test the import of cna data file in long format with: + * - two custom namespaces that should be imported + * - one unknown namespace that should be ignored + */ + @Test + public void testImportCnaDiscreteLongDataOnlyAddsSpecifiedCustomNamespaceColumns() throws Exception { + ObjectMapper mapper = new ObjectMapper(); + File file = new File("src/test/resources/data_cna_discrete_import_test_with_namespaces.txt"); + Set namespacesToImport = newHashSet("MyNamespace", "MyNamespace2"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance(), + namespacesToImport + ).importData(); + + // All namespace columns provided: + List results = getAnnotationJsonBy(geneticProfile.getGeneticProfileId()); + assertEquals(2, results.size()); + String resultAnnotationJson = results + .stream() + .filter(r -> r.entrezGeneId == 2115L) + .map(r -> r.annotationJson) + .findFirst().get(); + + // Namespace 'InvalidNamespace' should be ignored: + String expectedAnnotationJson = "{\"MyNamespace\": {\"column1\": \"MyValue1\", \"column2\": \"MyValue2\"}, \"MyNamespace2\": {\"blarp\": \"blorp\"}}"; + assertEquals( + mapper.readTree(results.get(0).annotationJson), + mapper.readTree(expectedAnnotationJson) + ); + assertEquals( + mapper.readTree(expectedAnnotationJson), + mapper.readTree(resultAnnotationJson) + ); + } + + /** + * Test the import of cna data file in long format with: + * - one row with both namespaces + * - one row with a missing namespace, imported as null + */ + @Test + public void testImportCnaDiscreteLongDataImportsMissingNamespacesAsNull() throws Exception { + ObjectMapper mapper = new ObjectMapper(); + File file = new File("src/test/resources/data_cna_discrete_import_test_with_namespaces.txt"); + Set namespacesToImport = newHashSet("MyNamespace", "MyNamespace2"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance(), + namespacesToImport + ).importData(); + + // All namespace columns provided: + List results = getAnnotationJsonBy(geneticProfile.getGeneticProfileId()); + assertEquals(2, results.size()); + String resultAnnotationJson = results + .stream() + .filter(r -> r.entrezGeneId == 2115L) + .map(r -> r.annotationJson) + .findFirst().get(); + String expectedAnnotationJson = "{\"MyNamespace\": {\"column1\": \"MyValue1\", \"column2\": \"MyValue2\"}, \"MyNamespace2\": {\"blarp\": \"blorp\"}}"; + assertEquals( + mapper.readTree(results.get(0).annotationJson), + mapper.readTree(expectedAnnotationJson) + ); + assertEquals( + mapper.readTree(expectedAnnotationJson), + mapper.readTree(resultAnnotationJson) + ); + + // Only one namespace column provided: + resultAnnotationJson = results + .stream() + .filter(r -> r.entrezGeneId == 27334L) + .map(r -> r.annotationJson) + .findFirst().get(); + expectedAnnotationJson = "{\"MyNamespace\": {\"column1\": null, \"column2\": null}, \"MyNamespace2\": {\"blarp\": \"bloerp\"}}"; + assertEquals( + mapper.readTree(expectedAnnotationJson), + mapper.readTree(resultAnnotationJson) + ); + } + + /** + * Test the import of cna data file in long format with: + * - two rows with the same gene and two different samples each with their own annotationJson + */ + @Test + public void testImportCnaDiscreteLongDataAddsCustomNamespaceColumnsForEachSample() throws Exception { + ObjectMapper mapper = new ObjectMapper(); + File file = new File("src/test/resources/data_cna_discrete_import_test_with_namespaces2.txt"); + Set namespaces = newHashSet("MyNamespace", "MyNamespace2"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance(), + namespaces + ).importData(); + + List results = getAnnotationJsonBy(geneticProfile.getGeneticProfileId()); + assertEquals(2, results.size()); + String expectedAnnotationJsonA1 = "{\"MyNamespace\": {\"column1\": \"v1a\", \"column2\": \"v2a\"}, \"MyNamespace2\": {\"blarp\": \"bloerp\"}}"; + String expectedAnnotationJsonA2 = "{\"MyNamespace\": {\"column1\": \"v1b\", \"column2\": \"v2b\"}, \"MyNamespace2\": {\"blarp\": \"bleurp\"}}"; + + String resultAnnotationJsonA1 = results + .stream() + .filter(r -> "TCGA-A1-A0SB-11".equals(r.stableId)) + .map(r -> r.annotationJson) + .findFirst().get(); + assertEquals( + mapper.readTree(expectedAnnotationJsonA1), + mapper.readTree(resultAnnotationJsonA1) + ); + String resultAnnotationJsonA2 = results + .stream() + .filter(r -> "TCGA-A2-A04U-11".equals(r.stableId)) + .map(r -> r.annotationJson) + .findFirst().get(); + assertEquals( + mapper.readTree(expectedAnnotationJsonA2), + mapper.readTree(resultAnnotationJsonA2) + ); + } + private List createPrimaryKeys(String sample, List cnaEvents) { return cnaEvents.stream().map(e -> { TestPdAnnotationPK pk = new TestPdAnnotationPK(); @@ -333,7 +471,7 @@ private void assertSampleExistsInGeneticProfile(String sampleId) throws DaoExcep } private String getGeneticProfileDatatype(long geneticProfileId) throws DaoException { - return query( + return runSelectQuery( "select DATATYPE " + "FROM genetic_profile " + "WHERE GENETIC_PROFILE_ID=" + geneticProfileId + " ;", @@ -341,6 +479,32 @@ private String getGeneticProfileDatatype(long geneticProfileId) throws DaoExcept ).get(0); } + class NamespaceAnnotationJson { + public int cnaEventId; + public int sampleId; + public int entrezGeneId; + public String stableId; + public String annotationJson; + } + + private List getAnnotationJsonBy(long geneticProfileId) throws DaoException { + return runSelectQuery( + "select cna_event.CNA_EVENT_ID, SAMPLE_ID, STABLE_ID, GENETIC_PROFILE_ID, ENTREZ_GENE_ID, ANNOTATION_JSON " + + "FROM sample_cna_event " + + "LEFT JOIN sample ON sample.INTERNAL_ID = sample_cna_event.SAMPLE_ID " + + "LEFT JOIN cna_event ON cna_event.CNA_EVENT_ID = sample_cna_event.CNA_EVENT_ID " + + "WHERE GENETIC_PROFILE_ID=" + geneticProfileId + " ;", + (ResultSet rs) -> { + NamespaceAnnotationJson result = new NamespaceAnnotationJson(); + result.cnaEventId = rs.getInt("CNA_EVENT_ID"); + result.sampleId = rs.getInt("SAMPLE_ID"); + result.stableId = rs.getString("STABLE_ID"); + result.entrezGeneId = rs.getInt("ENTREZ_GENE_ID"); + result.annotationJson = rs.getString("ANNOTATION_JSON"); + return result; + }); + } + private List getAllCnaPdAnnotations(List pks) throws DaoException { List pkStrings = new ArrayList<>(); for (TestPdAnnotationPK pk : pks) { @@ -349,8 +513,7 @@ private List getAllCnaPdAnnotations(List p pk.alterationEventId, pk.geneticProfileId, pk.sampleId )); } - - + String q = "SELECT DRIVER_TIERS_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_FILTER, " + "ALTERATION_EVENT_ID, GENETIC_PROFILE_ID, SAMPLE_ID " + "FROM alteration_driver_annotation "; @@ -358,7 +521,7 @@ private List getAllCnaPdAnnotations(List p q += "WHERE " + String.join(" OR ", pkStrings); } - return query( + return runSelectQuery( q, (ResultSet rs) -> { TestPdAnnotation line = new TestPdAnnotation(); @@ -377,7 +540,7 @@ private List getAllCnaPdAnnotations(List p } private List getAllGeneticAlterations() throws DaoException { - return query("SELECT * FROM genetic_alteration", (ResultSet rs) -> { + return runSelectQuery("SELECT * FROM genetic_alteration", (ResultSet rs) -> { TestGeneticAlteration line = new TestGeneticAlteration(); line.geneticProfileId = rs.getInt("GENETIC_PROFILE_ID"); line.geneticEntityId = rs.getInt("GENETIC_ENTITY_ID"); @@ -387,7 +550,7 @@ private List getAllGeneticAlterations() throws DaoExcepti } private TestGeneticAlteration getGeneticAlterationBy(long entrezId) throws DaoException { - return query("SELECT ga.GENETIC_PROFILE_ID, ga.GENETIC_ENTITY_ID, ga.VALUES, g.ENTREZ_GENE_ID " + + return runSelectQuery("SELECT ga.GENETIC_PROFILE_ID, ga.GENETIC_ENTITY_ID, ga.VALUES, g.ENTREZ_GENE_ID " + "FROM genetic_alteration AS ga " + "RIGHT JOIN gene AS g " + "ON g.GENETIC_ENTITY_ID = ga.GENETIC_ENTITY_ID " + @@ -403,7 +566,7 @@ private TestGeneticAlteration getGeneticAlterationBy(long entrezId) throws DaoEx } private TestGeneticProfileSample getGeneticProfileSample(long profileId) throws DaoException { - return query( + return runSelectQuery( "SELECT * FROM genetic_profile_samples WHERE GENETIC_PROFILE_ID=" + profileId, (ResultSet rs) -> { TestGeneticProfileSample line = new TestGeneticProfileSample(); @@ -413,7 +576,7 @@ private TestGeneticProfileSample getGeneticProfileSample(long profileId) throws }).get(0); } - private List query(String query, FunctionThrowsSql handler) throws DaoException { + private List runSelectQuery(String query, FunctionThrowsSql handler) throws DaoException { Connection con = null; PreparedStatement pstmt = null; ResultSet rs = null; diff --git a/core/src/test/resources/data_cna_discrete_import_test_with_namespaces.txt b/core/src/test/resources/data_cna_discrete_import_test_with_namespaces.txt new file mode 100644 index 00000000000..8fac01570e6 --- /dev/null +++ b/core/src/test/resources/data_cna_discrete_import_test_with_namespaces.txt @@ -0,0 +1,3 @@ +Hugo_Symbol Entrez_Gene_Id Sample_Id Value cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation MyNamespace.column1 MyNamespace.column2 MyNamespace2.blarp InvalidNamespace.column1 +ETV1 2115 TCGA-A1-A0SB-11 2 MyValue1 MyValue2 blorp InvalidValue +P2RY10 27334 TCGA-A1-A0SB-11 2 bloerp diff --git a/core/src/test/resources/data_cna_discrete_import_test_with_namespaces2.txt b/core/src/test/resources/data_cna_discrete_import_test_with_namespaces2.txt new file mode 100644 index 00000000000..47c8c8f4be3 --- /dev/null +++ b/core/src/test/resources/data_cna_discrete_import_test_with_namespaces2.txt @@ -0,0 +1,3 @@ +Hugo_Symbol Entrez_Gene_Id Sample_Id Value cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation MyNamespace.column1 MyNamespace.column2 MyNamespace2.blarp InvalidNamespace.column1 +P2RY10 27334 TCGA-A1-A0SB-11 2 v1a v2a bloerp +P2RY10 27334 TCGA-A2-A04U-11 2 v1b v2b bleurp diff --git a/core/src/test/scripts/test_data/study_es_0/data_cna_discrete.txt b/core/src/test/scripts/test_data/study_es_0/data_cna_discrete.txt index 741bc2143b3..a45f488a5e7 100644 --- a/core/src/test/scripts/test_data/study_es_0/data_cna_discrete.txt +++ b/core/src/test/scripts/test_data/study_es_0/data_cna_discrete.txt @@ -1,6305 +1,6305 @@ -Hugo_Symbol Entrez_Gene_Id Sample_Id Value cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation -ACAP3 116983 TCGA-A1-A0SB-01 0 -AGRN 375790 TCGA-A1-A0SB-01 0 -ATAD3A 55210 TCGA-A1-A0SB-01 0 -ATAD3B 83858 TCGA-A1-A0SB-01 0 -ATAD3C 219293 TCGA-A1-A0SB-01 0 -AURKAIP1 54998 TCGA-A1-A0SB-01 0 -ERCC5 2073 TCGA-A1-A0SB-01 0 -ACP3 55 TCGA-A1-A0SB-01 0 -ACAP3 116983 TCGA-A1-A0SD-01 -1 -AGRN 375790 TCGA-A1-A0SD-01 -1 -ATAD3A 55210 TCGA-A1-A0SD-01 -1 -ATAD3B 83858 TCGA-A1-A0SD-01 -1 -ATAD3C 219293 TCGA-A1-A0SD-01 -1 -AURKAIP1 54998 TCGA-A1-A0SD-01 -1 -ERCC5 2073 TCGA-A1-A0SD-01 -1 -ACP3 55 TCGA-A1-A0SD-01 0 -ACAP3 116983 TCGA-A1-A0SE-01 0 -AGRN 375790 TCGA-A1-A0SE-01 0 -ATAD3A 55210 TCGA-A1-A0SE-01 0 -ATAD3B 83858 TCGA-A1-A0SE-01 0 -ATAD3C 219293 TCGA-A1-A0SE-01 0 -AURKAIP1 54998 TCGA-A1-A0SE-01 0 -ERCC5 2073 TCGA-A1-A0SE-01 0 -ACP3 55 TCGA-A1-A0SE-01 0 -ACAP3 116983 TCGA-A1-A0SF-01 0 -AGRN 375790 TCGA-A1-A0SF-01 0 -ATAD3A 55210 TCGA-A1-A0SF-01 0 -ATAD3B 83858 TCGA-A1-A0SF-01 0 -ATAD3C 219293 TCGA-A1-A0SF-01 0 -AURKAIP1 54998 TCGA-A1-A0SF-01 0 -ERCC5 2073 TCGA-A1-A0SF-01 0 -ACP3 55 TCGA-A1-A0SF-01 0 -ACAP3 116983 TCGA-A1-A0SG-01 0 -AGRN 375790 TCGA-A1-A0SG-01 0 -ATAD3A 55210 TCGA-A1-A0SG-01 0 -ATAD3B 83858 TCGA-A1-A0SG-01 0 -ATAD3C 219293 TCGA-A1-A0SG-01 0 -AURKAIP1 54998 TCGA-A1-A0SG-01 0 -ERCC5 2073 TCGA-A1-A0SG-01 0 -ACP3 55 TCGA-A1-A0SG-01 0 -ACAP3 116983 TCGA-A1-A0SH-01 -1 -AGRN 375790 TCGA-A1-A0SH-01 -1 -ATAD3A 55210 TCGA-A1-A0SH-01 -1 -ATAD3B 83858 TCGA-A1-A0SH-01 -1 -ATAD3C 219293 TCGA-A1-A0SH-01 -1 -AURKAIP1 54998 TCGA-A1-A0SH-01 -1 -ERCC5 2073 TCGA-A1-A0SH-01 -1 -ACP3 55 TCGA-A1-A0SH-01 0 -ACAP3 116983 TCGA-A1-A0SI-01 0 -AGRN 375790 TCGA-A1-A0SI-01 0 -ATAD3A 55210 TCGA-A1-A0SI-01 0 -ATAD3B 83858 TCGA-A1-A0SI-01 0 -ATAD3C 219293 TCGA-A1-A0SI-01 0 -AURKAIP1 54998 TCGA-A1-A0SI-01 0 -ERCC5 2073 TCGA-A1-A0SI-01 0 -ACP3 55 TCGA-A1-A0SI-01 0 -ACAP3 116983 TCGA-A1-A0SJ-01 0 -AGRN 375790 TCGA-A1-A0SJ-01 0 -ATAD3A 55210 TCGA-A1-A0SJ-01 0 -ATAD3B 83858 TCGA-A1-A0SJ-01 0 -ATAD3C 219293 TCGA-A1-A0SJ-01 0 -AURKAIP1 54998 TCGA-A1-A0SJ-01 0 -ERCC5 2073 TCGA-A1-A0SJ-01 0 -ACP3 55 TCGA-A1-A0SJ-01 0 -ACAP3 116983 TCGA-A1-A0SK-01 0 -AGRN 375790 TCGA-A1-A0SK-01 0 -ATAD3A 55210 TCGA-A1-A0SK-01 0 -ATAD3B 83858 TCGA-A1-A0SK-01 0 -ATAD3C 219293 TCGA-A1-A0SK-01 0 -AURKAIP1 54998 TCGA-A1-A0SK-01 0 -ERCC5 2073 TCGA-A1-A0SK-01 0 -ACP3 55 TCGA-A1-A0SK-01 0 -ACAP3 116983 TCGA-A1-A0SM-01 -1 -AGRN 375790 TCGA-A1-A0SM-01 -1 -ATAD3A 55210 TCGA-A1-A0SM-01 -1 -ATAD3B 83858 TCGA-A1-A0SM-01 -1 -ATAD3C 219293 TCGA-A1-A0SM-01 -1 -AURKAIP1 54998 TCGA-A1-A0SM-01 -1 -ERCC5 2073 TCGA-A1-A0SM-01 -1 -ACP3 55 TCGA-A1-A0SM-01 0 -ACAP3 116983 TCGA-A1-A0SN-01 -1 -AGRN 375790 TCGA-A1-A0SN-01 -1 -ATAD3A 55210 TCGA-A1-A0SN-01 -1 -ATAD3B 83858 TCGA-A1-A0SN-01 -1 -ATAD3C 219293 TCGA-A1-A0SN-01 -1 -AURKAIP1 54998 TCGA-A1-A0SN-01 -1 -ERCC5 2073 TCGA-A1-A0SN-01 -1 -ACP3 55 TCGA-A1-A0SN-01 0 -ACAP3 116983 TCGA-A1-A0SO-01 -1 -AGRN 375790 TCGA-A1-A0SO-01 -1 -ATAD3A 55210 TCGA-A1-A0SO-01 -1 -ATAD3B 83858 TCGA-A1-A0SO-01 -1 -ATAD3C 219293 TCGA-A1-A0SO-01 -1 -AURKAIP1 54998 TCGA-A1-A0SO-01 -1 -ERCC5 2073 TCGA-A1-A0SO-01 -1 -ACP3 55 TCGA-A1-A0SO-01 0 -ACAP3 116983 TCGA-A1-A0SP-01 0 -AGRN 375790 TCGA-A1-A0SP-01 0 -ATAD3A 55210 TCGA-A1-A0SP-01 0 -ATAD3B 83858 TCGA-A1-A0SP-01 0 -ATAD3C 219293 TCGA-A1-A0SP-01 0 -AURKAIP1 54998 TCGA-A1-A0SP-01 0 -ERCC5 2073 TCGA-A1-A0SP-01 0 -ACP3 55 TCGA-A1-A0SP-01 0 -ACAP3 116983 TCGA-A1-A0SQ-01 0 -AGRN 375790 TCGA-A1-A0SQ-01 0 -ATAD3A 55210 TCGA-A1-A0SQ-01 0 -ATAD3B 83858 TCGA-A1-A0SQ-01 0 -ATAD3C 219293 TCGA-A1-A0SQ-01 0 -AURKAIP1 54998 TCGA-A1-A0SQ-01 0 -ERCC5 2073 TCGA-A1-A0SQ-01 0 -ACP3 55 TCGA-A1-A0SQ-01 0 -ACAP3 116983 TCGA-A2-A04N-01 0 -AGRN 375790 TCGA-A2-A04N-01 0 -ATAD3A 55210 TCGA-A2-A04N-01 0 -ATAD3B 83858 TCGA-A2-A04N-01 0 -ATAD3C 219293 TCGA-A2-A04N-01 0 -AURKAIP1 54998 TCGA-A2-A04N-01 0 -ERCC5 2073 TCGA-A2-A04N-01 0 -ACP3 55 TCGA-A2-A04N-01 0 -ACAP3 116983 TCGA-A2-A04P-01 0 -AGRN 375790 TCGA-A2-A04P-01 0 -ATAD3A 55210 TCGA-A2-A04P-01 0 -ATAD3B 83858 TCGA-A2-A04P-01 0 -ATAD3C 219293 TCGA-A2-A04P-01 0 -AURKAIP1 54998 TCGA-A2-A04P-01 0 -ERCC5 2073 TCGA-A2-A04P-01 0 -ACP3 55 TCGA-A2-A04P-01 0 -ACAP3 116983 TCGA-A2-A04Q-01 0 -AGRN 375790 TCGA-A2-A04Q-01 0 -ATAD3A 55210 TCGA-A2-A04Q-01 0 -ATAD3B 83858 TCGA-A2-A04Q-01 0 -ATAD3C 219293 TCGA-A2-A04Q-01 0 -AURKAIP1 54998 TCGA-A2-A04Q-01 0 -ERCC5 2073 TCGA-A2-A04Q-01 0 -ACP3 55 TCGA-A2-A04Q-01 0 -ACAP3 116983 TCGA-A2-A04R-01 -1 -AGRN 375790 TCGA-A2-A04R-01 -1 -ATAD3A 55210 TCGA-A2-A04R-01 -1 -ATAD3B 83858 TCGA-A2-A04R-01 -1 -ATAD3C 219293 TCGA-A2-A04R-01 -1 -AURKAIP1 54998 TCGA-A2-A04R-01 -1 -ERCC5 2073 TCGA-A2-A04R-01 -1 -ACP3 55 TCGA-A2-A04R-01 0 -ACAP3 116983 TCGA-A2-A04T-01 0 -AGRN 375790 TCGA-A2-A04T-01 0 -ATAD3A 55210 TCGA-A2-A04T-01 0 -ATAD3B 83858 TCGA-A2-A04T-01 0 -ATAD3C 219293 TCGA-A2-A04T-01 0 -AURKAIP1 54998 TCGA-A2-A04T-01 0 -ERCC5 2073 TCGA-A2-A04T-01 0 -ACP3 55 TCGA-A2-A04T-01 0 -ACAP3 116983 TCGA-A2-A04U-01 2 Putative_Passenger Test passenger Class 2 Class annotation -AGRN 375790 TCGA-A2-A04U-01 2 Putative_Driver Test driver Class 1 Class annotation -ATAD3A 55210 TCGA-A2-A04U-01 2 -ATAD3B 83858 TCGA-A2-A04U-01 2 -ATAD3C 219293 TCGA-A2-A04U-01 2 Putative_Passenger Test passenger -AURKAIP1 54998 TCGA-A2-A04U-01 2 -ERCC5 2073 TCGA-A2-A04U-01 2 Putative_Driver Test driver -ACP3 55 TCGA-A2-A04U-01 0 -ACAP3 116983 TCGA-A2-A04V-01 0 -AGRN 375790 TCGA-A2-A04V-01 0 -ATAD3A 55210 TCGA-A2-A04V-01 0 -ATAD3B 83858 TCGA-A2-A04V-01 0 -ATAD3C 219293 TCGA-A2-A04V-01 0 -AURKAIP1 54998 TCGA-A2-A04V-01 0 -ERCC5 2073 TCGA-A2-A04V-01 0 -ACP3 55 TCGA-A2-A04V-01 0 -ACAP3 116983 TCGA-A2-A04W-01 0 -AGRN 375790 TCGA-A2-A04W-01 0 -ATAD3A 55210 TCGA-A2-A04W-01 0 -ATAD3B 83858 TCGA-A2-A04W-01 0 -ATAD3C 219293 TCGA-A2-A04W-01 0 -AURKAIP1 54998 TCGA-A2-A04W-01 0 -ERCC5 2073 TCGA-A2-A04W-01 0 -ACP3 55 TCGA-A2-A04W-01 0 -ACAP3 116983 TCGA-A2-A04X-01 0 -AGRN 375790 TCGA-A2-A04X-01 0 -ATAD3A 55210 TCGA-A2-A04X-01 0 -ATAD3B 83858 TCGA-A2-A04X-01 0 -ATAD3C 219293 TCGA-A2-A04X-01 0 -AURKAIP1 54998 TCGA-A2-A04X-01 0 -ERCC5 2073 TCGA-A2-A04X-01 0 -ACP3 55 TCGA-A2-A04X-01 0 -ACAP3 116983 TCGA-A2-A04Y-01 1 -AGRN 375790 TCGA-A2-A04Y-01 1 -ATAD3A 55210 TCGA-A2-A04Y-01 1 -ATAD3B 83858 TCGA-A2-A04Y-01 1 -ATAD3C 219293 TCGA-A2-A04Y-01 1 -AURKAIP1 54998 TCGA-A2-A04Y-01 1 -ERCC5 2073 TCGA-A2-A04Y-01 1 -ACP3 55 TCGA-A2-A04Y-01 0 -ACAP3 116983 TCGA-A2-A0CL-01 0 -AGRN 375790 TCGA-A2-A0CL-01 0 -ATAD3A 55210 TCGA-A2-A0CL-01 0 -ATAD3B 83858 TCGA-A2-A0CL-01 0 -ATAD3C 219293 TCGA-A2-A0CL-01 0 -AURKAIP1 54998 TCGA-A2-A0CL-01 0 -ERCC5 2073 TCGA-A2-A0CL-01 0 -ACP3 55 TCGA-A2-A0CL-01 0 -ACAP3 116983 TCGA-A2-A0CM-01 0 -AGRN 375790 TCGA-A2-A0CM-01 0 -ATAD3A 55210 TCGA-A2-A0CM-01 0 -ATAD3B 83858 TCGA-A2-A0CM-01 0 -ATAD3C 219293 TCGA-A2-A0CM-01 0 -AURKAIP1 54998 TCGA-A2-A0CM-01 0 -ERCC5 2073 TCGA-A2-A0CM-01 0 -ACP3 55 TCGA-A2-A0CM-01 0 -ACAP3 116983 TCGA-A2-A0CP-01 0 -AGRN 375790 TCGA-A2-A0CP-01 0 -ATAD3A 55210 TCGA-A2-A0CP-01 0 -ATAD3B 83858 TCGA-A2-A0CP-01 0 -ATAD3C 219293 TCGA-A2-A0CP-01 0 -AURKAIP1 54998 TCGA-A2-A0CP-01 0 -ERCC5 2073 TCGA-A2-A0CP-01 0 -ACP3 55 TCGA-A2-A0CP-01 0 -ACAP3 116983 TCGA-A2-A0CQ-01 0 -AGRN 375790 TCGA-A2-A0CQ-01 0 -ATAD3A 55210 TCGA-A2-A0CQ-01 0 -ATAD3B 83858 TCGA-A2-A0CQ-01 0 -ATAD3C 219293 TCGA-A2-A0CQ-01 0 -AURKAIP1 54998 TCGA-A2-A0CQ-01 0 -ERCC5 2073 TCGA-A2-A0CQ-01 0 -ACP3 55 TCGA-A2-A0CQ-01 0 -ACAP3 116983 TCGA-A2-A0CS-01 -1 -AGRN 375790 TCGA-A2-A0CS-01 -1 -ATAD3A 55210 TCGA-A2-A0CS-01 -1 -ATAD3B 83858 TCGA-A2-A0CS-01 -1 -ATAD3C 219293 TCGA-A2-A0CS-01 -1 -AURKAIP1 54998 TCGA-A2-A0CS-01 -1 -ERCC5 2073 TCGA-A2-A0CS-01 -1 -ACP3 55 TCGA-A2-A0CS-01 0 -ACAP3 116983 TCGA-A2-A0CT-01 -1 -AGRN 375790 TCGA-A2-A0CT-01 -1 -ATAD3A 55210 TCGA-A2-A0CT-01 -1 -ATAD3B 83858 TCGA-A2-A0CT-01 -1 -ATAD3C 219293 TCGA-A2-A0CT-01 -1 -AURKAIP1 54998 TCGA-A2-A0CT-01 -1 -ERCC5 2073 TCGA-A2-A0CT-01 -1 -ACP3 55 TCGA-A2-A0CT-01 0 -ACAP3 116983 TCGA-A2-A0CU-01 0 -AGRN 375790 TCGA-A2-A0CU-01 0 -ATAD3A 55210 TCGA-A2-A0CU-01 0 -ATAD3B 83858 TCGA-A2-A0CU-01 0 -ATAD3C 219293 TCGA-A2-A0CU-01 0 -AURKAIP1 54998 TCGA-A2-A0CU-01 0 -ERCC5 2073 TCGA-A2-A0CU-01 0 -ACP3 55 TCGA-A2-A0CU-01 0 -ACAP3 116983 TCGA-A2-A0CV-01 0 -AGRN 375790 TCGA-A2-A0CV-01 0 -ATAD3A 55210 TCGA-A2-A0CV-01 0 -ATAD3B 83858 TCGA-A2-A0CV-01 0 -ATAD3C 219293 TCGA-A2-A0CV-01 0 -AURKAIP1 54998 TCGA-A2-A0CV-01 0 -ERCC5 2073 TCGA-A2-A0CV-01 0 -ACP3 55 TCGA-A2-A0CV-01 0 -ACAP3 116983 TCGA-A2-A0CW-01 -1 -AGRN 375790 TCGA-A2-A0CW-01 -1 -ATAD3A 55210 TCGA-A2-A0CW-01 -1 -ATAD3B 83858 TCGA-A2-A0CW-01 -1 -ATAD3C 219293 TCGA-A2-A0CW-01 -1 -AURKAIP1 54998 TCGA-A2-A0CW-01 -1 -ERCC5 2073 TCGA-A2-A0CW-01 -1 -ACP3 55 TCGA-A2-A0CW-01 0 -ACAP3 116983 TCGA-A2-A0CX-01 0 -AGRN 375790 TCGA-A2-A0CX-01 0 -ATAD3A 55210 TCGA-A2-A0CX-01 0 -ATAD3B 83858 TCGA-A2-A0CX-01 0 -ATAD3C 219293 TCGA-A2-A0CX-01 0 -AURKAIP1 54998 TCGA-A2-A0CX-01 0 -ERCC5 2073 TCGA-A2-A0CX-01 0 -ACP3 55 TCGA-A2-A0CX-01 0 -ACAP3 116983 TCGA-A2-A0D0-01 1 -AGRN 375790 TCGA-A2-A0D0-01 1 -ATAD3A 55210 TCGA-A2-A0D0-01 1 -ATAD3B 83858 TCGA-A2-A0D0-01 1 -ATAD3C 219293 TCGA-A2-A0D0-01 1 -AURKAIP1 54998 TCGA-A2-A0D0-01 1 -ERCC5 2073 TCGA-A2-A0D0-01 1 -ACP3 55 TCGA-A2-A0D0-01 0 -ACAP3 116983 TCGA-A2-A0D1-01 0 -AGRN 375790 TCGA-A2-A0D1-01 0 -ATAD3A 55210 TCGA-A2-A0D1-01 0 -ATAD3B 83858 TCGA-A2-A0D1-01 0 -ATAD3C 219293 TCGA-A2-A0D1-01 0 -AURKAIP1 54998 TCGA-A2-A0D1-01 0 -ERCC5 2073 TCGA-A2-A0D1-01 0 -ACP3 55 TCGA-A2-A0D1-01 0 -ACAP3 116983 TCGA-A2-A0D2-01 0 -AGRN 375790 TCGA-A2-A0D2-01 0 -ATAD3A 55210 TCGA-A2-A0D2-01 0 -ATAD3B 83858 TCGA-A2-A0D2-01 0 -ATAD3C 219293 TCGA-A2-A0D2-01 0 -AURKAIP1 54998 TCGA-A2-A0D2-01 0 -ERCC5 2073 TCGA-A2-A0D2-01 0 -ACP3 55 TCGA-A2-A0D2-01 0 -ACAP3 116983 TCGA-A2-A0D3-01 0 -AGRN 375790 TCGA-A2-A0D3-01 0 -ATAD3A 55210 TCGA-A2-A0D3-01 0 -ATAD3B 83858 TCGA-A2-A0D3-01 0 -ATAD3C 219293 TCGA-A2-A0D3-01 0 -AURKAIP1 54998 TCGA-A2-A0D3-01 0 -ERCC5 2073 TCGA-A2-A0D3-01 0 -ACP3 55 TCGA-A2-A0D3-01 0 -ACAP3 116983 TCGA-A2-A0D4-01 -1 -AGRN 375790 TCGA-A2-A0D4-01 -1 -ATAD3A 55210 TCGA-A2-A0D4-01 -1 -ATAD3B 83858 TCGA-A2-A0D4-01 -1 -ATAD3C 219293 TCGA-A2-A0D4-01 -1 -AURKAIP1 54998 TCGA-A2-A0D4-01 -1 -ERCC5 2073 TCGA-A2-A0D4-01 -1 -ACP3 55 TCGA-A2-A0D4-01 0 -ACAP3 116983 TCGA-A2-A0EM-01 0 -AGRN 375790 TCGA-A2-A0EM-01 0 -ATAD3A 55210 TCGA-A2-A0EM-01 0 -ATAD3B 83858 TCGA-A2-A0EM-01 0 -ATAD3C 219293 TCGA-A2-A0EM-01 0 -AURKAIP1 54998 TCGA-A2-A0EM-01 0 -ERCC5 2073 TCGA-A2-A0EM-01 0 -ACP3 55 TCGA-A2-A0EM-01 0 -ACAP3 116983 TCGA-A2-A0EN-01 -1 -AGRN 375790 TCGA-A2-A0EN-01 -1 -ATAD3A 55210 TCGA-A2-A0EN-01 -1 -ATAD3B 83858 TCGA-A2-A0EN-01 -1 -ATAD3C 219293 TCGA-A2-A0EN-01 -1 -AURKAIP1 54998 TCGA-A2-A0EN-01 -1 -ERCC5 2073 TCGA-A2-A0EN-01 -1 -ACP3 55 TCGA-A2-A0EN-01 0 -ACAP3 116983 TCGA-A2-A0EO-01 -1 -AGRN 375790 TCGA-A2-A0EO-01 -1 -ATAD3A 55210 TCGA-A2-A0EO-01 -1 -ATAD3B 83858 TCGA-A2-A0EO-01 -1 -ATAD3C 219293 TCGA-A2-A0EO-01 -1 -AURKAIP1 54998 TCGA-A2-A0EO-01 -1 -ERCC5 2073 TCGA-A2-A0EO-01 -1 -ACP3 55 TCGA-A2-A0EO-01 0 -ACAP3 116983 TCGA-A2-A0EQ-01 0 -AGRN 375790 TCGA-A2-A0EQ-01 0 -ATAD3A 55210 TCGA-A2-A0EQ-01 0 -ATAD3B 83858 TCGA-A2-A0EQ-01 0 -ATAD3C 219293 TCGA-A2-A0EQ-01 0 -AURKAIP1 54998 TCGA-A2-A0EQ-01 0 -ERCC5 2073 TCGA-A2-A0EQ-01 0 -ACP3 55 TCGA-A2-A0EQ-01 0 -ACAP3 116983 TCGA-A2-A0ER-01 0 -AGRN 375790 TCGA-A2-A0ER-01 0 -ATAD3A 55210 TCGA-A2-A0ER-01 0 -ATAD3B 83858 TCGA-A2-A0ER-01 0 -ATAD3C 219293 TCGA-A2-A0ER-01 0 -AURKAIP1 54998 TCGA-A2-A0ER-01 0 -ERCC5 2073 TCGA-A2-A0ER-01 0 -ACP3 55 TCGA-A2-A0ER-01 0 -ACAP3 116983 TCGA-A2-A0ES-01 0 -AGRN 375790 TCGA-A2-A0ES-01 0 -ATAD3A 55210 TCGA-A2-A0ES-01 0 -ATAD3B 83858 TCGA-A2-A0ES-01 0 -ATAD3C 219293 TCGA-A2-A0ES-01 0 -AURKAIP1 54998 TCGA-A2-A0ES-01 0 -ERCC5 2073 TCGA-A2-A0ES-01 0 -ACP3 55 TCGA-A2-A0ES-01 0 -ACAP3 116983 TCGA-A2-A0ET-01 -1 -AGRN 375790 TCGA-A2-A0ET-01 -1 -ATAD3A 55210 TCGA-A2-A0ET-01 -1 -ATAD3B 83858 TCGA-A2-A0ET-01 -1 -ATAD3C 219293 TCGA-A2-A0ET-01 -1 -AURKAIP1 54998 TCGA-A2-A0ET-01 -1 -ERCC5 2073 TCGA-A2-A0ET-01 -1 -ACP3 55 TCGA-A2-A0ET-01 0 -ACAP3 116983 TCGA-A2-A0EU-01 0 -AGRN 375790 TCGA-A2-A0EU-01 0 -ATAD3A 55210 TCGA-A2-A0EU-01 0 -ATAD3B 83858 TCGA-A2-A0EU-01 0 -ATAD3C 219293 TCGA-A2-A0EU-01 0 -AURKAIP1 54998 TCGA-A2-A0EU-01 0 -ERCC5 2073 TCGA-A2-A0EU-01 0 -ACP3 55 TCGA-A2-A0EU-01 0 -ACAP3 116983 TCGA-A2-A0EV-01 0 -AGRN 375790 TCGA-A2-A0EV-01 0 -ATAD3A 55210 TCGA-A2-A0EV-01 0 -ATAD3B 83858 TCGA-A2-A0EV-01 0 -ATAD3C 219293 TCGA-A2-A0EV-01 0 -AURKAIP1 54998 TCGA-A2-A0EV-01 0 -ERCC5 2073 TCGA-A2-A0EV-01 0 -ACP3 55 TCGA-A2-A0EV-01 0 -ACAP3 116983 TCGA-A2-A0EW-01 0 -AGRN 375790 TCGA-A2-A0EW-01 0 -ATAD3A 55210 TCGA-A2-A0EW-01 0 -ATAD3B 83858 TCGA-A2-A0EW-01 0 -ATAD3C 219293 TCGA-A2-A0EW-01 0 -AURKAIP1 54998 TCGA-A2-A0EW-01 0 -ERCC5 2073 TCGA-A2-A0EW-01 0 -ACP3 55 TCGA-A2-A0EW-01 0 -ACAP3 116983 TCGA-A2-A0EX-01 0 -AGRN 375790 TCGA-A2-A0EX-01 0 -ATAD3A 55210 TCGA-A2-A0EX-01 0 -ATAD3B 83858 TCGA-A2-A0EX-01 0 -ATAD3C 219293 TCGA-A2-A0EX-01 0 -AURKAIP1 54998 TCGA-A2-A0EX-01 0 -ERCC5 2073 TCGA-A2-A0EX-01 0 -ACP3 55 TCGA-A2-A0EX-01 0 -ACAP3 116983 TCGA-A2-A0EY-01 -1 -AGRN 375790 TCGA-A2-A0EY-01 -1 -ATAD3A 55210 TCGA-A2-A0EY-01 -1 -ATAD3B 83858 TCGA-A2-A0EY-01 -1 -ATAD3C 219293 TCGA-A2-A0EY-01 -1 -AURKAIP1 54998 TCGA-A2-A0EY-01 -1 -ERCC5 2073 TCGA-A2-A0EY-01 -1 -ACP3 55 TCGA-A2-A0EY-01 0 -ACAP3 116983 TCGA-A2-A0ST-01 0 -AGRN 375790 TCGA-A2-A0ST-01 0 -ATAD3A 55210 TCGA-A2-A0ST-01 0 -ATAD3B 83858 TCGA-A2-A0ST-01 0 -ATAD3C 219293 TCGA-A2-A0ST-01 0 -AURKAIP1 54998 TCGA-A2-A0ST-01 0 -ERCC5 2073 TCGA-A2-A0ST-01 0 -ACP3 55 TCGA-A2-A0ST-01 0 -ACAP3 116983 TCGA-A2-A0SU-01 0 -AGRN 375790 TCGA-A2-A0SU-01 0 -ATAD3A 55210 TCGA-A2-A0SU-01 0 -ATAD3B 83858 TCGA-A2-A0SU-01 0 -ATAD3C 219293 TCGA-A2-A0SU-01 0 -AURKAIP1 54998 TCGA-A2-A0SU-01 0 -ERCC5 2073 TCGA-A2-A0SU-01 0 -ACP3 55 TCGA-A2-A0SU-01 0 -ACAP3 116983 TCGA-A2-A0SV-01 0 -AGRN 375790 TCGA-A2-A0SV-01 0 -ATAD3A 55210 TCGA-A2-A0SV-01 0 -ATAD3B 83858 TCGA-A2-A0SV-01 0 -ATAD3C 219293 TCGA-A2-A0SV-01 0 -AURKAIP1 54998 TCGA-A2-A0SV-01 0 -ERCC5 2073 TCGA-A2-A0SV-01 0 -ACP3 55 TCGA-A2-A0SV-01 0 -ACAP3 116983 TCGA-A2-A0SW-01 0 -AGRN 375790 TCGA-A2-A0SW-01 0 -ATAD3A 55210 TCGA-A2-A0SW-01 0 -ATAD3B 83858 TCGA-A2-A0SW-01 0 -ATAD3C 219293 TCGA-A2-A0SW-01 0 -AURKAIP1 54998 TCGA-A2-A0SW-01 0 -ERCC5 2073 TCGA-A2-A0SW-01 0 -ACP3 55 TCGA-A2-A0SW-01 0 -ACAP3 116983 TCGA-A2-A0SX-01 0 -AGRN 375790 TCGA-A2-A0SX-01 0 -ATAD3A 55210 TCGA-A2-A0SX-01 0 -ATAD3B 83858 TCGA-A2-A0SX-01 0 -ATAD3C 219293 TCGA-A2-A0SX-01 0 -AURKAIP1 54998 TCGA-A2-A0SX-01 0 -ERCC5 2073 TCGA-A2-A0SX-01 0 -ACP3 55 TCGA-A2-A0SX-01 0 -ACAP3 116983 TCGA-A2-A0SY-01 0 -AGRN 375790 TCGA-A2-A0SY-01 0 -ATAD3A 55210 TCGA-A2-A0SY-01 0 -ATAD3B 83858 TCGA-A2-A0SY-01 0 -ATAD3C 219293 TCGA-A2-A0SY-01 0 -AURKAIP1 54998 TCGA-A2-A0SY-01 0 -ERCC5 2073 TCGA-A2-A0SY-01 0 -ACP3 55 TCGA-A2-A0SY-01 0 -ACAP3 116983 TCGA-A2-A0T0-01 0 -AGRN 375790 TCGA-A2-A0T0-01 0 -ATAD3A 55210 TCGA-A2-A0T0-01 0 -ATAD3B 83858 TCGA-A2-A0T0-01 0 -ATAD3C 219293 TCGA-A2-A0T0-01 0 -AURKAIP1 54998 TCGA-A2-A0T0-01 0 -ERCC5 2073 TCGA-A2-A0T0-01 0 -ACP3 55 TCGA-A2-A0T0-01 0 -ACAP3 116983 TCGA-A2-A0T1-01 0 -AGRN 375790 TCGA-A2-A0T1-01 0 -ATAD3A 55210 TCGA-A2-A0T1-01 0 -ATAD3B 83858 TCGA-A2-A0T1-01 0 -ATAD3C 219293 TCGA-A2-A0T1-01 0 -AURKAIP1 54998 TCGA-A2-A0T1-01 0 -ERCC5 2073 TCGA-A2-A0T1-01 0 -ACP3 55 TCGA-A2-A0T1-01 0 -ACAP3 116983 TCGA-A2-A0T2-01 1 -AGRN 375790 TCGA-A2-A0T2-01 1 -ATAD3A 55210 TCGA-A2-A0T2-01 1 -ATAD3B 83858 TCGA-A2-A0T2-01 1 -ATAD3C 219293 TCGA-A2-A0T2-01 1 -AURKAIP1 54998 TCGA-A2-A0T2-01 1 -ERCC5 2073 TCGA-A2-A0T2-01 1 -ACP3 55 TCGA-A2-A0T2-01 0 -ACAP3 116983 TCGA-A2-A0T3-01 0 -AGRN 375790 TCGA-A2-A0T3-01 0 -ATAD3A 55210 TCGA-A2-A0T3-01 0 -ATAD3B 83858 TCGA-A2-A0T3-01 0 -ATAD3C 219293 TCGA-A2-A0T3-01 0 -AURKAIP1 54998 TCGA-A2-A0T3-01 0 -ERCC5 2073 TCGA-A2-A0T3-01 0 -ACP3 55 TCGA-A2-A0T3-01 0 -ACAP3 116983 TCGA-A2-A0T4-01 -1 -AGRN 375790 TCGA-A2-A0T4-01 -1 -ATAD3A 55210 TCGA-A2-A0T4-01 -1 -ATAD3B 83858 TCGA-A2-A0T4-01 -1 -ATAD3C 219293 TCGA-A2-A0T4-01 -1 -AURKAIP1 54998 TCGA-A2-A0T4-01 -1 -ERCC5 2073 TCGA-A2-A0T4-01 -1 -ACP3 55 TCGA-A2-A0T4-01 0 -ACAP3 116983 TCGA-A2-A0T5-01 0 -AGRN 375790 TCGA-A2-A0T5-01 0 -ATAD3A 55210 TCGA-A2-A0T5-01 0 -ATAD3B 83858 TCGA-A2-A0T5-01 0 -ATAD3C 219293 TCGA-A2-A0T5-01 0 -AURKAIP1 54998 TCGA-A2-A0T5-01 0 -ERCC5 2073 TCGA-A2-A0T5-01 0 -ACP3 55 TCGA-A2-A0T5-01 0 -ACAP3 116983 TCGA-A2-A0T6-01 0 -AGRN 375790 TCGA-A2-A0T6-01 0 -ATAD3A 55210 TCGA-A2-A0T6-01 0 -ATAD3B 83858 TCGA-A2-A0T6-01 0 -ATAD3C 219293 TCGA-A2-A0T6-01 0 -AURKAIP1 54998 TCGA-A2-A0T6-01 0 -ERCC5 2073 TCGA-A2-A0T6-01 0 -ACP3 55 TCGA-A2-A0T6-01 0 -ACAP3 116983 TCGA-A2-A0T7-01 -1 -AGRN 375790 TCGA-A2-A0T7-01 -1 -ATAD3A 55210 TCGA-A2-A0T7-01 -1 -ATAD3B 83858 TCGA-A2-A0T7-01 -1 -ATAD3C 219293 TCGA-A2-A0T7-01 -1 -AURKAIP1 54998 TCGA-A2-A0T7-01 -1 -ERCC5 2073 TCGA-A2-A0T7-01 -1 -ACP3 55 TCGA-A2-A0T7-01 0 -ACAP3 116983 TCGA-A2-A0YC-01 0 -AGRN 375790 TCGA-A2-A0YC-01 0 -ATAD3A 55210 TCGA-A2-A0YC-01 0 -ATAD3B 83858 TCGA-A2-A0YC-01 0 -ATAD3C 219293 TCGA-A2-A0YC-01 0 -AURKAIP1 54998 TCGA-A2-A0YC-01 0 -ERCC5 2073 TCGA-A2-A0YC-01 0 -ACP3 55 TCGA-A2-A0YC-01 0 -ACAP3 116983 TCGA-A2-A0YD-01 0 -AGRN 375790 TCGA-A2-A0YD-01 0 -ATAD3A 55210 TCGA-A2-A0YD-01 0 -ATAD3B 83858 TCGA-A2-A0YD-01 0 -ATAD3C 219293 TCGA-A2-A0YD-01 0 -AURKAIP1 54998 TCGA-A2-A0YD-01 0 -ERCC5 2073 TCGA-A2-A0YD-01 0 -ACP3 55 TCGA-A2-A0YD-01 0 -ACAP3 116983 TCGA-A2-A0YE-01 0 -AGRN 375790 TCGA-A2-A0YE-01 0 -ATAD3A 55210 TCGA-A2-A0YE-01 0 -ATAD3B 83858 TCGA-A2-A0YE-01 0 -ATAD3C 219293 TCGA-A2-A0YE-01 0 -AURKAIP1 54998 TCGA-A2-A0YE-01 0 -ERCC5 2073 TCGA-A2-A0YE-01 0 -ACP3 55 TCGA-A2-A0YE-01 0 -ACAP3 116983 TCGA-A2-A0YF-01 -1 -AGRN 375790 TCGA-A2-A0YF-01 -1 -ATAD3A 55210 TCGA-A2-A0YF-01 -1 -ATAD3B 83858 TCGA-A2-A0YF-01 -1 -ATAD3C 219293 TCGA-A2-A0YF-01 -1 -AURKAIP1 54998 TCGA-A2-A0YF-01 -1 -ERCC5 2073 TCGA-A2-A0YF-01 -1 -ACP3 55 TCGA-A2-A0YF-01 0 -ACAP3 116983 TCGA-A2-A0YG-01 0 -AGRN 375790 TCGA-A2-A0YG-01 0 -ATAD3A 55210 TCGA-A2-A0YG-01 0 -ATAD3B 83858 TCGA-A2-A0YG-01 0 -ATAD3C 219293 TCGA-A2-A0YG-01 0 -AURKAIP1 54998 TCGA-A2-A0YG-01 0 -ERCC5 2073 TCGA-A2-A0YG-01 0 -ACP3 55 TCGA-A2-A0YG-01 0 -ACAP3 116983 TCGA-A2-A0YH-01 0 -AGRN 375790 TCGA-A2-A0YH-01 0 -ATAD3A 55210 TCGA-A2-A0YH-01 0 -ATAD3B 83858 TCGA-A2-A0YH-01 0 -ATAD3C 219293 TCGA-A2-A0YH-01 0 -AURKAIP1 54998 TCGA-A2-A0YH-01 0 -ERCC5 2073 TCGA-A2-A0YH-01 0 -ACP3 55 TCGA-A2-A0YH-01 0 -ACAP3 116983 TCGA-A2-A0YI-01 -1 -AGRN 375790 TCGA-A2-A0YI-01 -1 -ATAD3A 55210 TCGA-A2-A0YI-01 -1 -ATAD3B 83858 TCGA-A2-A0YI-01 -1 -ATAD3C 219293 TCGA-A2-A0YI-01 -1 -AURKAIP1 54998 TCGA-A2-A0YI-01 -1 -ERCC5 2073 TCGA-A2-A0YI-01 -1 -ACP3 55 TCGA-A2-A0YI-01 0 -ACAP3 116983 TCGA-A2-A0YJ-01 -1 -AGRN 375790 TCGA-A2-A0YJ-01 -1 -ATAD3A 55210 TCGA-A2-A0YJ-01 -1 -ATAD3B 83858 TCGA-A2-A0YJ-01 -1 -ATAD3C 219293 TCGA-A2-A0YJ-01 -1 -AURKAIP1 54998 TCGA-A2-A0YJ-01 -1 -ERCC5 2073 TCGA-A2-A0YJ-01 -1 -ACP3 55 TCGA-A2-A0YJ-01 0 -ACAP3 116983 TCGA-A2-A0YK-01 0 -AGRN 375790 TCGA-A2-A0YK-01 0 -ATAD3A 55210 TCGA-A2-A0YK-01 0 -ATAD3B 83858 TCGA-A2-A0YK-01 0 -ATAD3C 219293 TCGA-A2-A0YK-01 0 -AURKAIP1 54998 TCGA-A2-A0YK-01 0 -ERCC5 2073 TCGA-A2-A0YK-01 0 -ACP3 55 TCGA-A2-A0YK-01 0 -ACAP3 116983 TCGA-A2-A0YL-01 0 -AGRN 375790 TCGA-A2-A0YL-01 0 -ATAD3A 55210 TCGA-A2-A0YL-01 0 -ATAD3B 83858 TCGA-A2-A0YL-01 0 -ATAD3C 219293 TCGA-A2-A0YL-01 0 -AURKAIP1 54998 TCGA-A2-A0YL-01 0 -ERCC5 2073 TCGA-A2-A0YL-01 0 -ACP3 55 TCGA-A2-A0YL-01 0 -ACAP3 116983 TCGA-A2-A0YM-01 0 -AGRN 375790 TCGA-A2-A0YM-01 0 -ATAD3A 55210 TCGA-A2-A0YM-01 0 -ATAD3B 83858 TCGA-A2-A0YM-01 0 -ATAD3C 219293 TCGA-A2-A0YM-01 0 -AURKAIP1 54998 TCGA-A2-A0YM-01 0 -ERCC5 2073 TCGA-A2-A0YM-01 0 -ACP3 55 TCGA-A2-A0YM-01 0 -ACAP3 116983 TCGA-A2-A0YT-01 0 -AGRN 375790 TCGA-A2-A0YT-01 0 -ATAD3A 55210 TCGA-A2-A0YT-01 0 -ATAD3B 83858 TCGA-A2-A0YT-01 0 -ATAD3C 219293 TCGA-A2-A0YT-01 0 -AURKAIP1 54998 TCGA-A2-A0YT-01 0 -ERCC5 2073 TCGA-A2-A0YT-01 0 -ACP3 55 TCGA-A2-A0YT-01 0 -ACAP3 116983 TCGA-A2-A1FV-01 0 -AGRN 375790 TCGA-A2-A1FV-01 0 -ATAD3A 55210 TCGA-A2-A1FV-01 0 -ATAD3B 83858 TCGA-A2-A1FV-01 0 -ATAD3C 219293 TCGA-A2-A1FV-01 0 -AURKAIP1 54998 TCGA-A2-A1FV-01 0 -ERCC5 2073 TCGA-A2-A1FV-01 0 -ACP3 55 TCGA-A2-A1FV-01 0 -ACAP3 116983 TCGA-A2-A1FW-01 0 -AGRN 375790 TCGA-A2-A1FW-01 0 -ATAD3A 55210 TCGA-A2-A1FW-01 0 -ATAD3B 83858 TCGA-A2-A1FW-01 0 -ATAD3C 219293 TCGA-A2-A1FW-01 0 -AURKAIP1 54998 TCGA-A2-A1FW-01 0 -ERCC5 2073 TCGA-A2-A1FW-01 0 -ACP3 55 TCGA-A2-A1FW-01 0 -ACAP3 116983 TCGA-A2-A1FX-01 -1 -AGRN 375790 TCGA-A2-A1FX-01 -1 -ATAD3A 55210 TCGA-A2-A1FX-01 -1 -ATAD3B 83858 TCGA-A2-A1FX-01 -1 -ATAD3C 219293 TCGA-A2-A1FX-01 -1 -AURKAIP1 54998 TCGA-A2-A1FX-01 -1 -ERCC5 2073 TCGA-A2-A1FX-01 -1 -ACP3 55 TCGA-A2-A1FX-01 0 -ACAP3 116983 TCGA-A2-A1FZ-01 0 -AGRN 375790 TCGA-A2-A1FZ-01 0 -ATAD3A 55210 TCGA-A2-A1FZ-01 0 -ATAD3B 83858 TCGA-A2-A1FZ-01 0 -ATAD3C 219293 TCGA-A2-A1FZ-01 0 -AURKAIP1 54998 TCGA-A2-A1FZ-01 0 -ERCC5 2073 TCGA-A2-A1FZ-01 0 -ACP3 55 TCGA-A2-A1FZ-01 0 -ACAP3 116983 TCGA-A2-A1G0-01 1 -AGRN 375790 TCGA-A2-A1G0-01 1 -ATAD3A 55210 TCGA-A2-A1G0-01 1 -ATAD3B 83858 TCGA-A2-A1G0-01 1 -ATAD3C 219293 TCGA-A2-A1G0-01 1 -AURKAIP1 54998 TCGA-A2-A1G0-01 1 -ERCC5 2073 TCGA-A2-A1G0-01 1 -ACP3 55 TCGA-A2-A1G0-01 0 -ACAP3 116983 TCGA-A2-A1G1-01 0 -AGRN 375790 TCGA-A2-A1G1-01 0 -ATAD3A 55210 TCGA-A2-A1G1-01 0 -ATAD3B 83858 TCGA-A2-A1G1-01 0 -ATAD3C 219293 TCGA-A2-A1G1-01 0 -AURKAIP1 54998 TCGA-A2-A1G1-01 0 -ERCC5 2073 TCGA-A2-A1G1-01 0 -ACP3 55 TCGA-A2-A1G1-01 0 -ACAP3 116983 TCGA-A2-A1G4-01 0 -AGRN 375790 TCGA-A2-A1G4-01 0 -ATAD3A 55210 TCGA-A2-A1G4-01 0 -ATAD3B 83858 TCGA-A2-A1G4-01 0 -ATAD3C 219293 TCGA-A2-A1G4-01 0 -AURKAIP1 54998 TCGA-A2-A1G4-01 0 -ERCC5 2073 TCGA-A2-A1G4-01 0 -ACP3 55 TCGA-A2-A1G4-01 0 -ACAP3 116983 TCGA-A2-A1G6-01 0 -AGRN 375790 TCGA-A2-A1G6-01 0 -ATAD3A 55210 TCGA-A2-A1G6-01 0 -ATAD3B 83858 TCGA-A2-A1G6-01 0 -ATAD3C 219293 TCGA-A2-A1G6-01 0 -AURKAIP1 54998 TCGA-A2-A1G6-01 0 -ERCC5 2073 TCGA-A2-A1G6-01 0 -ACP3 55 TCGA-A2-A1G6-01 0 -ACAP3 116983 TCGA-A2-A259-01 0 -AGRN 375790 TCGA-A2-A259-01 0 -ATAD3A 55210 TCGA-A2-A259-01 0 -ATAD3B 83858 TCGA-A2-A259-01 0 -ATAD3C 219293 TCGA-A2-A259-01 0 -AURKAIP1 54998 TCGA-A2-A259-01 0 -ERCC5 2073 TCGA-A2-A259-01 0 -ACP3 55 TCGA-A2-A259-01 0 -ACAP3 116983 TCGA-A2-A25A-01 0 -AGRN 375790 TCGA-A2-A25A-01 0 -ATAD3A 55210 TCGA-A2-A25A-01 0 -ATAD3B 83858 TCGA-A2-A25A-01 0 -ATAD3C 219293 TCGA-A2-A25A-01 0 -AURKAIP1 54998 TCGA-A2-A25A-01 0 -ERCC5 2073 TCGA-A2-A25A-01 0 -ACP3 55 TCGA-A2-A25A-01 0 -ACAP3 116983 TCGA-A2-A25B-01 0 -AGRN 375790 TCGA-A2-A25B-01 0 -ATAD3A 55210 TCGA-A2-A25B-01 0 -ATAD3B 83858 TCGA-A2-A25B-01 0 -ATAD3C 219293 TCGA-A2-A25B-01 0 -AURKAIP1 54998 TCGA-A2-A25B-01 0 -ERCC5 2073 TCGA-A2-A25B-01 0 -ACP3 55 TCGA-A2-A25B-01 0 -ACAP3 116983 TCGA-A2-A25C-01 -1 -AGRN 375790 TCGA-A2-A25C-01 -1 -ATAD3A 55210 TCGA-A2-A25C-01 -1 -ATAD3B 83858 TCGA-A2-A25C-01 -1 -ATAD3C 219293 TCGA-A2-A25C-01 -1 -AURKAIP1 54998 TCGA-A2-A25C-01 -1 -ERCC5 2073 TCGA-A2-A25C-01 -1 -ACP3 55 TCGA-A2-A25C-01 0 -ACAP3 116983 TCGA-A2-A25D-01 0 -AGRN 375790 TCGA-A2-A25D-01 0 -ATAD3A 55210 TCGA-A2-A25D-01 0 -ATAD3B 83858 TCGA-A2-A25D-01 0 -ATAD3C 219293 TCGA-A2-A25D-01 0 -AURKAIP1 54998 TCGA-A2-A25D-01 0 -ERCC5 2073 TCGA-A2-A25D-01 0 -ACP3 55 TCGA-A2-A25D-01 0 -ACAP3 116983 TCGA-A2-A25E-01 0 -AGRN 375790 TCGA-A2-A25E-01 0 -ATAD3A 55210 TCGA-A2-A25E-01 0 -ATAD3B 83858 TCGA-A2-A25E-01 0 -ATAD3C 219293 TCGA-A2-A25E-01 0 -AURKAIP1 54998 TCGA-A2-A25E-01 0 -ERCC5 2073 TCGA-A2-A25E-01 0 -ACP3 55 TCGA-A2-A25E-01 0 -ACAP3 116983 TCGA-A2-A25F-01 0 -AGRN 375790 TCGA-A2-A25F-01 0 -ATAD3A 55210 TCGA-A2-A25F-01 0 -ATAD3B 83858 TCGA-A2-A25F-01 0 -ATAD3C 219293 TCGA-A2-A25F-01 0 -AURKAIP1 54998 TCGA-A2-A25F-01 0 -ERCC5 2073 TCGA-A2-A25F-01 0 -ACP3 55 TCGA-A2-A25F-01 0 -ACAP3 116983 TCGA-A7-A0CD-01 0 -AGRN 375790 TCGA-A7-A0CD-01 0 -ATAD3A 55210 TCGA-A7-A0CD-01 0 -ATAD3B 83858 TCGA-A7-A0CD-01 0 -ATAD3C 219293 TCGA-A7-A0CD-01 0 -AURKAIP1 54998 TCGA-A7-A0CD-01 0 -ERCC5 2073 TCGA-A7-A0CD-01 0 -ACP3 55 TCGA-A7-A0CD-01 0 -ACAP3 116983 TCGA-A7-A0CE-01 0 -AGRN 375790 TCGA-A7-A0CE-01 0 -ATAD3A 55210 TCGA-A7-A0CE-01 0 -ATAD3B 83858 TCGA-A7-A0CE-01 0 -ATAD3C 219293 TCGA-A7-A0CE-01 0 -AURKAIP1 54998 TCGA-A7-A0CE-01 0 -ERCC5 2073 TCGA-A7-A0CE-01 0 -ACP3 55 TCGA-A7-A0CE-01 0 -ACAP3 116983 TCGA-A7-A0CG-01 0 -AGRN 375790 TCGA-A7-A0CG-01 0 -ATAD3A 55210 TCGA-A7-A0CG-01 0 -ATAD3B 83858 TCGA-A7-A0CG-01 0 -ATAD3C 219293 TCGA-A7-A0CG-01 0 -AURKAIP1 54998 TCGA-A7-A0CG-01 0 -ERCC5 2073 TCGA-A7-A0CG-01 0 -ACP3 55 TCGA-A7-A0CG-01 0 -ACAP3 116983 TCGA-A7-A0CH-01 0 -AGRN 375790 TCGA-A7-A0CH-01 0 -ATAD3A 55210 TCGA-A7-A0CH-01 0 -ATAD3B 83858 TCGA-A7-A0CH-01 0 -ATAD3C 219293 TCGA-A7-A0CH-01 0 -AURKAIP1 54998 TCGA-A7-A0CH-01 0 -ERCC5 2073 TCGA-A7-A0CH-01 0 -ACP3 55 TCGA-A7-A0CH-01 0 -ACAP3 116983 TCGA-A7-A0CJ-01 0 -AGRN 375790 TCGA-A7-A0CJ-01 0 -ATAD3A 55210 TCGA-A7-A0CJ-01 0 -ATAD3B 83858 TCGA-A7-A0CJ-01 0 -ATAD3C 219293 TCGA-A7-A0CJ-01 0 -AURKAIP1 54998 TCGA-A7-A0CJ-01 0 -ERCC5 2073 TCGA-A7-A0CJ-01 0 -ACP3 55 TCGA-A7-A0CJ-01 0 -ACAP3 116983 TCGA-A7-A0D9-01 0 -AGRN 375790 TCGA-A7-A0D9-01 0 -ATAD3A 55210 TCGA-A7-A0D9-01 0 -ATAD3B 83858 TCGA-A7-A0D9-01 0 -ATAD3C 219293 TCGA-A7-A0D9-01 0 -AURKAIP1 54998 TCGA-A7-A0D9-01 0 -ERCC5 2073 TCGA-A7-A0D9-01 0 -ACP3 55 TCGA-A7-A0D9-01 0 -ACAP3 116983 TCGA-A7-A0DA-01 0 -AGRN 375790 TCGA-A7-A0DA-01 0 -ATAD3A 55210 TCGA-A7-A0DA-01 0 -ATAD3B 83858 TCGA-A7-A0DA-01 0 -ATAD3C 219293 TCGA-A7-A0DA-01 0 -AURKAIP1 54998 TCGA-A7-A0DA-01 0 -ERCC5 2073 TCGA-A7-A0DA-01 0 -ACP3 55 TCGA-A7-A0DA-01 0 -ACAP3 116983 TCGA-A7-A0DB-01 0 -AGRN 375790 TCGA-A7-A0DB-01 0 -ATAD3A 55210 TCGA-A7-A0DB-01 0 -ATAD3B 83858 TCGA-A7-A0DB-01 0 -ATAD3C 219293 TCGA-A7-A0DB-01 0 -AURKAIP1 54998 TCGA-A7-A0DB-01 0 -ERCC5 2073 TCGA-A7-A0DB-01 0 -ACP3 55 TCGA-A7-A0DB-01 0 -ACAP3 116983 TCGA-A7-A13D-01 0 -AGRN 375790 TCGA-A7-A13D-01 0 -ATAD3A 55210 TCGA-A7-A13D-01 0 -ATAD3B 83858 TCGA-A7-A13D-01 0 -ATAD3C 219293 TCGA-A7-A13D-01 0 -AURKAIP1 54998 TCGA-A7-A13D-01 0 -ERCC5 2073 TCGA-A7-A13D-01 0 -ACP3 55 TCGA-A7-A13D-01 0 -ACAP3 116983 TCGA-A7-A13E-01 0 -AGRN 375790 TCGA-A7-A13E-01 0 -ATAD3A 55210 TCGA-A7-A13E-01 0 -ATAD3B 83858 TCGA-A7-A13E-01 0 -ATAD3C 219293 TCGA-A7-A13E-01 0 -AURKAIP1 54998 TCGA-A7-A13E-01 0 -ERCC5 2073 TCGA-A7-A13E-01 0 -ACP3 55 TCGA-A7-A13E-01 0 -ACAP3 116983 TCGA-A7-A13F-01 -1 -AGRN 375790 TCGA-A7-A13F-01 -1 -ATAD3A 55210 TCGA-A7-A13F-01 -1 -ATAD3B 83858 TCGA-A7-A13F-01 -1 -ATAD3C 219293 TCGA-A7-A13F-01 -1 -AURKAIP1 54998 TCGA-A7-A13F-01 -1 -ERCC5 2073 TCGA-A7-A13F-01 -1 -ACP3 55 TCGA-A7-A13F-01 0 -ACAP3 116983 TCGA-A7-A13G-01 0 -AGRN 375790 TCGA-A7-A13G-01 0 -ATAD3A 55210 TCGA-A7-A13G-01 0 -ATAD3B 83858 TCGA-A7-A13G-01 0 -ATAD3C 219293 TCGA-A7-A13G-01 0 -AURKAIP1 54998 TCGA-A7-A13G-01 0 -ERCC5 2073 TCGA-A7-A13G-01 0 -ACP3 55 TCGA-A7-A13G-01 0 -ACAP3 116983 TCGA-A7-A26E-01 0 -AGRN 375790 TCGA-A7-A26E-01 0 -ATAD3A 55210 TCGA-A7-A26E-01 0 -ATAD3B 83858 TCGA-A7-A26E-01 0 -ATAD3C 219293 TCGA-A7-A26E-01 0 -AURKAIP1 54998 TCGA-A7-A26E-01 0 -ERCC5 2073 TCGA-A7-A26E-01 0 -ACP3 55 TCGA-A7-A26E-01 0 -ACAP3 116983 TCGA-A7-A26F-01 -2 -AGRN 375790 TCGA-A7-A26F-01 -2 -ATAD3A 55210 TCGA-A7-A26F-01 -2 Class 2 Class annotation -ATAD3B 83858 TCGA-A7-A26F-01 -2 Class 1 Class annotation -ATAD3C 219293 TCGA-A7-A26F-01 -2 -AURKAIP1 54998 TCGA-A7-A26F-01 -2 -ERCC5 2073 TCGA-A7-A26F-01 -2 Putative_Driver -ACP3 55 TCGA-A7-A26F-01 0 -ACAP3 116983 TCGA-A7-A26G-01 0 -AGRN 375790 TCGA-A7-A26G-01 0 -ATAD3A 55210 TCGA-A7-A26G-01 0 -ATAD3B 83858 TCGA-A7-A26G-01 0 -ATAD3C 219293 TCGA-A7-A26G-01 0 -AURKAIP1 54998 TCGA-A7-A26G-01 0 -ERCC5 2073 TCGA-A7-A26G-01 0 -ACP3 55 TCGA-A7-A26G-01 0 -ACAP3 116983 TCGA-A7-A26H-01 0 -AGRN 375790 TCGA-A7-A26H-01 0 -ATAD3A 55210 TCGA-A7-A26H-01 0 -ATAD3B 83858 TCGA-A7-A26H-01 0 -ATAD3C 219293 TCGA-A7-A26H-01 0 -AURKAIP1 54998 TCGA-A7-A26H-01 0 -ERCC5 2073 TCGA-A7-A26H-01 0 -ACP3 55 TCGA-A7-A26H-01 0 -ACAP3 116983 TCGA-A7-A26I-01 0 -AGRN 375790 TCGA-A7-A26I-01 0 -ATAD3A 55210 TCGA-A7-A26I-01 0 -ATAD3B 83858 TCGA-A7-A26I-01 0 -ATAD3C 219293 TCGA-A7-A26I-01 0 -AURKAIP1 54998 TCGA-A7-A26I-01 0 -ERCC5 2073 TCGA-A7-A26I-01 0 -ACP3 55 TCGA-A7-A26I-01 0 -ACAP3 116983 TCGA-A7-A26J-01 0 -AGRN 375790 TCGA-A7-A26J-01 0 -ATAD3A 55210 TCGA-A7-A26J-01 0 -ATAD3B 83858 TCGA-A7-A26J-01 0 -ATAD3C 219293 TCGA-A7-A26J-01 0 -AURKAIP1 54998 TCGA-A7-A26J-01 0 -ERCC5 2073 TCGA-A7-A26J-01 0 -ACP3 55 TCGA-A7-A26J-01 0 -ACAP3 116983 TCGA-A8-A06N-01 0 -AGRN 375790 TCGA-A8-A06N-01 0 -ATAD3A 55210 TCGA-A8-A06N-01 0 -ATAD3B 83858 TCGA-A8-A06N-01 0 -ATAD3C 219293 TCGA-A8-A06N-01 0 -AURKAIP1 54998 TCGA-A8-A06N-01 0 -ERCC5 2073 TCGA-A8-A06N-01 0 -ACP3 55 TCGA-A8-A06N-01 0 -ACAP3 116983 TCGA-A8-A06O-01 0 -AGRN 375790 TCGA-A8-A06O-01 0 -ATAD3A 55210 TCGA-A8-A06O-01 0 -ATAD3B 83858 TCGA-A8-A06O-01 0 -ATAD3C 219293 TCGA-A8-A06O-01 0 -AURKAIP1 54998 TCGA-A8-A06O-01 0 -ERCC5 2073 TCGA-A8-A06O-01 0 -ACP3 55 TCGA-A8-A06O-01 0 -ACAP3 116983 TCGA-A8-A06P-01 0 -AGRN 375790 TCGA-A8-A06P-01 0 -ATAD3A 55210 TCGA-A8-A06P-01 0 -ATAD3B 83858 TCGA-A8-A06P-01 0 -ATAD3C 219293 TCGA-A8-A06P-01 0 -AURKAIP1 54998 TCGA-A8-A06P-01 0 -ERCC5 2073 TCGA-A8-A06P-01 0 -ACP3 55 TCGA-A8-A06P-01 0 -ACAP3 116983 TCGA-A8-A06Q-01 0 -AGRN 375790 TCGA-A8-A06Q-01 0 -ATAD3A 55210 TCGA-A8-A06Q-01 0 -ATAD3B 83858 TCGA-A8-A06Q-01 0 -ATAD3C 219293 TCGA-A8-A06Q-01 0 -AURKAIP1 54998 TCGA-A8-A06Q-01 0 -ERCC5 2073 TCGA-A8-A06Q-01 0 -ACP3 55 TCGA-A8-A06Q-01 0 -ACAP3 116983 TCGA-A8-A06R-01 0 -AGRN 375790 TCGA-A8-A06R-01 0 -ATAD3A 55210 TCGA-A8-A06R-01 0 -ATAD3B 83858 TCGA-A8-A06R-01 0 -ATAD3C 219293 TCGA-A8-A06R-01 0 -AURKAIP1 54998 TCGA-A8-A06R-01 0 -ERCC5 2073 TCGA-A8-A06R-01 0 -ACP3 55 TCGA-A8-A06R-01 0 -ACAP3 116983 TCGA-A8-A06T-01 -1 -AGRN 375790 TCGA-A8-A06T-01 -1 -ATAD3A 55210 TCGA-A8-A06T-01 -1 -ATAD3B 83858 TCGA-A8-A06T-01 -1 -ATAD3C 219293 TCGA-A8-A06T-01 -1 -AURKAIP1 54998 TCGA-A8-A06T-01 -1 -ERCC5 2073 TCGA-A8-A06T-01 -1 -ACP3 55 TCGA-A8-A06T-01 0 -ACAP3 116983 TCGA-A8-A06U-01 -1 -AGRN 375790 TCGA-A8-A06U-01 -1 -ATAD3A 55210 TCGA-A8-A06U-01 -1 -ATAD3B 83858 TCGA-A8-A06U-01 -1 -ATAD3C 219293 TCGA-A8-A06U-01 -1 -AURKAIP1 54998 TCGA-A8-A06U-01 -1 -ERCC5 2073 TCGA-A8-A06U-01 -1 -ACP3 55 TCGA-A8-A06U-01 0 -ACAP3 116983 TCGA-A8-A06X-01 0 -AGRN 375790 TCGA-A8-A06X-01 0 -ATAD3A 55210 TCGA-A8-A06X-01 0 -ATAD3B 83858 TCGA-A8-A06X-01 0 -ATAD3C 219293 TCGA-A8-A06X-01 0 -AURKAIP1 54998 TCGA-A8-A06X-01 0 -ERCC5 2073 TCGA-A8-A06X-01 0 -ACP3 55 TCGA-A8-A06X-01 0 -ACAP3 116983 TCGA-A8-A06Y-01 -1 -AGRN 375790 TCGA-A8-A06Y-01 -1 -ATAD3A 55210 TCGA-A8-A06Y-01 -1 -ATAD3B 83858 TCGA-A8-A06Y-01 -1 -ATAD3C 219293 TCGA-A8-A06Y-01 -1 -AURKAIP1 54998 TCGA-A8-A06Y-01 -1 -ERCC5 2073 TCGA-A8-A06Y-01 -1 -ACP3 55 TCGA-A8-A06Y-01 0 -ACAP3 116983 TCGA-A8-A06Z-01 1 -AGRN 375790 TCGA-A8-A06Z-01 1 -ATAD3A 55210 TCGA-A8-A06Z-01 1 -ATAD3B 83858 TCGA-A8-A06Z-01 1 -ATAD3C 219293 TCGA-A8-A06Z-01 1 -AURKAIP1 54998 TCGA-A8-A06Z-01 1 -ERCC5 2073 TCGA-A8-A06Z-01 1 -ACP3 55 TCGA-A8-A06Z-01 0 -ACAP3 116983 TCGA-A8-A075-01 -1 -AGRN 375790 TCGA-A8-A075-01 -1 -ATAD3A 55210 TCGA-A8-A075-01 -1 -ATAD3B 83858 TCGA-A8-A075-01 -1 -ATAD3C 219293 TCGA-A8-A075-01 -1 -AURKAIP1 54998 TCGA-A8-A075-01 -1 -ERCC5 2073 TCGA-A8-A075-01 -1 -ACP3 55 TCGA-A8-A075-01 0 -ACAP3 116983 TCGA-A8-A076-01 -1 -AGRN 375790 TCGA-A8-A076-01 -1 -ATAD3A 55210 TCGA-A8-A076-01 -1 -ATAD3B 83858 TCGA-A8-A076-01 -1 -ATAD3C 219293 TCGA-A8-A076-01 -1 -AURKAIP1 54998 TCGA-A8-A076-01 -1 -ERCC5 2073 TCGA-A8-A076-01 -1 -ACP3 55 TCGA-A8-A076-01 0 -ACAP3 116983 TCGA-A8-A079-01 -1 -AGRN 375790 TCGA-A8-A079-01 -1 -ATAD3A 55210 TCGA-A8-A079-01 -1 -ATAD3B 83858 TCGA-A8-A079-01 -1 -ATAD3C 219293 TCGA-A8-A079-01 -1 -AURKAIP1 54998 TCGA-A8-A079-01 -1 -ERCC5 2073 TCGA-A8-A079-01 -1 -ACP3 55 TCGA-A8-A079-01 0 -ACAP3 116983 TCGA-A8-A07B-01 -1 -AGRN 375790 TCGA-A8-A07B-01 -1 -ATAD3A 55210 TCGA-A8-A07B-01 -1 -ATAD3B 83858 TCGA-A8-A07B-01 -1 -ATAD3C 219293 TCGA-A8-A07B-01 -1 -AURKAIP1 54998 TCGA-A8-A07B-01 -1 -ERCC5 2073 TCGA-A8-A07B-01 -1 -ACP3 55 TCGA-A8-A07B-01 0 -ACAP3 116983 TCGA-A8-A07E-01 0 -AGRN 375790 TCGA-A8-A07E-01 0 -ATAD3A 55210 TCGA-A8-A07E-01 0 -ATAD3B 83858 TCGA-A8-A07E-01 0 -ATAD3C 219293 TCGA-A8-A07E-01 0 -AURKAIP1 54998 TCGA-A8-A07E-01 0 -ERCC5 2073 TCGA-A8-A07E-01 0 -ACP3 55 TCGA-A8-A07E-01 0 -ACAP3 116983 TCGA-A8-A07F-01 -1 -AGRN 375790 TCGA-A8-A07F-01 -1 -ATAD3A 55210 TCGA-A8-A07F-01 -1 -ATAD3B 83858 TCGA-A8-A07F-01 -1 -ATAD3C 219293 TCGA-A8-A07F-01 -1 -AURKAIP1 54998 TCGA-A8-A07F-01 -1 -ERCC5 2073 TCGA-A8-A07F-01 -1 -ACP3 55 TCGA-A8-A07F-01 0 -ACAP3 116983 TCGA-A8-A07G-01 0 -AGRN 375790 TCGA-A8-A07G-01 0 -ATAD3A 55210 TCGA-A8-A07G-01 0 -ATAD3B 83858 TCGA-A8-A07G-01 0 -ATAD3C 219293 TCGA-A8-A07G-01 0 -AURKAIP1 54998 TCGA-A8-A07G-01 0 -ERCC5 2073 TCGA-A8-A07G-01 0 -ACP3 55 TCGA-A8-A07G-01 0 -ACAP3 116983 TCGA-A8-A07I-01 0 -AGRN 375790 TCGA-A8-A07I-01 0 -ATAD3A 55210 TCGA-A8-A07I-01 0 -ATAD3B 83858 TCGA-A8-A07I-01 0 -ATAD3C 219293 TCGA-A8-A07I-01 0 -AURKAIP1 54998 TCGA-A8-A07I-01 0 -ERCC5 2073 TCGA-A8-A07I-01 0 -ACP3 55 TCGA-A8-A07I-01 0 -ACAP3 116983 TCGA-A8-A07J-01 0 -AGRN 375790 TCGA-A8-A07J-01 0 -ATAD3A 55210 TCGA-A8-A07J-01 0 -ATAD3B 83858 TCGA-A8-A07J-01 0 -ATAD3C 219293 TCGA-A8-A07J-01 0 -AURKAIP1 54998 TCGA-A8-A07J-01 0 -ERCC5 2073 TCGA-A8-A07J-01 0 -ACP3 55 TCGA-A8-A07J-01 0 -ACAP3 116983 TCGA-A8-A07L-01 -1 -AGRN 375790 TCGA-A8-A07L-01 -1 -ATAD3A 55210 TCGA-A8-A07L-01 -1 -ATAD3B 83858 TCGA-A8-A07L-01 -1 -ATAD3C 219293 TCGA-A8-A07L-01 -1 -AURKAIP1 54998 TCGA-A8-A07L-01 -1 -ERCC5 2073 TCGA-A8-A07L-01 -1 -ACP3 55 TCGA-A8-A07L-01 0 -ACAP3 116983 TCGA-A8-A07O-01 0 -AGRN 375790 TCGA-A8-A07O-01 0 -ATAD3A 55210 TCGA-A8-A07O-01 0 -ATAD3B 83858 TCGA-A8-A07O-01 0 -ATAD3C 219293 TCGA-A8-A07O-01 0 -AURKAIP1 54998 TCGA-A8-A07O-01 0 -ERCC5 2073 TCGA-A8-A07O-01 0 -ACP3 55 TCGA-A8-A07O-01 0 -ACAP3 116983 TCGA-A8-A07P-01 0 -AGRN 375790 TCGA-A8-A07P-01 0 -ATAD3A 55210 TCGA-A8-A07P-01 0 -ATAD3B 83858 TCGA-A8-A07P-01 0 -ATAD3C 219293 TCGA-A8-A07P-01 0 -AURKAIP1 54998 TCGA-A8-A07P-01 0 -ERCC5 2073 TCGA-A8-A07P-01 0 -ACP3 55 TCGA-A8-A07P-01 0 -ACAP3 116983 TCGA-A8-A07R-01 0 -AGRN 375790 TCGA-A8-A07R-01 0 -ATAD3A 55210 TCGA-A8-A07R-01 0 -ATAD3B 83858 TCGA-A8-A07R-01 0 -ATAD3C 219293 TCGA-A8-A07R-01 0 -AURKAIP1 54998 TCGA-A8-A07R-01 0 -ERCC5 2073 TCGA-A8-A07R-01 0 -ACP3 55 TCGA-A8-A07R-01 0 -ACAP3 116983 TCGA-A8-A07S-01 0 -AGRN 375790 TCGA-A8-A07S-01 0 -ATAD3A 55210 TCGA-A8-A07S-01 0 -ATAD3B 83858 TCGA-A8-A07S-01 0 -ATAD3C 219293 TCGA-A8-A07S-01 0 -AURKAIP1 54998 TCGA-A8-A07S-01 0 -ERCC5 2073 TCGA-A8-A07S-01 0 -ACP3 55 TCGA-A8-A07S-01 0 -ACAP3 116983 TCGA-A8-A07U-01 0 -AGRN 375790 TCGA-A8-A07U-01 0 -ATAD3A 55210 TCGA-A8-A07U-01 0 -ATAD3B 83858 TCGA-A8-A07U-01 0 -ATAD3C 219293 TCGA-A8-A07U-01 0 -AURKAIP1 54998 TCGA-A8-A07U-01 0 -ERCC5 2073 TCGA-A8-A07U-01 0 -ACP3 55 TCGA-A8-A07U-01 0 -ACAP3 116983 TCGA-A8-A07W-01 0 -AGRN 375790 TCGA-A8-A07W-01 0 -ATAD3A 55210 TCGA-A8-A07W-01 0 -ATAD3B 83858 TCGA-A8-A07W-01 0 -ATAD3C 219293 TCGA-A8-A07W-01 0 -AURKAIP1 54998 TCGA-A8-A07W-01 0 -ERCC5 2073 TCGA-A8-A07W-01 0 -ACP3 55 TCGA-A8-A07W-01 0 -ACAP3 116983 TCGA-A8-A07Z-01 0 -AGRN 375790 TCGA-A8-A07Z-01 0 -ATAD3A 55210 TCGA-A8-A07Z-01 0 -ATAD3B 83858 TCGA-A8-A07Z-01 0 -ATAD3C 219293 TCGA-A8-A07Z-01 0 -AURKAIP1 54998 TCGA-A8-A07Z-01 0 -ERCC5 2073 TCGA-A8-A07Z-01 0 -ACP3 55 TCGA-A8-A07Z-01 0 -ACAP3 116983 TCGA-A8-A081-01 -1 -AGRN 375790 TCGA-A8-A081-01 -1 -ATAD3A 55210 TCGA-A8-A081-01 -1 -ATAD3B 83858 TCGA-A8-A081-01 -1 -ATAD3C 219293 TCGA-A8-A081-01 -1 -AURKAIP1 54998 TCGA-A8-A081-01 -1 -ERCC5 2073 TCGA-A8-A081-01 -1 -ACP3 55 TCGA-A8-A081-01 0 -ACAP3 116983 TCGA-A8-A082-01 0 -AGRN 375790 TCGA-A8-A082-01 0 -ATAD3A 55210 TCGA-A8-A082-01 0 -ATAD3B 83858 TCGA-A8-A082-01 0 -ATAD3C 219293 TCGA-A8-A082-01 0 -AURKAIP1 54998 TCGA-A8-A082-01 0 -ERCC5 2073 TCGA-A8-A082-01 0 -ACP3 55 TCGA-A8-A082-01 0 -ACAP3 116983 TCGA-A8-A083-01 0 -AGRN 375790 TCGA-A8-A083-01 0 -ATAD3A 55210 TCGA-A8-A083-01 0 -ATAD3B 83858 TCGA-A8-A083-01 0 -ATAD3C 219293 TCGA-A8-A083-01 0 -AURKAIP1 54998 TCGA-A8-A083-01 0 -ERCC5 2073 TCGA-A8-A083-01 0 -ACP3 55 TCGA-A8-A083-01 0 -ACAP3 116983 TCGA-A8-A084-01 -1 -AGRN 375790 TCGA-A8-A084-01 -1 -ATAD3A 55210 TCGA-A8-A084-01 -1 -ATAD3B 83858 TCGA-A8-A084-01 -1 -ATAD3C 219293 TCGA-A8-A084-01 -1 -AURKAIP1 54998 TCGA-A8-A084-01 -1 -ERCC5 2073 TCGA-A8-A084-01 -1 -ACP3 55 TCGA-A8-A084-01 0 -ACAP3 116983 TCGA-A8-A085-01 0 -AGRN 375790 TCGA-A8-A085-01 0 -ATAD3A 55210 TCGA-A8-A085-01 0 -ATAD3B 83858 TCGA-A8-A085-01 0 -ATAD3C 219293 TCGA-A8-A085-01 0 -AURKAIP1 54998 TCGA-A8-A085-01 0 -ERCC5 2073 TCGA-A8-A085-01 0 -ACP3 55 TCGA-A8-A085-01 0 -ACAP3 116983 TCGA-A8-A086-01 0 -AGRN 375790 TCGA-A8-A086-01 0 -ATAD3A 55210 TCGA-A8-A086-01 0 -ATAD3B 83858 TCGA-A8-A086-01 0 -ATAD3C 219293 TCGA-A8-A086-01 0 -AURKAIP1 54998 TCGA-A8-A086-01 0 -ERCC5 2073 TCGA-A8-A086-01 0 -ACP3 55 TCGA-A8-A086-01 0 -ACAP3 116983 TCGA-A8-A08A-01 0 -AGRN 375790 TCGA-A8-A08A-01 0 -ATAD3A 55210 TCGA-A8-A08A-01 0 -ATAD3B 83858 TCGA-A8-A08A-01 0 -ATAD3C 219293 TCGA-A8-A08A-01 0 -AURKAIP1 54998 TCGA-A8-A08A-01 0 -ERCC5 2073 TCGA-A8-A08A-01 0 -ACP3 55 TCGA-A8-A08A-01 0 -ACAP3 116983 TCGA-A8-A08B-01 0 -AGRN 375790 TCGA-A8-A08B-01 0 -ATAD3A 55210 TCGA-A8-A08B-01 0 -ATAD3B 83858 TCGA-A8-A08B-01 0 -ATAD3C 219293 TCGA-A8-A08B-01 0 -AURKAIP1 54998 TCGA-A8-A08B-01 0 -ERCC5 2073 TCGA-A8-A08B-01 0 -ACP3 55 TCGA-A8-A08B-01 0 -ACAP3 116983 TCGA-A8-A08C-01 0 -AGRN 375790 TCGA-A8-A08C-01 0 -ATAD3A 55210 TCGA-A8-A08C-01 0 -ATAD3B 83858 TCGA-A8-A08C-01 0 -ATAD3C 219293 TCGA-A8-A08C-01 0 -AURKAIP1 54998 TCGA-A8-A08C-01 0 -ERCC5 2073 TCGA-A8-A08C-01 0 -ACP3 55 TCGA-A8-A08C-01 0 -ACAP3 116983 TCGA-A8-A08F-01 0 -AGRN 375790 TCGA-A8-A08F-01 0 -ATAD3A 55210 TCGA-A8-A08F-01 0 -ATAD3B 83858 TCGA-A8-A08F-01 0 -ATAD3C 219293 TCGA-A8-A08F-01 0 -AURKAIP1 54998 TCGA-A8-A08F-01 0 -ERCC5 2073 TCGA-A8-A08F-01 0 -ACP3 55 TCGA-A8-A08F-01 0 -ACAP3 116983 TCGA-A8-A08G-01 0 -AGRN 375790 TCGA-A8-A08G-01 0 -ATAD3A 55210 TCGA-A8-A08G-01 0 -ATAD3B 83858 TCGA-A8-A08G-01 0 -ATAD3C 219293 TCGA-A8-A08G-01 0 -AURKAIP1 54998 TCGA-A8-A08G-01 0 -ERCC5 2073 TCGA-A8-A08G-01 0 -ACP3 55 TCGA-A8-A08G-01 0 -ACAP3 116983 TCGA-A8-A08H-01 0 -AGRN 375790 TCGA-A8-A08H-01 0 -ATAD3A 55210 TCGA-A8-A08H-01 0 -ATAD3B 83858 TCGA-A8-A08H-01 0 -ATAD3C 219293 TCGA-A8-A08H-01 0 -AURKAIP1 54998 TCGA-A8-A08H-01 0 -ERCC5 2073 TCGA-A8-A08H-01 0 -ACP3 55 TCGA-A8-A08H-01 0 -ACAP3 116983 TCGA-A8-A08I-01 -1 -AGRN 375790 TCGA-A8-A08I-01 -1 -ATAD3A 55210 TCGA-A8-A08I-01 -1 -ATAD3B 83858 TCGA-A8-A08I-01 -1 -ATAD3C 219293 TCGA-A8-A08I-01 -1 -AURKAIP1 54998 TCGA-A8-A08I-01 -1 -ERCC5 2073 TCGA-A8-A08I-01 -1 -ACP3 55 TCGA-A8-A08I-01 0 -ACAP3 116983 TCGA-A8-A08J-01 -1 -AGRN 375790 TCGA-A8-A08J-01 -1 -ATAD3A 55210 TCGA-A8-A08J-01 -1 -ATAD3B 83858 TCGA-A8-A08J-01 -1 -ATAD3C 219293 TCGA-A8-A08J-01 -1 -AURKAIP1 54998 TCGA-A8-A08J-01 -1 -ERCC5 2073 TCGA-A8-A08J-01 -1 -ACP3 55 TCGA-A8-A08J-01 0 -ACAP3 116983 TCGA-A8-A08L-01 0 -AGRN 375790 TCGA-A8-A08L-01 0 -ATAD3A 55210 TCGA-A8-A08L-01 0 -ATAD3B 83858 TCGA-A8-A08L-01 0 -ATAD3C 219293 TCGA-A8-A08L-01 0 -AURKAIP1 54998 TCGA-A8-A08L-01 0 -ERCC5 2073 TCGA-A8-A08L-01 0 -ACP3 55 TCGA-A8-A08L-01 0 -ACAP3 116983 TCGA-A8-A08O-01 -1 -AGRN 375790 TCGA-A8-A08O-01 -1 -ATAD3A 55210 TCGA-A8-A08O-01 -1 -ATAD3B 83858 TCGA-A8-A08O-01 -1 -ATAD3C 219293 TCGA-A8-A08O-01 -1 -AURKAIP1 54998 TCGA-A8-A08O-01 -1 -ERCC5 2073 TCGA-A8-A08O-01 -1 -ACP3 55 TCGA-A8-A08O-01 0 -ACAP3 116983 TCGA-A8-A08P-01 0 -AGRN 375790 TCGA-A8-A08P-01 0 -ATAD3A 55210 TCGA-A8-A08P-01 0 -ATAD3B 83858 TCGA-A8-A08P-01 0 -ATAD3C 219293 TCGA-A8-A08P-01 0 -AURKAIP1 54998 TCGA-A8-A08P-01 0 -ERCC5 2073 TCGA-A8-A08P-01 0 -ACP3 55 TCGA-A8-A08P-01 0 -ACAP3 116983 TCGA-A8-A08R-01 0 -AGRN 375790 TCGA-A8-A08R-01 0 -ATAD3A 55210 TCGA-A8-A08R-01 0 -ATAD3B 83858 TCGA-A8-A08R-01 0 -ATAD3C 219293 TCGA-A8-A08R-01 0 -AURKAIP1 54998 TCGA-A8-A08R-01 0 -ERCC5 2073 TCGA-A8-A08R-01 0 -ACP3 55 TCGA-A8-A08R-01 0 -ACAP3 116983 TCGA-A8-A08S-01 -1 -AGRN 375790 TCGA-A8-A08S-01 -1 -ATAD3A 55210 TCGA-A8-A08S-01 -1 -ATAD3B 83858 TCGA-A8-A08S-01 -1 -ATAD3C 219293 TCGA-A8-A08S-01 -1 -AURKAIP1 54998 TCGA-A8-A08S-01 -1 -ERCC5 2073 TCGA-A8-A08S-01 -1 -ACP3 55 TCGA-A8-A08S-01 0 -ACAP3 116983 TCGA-A8-A08T-01 0 -AGRN 375790 TCGA-A8-A08T-01 0 -ATAD3A 55210 TCGA-A8-A08T-01 0 -ATAD3B 83858 TCGA-A8-A08T-01 0 -ATAD3C 219293 TCGA-A8-A08T-01 0 -AURKAIP1 54998 TCGA-A8-A08T-01 0 -ERCC5 2073 TCGA-A8-A08T-01 0 -ACP3 55 TCGA-A8-A08T-01 0 -ACAP3 116983 TCGA-A8-A08X-01 0 -AGRN 375790 TCGA-A8-A08X-01 0 -ATAD3A 55210 TCGA-A8-A08X-01 0 -ATAD3B 83858 TCGA-A8-A08X-01 0 -ATAD3C 219293 TCGA-A8-A08X-01 0 -AURKAIP1 54998 TCGA-A8-A08X-01 0 -ERCC5 2073 TCGA-A8-A08X-01 0 -ACP3 55 TCGA-A8-A08X-01 0 -ACAP3 116983 TCGA-A8-A08Z-01 0 -AGRN 375790 TCGA-A8-A08Z-01 0 -ATAD3A 55210 TCGA-A8-A08Z-01 0 -ATAD3B 83858 TCGA-A8-A08Z-01 0 -ATAD3C 219293 TCGA-A8-A08Z-01 0 -AURKAIP1 54998 TCGA-A8-A08Z-01 0 -ERCC5 2073 TCGA-A8-A08Z-01 0 -ACP3 55 TCGA-A8-A08Z-01 0 -ACAP3 116983 TCGA-A8-A090-01 0 -AGRN 375790 TCGA-A8-A090-01 0 -ATAD3A 55210 TCGA-A8-A090-01 0 -ATAD3B 83858 TCGA-A8-A090-01 0 -ATAD3C 219293 TCGA-A8-A090-01 0 -AURKAIP1 54998 TCGA-A8-A090-01 0 -ERCC5 2073 TCGA-A8-A090-01 0 -ACP3 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TCGA-EW-A2FV-01 0 +AURKAIP1 54998 TCGA-EW-A2FV-01 0 +ERCC5 2073 TCGA-EW-A2FV-01 0 +ACP3 55 TCGA-EW-A2FV-01 0 +ACAP3 116983 TCGA-EW-A2FW-01 -1 +AGRN 375790 TCGA-EW-A2FW-01 -1 +ATAD3A 55210 TCGA-EW-A2FW-01 -1 +ATAD3B 83858 TCGA-EW-A2FW-01 -1 +ATAD3C 219293 TCGA-EW-A2FW-01 -1 +AURKAIP1 54998 TCGA-EW-A2FW-01 -1 +ERCC5 2073 TCGA-EW-A2FW-01 -1 +ACP3 55 TCGA-EW-A2FW-01 0 +ACAP3 116983 TCGA-GI-A2C8-01 -1 +AGRN 375790 TCGA-GI-A2C8-01 -1 +ATAD3A 55210 TCGA-GI-A2C8-01 -1 +ATAD3B 83858 TCGA-GI-A2C8-01 -1 +ATAD3C 219293 TCGA-GI-A2C8-01 -1 +AURKAIP1 54998 TCGA-GI-A2C8-01 -1 +ERCC5 2073 TCGA-GI-A2C8-01 -1 +ACP3 55 TCGA-GI-A2C8-01 0 +ACAP3 116983 TEST_SAMPLE_1 0 +AGRN 375790 TEST_SAMPLE_1 0 +ATAD3A 55210 TEST_SAMPLE_1 0 +ATAD3B 83858 TEST_SAMPLE_1 0 +ATAD3C 219293 TEST_SAMPLE_1 0 +AURKAIP1 54998 TEST_SAMPLE_1 0 +ERCC5 2073 TEST_SAMPLE_1 0 +ACP3 55 TEST_SAMPLE_1 0 +ACAP3 116983 TEST_SAMPLE_2 0 +AGRN 375790 TEST_SAMPLE_2 0 +ATAD3A 55210 TEST_SAMPLE_2 0 +ATAD3B 83858 TEST_SAMPLE_2 0 +ATAD3C 219293 TEST_SAMPLE_2 0 +AURKAIP1 54998 TEST_SAMPLE_2 0 +ERCC5 2073 TEST_SAMPLE_2 0 +ACP3 55 TEST_SAMPLE_2 0 +ACAP3 116983 TEST_SAMPLE_3 0 +AGRN 375790 TEST_SAMPLE_3 0 +ATAD3A 55210 TEST_SAMPLE_3 0 +ATAD3B 83858 TEST_SAMPLE_3 0 +ATAD3C 219293 TEST_SAMPLE_3 0 +AURKAIP1 54998 TEST_SAMPLE_3 0 +ERCC5 2073 TEST_SAMPLE_3 0 +ACP3 55 TEST_SAMPLE_3 0 +ACAP3 116983 TEST_SAMPLE_4 0 +AGRN 375790 TEST_SAMPLE_4 0 +ATAD3A 55210 TEST_SAMPLE_4 0 +ATAD3B 83858 TEST_SAMPLE_4 0 +ATAD3C 219293 TEST_SAMPLE_4 0 +AURKAIP1 54998 TEST_SAMPLE_4 0 +ERCC5 2073 TEST_SAMPLE_4 0 +ACP3 55 TEST_SAMPLE_4 0 +ACAP3 116983 TEST_SAMPLE_7 0 +AGRN 375790 TEST_SAMPLE_7 0 +ATAD3A 55210 TEST_SAMPLE_7 0 +ATAD3B 83858 TEST_SAMPLE_7 0 +ATAD3C 219293 TEST_SAMPLE_7 0 +AURKAIP1 54998 TEST_SAMPLE_7 0 +ERCC5 2073 TEST_SAMPLE_7 0 +ACP3 55 TEST_SAMPLE_7 0 +ACAP3 116983 TEST_SAMPLE_8 0 +AGRN 375790 TEST_SAMPLE_8 0 +ATAD3A 55210 TEST_SAMPLE_8 0 +ATAD3B 83858 TEST_SAMPLE_8 0 +ATAD3C 219293 TEST_SAMPLE_8 0 +AURKAIP1 54998 TEST_SAMPLE_8 0 +ERCC5 2073 TEST_SAMPLE_8 0 +ACP3 55 TEST_SAMPLE_8 0 +ACAP3 116983 TEST_SAMPLE_12 0 +AGRN 375790 TEST_SAMPLE_12 0 +ATAD3A 55210 TEST_SAMPLE_12 0 +ATAD3B 83858 TEST_SAMPLE_12 0 +ATAD3C 219293 TEST_SAMPLE_12 0 +AURKAIP1 54998 TEST_SAMPLE_12 0 +ERCC5 2073 TEST_SAMPLE_12 0 +ACP3 55 TEST_SAMPLE_12 0 +ACAP3 116983 TEST_SAMPLE_13 0 +AGRN 375790 TEST_SAMPLE_13 0 +ATAD3A 55210 TEST_SAMPLE_13 0 +ATAD3B 83858 TEST_SAMPLE_13 0 +ATAD3C 219293 TEST_SAMPLE_13 0 +AURKAIP1 54998 TEST_SAMPLE_13 0 +ERCC5 2073 TEST_SAMPLE_13 0 +ACP3 55 TEST_SAMPLE_13 0 +ACAP3 116983 TEST_SAMPLE_14 0 +AGRN 375790 TEST_SAMPLE_14 0 +ATAD3A 55210 TEST_SAMPLE_14 0 +ATAD3B 83858 TEST_SAMPLE_14 0 +ATAD3C 219293 TEST_SAMPLE_14 0 +AURKAIP1 54998 TEST_SAMPLE_14 0 +ERCC5 2073 TEST_SAMPLE_14 0 +ACP3 55 TEST_SAMPLE_14 0 +ACAP3 116983 TEST_SAMPLE_15 0 +AGRN 375790 TEST_SAMPLE_15 0 +ATAD3A 55210 TEST_SAMPLE_15 0 +ATAD3B 83858 TEST_SAMPLE_15 0 +ATAD3C 219293 TEST_SAMPLE_15 0 +AURKAIP1 54998 TEST_SAMPLE_15 0 +ERCC5 2073 TEST_SAMPLE_15 0 +ACP3 55 TEST_SAMPLE_15 0 diff --git a/core/src/test/scripts/test_data/study_es_0/meta_cna_discrete.txt b/core/src/test/scripts/test_data/study_es_0/meta_cna_discrete.txt index 8bcc1727d1f..3cc10e71e0c 100644 --- a/core/src/test/scripts/test_data/study_es_0/meta_cna_discrete.txt +++ b/core/src/test/scripts/test_data/study_es_0/meta_cna_discrete.txt @@ -6,3 +6,4 @@ show_profile_in_analysis_tab: true profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. profile_name: Putative copy-number alterations from GISTIC data_filename: data_cna_discrete.txt +namespaces: MyNamespace,MyNamespace2 diff --git a/db-scripts/src/main/resources/cgds.sql b/db-scripts/src/main/resources/cgds.sql index f28432e323d..00581970e2b 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -601,6 +601,7 @@ CREATE TABLE `sample_cna_event` ( `CNA_EVENT_ID` int(255) NOT NULL, `SAMPLE_ID` int(11) NOT NULL, `GENETIC_PROFILE_ID` int(11) NOT NULL, + `ANNOTATION_JSON` JSON, KEY (`GENETIC_PROFILE_ID`,`SAMPLE_ID`), PRIMARY KEY (`CNA_EVENT_ID`, `SAMPLE_ID`, `GENETIC_PROFILE_ID`), FOREIGN KEY (`CNA_EVENT_ID`) REFERENCES `cna_event` (`CNA_EVENT_ID`), @@ -760,4 +761,5 @@ CREATE TABLE `resource_study` ( ); -- THIS MUST BE KEPT IN SYNC WITH db.version PROPERTY IN pom.xml -INSERT INTO info VALUES ('2.12.14', NULL); +INSERT INTO info VALUES ('2.12.15', NULL); + diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index c3c4fa5a069..c948177be2c 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -992,3 +992,7 @@ ALTER TABLE `structural_variant` DROP COLUMN `SITE2_EXON`; ALTER TABLE `structural_variant` DROP COLUMN `CENTER`; ALTER TABLE `structural_variant` DROP COLUMN `EXTERNAL_ANNOTATION`; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.14"; + +##version: 2.12.15 +ALTER TABLE `sample_cna_event` ADD COLUMN `ANNOTATION_JSON` JSON AFTER `GENETIC_PROFILE_ID`; +UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.15"; diff --git a/model/src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java b/model/src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java index 054c68164c0..cbeb2862d16 100644 --- a/model/src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java +++ b/model/src/main/java/org/cbioportal/model/DiscreteCopyNumberData.java @@ -1,13 +1,19 @@ package org.cbioportal.model; +import com.fasterxml.jackson.annotation.JsonRawValue; +import io.swagger.annotations.ApiModelProperty; + import java.io.Serializable; import javax.validation.constraints.NotNull; public class DiscreteCopyNumberData extends Alteration implements Serializable { - @NotNull private Integer alteration; - + + @JsonRawValue + @ApiModelProperty(dataType = "java.util.Map") + private String annotationJson; + public Integer getAlteration() { return alteration; } @@ -15,4 +21,13 @@ public Integer getAlteration() { public void setAlteration(Integer alteration) { this.alteration = alteration; } + + public String getAnnotationJson() { + return annotationJson; + } + + public void setAnnotationJson(String annotationJson) { + this.annotationJson = annotationJson; + } + } diff --git a/model/src/main/java/org/cbioportal/model/MolecularProfile.java b/model/src/main/java/org/cbioportal/model/MolecularProfile.java index 3fc68a66f5a..b7aefb1c903 100644 --- a/model/src/main/java/org/cbioportal/model/MolecularProfile.java +++ b/model/src/main/java/org/cbioportal/model/MolecularProfile.java @@ -36,6 +36,22 @@ public enum ImportType { DISCRETE_LONG; } + public enum CnaDatatype { + DISCRETE, + DISCRETE_LONG; + + public static CnaDatatype findByName(String name) { + CnaDatatype result = null; + for (CnaDatatype value : values()) { + if (value.name().equalsIgnoreCase(name)) { + result = value; + break; + } + } + return result; + } + } + private Integer molecularProfileId; @NotNull private String stableId; diff --git a/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml b/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml index 0caffb5697d..b896d57e32d 100644 --- a/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml +++ b/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml @@ -6,6 +6,7 @@ cna_event.ENTREZ_GENE_ID as entrezGeneId, cna_event.ALTERATION AS alteration, + sample_cna_event.ANNOTATION_JSON as annotationJson, genetic_profile.STABLE_ID AS molecularProfileId, sample.STABLE_ID AS sampleId, patient.STABLE_ID AS patientId, diff --git a/persistence/persistence-mybatis/src/test/resources/testSql.sql b/persistence/persistence-mybatis/src/test/resources/testSql.sql index b8e4a3adc1b..bdfcef6f34f 100644 --- a/persistence/persistence-mybatis/src/test/resources/testSql.sql +++ b/persistence/persistence-mybatis/src/test/resources/testSql.sql @@ -421,9 +421,9 @@ INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION) VALUES (1,207,-2) INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION) VALUES (2,208,2); INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION) VALUES (3,207,2); -INSERT INTO sample_cna_event (CNA_EVENT_ID,SAMPLE_ID,GENETIC_PROFILE_ID) VALUES (1,1,2); -INSERT INTO sample_cna_event (CNA_EVENT_ID,SAMPLE_ID,GENETIC_PROFILE_ID) VALUES (2,1,2); -INSERT INTO sample_cna_event (CNA_EVENT_ID,SAMPLE_ID,GENETIC_PROFILE_ID) VALUES (3,2,2); +INSERT INTO sample_cna_event (CNA_EVENT_ID,SAMPLE_ID,GENETIC_PROFILE_ID, ANNOTATION_JSON) VALUES (1,1,2, '{"columnName":{"fieldName":"fieldValue"}}'); +INSERT INTO sample_cna_event (CNA_EVENT_ID,SAMPLE_ID,GENETIC_PROFILE_ID, ANNOTATION_JSON) VALUES (2,1,2, '{"columnName":{"fieldName":"fieldValue"}}'); +INSERT INTO sample_cna_event (CNA_EVENT_ID,SAMPLE_ID,GENETIC_PROFILE_ID, ANNOTATION_JSON) VALUES (3,2,2, '{"columnName":{"fieldName":"fieldValue"}}'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (1,2,1, 'Putative_Driver', 'Pathogenic', 'Tier 1', 'Highly Actionable'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (3,2,2, 'Putative_Passenger', 'Pathogenic', 'Tier 2', 'Potentially Actionable'); diff --git a/pom.xml b/pom.xml index 7e7c4a53d61..a45530aab87 100644 --- a/pom.xml +++ b/pom.xml @@ -315,7 +315,7 @@ 720 - 2.12.14 + 2.12.15 diff --git a/service/src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java b/service/src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java index 79a74b2ca70..c862e7924ce 100644 --- a/service/src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java +++ b/service/src/main/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImpl.java @@ -1,7 +1,12 @@ package org.cbioportal.service.impl; -import org.cbioportal.model.*; +import org.cbioportal.model.CNA; +import org.cbioportal.model.CopyNumberCount; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.DiscreteCopyNumberData; import org.cbioportal.model.GeneFilterQuery; +import org.cbioportal.model.GeneMolecularData; +import org.cbioportal.model.MolecularProfile; import org.cbioportal.model.meta.BaseMeta; import org.cbioportal.persistence.DiscreteCopyNumberRepository; import org.cbioportal.service.DiscreteCopyNumberService; diff --git a/service/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java b/service/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java index beaa290db64..199865c11bd 100644 --- a/service/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java +++ b/service/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java @@ -64,6 +64,64 @@ public void getDiscreteCopyNumbersInMultipleMolecularProfilesHomdelOrAmp() { Assert.assertEquals(toStrings(returned), toStrings(actual)); } + @Test + public void getDiscreteCopyNumbersWithAnnotationJson() { + List returned = Arrays.asList( + discreteCopyNumberData("sample1", "study1", -2), + discreteCopyNumberData("sample2", "study2", 2) + ); + returned.get(0).setAnnotationJson("{\"columnName\":{\"fieldName\":\"fieldValue\"}}"); + List profiles = Arrays.asList("profile1", "profile2"); + List samples = Arrays.asList("sample1", "sample2"); + List geneIds = Arrays.asList(0, 1); + List alterationTypes = Arrays.asList(-2, 2); + + Mockito.when(discreteCopyNumberRepository.getDiscreteCopyNumbersInMultipleMolecularProfiles( + profiles, + samples, + geneIds, + alterationTypes, + PROJECTION + )) + .thenReturn( + returned + ); + + List actual = discreteCopyNumberService.getDiscreteCopyNumbersInMultipleMolecularProfiles( + profiles, samples, geneIds, alterationTypes, PROJECTION + ); + + Assert.assertEquals(toStrings(returned), toStrings(actual)); + } + @Test + public void getDiscreteCopyNumbersWithoutAnnotationJson() { + List returned = Arrays.asList( + discreteCopyNumberData("sample1", "study1", -2), + discreteCopyNumberData("sample2", "study2", 2) + ); + List profiles = Arrays.asList("profile1", "profile2"); + List samples = Arrays.asList("sample1", "sample2"); + List geneIds = Arrays.asList(0, 1); + List alterationTypes = Arrays.asList(-2, 2); + + Mockito.when(discreteCopyNumberRepository.getDiscreteCopyNumbersInMultipleMolecularProfiles( + profiles, + samples, + geneIds, + alterationTypes, + PROJECTION + )) + .thenReturn( + returned + ); + + List actual = discreteCopyNumberService.getDiscreteCopyNumbersInMultipleMolecularProfiles( + profiles, samples, geneIds, alterationTypes, PROJECTION + ); + Assert.assertNull(returned.get(0).getAnnotationJson()); + Assert.assertEquals(toStrings(returned), toStrings(actual)); + } + @Test public void getDiscreteCopyNumbersInMultipleMolecularProfilesAllAlterationTypes() { List returned = Arrays.asList( diff --git a/web/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java b/web/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java index 88a8d99ea78..ba3d05f857b 100644 --- a/web/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java +++ b/web/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java @@ -46,8 +46,9 @@ import org.cbioportal.model.ClinicalDataCount; import org.cbioportal.model.ClinicalEvent; import org.cbioportal.model.ClinicalEventData; -import org.cbioportal.model.DataAccessToken; import org.cbioportal.model.CopyNumberSeg; +import org.cbioportal.model.DataAccessToken; +import org.cbioportal.model.DiscreteCopyNumberData; import org.cbioportal.model.Gene; import org.cbioportal.model.GenePanel; import org.cbioportal.model.GenePanelToGene; @@ -64,15 +65,8 @@ import org.cbioportal.model.ResourceDefinition; import org.cbioportal.model.Sample; import org.cbioportal.model.SampleList; -import org.cbioportal.session_service.domain.Session; import org.cbioportal.model.TypeOfCancer; -import org.cbioportal.web.parameter.CustomDataSession; -import org.cbioportal.web.parameter.PageSettings; -import org.cbioportal.web.parameter.PageSettingsData; -import org.cbioportal.web.parameter.StudyPageSettings; -import org.cbioportal.web.parameter.VirtualStudy; -import org.cbioportal.web.parameter.VirtualStudyData; -import org.cbioportal.web.CustomAttributeWithData; +import org.cbioportal.session_service.domain.Session; import org.cbioportal.web.mixin.CancerStudyMixin; import org.cbioportal.web.mixin.ClinicalAttributeCountMixin; import org.cbioportal.web.mixin.ClinicalAttributeMixin; @@ -82,6 +76,7 @@ import org.cbioportal.web.mixin.ClinicalEventMixin; import org.cbioportal.web.mixin.CopyNumberSegMixin; import org.cbioportal.web.mixin.DataAccessTokenMixin; +import org.cbioportal.web.mixin.DiscreteCopyNumberDataMixin; import org.cbioportal.web.mixin.GeneMixin; import org.cbioportal.web.mixin.GenePanelMixin; import org.cbioportal.web.mixin.GenePanelToGeneMixin; @@ -98,9 +93,16 @@ import org.cbioportal.web.mixin.ResourceDefinitionMixin; import org.cbioportal.web.mixin.SampleListMixin; import org.cbioportal.web.mixin.SampleMixin; -import org.cbioportal.web.mixin.SessionMixin; import org.cbioportal.web.mixin.SessionDataMixin; +import org.cbioportal.web.mixin.SessionMixin; import org.cbioportal.web.mixin.TypeOfCancerMixin; +import org.cbioportal.web.parameter.CustomDataSession; +import org.cbioportal.web.parameter.PageSettings; +import org.cbioportal.web.parameter.PageSettingsData; +import org.cbioportal.web.parameter.StudyPageSettings; +import org.cbioportal.web.parameter.VirtualStudy; +import org.cbioportal.web.parameter.VirtualStudyData; +import org.cbioportal.web.CustomAttributeWithData; public class CustomObjectMapper extends ObjectMapper { @@ -118,6 +120,7 @@ public CustomObjectMapper() { mixinMap.put(ClinicalEventData.class, ClinicalEventDataMixin.class); mixinMap.put(CopyNumberSeg.class, CopyNumberSegMixin.class); mixinMap.put(DataAccessToken.class, DataAccessTokenMixin.class); + mixinMap.put(DiscreteCopyNumberData.class, DiscreteCopyNumberDataMixin.class); mixinMap.put(Gene.class, GeneMixin.class); mixinMap.put(GenePanel.class, GenePanelMixin.class); mixinMap.put(GenePanelToGene.class, GenePanelToGeneMixin.class); diff --git a/web/src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java b/web/src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java new file mode 100644 index 00000000000..f8c904f252b --- /dev/null +++ b/web/src/main/java/org/cbioportal/web/mixin/DiscreteCopyNumberDataMixin.java @@ -0,0 +1,9 @@ +package org.cbioportal.web.mixin; + +import com.fasterxml.jackson.annotation.JsonProperty; + +public class DiscreteCopyNumberDataMixin { + + @JsonProperty("namespaceColumns") + private String annotationJson; +} \ No newline at end of file diff --git a/web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java b/web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java index 0bf7adbfa65..da53f3137dd 100644 --- a/web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java @@ -41,6 +41,7 @@ public class DiscreteCopyNumberControllerTest { private static final String TEST_SAMPLE_STABLE_ID_1 = "test_sample_stable_id_1"; private static final int TEST_ENTREZ_GENE_ID_1 = 1; private static final int TEST_ALTERATION_1 = 1; + private static final String TEST_ANNOTATION_JSON_1 = "{\"columnName\":{\"fieldName\":\"fieldValue\"}}"; private static final String TEST_HUGO_GENE_SYMBOL_1 = "test_hugo_gene_symbol_1"; private static final String TEST_TYPE_1 = "test_type_1"; private static final String TEST_CYTOBAND_1 = "test_cytoband_1"; @@ -102,6 +103,7 @@ public void getDiscreteCopyNumbersInMolecularProfileBySampleListIdDefaultProject .andExpect(MockMvcResultMatchers.jsonPath("$[0].sampleId").value(TEST_SAMPLE_STABLE_ID_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].entrezGeneId").value(TEST_ENTREZ_GENE_ID_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].alteration").value(TEST_ALTERATION_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].namespaceColumns.columnName.fieldName").value("fieldValue")) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[1].molecularProfileId") .value(TEST_MOLECULAR_PROFILE_STABLE_ID_2)) @@ -111,6 +113,25 @@ public void getDiscreteCopyNumbersInMolecularProfileBySampleListIdDefaultProject .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist()); } + @Test + public void getDiscreteCopyNumbersWithoutAnnotationJson() throws Exception { + + List discreteCopyNumberDataList = createExampleDiscreteCopyNumberData(); + discreteCopyNumberDataList.get(0).setAnnotationJson(null); + Mockito.when(discreteCopyNumberService.getDiscreteCopyNumbersInMolecularProfileBySampleListId( + Mockito.any(), Mockito.any(), Mockito.any(), + Mockito.any(), Mockito.any())).thenReturn(discreteCopyNumberDataList); + + mockMvc.perform(MockMvcRequestBuilders.get("/molecular-profiles/test_molecular_profile_id/discrete-copy-number") + .param("sampleListId", TEST_SAMPLE_LIST_ID) + .param("discreteCopyNumberEventType", DiscreteCopyNumberEventType.HOMDEL_AND_AMP.name()) + .accept(MediaType.APPLICATION_JSON)) + .andExpect(MockMvcResultMatchers.status().isOk()) + .andExpect(MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON)) + .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2))) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].namespaceColumns").doesNotExist()); + } + @Test public void getDiscreteCopyNumbersInMolecularProfileBySampleListIdDetailedProjection() throws Exception { @@ -339,6 +360,7 @@ private List createExampleDiscreteCopyNumberData() { discreteCopyNumberData1.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1); discreteCopyNumberData1.setAlteration(TEST_ALTERATION_1); discreteCopyNumberDataList.add(discreteCopyNumberData1); + discreteCopyNumberData1.setAnnotationJson(TEST_ANNOTATION_JSON_1); DiscreteCopyNumberData discreteCopyNumberData2 = new DiscreteCopyNumberData(); discreteCopyNumberData2.setMolecularProfileId(TEST_MOLECULAR_PROFILE_STABLE_ID_2); discreteCopyNumberData2.setSampleId(TEST_SAMPLE_STABLE_ID_2);