From 11d72175569d337df5a87501486a09ffb32fa0c2 Mon Sep 17 00:00:00 2001 From: Bas Leenknegt Date: Thu, 8 Sep 2022 13:47:07 +0200 Subject: [PATCH 1/3] Add new CNA long data format --- .../mskcc/cbio/portal/dao/DaoCnaEvent.java | 7 +- .../portal/dao/DaoGeneticProfileSamples.java | 2 +- .../cbio/portal/model/CanonicalGene.java | 2 - .../org/mskcc/cbio/portal/model/CnaEvent.java | 6 +- .../scripts/GeneticAlterationImporter.java | 59 + .../scripts/ImportCnaDiscreteLongData.java | 331 + .../portal/scripts/ImportProfileData.java | 42 +- .../portal/scripts/ImportTabDelimData.java | 580 +- .../org/mskcc/cbio/portal/util/CnaUtil.java | 112 + .../scripts/importer/allowed_data_types.txt | 2 + .../portal/dao/TestDaoGeneticProfile.java | 10 +- .../TestImportCnaDiscreteLongData.java | 438 ++ .../scripts/TestImportTabDelimData.java | 10 +- .../data_cna_discrete_import_test.txt | 26 + core/src/test/resources/seed_mini.sql | 9 + .../scripts/system_tests_validate_studies.py | 16 + .../study_es_0/data_cna_discrete.txt | 6314 ++++++++++++++++- .../study_es_0/meta_cna_discrete.txt | 4 +- .../data_clinical_samples.txt | 850 +++ .../data_cna_discrete.txt | 9 + .../data_cna_pd_annotations.txt | 2 +- .../data_mutations_extended.maf | 3 + .../meta_clinical_samples.txt | 4 + .../meta_cna_discrete.txt | 10 + .../meta_mutations_extended.txt | 10 + .../meta_study.txt | 10 + docs/Testing.md | 7 +- .../web/DiscreteCopyNumberControllerTest.java | 1 - 28 files changed, 8540 insertions(+), 336 deletions(-) create mode 100644 core/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java create mode 100644 core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java create mode 100644 core/src/main/java/org/mskcc/cbio/portal/util/CnaUtil.java create mode 100644 core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java create mode 100644 core/src/test/resources/data_cna_discrete_import_test.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_clinical_samples.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_cna_discrete.txt rename core/src/test/scripts/test_data/{study_es_0 => study_es_0_legacy_cna_discrete}/data_cna_pd_annotations.txt (92%) create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_mutations_extended.maf create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_clinical_samples.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_cna_discrete.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_mutations_extended.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_study.txt 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 4c5676ba2e7..6a7ab06ae9c 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 @@ -70,8 +70,11 @@ public static void addCaseCnaEvent(CnaEvent cnaEvent, boolean newCnaEvent) throw || (cnaEvent.getDriverTiersFilter() != null && !cnaEvent.getDriverTiersFilter().isEmpty() - && !cnaEvent.getDriverTiersFilter().toLowerCase().equals("na"))) { - MySQLbulkLoader.getMySQLbulkLoader("alteration_driver_annotation").insertRecord( + && !cnaEvent.getDriverTiersFilter().toLowerCase().equals("na")) + ) { + MySQLbulkLoader + .getMySQLbulkLoader("alteration_driver_annotation") + .insertRecord( Long.toString(eventId), Integer.toString(cnaEvent.getCnaProfileId()), Integer.toString(cnaEvent.getSampleId()), diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfileSamples.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfileSamples.java index ef194fe614a..b8346957354 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfileSamples.java +++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfileSamples.java @@ -56,7 +56,7 @@ private DaoGeneticProfileSamples() {} * @return number of rows added. * @throws DaoException Data Access Exception. */ - public static int addGeneticProfileSamples(int geneticProfileId, ArrayList orderedSampleList) + public static int addGeneticProfileSamples(int geneticProfileId, List orderedSampleList) throws DaoException { Connection con = null; PreparedStatement pstmt = null; diff --git a/core/src/main/java/org/mskcc/cbio/portal/model/CanonicalGene.java b/core/src/main/java/org/mskcc/cbio/portal/model/CanonicalGene.java index 5540ecc715e..b3ed90d5db1 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/model/CanonicalGene.java +++ b/core/src/main/java/org/mskcc/cbio/portal/model/CanonicalGene.java @@ -32,8 +32,6 @@ package org.mskcc.cbio.portal.model; -import org.mskcc.cbio.portal.dao.DaoException; - import java.util.*; import java.io.Serializable; 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 7da265d1b3c..2dc35b96335 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 @@ -72,7 +72,7 @@ public void setGene(CanonicalGene gene) { public void setEntrezGeneId(long entrezGeneId) { setGene(DaoGeneOptimized.getInstance().getGene(entrezGeneId)); if (gene == null) { - throw new IllegalArgumentException("Could not find entrez gene id: "+entrezGeneId); + throw new IllegalArgumentException("Could not find entrez gene id: " + entrezGeneId); } } @@ -99,6 +99,10 @@ public int hashCode() { return hash; } + /** + * Compare by gene and alteration, + * but not by eventId + */ @Override public boolean equals(Object obj) { if (obj == null) { diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java new file mode 100644 index 00000000000..32aa43f2380 --- /dev/null +++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java @@ -0,0 +1,59 @@ +package org.mskcc.cbio.portal.scripts; + +import org.mskcc.cbio.portal.dao.DaoException; +import org.mskcc.cbio.portal.dao.DaoGeneticAlteration; +import org.mskcc.cbio.portal.model.CanonicalGene; +import org.mskcc.cbio.portal.util.ProgressMonitor; + +import java.util.*; + +import static java.lang.String.format; + +public class GeneticAlterationImporter { + + private final int geneticProfileId; + private Set importSetOfGenes = new HashSet<>(); + private DaoGeneticAlteration daoGeneticAlteration; + + public GeneticAlterationImporter( + int geneticProfileId, + DaoGeneticAlteration daoGeneticAlteration + ) { + this.geneticProfileId = geneticProfileId; + this.daoGeneticAlteration = daoGeneticAlteration; + } + + /** + * Check that we have not already imported information regarding this gene. + * This is an important check, because a GISTIC or RAE file may contain + * multiple rows for the same gene, and we only want to import the first row. + */ + public boolean store( + String[] values, + CanonicalGene gene, + String geneSymbol + ) throws DaoException { + try { + if (importSetOfGenes.add(gene.getEntrezGeneId())) { + daoGeneticAlteration.addGeneticAlterations(geneticProfileId, gene.getEntrezGeneId(), values); + return true; + } else { + String geneSymbolMessage = ""; + if (geneSymbol != null && !geneSymbol.equalsIgnoreCase(gene.getHugoGeneSymbolAllCaps())) { + geneSymbolMessage = " (given as alias in your file as: " + geneSymbol + ")"; + } + ProgressMonitor.logWarning(format( + "Gene %s (%d)%s found to be duplicated in your file. Duplicated row will be ignored!", + gene.getHugoGeneSymbolAllCaps(), + gene.getEntrezGeneId(), + geneSymbolMessage) + ); + return false; + } + } catch (Exception e) { + throw new RuntimeException("Aborted: Error found for row starting with " + geneSymbol + ": " + e.getMessage()); + } + } + + +} 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 new file mode 100644 index 00000000000..c76b0af0b8e --- /dev/null +++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java @@ -0,0 +1,331 @@ +/* + * Copyright (c) 2018 - 2022 The Hyve B.V. + * This code is licensed under the GNU Affero General Public License (AGPL), + * version 3, or (at your option) any later version. + */ + +/* + * This file is part of cBioPortal. + * + * cBioPortal is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ +package org.mskcc.cbio.portal.scripts; + +import com.google.common.base.*; +import com.google.common.collect.*; +import org.mskcc.cbio.portal.dao.*; +import org.mskcc.cbio.portal.model.*; +import org.mskcc.cbio.portal.util.*; + +import java.io.*; +import java.util.Optional; +import java.util.*; +import java.util.stream.*; + +import static com.google.common.collect.Lists.*; +import static java.lang.String.*; + +public class ImportCnaDiscreteLongData { + + private final File cnaFile; + private final int geneticProfileId; + private final GeneticAlterationImporter geneticAlterationGeneImporter; + private String genePanel; + private final DaoGeneOptimized daoGene; + private CnaUtil cnaUtil; + private Set existingCnaEvents = new HashSet<>(); + private int samplesSkipped = 0; + + private final ArrayList sampleIdGeneticProfileIds = new ArrayList<>(); + + public ImportCnaDiscreteLongData( + File cnaFile, + int geneticProfileId, + String genePanel, + DaoGeneOptimized daoGene, + DaoGeneticAlteration daoGeneticAlteration + ) { + this.cnaFile = cnaFile; + this.geneticProfileId = geneticProfileId; + this.genePanel = genePanel; + this.daoGene = daoGene; + this.geneticAlterationGeneImporter = new GeneticAlterationImporter(geneticProfileId, daoGeneticAlteration); + } + + public void importData() throws Exception { + FileReader reader = new FileReader(this.cnaFile); + BufferedReader buf = new BufferedReader(reader); + + // Pass first line with headers to util: + String line = buf.readLine(); + int lineIndex = 1; + this.cnaUtil = new CnaUtil(line); + + GeneticProfile geneticProfile = DaoGeneticProfile.getGeneticProfileById(geneticProfileId); + + boolean isDiscretizedCnaProfile = geneticProfile != null + && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.COPY_NUMBER_ALTERATION + && geneticProfile.showProfileInAnalysisTab(); + + if (isDiscretizedCnaProfile) { + existingCnaEvents.addAll(DaoCnaEvent.getAllCnaEvents()); + MySQLbulkLoader.bulkLoadOn(); + } + + CnaImportData toImport = new CnaImportData(); + + while ((line = buf.readLine()) != null) { + lineIndex++; + ProgressMonitor.incrementCurValue(); + ConsoleUtil.showProgress(); + this.extractDataToImport(geneticProfile, line, lineIndex, toImport); + } + + DaoGeneticProfileSamples.addGeneticProfileSamples( + geneticProfileId, + newArrayList(toImport.eventsTable.columnKeySet()) + ); + + for (Long entrezId : toImport.eventsTable.rowKeySet()) { + boolean added = storeGeneticAlterations(toImport, entrezId); + if (added) { + storeCnaEvents(toImport, entrezId); + } else { + ProgressMonitor.logWarning("Values not added to gene with entrezId: " + entrezId + ". Skip creation of cna events."); + } + } + + ProgressMonitor.setCurrentMessage(" --> total number of samples skipped (normal samples): " + getSamplesSkipped() + ); + buf.close(); + MySQLbulkLoader.flushAll(); + } + + /** + * First we collect all the events + * to import all events related to a single gene in one query: + */ + public void extractDataToImport( + GeneticProfile geneticProfile, + String line, + int lineIndex, + CnaImportData importContainer + ) throws Exception { + boolean hasData = !line.startsWith("#") && line.trim().length() > 0; + if (!hasData) { + return; + } + String[] lineParts = line.split("\t", -1); + CanonicalGene gene = this.getGene(cnaUtil.getEntrezSymbol(lineParts), lineParts, cnaUtil); + importContainer.genes.add(gene); + + if (gene == null) { + return; + } + + int cancerStudyId = geneticProfile.getCancerStudyId(); + + String sampleIdStr = cnaUtil.getSampleIdStr(lineParts); + Sample sample = findSample(sampleIdStr, cancerStudyId); + createSampleProfile(sample); + + long entrezId = gene.getEntrezGeneId(); + int sampleId = sample.getInternalId(); + CnaEventImportData eventContainer = new CnaEventImportData(); + Table geneBySampleEventTable = importContainer.eventsTable; + + if (!geneBySampleEventTable.contains(entrezId, sample.getInternalId())) { + geneBySampleEventTable.put(entrezId, sampleId, eventContainer); + } else { + ProgressMonitor.logWarning(format("Skipping line %d with duplicate gene %d and sample %d", lineIndex, entrezId, sampleId)); + } + + eventContainer.geneticEvent = cnaUtil.createEvent(geneticProfile, sample.getInternalId(), lineParts); + } + + /** + * Store all cna events related to a single gene + */ + private void storeCnaEvents(CnaImportData toImport, Long entrezId) throws DaoException { + List events = toImport.eventsTable + .row(entrezId) + .values() + .stream() + .filter(v -> v.geneticEvent != null) + .map(v -> v.geneticEvent) + .collect(Collectors.toList()); + CnaUtil.storeCnaEvents(existingCnaEvents, events); + } + + /** + * Store all events related to a single gene + */ + private boolean storeGeneticAlterations(CnaImportData toImport, Long entrezId) throws DaoException { + String[] values = toImport.eventsTable + .row(entrezId) + .values() + .stream() + .filter(v -> v.geneticEvent != null) + .map(v -> "" + v + .geneticEvent + .getAlteration() + .getCode() + ) + .toArray(String[]::new); + + Optional gene = toImport.genes + .stream() + .filter(g -> g != null && g.getEntrezGeneId() == entrezId) + .findFirst(); + + if (!gene.isPresent()) { + ProgressMonitor.logWarning("No gene found for entrezId: " + entrezId); + return false; + } + + String geneSymbol = !Strings.isNullOrEmpty(gene.get().getHugoGeneSymbolAllCaps()) + ? gene.get().getHugoGeneSymbolAllCaps() + : "" + entrezId; + + return this.geneticAlterationGeneImporter.store(values, gene.get(), geneSymbol); + } + + /** + * @return null when no gene could be found + */ + private CanonicalGene getGene( + long entrez, + String[] parts, + CnaUtil util + ) { + + String hugoSymbol = util.getHugoSymbol(parts); + + if (Strings.isNullOrEmpty(hugoSymbol) && entrez == 0) { + ProgressMonitor.logWarning("Ignoring line with no Hugo_Symbol and no Entrez_Id"); + return null; + } + if (entrez != 0) { + //try entrez: + return this.daoGene.getGene(entrez); + } else if (!Strings.isNullOrEmpty(hugoSymbol)) { + //try hugo: + if (hugoSymbol.contains("///") || hugoSymbol.contains("---")) { + // Ignore gene IDs separated by ///. This indicates that + // the line contains information regarding multiple genes, and + // we cannot currently handle this. + // Also, ignore gene IDs that are specified as ---. This indicates + // the line contains information regarding an unknown gene, and + // we cannot currently handle this. + ProgressMonitor.logWarning("Ignoring gene ID: " + hugoSymbol); + return null; + } + int ix = hugoSymbol.indexOf("|"); + if (ix > 0) { + hugoSymbol = hugoSymbol.substring(0, ix); + } + List genes = daoGene.getGene(hugoSymbol, true); + if (genes.size() > 1) { + throw new IllegalStateException("Found multiple genes for Hugo symbol " + hugoSymbol + " while importing cna"); + } + return genes.get(0); + } else { + ProgressMonitor.logWarning("Entrez_Id " + entrez + " not found. Record will be skipped for this gene."); + return null; + } + } + + /** + * Find sample and create sample profile when needed + * + * @return boolean created or not + */ + public boolean createSampleProfile( + Sample sample + ) throws Exception { + boolean inDatabase = DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId); + Integer genePanelID = (genePanel == null) ? null : GeneticProfileUtil.getGenePanelId(genePanel); + SampleIdGeneticProfileId toCreate = new SampleIdGeneticProfileId(sample.getInternalId(), geneticProfileId); + boolean isQueued = this.sampleIdGeneticProfileIds.contains(toCreate); + if (!inDatabase && !isQueued) { + DaoSampleProfile.addSampleProfile(sample.getInternalId(), geneticProfileId, genePanelID); + this.sampleIdGeneticProfileIds.add(toCreate); + return true; + } + return false; + } + + + private static class SampleIdGeneticProfileId { + public int sampleId; + public int geneticProfileId; + + public SampleIdGeneticProfileId(int sampleId, int geneticProfileId) { + this.sampleId = sampleId; + this.geneticProfileId = geneticProfileId; + } + + @Override + public boolean equals(Object o) { + if (this == o) + return true; + if (o == null || getClass() != o.getClass()) + return false; + + SampleIdGeneticProfileId that = (SampleIdGeneticProfileId) o; + return sampleId == that.sampleId + && geneticProfileId == that.geneticProfileId; + } + } + + /** + * Find sample and create sample profile when needed + */ + public Sample findSample( + String sampleId, + int cancerStudyId + ) throws Exception { + Sample sample = DaoSample.getSampleByCancerStudyAndSampleId( + cancerStudyId, + StableIdUtil.getSampleId(sampleId) + ); + // can be null in case of 'normal' sample, throw exception if not 'normal' and sample not found in db + if (sample == null) { + if (StableIdUtil.isNormal(sampleId)) { + samplesSkipped++; + return null; + } else { + throw new RuntimeException("Unknown sample id '" + StableIdUtil.getSampleId(sampleId)); + } + } + return sample; + } + + private class CnaImportData { + // Entrez ID x Sample ID table: + public Table eventsTable = HashBasedTable.create(); + public Set genes = new HashSet<>(); + } + + private class CnaEventImportData { + public int line; + public CnaEvent geneticEvent; + public String geneSymbol; + } + + public int getSamplesSkipped() { + return samplesSkipped; + } +} + 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 b902ee5574c..0f27636f6a7 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 @@ -33,13 +33,11 @@ package org.mskcc.cbio.portal.scripts; import java.io.*; -import java.util.ArrayList; -import java.util.Date; import java.util.Set; import joptsimple.*; -import org.cbioportal.model.EntityType; +import org.mskcc.cbio.portal.dao.*; import org.mskcc.cbio.portal.model.*; import org.mskcc.cbio.portal.util.*; @@ -52,6 +50,15 @@ public class ImportProfileData extends ConsoleRunnable { public void run() { + DaoGeneOptimized daoGene; + DaoGeneticAlteration daoGeneticAlteration; + try { + daoGene = DaoGeneOptimized.getInstance(); + daoGeneticAlteration = DaoGeneticAlteration.getInstance(); + } catch (DaoException e) { + throw new RuntimeException("Could not create dao instances", e); + } + try { // Parse arguments // using a real options parser, helps avoid bugs @@ -110,11 +117,36 @@ public void run() { genericAssayProfileImporter.importData(numLines); } else { // use ImportTabDelimData importer for non-patient level data - ImportTabDelimData genericAssayProfileImporter = new ImportTabDelimData(dataFile, geneticProfile.getTargetLine(), geneticProfile.getGeneticProfileId(), genePanel, geneticProfile.getOtherMetaDataField("generic_entity_meta_properties")); + ImportTabDelimData genericAssayProfileImporter = new ImportTabDelimData( + dataFile, + geneticProfile.getTargetLine(), + geneticProfile.getGeneticProfileId(), + genePanel, + geneticProfile.getOtherMetaDataField("generic_entity_meta_properties"), + daoGeneticAlteration + ); genericAssayProfileImporter.importData(numLines); } + } else if( + geneticProfile.getGeneticAlterationType() == GeneticAlterationType.COPY_NUMBER_ALTERATION + && geneticProfile.getDatatype().equals("DISCRETE_LONG") + ) { + ImportCnaDiscreteLongData importer = new ImportCnaDiscreteLongData( + dataFile, + geneticProfile.getGeneticProfileId(), + genePanel, + daoGene, + daoGeneticAlteration + ); + importer.importData(); } else { - ImportTabDelimData importer = new ImportTabDelimData(dataFile, geneticProfile.getTargetLine(), geneticProfile.getGeneticProfileId(), genePanel); + ImportTabDelimData importer = new ImportTabDelimData( + dataFile, + geneticProfile.getTargetLine(), + geneticProfile.getGeneticProfileId(), + genePanel, + daoGeneticAlteration + ); String pdAnnotationsFilename = geneticProfile.getOtherMetaDataField("pd_annotations_filename"); if (pdAnnotationsFilename != null && !"".equals(pdAnnotationsFilename)) { importer.setPdAnnotationsFile(new File(dataFile.getParent(), pdAnnotationsFilename)); diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java index cd151f75708..b984abf4388 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java @@ -28,7 +28,7 @@ * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see . -*/ + */ package org.mskcc.cbio.portal.scripts; @@ -41,8 +41,6 @@ import org.apache.commons.lang3.ArrayUtils; import org.cbioportal.model.EntityType; -import org.cbioportal.model.GeneticEntity; -import org.cbioportal.model.meta.GenericAssayMeta; import org.mskcc.cbio.portal.dao.*; import org.mskcc.cbio.portal.model.*; import org.mskcc.cbio.portal.util.*; @@ -60,8 +58,7 @@ public class ImportTabDelimData { public static final String CNA_VALUE_HOMOZYGOUS_DELETION = "-2"; public static final String CNA_VALUE_PARTIAL_DELETION = "-1.5"; public static final String CNA_VALUE_ZERO = "0"; - private HashSet importSetOfGenes = new HashSet(); - private HashSet importedGeneticEntitySet = new HashSet<>(); + private HashSet importedGeneticEntitySet = new HashSet<>(); private File dataFile; private String targetLine; private int geneticProfileId; @@ -73,25 +70,37 @@ public class ImportTabDelimData { private String genericEntityProperties; private File pdAnnotationsFile; private Map, Map> pdAnnotations; + private final GeneticAlterationImporter geneticAlterationImporter; /** * Constructor. * - * @param dataFile Data File containing Copy Number Alteration, MRNA Expression Data, or protein RPPA data - * @param targetLine The line we want to import. - * If null, all lines are imported. - * @param geneticProfileId GeneticProfile ID. - * @param genePanel GenePanel + * @param dataFile Data File containing Copy Number Alteration, MRNA Expression Data, or protein RPPA data + * @param targetLine The line we want to import. + * If null, all lines are imported. + * @param geneticProfileId GeneticProfile ID. + * @param genePanel GenePanel * @param genericEntityProperties Generic Assay Entities. * - * @deprecated : TODO shall we deprecate this feature (i.e. the targetLine)? + * @deprecated : TODO shall we deprecate this feature (i.e. the targetLine)? */ - public ImportTabDelimData(File dataFile, String targetLine, int geneticProfileId, String genePanel, String genericEntityProperties) { + public ImportTabDelimData( + File dataFile, + String targetLine, + int geneticProfileId, + String genePanel, + String genericEntityProperties, + DaoGeneticAlteration daoGeneticAlteration + ) { this.dataFile = dataFile; this.targetLine = targetLine; this.geneticProfileId = geneticProfileId; this.genePanel = genePanel; this.genericEntityProperties = genericEntityProperties; + this.geneticAlterationImporter = new GeneticAlterationImporter( + geneticProfileId, + daoGeneticAlteration + ); } /** @@ -102,13 +111,20 @@ public ImportTabDelimData(File dataFile, String targetLine, int geneticProfileId * If null, all lines are imported. * @param geneticProfileId GeneticProfile ID. * - * @deprecated : TODO shall we deprecate this feature (i.e. the targetLine)? + * @deprecated : TODO shall we deprecate this feature (i.e. the targetLine)? */ - public ImportTabDelimData(File dataFile, String targetLine, int geneticProfileId, String genePanel) { + public ImportTabDelimData( + File dataFile, + String targetLine, + int geneticProfileId, + String genePanel, + DaoGeneticAlteration daoGeneticAlteration + ) { this.dataFile = dataFile; this.targetLine = targetLine; this.geneticProfileId = geneticProfileId; this.genePanel = genePanel; + this.geneticAlterationImporter = new GeneticAlterationImporter(geneticProfileId, daoGeneticAlteration); } /** @@ -117,10 +133,16 @@ public ImportTabDelimData(File dataFile, String targetLine, int geneticProfileId * @param dataFile Data File containing Copy Number Alteration, MRNA Expression Data, or protein RPPA data * @param geneticProfileId GeneticProfile ID. */ - public ImportTabDelimData(File dataFile, int geneticProfileId, String genePanel) { + public ImportTabDelimData( + File dataFile, + int geneticProfileId, + String genePanel, + DaoGeneticAlteration daoGeneticAlteration + ) { this.dataFile = dataFile; this.geneticProfileId = geneticProfileId; this.genePanel = genePanel; + this.geneticAlterationImporter = new GeneticAlterationImporter(geneticProfileId, daoGeneticAlteration); } /** @@ -137,21 +159,21 @@ public void importData(int numLines) throws IOException, DaoException { BufferedReader buf = new BufferedReader(reader); String headerLine = buf.readLine(); String parts[] = headerLine.split("\t"); - + //Whether data regards CNA or RPPA: - boolean isDiscretizedCnaProfile = geneticProfile!=null - && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.COPY_NUMBER_ALTERATION - && geneticProfile.showProfileInAnalysisTab(); - boolean isRppaProfile = geneticProfile!=null - && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.PROTEIN_LEVEL - && "Composite.Element.Ref".equalsIgnoreCase(parts[0]); - boolean isGsvaProfile = geneticProfile!=null - && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.GENESET_SCORE - && parts[0].equalsIgnoreCase("geneset_id"); - boolean isGenericAssayProfile = geneticProfile!=null - && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.GENERIC_ASSAY - && parts[0].equalsIgnoreCase("ENTITY_STABLE_ID"); - + boolean isDiscretizedCnaProfile = geneticProfile != null + && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.COPY_NUMBER_ALTERATION + && geneticProfile.showProfileInAnalysisTab(); + boolean isRppaProfile = geneticProfile != null + && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.PROTEIN_LEVEL + && "Composite.Element.Ref".equalsIgnoreCase(parts[0]); + boolean isGsvaProfile = geneticProfile != null + && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.GENESET_SCORE + && parts[0].equalsIgnoreCase("geneset_id"); + boolean isGenericAssayProfile = geneticProfile != null + && geneticProfile.getGeneticAlterationType() == GeneticAlterationType.GENERIC_ASSAY + && parts[0].equalsIgnoreCase("ENTITY_STABLE_ID"); + int numRecordsToAdd = 0; int samplesSkipped = 0; try { @@ -176,7 +198,7 @@ public void importData(int numLines) throws IOException, DaoException { } else if (hugoSymbolIndex == -1 && entrezGeneIdIndex == -1) { throw new RuntimeException("Error: at least one of the following columns should be present: Hugo_Symbol or Entrez_Gene_Id"); } - + String sampleIds[]; sampleIds = new String[parts.length - sampleStartIndex]; System.arraycopy(parts, sampleStartIndex, sampleIds, 0, parts.length - sampleStartIndex); @@ -189,12 +211,12 @@ public void importData(int numLines) throws IOException, DaoException { pdAnnotationsForStableSampleIds = readPdAnnotations(this.pdAnnotationsFile); } // link Samples to the genetic profile - ArrayList orderedSampleList = new ArrayList(); - ArrayList filteredSampleIndices = new ArrayList(); + ArrayList orderedSampleList = new ArrayList(); + ArrayList filteredSampleIndices = new ArrayList(); this.pdAnnotations = new HashMap<>(); for (int i = 0; i < sampleIds.length; i++) { Sample sample = DaoSample.getSampleByCancerStudyAndSampleId(geneticProfile.getCancerStudyId(), - StableIdUtil.getSampleId(sampleIds[i])); + StableIdUtil.getSampleId(sampleIds[i])); // can be null in case of 'normal' sample, throw exception if not 'normal' and sample not found in db if (sample == null) { if (StableIdUtil.isNormal(sampleIds[i])) { @@ -213,7 +235,7 @@ public void importData(int numLines) throws IOException, DaoException { orderedSampleList.add(sample.getInternalId()); if (pdAnnotationsForStableSampleIds != null) { Set> keys = new HashSet<>(pdAnnotationsForStableSampleIds.keySet()); - for (Map.Entry stableSampleIdToGeneKey: keys) { + for (Map.Entry stableSampleIdToGeneKey : keys) { if (stableSampleIdToGeneKey.getKey().equals(sample.getStableId())) { Long entrezGeneId = stableSampleIdToGeneKey.getValue(); Map pdAnnotationsDetails = pdAnnotationsForStableSampleIds.get(stableSampleIdToGeneKey); @@ -232,56 +254,53 @@ public void importData(int numLines) throws IOException, DaoException { if (samplesSkipped > 0) { ProgressMonitor.setCurrentMessage(" --> total number of samples skipped (normal samples): " + samplesSkipped); } - ProgressMonitor.setCurrentMessage(" --> total number of data lines: " + (numLines-1)); - + ProgressMonitor.setCurrentMessage(" --> total number of data lines: " + (numLines - 1)); + DaoGeneticProfileSamples.addGeneticProfileSamples(geneticProfileId, orderedSampleList); - + //Gene cache: DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance(); - + //Object to insert records in the generic 'genetic_alteration' table: DaoGeneticAlteration daoGeneticAlteration = DaoGeneticAlteration.getInstance(); - + //cache for data found in cna_event' table: - Map existingCnaEvents = null; + Set existingCnaEvents = new HashSet<>(); if (isDiscretizedCnaProfile) { - existingCnaEvents = new HashMap(); - for (CnaEvent.Event event : DaoCnaEvent.getAllCnaEvents()) { - existingCnaEvents.put(event, event); - } + existingCnaEvents.addAll(DaoCnaEvent.getAllCnaEvents()); MySQLbulkLoader.bulkLoadOn(); } // load entities map from database Map genericAssayStableIdToEntityIdMap = Collections.emptyMap(); - if (isGenericAssayProfile) { - genericAssayStableIdToEntityIdMap = GenericAssayMetaUtils.buildGenericAssayStableIdToEntityIdMap(); + if (isGenericAssayProfile) { + genericAssayStableIdToEntityIdMap = GenericAssayMetaUtils.buildGenericAssayStableIdToEntityIdMap(); } - + int lenParts = parts.length; - + String line = buf.readLine(); while (line != null) { ProgressMonitor.incrementCurValue(); ConsoleUtil.showProgress(); boolean recordAdded = false; - + // either parse line as geneset or gene for importing into 'genetic_alteration' table if (isGsvaProfile) { - recordAdded = parseGenesetLine(line, lenParts, sampleStartIndex, genesetIdIndex, - filteredSampleIndices, daoGeneticAlteration); + recordAdded = parseGenesetLine(line, lenParts, sampleStartIndex, genesetIdIndex, + filteredSampleIndices, daoGeneticAlteration); } else if (isGenericAssayProfile) { - recordAdded = parseGenericAssayLine(line, lenParts, sampleStartIndex, genericAssayIdIndex, - filteredSampleIndices, daoGeneticAlteration, genericAssayStableIdToEntityIdMap); + recordAdded = parseGenericAssayLine(line, lenParts, sampleStartIndex, genericAssayIdIndex, + filteredSampleIndices, daoGeneticAlteration, genericAssayStableIdToEntityIdMap); } else { - recordAdded = parseLine(line, lenParts, sampleStartIndex, - hugoSymbolIndex, entrezGeneIdIndex, rppaGeneRefIndex, - isRppaProfile, isDiscretizedCnaProfile, - daoGene, - filteredSampleIndices, orderedSampleList, - existingCnaEvents, daoGeneticAlteration); + recordAdded = parseLine(line, lenParts, sampleStartIndex, + hugoSymbolIndex, entrezGeneIdIndex, rppaGeneRefIndex, + isRppaProfile, isDiscretizedCnaProfile, + daoGene, + filteredSampleIndices, orderedSampleList, + existingCnaEvents); } - + // increment number of records added or entries skipped if (recordAdded) { numRecordsToAdd++; @@ -289,13 +308,13 @@ public void importData(int numLines) throws IOException, DaoException { else { entriesSkipped++; } - + line = buf.readLine(); } if (MySQLbulkLoader.isBulkLoad()) { - MySQLbulkLoader.flushAll(); + MySQLbulkLoader.flushAll(); } - + if (isRppaProfile) { ProgressMonitor.setCurrentMessage(" --> total number of extra records added because of multiple genes in one line: " + nrExtraRecords); } @@ -304,13 +323,13 @@ public void importData(int numLines) throws IOException, DaoException { } if (numRecordsToAdd == 0) { - throw new DaoException ("Something has gone wrong! I did not save any records" + - " to the database!"); + throw new DaoException("Something has gone wrong! I did not save any records" + + " to the database!"); } } finally { buf.close(); - } + } } private Map, Map> readPdAnnotations(File pdAnnotationsFile) { @@ -367,143 +386,141 @@ private Map, Map> readPdAnnotations(File } reader.close(); } catch (IOException e) { - throw new RuntimeException("Can't read PD annotation file", e); + throw new RuntimeException("Can't read PD annotation file", e); } return pdAnnotations; } /** - * Attempt to create a genetic_alteration record based on the current line read from a profile data file. - *
    - *
  1. Commented out lines and blank lines are always skipped (returns false) - *
  2. The line is split into columns by the tab delimiter - *
  3. The involved genes (list of entrez_gene_ids) are determined: - *
      - *
    1. Hugo_Symbol and Entrez_Gene_Id column indices are read and validated - *
    2. if neither are available, the line is skipped - *
    3. if Hugo_Symbol contains '///' or '---', the line is skipped - *
    4. rppaProfile parsing has special rules for determining the involved genes - *
    5. if Entrez_Gene_Id is available, use that to determine the involved genes - *
    6. if Hugo_Symbol is available, use that to determine the involved genes (truncate symbols with '|' in them) - *
    7. if the involved genes list is still empty, the line is skipped (returns false) - *
    - *
  4. Both gene_alias and gene records are examined to see how many genes of type 'miRNA' are matched - *
  5. If any matched record is of type 'miRNA': - *
      - *
    • Loop through each gene or gene_alias of type 'miRNA' and attempt to store the record under that gene in genetic_alteration - *
    • If no records were successfully stored in genetic_alteration, log the failure - *
    - *
  6. If no matched record is of type 'miRNA': - *
  7. if there is exactly 1 involved gene (using only the gene table if sufficient, or gene_alias if neccessary): - *
      - *
    1. if this is a 'discretizedCnaProfile', normalize the CNA values and create a list of cnaEvents to be added - *
    2. attempt to store the record in genetic_alteration - *
    3. if the record is successfully stored (not duplicated), create (or update) records in sample_cna_event for the created list of cnaEvents (if any) - *
    - *
  8. if there are several involved genes and the profile is an rppaProfile, loop through the genes; for each one: - *
      - *
    1. attempt to store the record under that gene in genetic_alteration - *
    2. count the number of successfully imported records (for logging) - *
    - *
      - *
    • after looping through all involved genes, check whether any records were successfully stored in genetic_alteration - if not log the failure - *
    - *
  9. if there are several involved genes and the profile is not an rppaProfile, log a failure to import the current line due to ambiguous gene symbol - *
- *
  • If a record was (or more than one were) successfully stored in genetic_alteration, return true ; else false - * - *

    - * During the import of any single profile data file, at most one record per Entrez_Gene_Id will be successfuly imported to genetic_alteration. - * Each attempt to import is done through a call to the function storeGeneticAlterations(). - * That function will check an instance variable importSetOfGenes, and if the gene has been previously imported, no new attempt is made (failure). - * Each time a gene is successfully imported, it is added to importSetOfGenes. - *

    - * MicroRNA are treated specially because of the possible presence of constructed combination forms (such as 'MIR-100/100*' and 'MIR-100/100'). - * In these cases a Hugo_Symbol such as 'hsa-mir-100' may be expected to match the (fake) Entrez_Gene_Id for both of these combination forms. - * In that case, we want to import several copies of the genetic alteration profile line .. one for each matched gene of type 'miRNA'. - * This allows the visualization of both CNA event profiles for the microRNA precursor with expression profiles for the microRNA mature form. - *

    - * The current implementation of this code does not attempt to "merge" / "unify" lines in the profile data file which have duplicated Entrez_Gene_Id. - * Instead, the first encountered line which maps to the Entrez_Gene_Id will be stored as a record in genetic_alteration (returns true). - * Later lines which attempt to store a record with that Entrez_Gene_Id will not be stored as a record in genetic_alteration (returns false). - * For microRNA gene aliases it is possible that complex interactions will occur, where an earlier line in the data file stores a record under several Entrez_Gene_Ids, and a later line in the file fails to store records under some of those previously 'used' Entrez_Gene_Ids, but succeeds in storing a record under one or more not previously used Entrez_Gene_Ids. So a microRNA line from the file may be imported "partially successfully" (returns true). - *

    - * Examples Cases:
    - * Gene records are P1, P2, P3, P4 (protein coding), M1, M2, M3 (microRNA). - * Gene_Symbol AMA is gene_alias for M1 and M2, Gene_Symbol AMB is gene_alias for M2 and M3, Gene_Symbol AAMBIG is gene_alias for P3 and P4. Gene_Symbol AMIXED is gene_alias for P1 and M3. - *

    - * Case_1 (the last two lines will be skipped and logged like "Gene P1 (#) found to be duplicated in your file. Duplicated row will be ignored!")
    - * - *
    Hugo_SymbolSample1... - *
    P10... - *
    P20... - *
    P10... - *
    P10... - *
    - *

    - * Case_2 (the last line will be skipped and logged like "Gene M1 (#) (given as alias in your file as: AMA) found to be duplicated in your file. Duplicated row will be ignored!" , "Gene M2 (#) (given as alias in your file as: AMA) found to be duplicated in your file. Duplicated row will be ignored!" , "Could not store microRNA or RPPA data" )
    - * - *
    Hugo_SymbolSample1... - *
    AMA0... - *
    AMA0... - *
    - *

    - * Case_3 (the last line in the file will fail with log messages like "Gene symbol AAMBIG found to be ambiguous. Record will be skipped for this gene.")
    - * - *
    Hugo_SymbolSample1... - *
    P10... - *
    P20... - *
    AAMBIG0... - *
    - *

    - * Case_4 (the second to last line will partially succeed, storing a record in genetic_alteration for gene M3 but failing for M2 with a log message like "Gene M2 (#) (given as alias in your file as: AMB) found to be duplicated in your file. Duplicated row will be ignored!" ; the last line in the file will fail with log messages like "Gene M3 (#) (given as alias in your file as: AMIXED) found to be duplicated in your file. Duplicated row will be ignored!" , "Gene symbol AMIXED found to be ambiguous (a mixture of microRNA and other types). Record will be skipped for this gene.")
    - * - *
    Hugo_SymbolSample1... - *
    AMA0... - *
    AMB0... - *
    AMIXED0... - *
    - * - * @param line the line from the profile data file to be parsed - * @param nrColumns the number of columns, defined by the header line - * @param sampleStartIndex the index of the first column with a sample name in the header field - * @param hugoSymbolIndex the index of the column Hugo_Symbol - * @param entrezGeneIdIndex the index of the column Entrez_Gene_Id - * @param rppaGeneRefIndex the index of the column Composite.Element.Ref - * @param isRppaProfile true if this is an rppa profile (i.e. alteration type is PROTEIN_LEVEL and the first column is Composite.Element.Ref) - * @param isDiscretizedCnaProfile true if this is a discretized CNA profile (i.e. alteration type COPY_NUMBER_ALTERATION and showProfileInAnalysisTab is true) - * @param daoGene an instance of DaoGeneOptimized ... for use in resolving gene symbols - * @param filteredSampleIndicesList not used (dead code) - * @param orderedSampleList a list of the internal sample ids corresponding to the sample names in the header line - * @param existingCnaEvents a collection of CnaEvents, to be added to or updated during parsing of individual lines - * @param daoGeneticAlteration in instance of DaoGeneticAlteration ... for use in storing records in the genetic_alteration table - * @return true if any record was stored in genetic_alteration, else false - * @throws DaoException if any DaoException is thrown while using daoGene or daoGeneticAlteration - */ - private boolean parseLine(String line, int nrColumns, int sampleStartIndex, - int hugoSymbolIndex, int entrezGeneIdIndex, int rppaGeneRefIndex, - boolean isRppaProfile, boolean isDiscretizedCnaProfile, - DaoGeneOptimized daoGene, - List filteredSampleIndices, List orderedSampleList, - Map existingCnaEvents, DaoGeneticAlteration daoGeneticAlteration - ) throws DaoException { - + * Attempt to create a genetic_alteration record based on the current line read from a profile data file. + *

      + *
    1. Commented out lines and blank lines are always skipped (returns false) + *
    2. The line is split into columns by the tab delimiter + *
    3. The involved genes (list of entrez_gene_ids) are determined: + *
        + *
      1. Hugo_Symbol and Entrez_Gene_Id column indices are read and validated + *
      2. if neither are available, the line is skipped + *
      3. if Hugo_Symbol contains '///' or '---', the line is skipped + *
      4. rppaProfile parsing has special rules for determining the involved genes + *
      5. if Entrez_Gene_Id is available, use that to determine the involved genes + *
      6. if Hugo_Symbol is available, use that to determine the involved genes (truncate symbols with '|' in them) + *
      7. if the involved genes list is still empty, the line is skipped (returns false) + *
      + *
    4. Both gene_alias and gene records are examined to see how many genes of type 'miRNA' are matched + *
    5. If any matched record is of type 'miRNA': + *
        + *
      • Loop through each gene or gene_alias of type 'miRNA' and attempt to store the record under that gene in genetic_alteration + *
      • If no records were successfully stored in genetic_alteration, log the failure + *
      + *
    6. If no matched record is of type 'miRNA': + *
    7. if there is exactly 1 involved gene (using only the gene table if sufficient, or gene_alias if neccessary): + *
        + *
      1. if this is a 'discretizedCnaProfile', normalize the CNA values and create a list of cnaEvents to be added + *
      2. attempt to store the record in genetic_alteration + *
      3. if the record is successfully stored (not duplicated), create (or update) records in sample_cna_event for the created list of cnaEvents (if any) + *
      + *
    8. if there are several involved genes and the profile is an rppaProfile, loop through the genes; for each one: + *
        + *
      1. attempt to store the record under that gene in genetic_alteration + *
      2. count the number of successfully imported records (for logging) + *
      + *
        + *
      • after looping through all involved genes, check whether any records were successfully stored in genetic_alteration - if not log the failure + *
      + *
    9. if there are several involved genes and the profile is not an rppaProfile, log a failure to import the current line due to ambiguous gene symbol + *
    + *
  • If a record was (or more than one were) successfully stored in genetic_alteration, return true ; else false + * + *

    + * During the import of any single profile data file, at most one record per Entrez_Gene_Id will be successfuly imported to genetic_alteration. + * Each attempt to import is done through a call to the function storeGeneticAlterations(). + * That function will check an instance variable importSetOfGenes, and if the gene has been previously imported, no new attempt is made (failure). + * Each time a gene is successfully imported, it is added to importSetOfGenes. + *

    + * MicroRNA are treated specially because of the possible presence of constructed combination forms (such as 'MIR-100/100*' and 'MIR-100/100'). + * In these cases a Hugo_Symbol such as 'hsa-mir-100' may be expected to match the (fake) Entrez_Gene_Id for both of these combination forms. + * In that case, we want to import several copies of the genetic alteration profile line .. one for each matched gene of type 'miRNA'. + * This allows the visualization of both CNA event profiles for the microRNA precursor with expression profiles for the microRNA mature form. + *

    + * The current implementation of this code does not attempt to "merge" / "unify" lines in the profile data file which have duplicated Entrez_Gene_Id. + * Instead, the first encountered line which maps to the Entrez_Gene_Id will be stored as a record in genetic_alteration (returns true). + * Later lines which attempt to store a record with that Entrez_Gene_Id will not be stored as a record in genetic_alteration (returns false). + * For microRNA gene aliases it is possible that complex interactions will occur, where an earlier line in the data file stores a record under several Entrez_Gene_Ids, and a later line in the file fails to store records under some of those previously 'used' Entrez_Gene_Ids, but succeeds in storing a record under one or more not previously used Entrez_Gene_Ids. So a microRNA line from the file may be imported "partially successfully" (returns true). + *

    + * Examples Cases:
    + * Gene records are P1, P2, P3, P4 (protein coding), M1, M2, M3 (microRNA). + * Gene_Symbol AMA is gene_alias for M1 and M2, Gene_Symbol AMB is gene_alias for M2 and M3, Gene_Symbol AAMBIG is gene_alias for P3 and P4. Gene_Symbol AMIXED is gene_alias for P1 and M3. + *

    + * Case_1 (the last two lines will be skipped and logged like "Gene P1 (#) found to be duplicated in your file. Duplicated row will be ignored!")
    + * + *
    Hugo_SymbolSample1... + *
    P10... + *
    P20... + *
    P10... + *
    P10... + *
    + *

    + * Case_2 (the last line will be skipped and logged like "Gene M1 (#) (given as alias in your file as: AMA) found to be duplicated in your file. Duplicated row will be ignored!" , "Gene M2 (#) (given as alias in your file as: AMA) found to be duplicated in your file. Duplicated row will be ignored!" , "Could not store microRNA or RPPA data" )
    + * + *
    Hugo_SymbolSample1... + *
    AMA0... + *
    AMA0... + *
    + *

    + * Case_3 (the last line in the file will fail with log messages like "Gene symbol AAMBIG found to be ambiguous. Record will be skipped for this gene.")
    + * + *
    Hugo_SymbolSample1... + *
    P10... + *
    P20... + *
    AAMBIG0... + *
    + *

    + * Case_4 (the second to last line will partially succeed, storing a record in genetic_alteration for gene M3 but failing for M2 with a log message like "Gene M2 (#) (given as alias in your file as: AMB) found to be duplicated in your file. Duplicated row will be ignored!" ; the last line in the file will fail with log messages like "Gene M3 (#) (given as alias in your file as: AMIXED) found to be duplicated in your file. Duplicated row will be ignored!" , "Gene symbol AMIXED found to be ambiguous (a mixture of microRNA and other types). Record will be skipped for this gene.")
    + * + *
    Hugo_SymbolSample1... + *
    AMA0... + *
    AMB0... + *
    AMIXED0... + *
    + * + * @param line the line from the profile data file to be parsed + * @param nrColumns the number of columns, defined by the header line + * @param sampleStartIndex the index of the first column with a sample name in the header field + * @param hugoSymbolIndex the index of the column Hugo_Symbol + * @param entrezGeneIdIndex the index of the column Entrez_Gene_Id + * @param rppaGeneRefIndex the index of the column Composite.Element.Ref + * @param isRppaProfile true if this is an rppa profile (i.e. alteration type is PROTEIN_LEVEL and the first column is Composite.Element.Ref) + * @param isDiscretizedCnaProfile true if this is a discretized CNA profile (i.e. alteration type COPY_NUMBER_ALTERATION and showProfileInAnalysisTab is true) + * @param daoGene an instance of DaoGeneOptimized ... for use in resolving gene symbols + * @param orderedSampleList a list of the internal sample ids corresponding to the sample names in the header line + * @param existingCnaEvents a collection of CnaEvents, to be added to or updated during parsing of individual lines + * @return true if any record was stored in genetic_alteration, else false + * @throws DaoException if any DaoException is thrown while using daoGene or daoGeneticAlteration + */ + private boolean parseLine(String line, int nrColumns, int sampleStartIndex, + int hugoSymbolIndex, int entrezGeneIdIndex, int rppaGeneRefIndex, + boolean isRppaProfile, boolean isDiscretizedCnaProfile, + DaoGeneOptimized daoGene, + List filteredSampleIndices, List orderedSampleList, + Set existingCnaEvents + ) throws DaoException { + //TODO: refactor this entire function - split functionality into smaller units / subroutines - boolean recordStored = false; - + boolean recordStored = false; + // Ignore lines starting with # if (!line.startsWith("#") && line.trim().length() > 0) { - String[] parts = line.split("\t",-1); - - if (parts.length>nrColumns) { - if (line.split("\t").length>nrColumns) { + String[] parts = line.split("\t", -1); + + if (parts.length > nrColumns) { + if (line.split("\t").length > nrColumns) { ProgressMonitor.logWarning("Ignoring line with more fields (" + parts.length - + ") than specified in the headers(" + nrColumns + "): \n"+parts[0]); + + ") than specified in the headers(" + nrColumns + "): \n" + parts[0]); return false; } } - String values[] = (String[]) ArrayUtils.subarray(parts, sampleStartIndex, parts.length>nrColumns?nrColumns:parts.length); + String values[] = (String[]) ArrayUtils.subarray(parts, sampleStartIndex, parts.length > nrColumns ? nrColumns : parts.length); values = filterOutNormalValues(filteredSampleIndices, values); String geneSymbol = null; @@ -514,7 +531,7 @@ private boolean parseLine(String line, int nrColumns, int sampleStartIndex, if (rppaGeneRefIndex != -1) { geneSymbol = parts[rppaGeneRefIndex]; } - if (geneSymbol!=null && geneSymbol.isEmpty()) { + if (geneSymbol != null && geneSymbol.isEmpty()) { geneSymbol = null; } if (isRppaProfile && geneSymbol == null) { @@ -523,10 +540,10 @@ private boolean parseLine(String line, int nrColumns, int sampleStartIndex, } //get entrez String entrez = null; - if (entrezGeneIdIndex!=-1) { + if (entrezGeneIdIndex != -1) { entrez = parts[entrezGeneIdIndex]; } - if (entrez!=null) { + if (entrez != null) { if (entrez.isEmpty()) { entrez = null; } @@ -534,12 +551,12 @@ else if (!entrez.matches("[0-9]+")) { //TODO - would be better to give an exception in some cases, like negative Entrez values ProgressMonitor.logWarning("Ignoring line with invalid Entrez_Id " + entrez); return false; - } + } } - + //If all are empty, skip line: if (geneSymbol == null && entrez == null) { - ProgressMonitor.logWarning("Ignoring line with no Hugo_Symbol or Entrez_Id value"); + ProgressMonitor.logWarning("Ignoring line with no Hugo_Symbol and no Entrez_Id"); return false; } else { if (geneSymbol != null && (geneSymbol.contains("///") || geneSymbol.contains("---"))) { @@ -560,7 +577,7 @@ else if (!entrez.matches("[0-9]+")) { //will be null when there is a parse error in this case, so we //can return here and avoid duplicated messages: return false; - } + } if (genes.isEmpty()) { String gene = (geneSymbol != null) ? geneSymbol : entrez; ProgressMonitor.logWarning("Gene not found for: [" + gene @@ -580,7 +597,7 @@ else if (!entrez.matches("[0-9]+")) { if ((genes == null || genes.isEmpty()) && geneSymbol != null) { // deal with multiple symbols separate by |, use the first one int ix = geneSymbol.indexOf("|"); - if (ix>0) { + if (ix > 0) { geneSymbol = geneSymbol.substring(0, ix); } genes = daoGene.getGene(geneSymbol, true); @@ -616,8 +633,7 @@ else if (!entrez.matches("[0-9]+")) { if (!microRNAGenes.isEmpty()) { // for micro rna, duplicate the data for (CanonicalGene gene : microRNAGenes) { - boolean result = storeGeneticAlterations(values, daoGeneticAlteration, gene, geneSymbol); - if (result == true) { + if (this.geneticAlterationImporter.store(values, gene, geneSymbol)) { recordStored = true; } } @@ -637,20 +653,21 @@ else if (!entrez.matches("[0-9]+")) { // none of the matched genes are type "miRNA" if (genes.size() == 1) { List cnaEventsToAdd = new ArrayList(); - + if (isDiscretizedCnaProfile) { long entrezGeneId = genes.get(0).getEntrezGeneId(); for (int i = 0; i < values.length; i++) { - + // temporary solution -- change partial deletion back to full deletion. if (values[i].equals(CNA_VALUE_PARTIAL_DELETION)) { values[i] = CNA_VALUE_HOMOZYGOUS_DELETION; } - if (values[i].equals(CNA_VALUE_AMPLIFICATION) + if (values[i].equals(CNA_VALUE_AMPLIFICATION) // || values[i].equals(CNA_VALUE_GAIN) >> skipping GAIN, ZERO, HEMIZYGOUS_DELETION to minimize size of dataset in DB // || values[i].equals(CNA_VALUE_ZERO) // || values[i].equals(CNA_VALUE_HEMIZYGOUS_DELETION) - || values[i].equals(CNA_VALUE_HOMOZYGOUS_DELETION)) { + || values[i].equals(CNA_VALUE_HOMOZYGOUS_DELETION) + ) { Integer sampleId = orderedSampleList.get(i); CnaEvent cnaEvent = new CnaEvent(sampleId, geneticProfileId, entrezGeneId, Short.parseShort(values[i])); //delayed add: @@ -666,25 +683,16 @@ else if (!entrez.matches("[0-9]+")) { } } } - recordStored = storeGeneticAlterations(values, daoGeneticAlteration, genes.get(0), geneSymbol); + // Store all values per gene: + recordStored = this.geneticAlterationImporter.store(values, genes.get(0), geneSymbol); //only add extra CNA related records if the step above worked, otherwise skip: if (recordStored) { - for (CnaEvent cnaEvent : cnaEventsToAdd) { - if (existingCnaEvents.containsKey(cnaEvent.getEvent())) { - cnaEvent.setEventId(existingCnaEvents.get(cnaEvent.getEvent()).getEventId()); - DaoCnaEvent.addCaseCnaEvent(cnaEvent, false); - } else { - //cnaEvent.setEventId(++cnaEventId); not needed anymore, column now has AUTO_INCREMENT - DaoCnaEvent.addCaseCnaEvent(cnaEvent, true); - existingCnaEvents.put(cnaEvent.getEvent(), cnaEvent.getEvent()); - } - } - } + CnaUtil.storeCnaEvents(existingCnaEvents, cnaEventsToAdd); + } } else { if (isRppaProfile) { // for protein data, duplicate the data for (CanonicalGene gene : genes) { - boolean result = storeGeneticAlterations(values, daoGeneticAlteration, gene, geneSymbol); - if (result == true) { + if (this.geneticAlterationImporter.store(values, gene, geneSymbol)) { recordStored = true; nrExtraRecords++; } @@ -710,7 +718,7 @@ else if (!entrez.matches("[0-9]+")) { } return recordStored; } - + /** * Parses line for gene set record and stores record in 'genetic_alteration' table. * @param line @@ -720,33 +728,33 @@ else if (!entrez.matches("[0-9]+")) { * @param filteredSampleIndices * @param daoGeneticAlteration * @return - * @throws DaoException + * @throws DaoException */ private boolean parseGenesetLine(String line, int nrColumns, int sampleStartIndex, int genesetIdIndex, - List filteredSampleIndices, DaoGeneticAlteration daoGeneticAlteration) throws DaoException { + List filteredSampleIndices, DaoGeneticAlteration daoGeneticAlteration) throws DaoException { boolean storedRecord = false; - + if (!line.startsWith("#") && line.trim().length() > 0) { - String[] parts = line.split("\t",-1); + String[] parts = line.split("\t", -1); - if (parts.length>nrColumns) { - if (line.split("\t").length>nrColumns) { + if (parts.length > nrColumns) { + if (line.split("\t").length > nrColumns) { ProgressMonitor.logWarning("Ignoring line with more fields (" + parts.length - + ") than specified in the headers(" + nrColumns + "): \n"+parts[0]); + + ") than specified in the headers(" + nrColumns + "): \n" + parts[0]); return false; } } - - String values[] = (String[]) ArrayUtils.subarray(parts, sampleStartIndex, parts.length>nrColumns?nrColumns:parts.length); + + String values[] = (String[]) ArrayUtils.subarray(parts, sampleStartIndex, parts.length > nrColumns ? nrColumns : parts.length); // trim whitespace from values values = Stream.of(values).map(String::trim).toArray(String[]::new); values = filterOutNormalValues(filteredSampleIndices, values); - + Geneset geneset = DaoGeneset.getGenesetByExternalId(parts[genesetIdIndex]); - if (geneset != null) { - storedRecord = storeGeneticEntityGeneticAlterations(values, daoGeneticAlteration, geneset.getGeneticEntityId(), - EntityType.GENESET, geneset.getExternalId()); + if (geneset != null) { + storedRecord = storeGeneticEntityGeneticAlterations(values, daoGeneticAlteration, geneset.getGeneticEntityId(), + EntityType.GENESET, geneset.getExternalId()); } else { ProgressMonitor.logWarning("Geneset " + parts[genesetIdIndex] + " not found in DB. Record will be skipped."); @@ -757,46 +765,46 @@ private boolean parseGenesetLine(String line, int nrColumns, int sampleStartInde /** * Parses line for generic assay profile record and stores record in 'genetic_alteration' table. - * @param line row from the separated-text that contains one or more values on a single sample + * @param line row from the separated-text that contains one or more values on a single sample * @param nrColumns - * @param sampleStartIndex index of the first sample column - * @param genericAssayIdIndex index of the column that uniquely identifies a sample + * @param sampleStartIndex index of the first sample column + * @param genericAssayIdIndex index of the column that uniquely identifies a sample * @param filteredSampleIndices * @param daoGeneticAlteration * @return - * @throws DaoException + * @throws DaoException */ private boolean parseGenericAssayLine(String line, int nrColumns, int sampleStartIndex, int genericAssayIdIndex, - List filteredSampleIndices, DaoGeneticAlteration daoGeneticAlteration, Map genericAssayStableIdToEntityIdMap) throws DaoException { + List filteredSampleIndices, DaoGeneticAlteration daoGeneticAlteration, Map genericAssayStableIdToEntityIdMap) throws DaoException { boolean recordIsStored = false; - + if (!line.startsWith("#") && line.trim().length() > 0) { String[] parts = line.split("\t", -1); if (parts.length > nrColumns) { if (line.split("\t").length > nrColumns) { ProgressMonitor.logWarning("Ignoring line with more fields (" + parts.length - + ") than specified in the headers(" + nrColumns + "): \n"+parts[0]); + + ") than specified in the headers(" + nrColumns + "): \n" + parts[0]); return false; } } - - String values[] = (String[]) ArrayUtils.subarray(parts, sampleStartIndex, parts.length>nrColumns?nrColumns:parts.length); + + String values[] = (String[]) ArrayUtils.subarray(parts, sampleStartIndex, parts.length > nrColumns ? nrColumns : parts.length); // trim whitespace from values values = Stream.of(values).map(String::trim).toArray(String[]::new); values = filterOutNormalValues(filteredSampleIndices, values); - + String stableId = parts[genericAssayIdIndex]; Integer entityId = genericAssayStableIdToEntityIdMap.getOrDefault(stableId, null); - - if (entityId == null) { + + if (entityId == null) { ProgressMonitor.logWarning("Generic Assay entity " + parts[genericAssayIdIndex] + " not found in DB. Record will be skipped."); } else { - recordIsStored = storeGeneticEntityGeneticAlterations(values, daoGeneticAlteration, entityId, - EntityType.GENERIC_ASSAY, stableId); + recordIsStored = storeGeneticEntityGeneticAlterations(values, daoGeneticAlteration, entityId, + EntityType.GENERIC_ASSAY, stableId); } return recordIsStored; @@ -805,51 +813,25 @@ private boolean parseGenericAssayLine(String line, int nrColumns, int sampleStar return recordIsStored; } - private boolean storeGeneticAlterations(String[] values, DaoGeneticAlteration daoGeneticAlteration, - CanonicalGene gene, String geneSymbol) throws DaoException { - // Check that we have not already imported information regarding this gene. - // This is an important check, because a GISTIC or RAE file may contain - // multiple rows for the same gene, and we only want to import the first row. - try { - if (!importSetOfGenes.contains(gene.getEntrezGeneId())) { - daoGeneticAlteration.addGeneticAlterations(geneticProfileId, gene.getEntrezGeneId(), values); - importSetOfGenes.add(gene.getEntrezGeneId()); - return true; - } - else { - //TODO - review this part - maybe it should be an Exception instead of just a warning. - String geneSymbolMessage = ""; - if (geneSymbol != null && !geneSymbol.equalsIgnoreCase(gene.getHugoGeneSymbolAllCaps())) - geneSymbolMessage = " (given as alias in your file as: " + geneSymbol + ")"; - ProgressMonitor.logWarning("Gene " + gene.getHugoGeneSymbolAllCaps() + " (" + gene.getEntrezGeneId() + ")" + geneSymbolMessage + " found to be duplicated in your file. Duplicated row will be ignored!"); - return false; - } - } - catch (Exception e) - { - throw new RuntimeException("Aborted: Error found for row starting with " + geneSymbol + ": " + e.getMessage()); - } - } - /** - * Stores genetic alteration data for a genetic entity. + * Stores genetic alteration data for a genetic entity. * @param values * @param daoGeneticAlteration - * @param geneticEntityId - internal id for genetic entity - * @param geneticEntityType - "GENE", "GENESET", "PHOSPHOPROTEIN" - * @param geneticEntityName - hugo symbol for "GENE", external id for "GENESET", phospho gene name for "PHOSPHOPROTEIN" + * @param geneticEntityId - internal id for genetic entity + * @param geneticEntityType - "GENE", "GENESET", "PHOSPHOPROTEIN" + * @param geneticEntityName - hugo symbol for "GENE", external id for "GENESET", phospho gene name for "PHOSPHOPROTEIN" * @return boolean indicating if record was stored successfully or not */ private boolean storeGeneticEntityGeneticAlterations(String[] values, DaoGeneticAlteration daoGeneticAlteration, - Integer geneticEntityId, EntityType geneticEntityType, String geneticEntityName) { + Integer geneticEntityId, EntityType geneticEntityType, String geneticEntityName) { try { if (importedGeneticEntitySet.add(geneticEntityId)) { daoGeneticAlteration.addGeneticAlterationsForGeneticEntity(geneticProfile.getGeneticProfileId(), geneticEntityId, values); return true; } else { - ProgressMonitor.logWarning("Data for genetic entity " + geneticEntityName - + " [" + geneticEntityType +"] already imported from file. Record will be skipped."); + ProgressMonitor.logWarning("Data for genetic entity " + geneticEntityName + + " [" + geneticEntityType + "] already imported from file. Record will be skipped."); return false; } } @@ -860,9 +842,9 @@ private boolean storeGeneticEntityGeneticAlterations(String[] values, DaoGenetic /** * Tries to parse the genes and look them up in DaoGeneOptimized - * + * * @param antibodyWithGene - * @return returns null if something was wrong, e.g. could not parse the antibodyWithGene string; returns + * @return returns null if something was wrong, e.g. could not parse the antibodyWithGene string; returns * a list with 0 or more elements otherwise. * @throws DaoException */ @@ -891,7 +873,7 @@ private List parseRPPAGenes(String antibodyWithGene) throws DaoEx } else { CanonicalGene gene = daoGene.getNonAmbiguousGene(symbol, true); - if (gene!=null) { + if (gene != null) { genes.add(gene); } else { @@ -908,7 +890,7 @@ private List parseRPPAGenes(String antibodyWithGene) throws DaoEx for (String symbol : symbolsNotFound) { ProgressMonitor.logWarning("Gene " + symbol + " not found in DB. Record will be skipped for this gene."); } - + Pattern p = Pattern.compile("(p[STY][0-9]+(?:_[STY][0-9]+)*)"); Matcher m = p.matcher(arrayId); String residue; @@ -921,7 +903,7 @@ private List parseRPPAGenes(String antibodyWithGene) throws DaoEx return importPhosphoGene(genes, residue); } } - + private List importPhosphoGene(List genes, String residue) throws DaoException { DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance(); List phosphoGenes = new ArrayList(); @@ -929,10 +911,10 @@ private List importPhosphoGene(List genes, String Set aliases = new HashSet(); aliases.add("rppa-phospho"); aliases.add("phosphoprotein"); - aliases.add("phospho"+gene.getStandardSymbol()); - String phosphoSymbol = gene.getStandardSymbol()+"_"+residue; + aliases.add("phospho" + gene.getStandardSymbol()); + String phosphoSymbol = gene.getStandardSymbol() + "_" + residue; CanonicalGene phosphoGene = daoGene.getGene(phosphoSymbol); - if (phosphoGene==null) { + if (phosphoGene == null) { ProgressMonitor.logWarning("Phosphoprotein " + phosphoSymbol + " not yet known in DB. Adding it to `gene` table with 3 aliases in `gene_alias` table."); phosphoGene = new CanonicalGene(phosphoSymbol, aliases); phosphoGene.setType(CanonicalGene.PHOSPHOPROTEIN_TYPE); @@ -943,7 +925,7 @@ private List importPhosphoGene(List genes, String return phosphoGenes; } - + // returns index for geneset id column private int getGenesetIdIndex(String[] headers) { return getColIndexByName(headers, "geneset_id"); @@ -952,22 +934,22 @@ private int getGenesetIdIndex(String[] headers) { private int getGenericAssayIdIndex(String[] headers) { return getColIndexByName(headers, "ENTITY_STABLE_ID"); } - + private int getHugoSymbolIndex(String[] headers) { return getColIndexByName(headers, "Hugo_Symbol"); } - + private int getEntrezGeneIdIndex(String[] headers) { return getColIndexByName(headers, "Entrez_Gene_Id"); } - + private int getRppaGeneRefIndex(String[] headers) { return getColIndexByName(headers, "Composite.Element.Ref"); } - + // helper function for finding the index of a column by name private int getColIndexByName(String[] headers, String colName) { - for (int i=0; i featureColNames = new ArrayList(); featureColNames.add("Gene Symbol"); @@ -999,12 +981,12 @@ private int getStartIndex(String[] headers, int ...featureColIds) { } int startIndex = -1; - - for (int i=0; i e.equalsIgnoreCase(h)) + if (featureColNames.stream().noneMatch(e -> e.equalsIgnoreCase(h)) && i > lastFeatureCol) { //then we consider this the start of the sample columns: startIndex = i; @@ -1013,7 +995,7 @@ private int getStartIndex(String[] headers, int ...featureColIds) { } if (startIndex == -1) throw new RuntimeException("Could not find a sample column in the file"); - + return startIndex; } 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 new file mode 100644 index 00000000000..f69178e304c --- /dev/null +++ b/core/src/main/java/org/mskcc/cbio/portal/util/CnaUtil.java @@ -0,0 +1,112 @@ +package org.mskcc.cbio.portal.util; + +import org.cbioportal.model.*; +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 java.util.*; + +import static org.mskcc.cbio.portal.scripts.ImportTabDelimData.*; + +public class CnaUtil { + + private final HashMap columnIndexMap; + + public static final String HUGO_SYMBOL = "Hugo_Symbol"; + public static final String ENTREZ_GENE_ID = "Entrez_Gene_Id"; + public static final String SAMPLE_ID = "Sample_Id"; + public static final String VALUE = "Value"; + public static final String CBP_DRIVER = "cbp_driver"; + public static final String CBP_DRIVER_ANNOTATION = "cbp_driver_annotation"; + public static final String CBP_DRIVER_TIERS = "cbp_driver_tiers"; + + public static void storeCnaEvents( + Set existingCnaEvents, + List cnaEventsToAdd + ) throws DaoException { + for (CnaEvent cnaEvent : cnaEventsToAdd) { + if (!CNA.AMP.equals(cnaEvent.getAlteration()) && !CNA.HOMDEL.equals(cnaEvent.getAlteration())) { + continue; + } + Optional existingCnaEvent = existingCnaEvents + .stream() + .filter(e -> e.equals(cnaEvent.getEvent())) + .findFirst(); + if (existingCnaEvent.isPresent()) { + cnaEvent.setEventId(existingCnaEvent.get().getEventId()); + DaoCnaEvent.addCaseCnaEvent(cnaEvent, false); + } else { + DaoCnaEvent.addCaseCnaEvent(cnaEvent, true); + existingCnaEvents.add(cnaEvent.getEvent()); + } + } + } + + 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) { + int cnaProfileId = geneticProfile.getGeneticProfileId(); + long entrezGeneId = getEntrezSymbol(parts); + short alteration = createAlteration(parts); + CnaEvent cna = new CnaEvent(sampleId, cnaProfileId, entrezGeneId, alteration); + cna.setDriverFilter(TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.CBP_DRIVER), parts)); + 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)); + return cna; + } + + public long getEntrezSymbol(String[] parts) { + String entrezAsString = TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.ENTREZ_GENE_ID), parts); + if (entrezAsString.isEmpty()) { + return 0; + } else if (!entrezAsString.matches("^\\d+$")) { + ProgressMonitor.logWarning("Ignoring line with invalid Entrez_Id " + entrezAsString); + return 0; + } + return TabDelimitedFileUtil.getPartLong(getColumnIndex(CnaUtil.ENTREZ_GENE_ID), parts); + } + + public String getHugoSymbol(String[] parts) { + return TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.HUGO_SYMBOL), parts); + } + + private short createAlteration(String[] parts) { + String value = TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.VALUE), parts); + String result = value; + // temporary solution -- change partial deletion back to full deletion. + if (value.equals(CNA_VALUE_PARTIAL_DELETION)) { + result = CNA_VALUE_HOMOZYGOUS_DELETION; + } + return Integer.valueOf(result).shortValue(); + } + + public int getColumnIndex(String colName) { + Integer index = this.columnIndexMap.get(colName.toLowerCase()); + if (index == null) { + index = -1; + } + return index; + } + + public String getSampleIdStr(String[] parts) { + return TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.SAMPLE_ID), parts); + } +} diff --git a/core/src/main/scripts/importer/allowed_data_types.txt b/core/src/main/scripts/importer/allowed_data_types.txt index adea1c858da..671bc447380 100644 --- a/core/src/main/scripts/importer/allowed_data_types.txt +++ b/core/src/main/scripts/importer/allowed_data_types.txt @@ -6,9 +6,11 @@ # when specific important combinations were found to be missing in their study directory. GENETIC_ALTERATION_TYPE DATATYPE STABLE_ID COPY_NUMBER_ALTERATION DISCRETE cna +COPY_NUMBER_ALTERATION DISCRETE_LONG cna COPY_NUMBER_ALTERATION DISCRETE cna_rae COPY_NUMBER_ALTERATION DISCRETE cna_consensus COPY_NUMBER_ALTERATION DISCRETE gistic +COPY_NUMBER_ALTERATION DISCRETE_LONG gistic COPY_NUMBER_ALTERATION CONTINUOUS linear_CNA COPY_NUMBER_ALTERATION LOG2-VALUE log2CNA MUTATION_EXTENDED MAF mutations diff --git a/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfile.java b/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfile.java index 6add7177219..8fe0569b8f9 100644 --- a/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfile.java +++ b/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoGeneticProfile.java @@ -65,7 +65,7 @@ public void setUp() throws DaoException public void testDaoGetAllGeneticProfiles() throws DaoException { ArrayList list = DaoGeneticProfile.getAllGeneticProfiles(studyId); - assertEquals(6, list.size()); + assertEquals(7, list.size()); } @Test @@ -127,12 +127,12 @@ public void testDaoDeleteGeneticProfile() throws DaoException { GeneticProfile geneticProfile = DaoGeneticProfile.getGeneticProfileById(2); - assertEquals(6, DaoGeneticProfile.getCount()); + assertEquals(7, DaoGeneticProfile.getCount()); DaoGeneticProfile.deleteGeneticProfile(geneticProfile); - assertEquals(5, DaoGeneticProfile.getCount()); + assertEquals(6, DaoGeneticProfile.getCount()); ArrayList list = DaoGeneticProfile.getAllGeneticProfiles(studyId); - assertEquals(5, list.size()); + assertEquals(6, list.size()); geneticProfile = list.get(0); assertEquals(studyId, geneticProfile.getCancerStudyId()); assertEquals("mRNA expression (microarray)", geneticProfile.getProfileName()); @@ -148,7 +148,7 @@ public void testDaoUpdateGeneticProfile() throws DaoException { geneticProfile.getGeneticProfileId(), "Updated Name", "Updated Description")); ArrayList list = DaoGeneticProfile.getAllGeneticProfiles(studyId); - assertEquals(6, list.size()); + assertEquals(7, list.size()); geneticProfile = list.get(0); assertEquals(studyId, geneticProfile.getCancerStudyId()); assertEquals("Updated Name", geneticProfile.getProfileName()); 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 new file mode 100644 index 00000000000..4eabb6e1324 --- /dev/null +++ b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java @@ -0,0 +1,438 @@ +/* + * Copyright (c) 2018 The Hyve B.V. + * This code is licensed under the GNU Affero General Public License (AGPL), + * version 3, or (at your option) any later version. + */ + +/* + * This file is part of cBioPortal. + * + * cBioPortal is free software: you can redistribute it and/or modify + * it under the terms of the GNU Affero General Public License as + * published by the Free Software Foundation, either version 3 of the + * License. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + */ + +/* + * @author Sander Tan + */ + +package org.mskcc.cbio.portal.scripts; + +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.*; +import org.mskcc.cbio.portal.model.CnaEvent; +import org.mskcc.cbio.portal.model.GeneticProfile; +import org.mskcc.cbio.portal.model.Sample; +import org.mskcc.cbio.portal.util.StableIdUtil; +import org.springframework.test.annotation.Rollback; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; +import org.springframework.transaction.annotation.Transactional; + +import java.io.File; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.List; + +import static com.google.common.collect.Lists.newArrayList; +import static java.util.stream.Collectors.joining; +import static java.util.stream.Collectors.toList; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +@RunWith(SpringJUnit4ClassRunner.class) +@ContextConfiguration(locations = {"classpath:/applicationContext-dao.xml"}) +@Rollback +@Transactional +public class TestImportCnaDiscreteLongData { + int studyId; + GeneticProfile geneticProfile; + String genePanel = "TESTPANEL_CNA_DISCRETE_LONG_FORMAT"; + + @Before + public void setUp() throws DaoException { + studyId = DaoCancerStudy + .getCancerStudyByStableId("study_tcga_pub") + .getInternalId(); + this.geneticProfile = DaoGeneticProfile + .getGeneticProfileByStableId("study_tcga_pub_cna_long"); + } + + @After + public void cleanUp() throws DaoException { + MySQLbulkLoader.flushAll(); + } + + /** + * Test the import of cna data file in long format with 2 samples + */ + @Test + public void testImportCnaDiscreteLongDataAddsSamples() throws Exception { + File file = new File("src/test/resources/data_cna_discrete_import_test.txt"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance() + ).importData(); + + // Test new samples are added: + List expectedSampleIds = newArrayList("TCGA-A1-A0SB-11", "TCGA-A2-A04U-11"); + for (String id : expectedSampleIds) { + assertSampleExistsInGeneticProfile(id); + } + } + + /** + * Test the import of cna data file in long format with: + * - 10 cna events (-2, -1.5 or 2) + * - 4 non-cna events (0, -1, 1) + */ + @Test + public void testImportCnaDiscreteLongDataAddsCnaEvents() throws Exception { + List beforeCnaEvents = DaoCnaEvent.getAllCnaEvents(); + assertEquals(beforeCnaEvents.size(), 17); + + File file = new File("src/test/resources/data_cna_discrete_import_test.txt"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance() + ).importData(); + + List resultCnaEvents = DaoCnaEvent.getAllCnaEvents(); + + // Test all cna events are added: + int expectedCnaEventCount = 10; + int expectedNewCnaEvents = beforeCnaEvents.size() + expectedCnaEventCount; + assertEquals( + expectedNewCnaEvents, + resultCnaEvents.size() + ); + + // Test gene with homozygous deletion and amplification has two cna events: + List cnaEvents = resultCnaEvents + .stream() + .filter(e -> e.getGene().getEntrezGeneId() == 2115) + .map(e -> e.getAlteration().getDescription()) + .collect(toList()); + assertEquals(2, cnaEvents.size()); + assertTrue(newArrayList("Amplified", "Homozygously deleted").containsAll(cnaEvents)); + + // Test gene with partial deletion and amplification has two cna events: + List convertedCnaEvents = resultCnaEvents + .stream() + .filter(e -> e.getGene().getEntrezGeneId() == 3983) + .map(e -> e.getAlteration().getDescription()) + .collect(toList()); + assertEquals(2, cnaEvents.size()); + assertTrue(newArrayList("Amplified", "Homozygously deleted").containsAll(cnaEvents)); + + // Test gene with homozygous deletion and amplification has no cna events: + List skippedCnaEvents = resultCnaEvents + .stream() + .filter(e -> e.getGene().getEntrezGeneId() == 56914) + .collect(toList()); + assertEquals(0, skippedCnaEvents.size()); + } + + /** + * Test the import of cna data file in long format with 7 genes + */ + @Test + public void testImportCnaDiscreteLongDataAddsGeneticAlterations() throws Exception { + List beforeGeneticAlterations = getAllGeneticAlterations(); + assertEquals(beforeGeneticAlterations.size(), 42); + + File file = new File("src/test/resources/data_cna_discrete_import_test.txt"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance() + ).importData(); + + // Test genetic alterations are added for all genes: + List resultGeneticAlterations = getAllGeneticAlterations(); + List expectedEntrezIds = newArrayList(2115L, 27334L, 57670L, 80070L, 3983L, 56914L, 2261L); + assertEquals(beforeGeneticAlterations.size() + expectedEntrezIds.size(), resultGeneticAlterations.size()); + } + + /** + * Test the imported events match the imported genetic profile samples + */ + @Test + public void testImportCnaDiscreteLongDataAddsGeneticAlterationsAndProfileSamplesInCorrectOrder() throws Exception { + List beforeGeneticAlterations = getAllGeneticAlterations(); + assertEquals(beforeGeneticAlterations.size(), 42); + + File file = new File("src/test/resources/data_cna_discrete_import_test.txt"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance() + ).importData(); + + // Test order of genetic alteration values: + TestGeneticAlteration geneticAlteration = getGeneticAlterationBy(2115L); + assertEquals(geneticProfile.getGeneticProfileId(), geneticAlteration.geneticProfileId); + assertEquals("2,-2,", geneticAlteration.values); + + // Test order of samples in genetic profile samples matches the order in genetic alteration: + TestGeneticProfileSample geneticProfileSample = getGeneticProfileSample(geneticProfile.getGeneticProfileId()); + assertEquals("21,20,", geneticProfileSample.orderedSampleList); + } + + /** + * Test genetic events are imported, even when not imported as cna event + */ + @Test + public void testImportCnaDiscreteLongDataAddsGeneticAlterationsFromNonCnaEvents() throws Exception { + List beforeGeneticAlterations = getAllGeneticAlterations(); + assertEquals(beforeGeneticAlterations.size(), 42); + + File file = new File("src/test/resources/data_cna_discrete_import_test.txt"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance() + ).importData(); + + // Test genetic alteration are added of non-cna event: + TestGeneticAlteration geneticAlteration = getGeneticAlterationBy(56914); + assertEquals(geneticProfile.getGeneticProfileId(), geneticAlteration.geneticProfileId); + assertEquals("0,1,", geneticAlteration.values); + TestGeneticProfileSample geneticProfileSample = getGeneticProfileSample(geneticProfile.getGeneticProfileId()); + assertEquals("21,20,", geneticProfileSample.orderedSampleList); + } + + /** + * Test genetic events are imported, even when not imported as cna event + */ + @Test + public void testImportCnaDiscreteLongDataIgnoresLineWithDuplicateGene() throws Exception { + List beforeGeneticAlterations = getAllGeneticAlterations(); + assertEquals(beforeGeneticAlterations.size(), 42); + + File file = new File("src/test/resources/data_cna_discrete_import_test.txt"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance() + ).importData(); + + // Test genetic alteration are deduplicated: + TestGeneticAlteration geneticAlteration = getGeneticAlterationBy(57670); + assertEquals(geneticProfile.getGeneticProfileId(), geneticAlteration.geneticProfileId); + // Should not be "2,-2,2" or (2,2): + assertEquals("2,-2,", geneticAlteration.values); + } + + /** + * Test the import of cna data file in long format with: + * - 3 cna events with pd annotations + */ + @Test + public void testImportCnaDiscreteLongDataAddsPdAnnotations() throws Exception { + File file = new File("src/test/resources/data_cna_discrete_import_test.txt"); + new ImportCnaDiscreteLongData( + file, + geneticProfile.getGeneticProfileId(), + genePanel, + DaoGeneOptimized.getInstance(), + DaoGeneticAlteration.getInstance() + ).importData(); + List genes = newArrayList(3983L, 27334L, 2115L); + List resultCnaEvents = DaoCnaEvent.getAllCnaEvents() + .stream() + .filter(event -> genes.contains(event.getGene().getEntrezGeneId())) + .collect(toList()); + String sample = "TCGA-A2-A04U-11"; + List allCnaPdAnnotations = getAllCnaPdAnnotations(createPrimaryKeys(sample, resultCnaEvents)); + assertEquals(3, allCnaPdAnnotations.size()); + String allDriverTiersFilters = allCnaPdAnnotations + .stream() + .map(a -> a.driverTiersFilter) + .collect(joining(",")); + assertEquals("Class 2,Class 1,NA", allDriverTiersFilters); + } + + private List createPrimaryKeys(String sample, List cnaEvents) { + return cnaEvents.stream().map(e -> { + TestPdAnnotationPK pk = new TestPdAnnotationPK(); + pk.geneticProfileId = geneticProfile.getGeneticProfileId(); + pk.sampleId = DaoSample.getSampleByCancerStudyAndSampleId( + geneticProfile.getCancerStudyId(), + StableIdUtil.getSampleId(sample) + ).getInternalId(); + pk.alterationEventId = e.getEventId(); + return pk; + }).collect(toList()); + } + + private void assertSampleExistsInGeneticProfile(String sampleId) throws DaoException { + String sampleStableId = StableIdUtil.getSampleId(sampleId); + + Sample sample = DaoSample.getSampleByCancerStudyAndSampleId( + geneticProfile.getCancerStudyId(), + sampleStableId + ); + Assert.assertNotNull(sample); + Assert.assertTrue(DaoSampleProfile.sampleExistsInGeneticProfile( + sample.getInternalId(), + geneticProfile.getGeneticProfileId() + )); + } + + private List getAllCnaPdAnnotations(List pks) throws DaoException { + List pkStrings = new ArrayList<>(); + for (TestPdAnnotationPK pk : pks) { + pkStrings.add(String.format( + "( ALTERATION_EVENT_ID=%d AND GENETIC_PROFILE_ID=%d AND SAMPLE_ID=%d )", + 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 "; + if (pks.size() > 0) { + q += "WHERE " + String.join(" OR ", pkStrings); + } + + System.out.println("pkq:" + q); + return query( + q, + (ResultSet rs) -> { + TestPdAnnotation line = new TestPdAnnotation(); + line.driverFilter = rs.getString("DRIVER_FILTER"); + line.driverTiersFilter = rs.getString("DRIVER_TIERS_FILTER"); + line.driverFilterAnnotation = rs.getString("DRIVER_FILTER_ANNOTATION"); + line.driverTiersFilterAnnotation = rs.getString("DRIVER_TIERS_FILTER_ANNOTATION"); + + line.pk = new TestPdAnnotationPK(); + line.pk.alterationEventId = rs.getInt("ALTERATION_EVENT_ID"); + line.pk.geneticProfileId = rs.getInt("GENETIC_PROFILE_ID"); + line.pk.sampleId = rs.getInt("SAMPLE_ID"); + + return line; + }); + } + + private List getAllGeneticAlterations() throws DaoException { + return query("SELECT * FROM genetic_alteration", (ResultSet rs) -> { + TestGeneticAlteration line = new TestGeneticAlteration(); + line.geneticProfileId = rs.getInt("GENETIC_PROFILE_ID"); + line.geneticEntityId = rs.getInt("GENETIC_ENTITY_ID"); + line.values = rs.getString("VALUES"); + return line; + }); + } + + private TestGeneticAlteration getGeneticAlterationBy(long entrezId) throws DaoException { + return query("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 " + + "WHERE g.ENTREZ_GENE_ID=" + entrezId, + (ResultSet rs) -> { + TestGeneticAlteration line = new TestGeneticAlteration(); + line.geneticProfileId = rs.getInt("GENETIC_PROFILE_ID"); + line.geneticEntityId = rs.getInt("GENETIC_ENTITY_ID"); + line.values = rs.getString("VALUES"); + line.entrezId = rs.getLong("ENTREZ_GENE_ID"); + return line; + }).get(0); + } + + private TestGeneticProfileSample getGeneticProfileSample(long profileId) throws DaoException { + return query( + "SELECT * FROM genetic_profile_samples WHERE GENETIC_PROFILE_ID=" + profileId, + (ResultSet rs) -> { + TestGeneticProfileSample line = new TestGeneticProfileSample(); + line.geneticProfileId = rs.getInt("GENETIC_PROFILE_ID"); + line.orderedSampleList = rs.getString("ORDERED_SAMPLE_LIST"); + return line; + }).get(0); + } + + private List query(String query, FunctionThrowsSql handler) throws DaoException { + Connection con = null; + PreparedStatement pstmt = null; + ResultSet rs = null; + List result = new ArrayList<>(); + try { + con = JdbcUtil.getDbConnection(DaoGeneticAlteration.class); + pstmt = con.prepareStatement(query); + rs = pstmt.executeQuery(); + while (rs.next()) { + result.add(handler.apply(rs)); + } + return result; + } catch (SQLException e) { + throw new DaoException(e); + } finally { + JdbcUtil.closeAll(DaoGeneticAlteration.class, con, pstmt, rs); + } + } + +} + +class TestGeneticAlteration { + public int geneticProfileId; + public int geneticEntityId; + public String values; + public long entrezId; +} + +class TestGeneticProfileSample { + public int geneticProfileId; + public String orderedSampleList; +} + +class TestPdAnnotationPK { + public long alterationEventId; + public int sampleId; + public int geneticProfileId; +} + +class TestPdAnnotation { + public TestPdAnnotationPK pk; + public String driverTiersFilterAnnotation; + public String driverTiersFilter; + public String driverFilterAnnotation; + public String driverFilter; +} + +@FunctionalInterface +interface FunctionThrowsSql { + R apply(T t) throws SQLException; +} diff --git a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportTabDelimData.java b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportTabDelimData.java index 23fd05b379d..4c9f9f8ced8 100644 --- a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportTabDelimData.java +++ b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportTabDelimData.java @@ -150,7 +150,7 @@ private void runImportCnaData() throws DaoException, IOException{ ProgressMonitor.setConsoleMode(false); // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/cna_test.txt"); - ImportTabDelimData parser = new ImportTabDelimData(file, "Barry", geneticProfileId, null); + ImportTabDelimData parser = new ImportTabDelimData(file, "Barry", geneticProfileId, null, DaoGeneticAlteration.getInstance()); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); @@ -215,7 +215,7 @@ private void runImportCnaData2() throws DaoException, IOException{ ProgressMonitor.setConsoleMode(false); // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/cna_test2.txt"); - ImportTabDelimData parser = new ImportTabDelimData(file, geneticProfileId, null); + ImportTabDelimData parser = new ImportTabDelimData(file, geneticProfileId, null, DaoGeneticAlteration.getInstance()); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); @@ -300,7 +300,7 @@ private void runImportRnaData1() throws DaoException, IOException{ // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/mrna_test.txt"); addTestPatientAndSampleRecords(file); - ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null); + ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null, DaoGeneticAlteration.getInstance()); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); ConsoleUtil.showMessages(); @@ -354,7 +354,7 @@ public void testImportmRnaData2() throws Exception { // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/tabDelimitedData/data_expression2.txt"); addTestPatientAndSampleRecords(file); - ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null); + ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null, DaoGeneticAlteration.getInstance()); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); @@ -447,7 +447,7 @@ public void testImportRppaData() throws Exception { // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/tabDelimitedData/data_rppa.txt"); addTestPatientAndSampleRecords(file); - ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null); + ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null, DaoGeneticAlteration.getInstance()); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); ConsoleUtil.showMessages(); diff --git a/core/src/test/resources/data_cna_discrete_import_test.txt b/core/src/test/resources/data_cna_discrete_import_test.txt new file mode 100644 index 00000000000..643010a3ec8 --- /dev/null +++ b/core/src/test/resources/data_cna_discrete_import_test.txt @@ -0,0 +1,26 @@ +Hugo_Symbol Entrez_Gene_Id Sample_Id Value cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation +ETV1 2115 TCGA-A1-A0SB-11 2 +P2RY10 27334 TCGA-A1-A0SB-11 2 +KIAA1549 57670 TCGA-A1-A0SB-11 2 +ADAMTS20 80070 TCGA-A1-A0SB-11 2 +ABLIM1 3983 TCGA-A1-A0SB-11 2 + +ETV1 2115 TCGA-A2-A04U-11 -2 Putative_Passenger Test passenger Class 2 Class annotation +P2RY10 27334 TCGA-A2-A04U-11 -2 Putative_Driver Test driver Class 1 Class annotation +KIAA1549 57670 TCGA-A2-A04U-11 -2 +ADAMTS20 80070 TCGA-A2-A04U-11 -2 + +# partial deletion gets converted into full deletion: +ABLIM1 3983 TCGA-A2-A04U-11 -1.5 Putative_Passenger Test passenger + +# Ignore hemizygous deletion and value gain: +OTOR 56914 TCGA-A2-A04U-11 0 +OTOR 56914 TCGA-A1-A0SB-11 1 +FGFR3 2261 TCGA-A2-A04U-11 0 Putative_Driver Test driver +FGFR3 2261 TCGA-A1-A0SB-11 -1 + +# This line references two genes: it will be ignored +AKT1 /// AKT2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 + +# This gene-sample combi already exists: it will be ignored +KIAA1549 57670 TCGA-A2-A04U-11 2 diff --git a/core/src/test/resources/seed_mini.sql b/core/src/test/resources/seed_mini.sql index e1bfcca4ef8..fd98ec7d340 100644 --- a/core/src/test/resources/seed_mini.sql +++ b/core/src/test/resources/seed_mini.sql @@ -318,6 +318,10 @@ INSERT INTO "genetic_profile" ("GENETIC_PROFILE_ID","STABLE_ID","CANCER_STUDY_ID INSERT INTO "genetic_profile" ("GENETIC_PROFILE_ID","STABLE_ID","CANCER_STUDY_ID","GENETIC_ALTERATION_TYPE","DATATYPE","NAME","DESCRIPTION","SHOW_PROFILE_IN_ANALYSIS_TAB") VALUES (5,'study_tcga_pub_methylation_hm27',1,'METHYLATION','CONTINUOUS','Methylation (HM27)','Methylation beta-values (HM27 platform). For genes with multiple methylation probes,the probe least correlated with expression is selected.','0'); INSERT INTO "genetic_profile" ("GENETIC_PROFILE_ID","STABLE_ID","CANCER_STUDY_ID","GENETIC_ALTERATION_TYPE","DATATYPE","NAME","DESCRIPTION","SHOW_PROFILE_IN_ANALYSIS_TAB") VALUES (6,'study_tcga_pub_mutations',1,'MUTATION_EXTENDED','MAF','Mutations','Mutation data from whole exome sequencing.','1'); INSERT INTO "genetic_profile" ("GENETIC_PROFILE_ID","STABLE_ID","CANCER_STUDY_ID","GENETIC_ALTERATION_TYPE","DATATYPE","NAME","DESCRIPTION","SHOW_PROFILE_IN_ANALYSIS_TAB") VALUES (7,'study_tcga_pub_structural_variants',1,'STRUCTURAL_VARIANT','SV','Structural Variants','Structural Variants test data.','1'); +INSERT INTO "genetic_profile" ("GENETIC_PROFILE_ID","STABLE_ID","CANCER_STUDY_ID","GENETIC_ALTERATION_TYPE","DATATYPE","NAME","DESCRIPTION","SHOW_PROFILE_IN_ANALYSIS_TAB") VALUES (8,'study_tcga_pub_cna_long',1,'COPY_NUMBER_ALTERATION','DISCRETE_LONG','CNA values','CNA values dummy data','1'); + +-- gene_panel +INSERT INTO gene_panel (INTERNAL_ID,STABLE_ID,DESCRIPTION) VALUES (1,'TESTPANEL_CNA_DISCRETE_LONG_FORMAT','Some test panel'); -- genetic_alteration INSERT INTO "genetic_alteration" ("GENETIC_PROFILE_ID","GENETIC_ENTITY_ID","VALUES") VALUES (2,(Select "GENETIC_ENTITY_ID" from "gene" where "ENTREZ_GENE_ID" = 10000),'0,0,1,2,0,1,1,1,0,1,1,1,0,1,'); @@ -388,6 +392,8 @@ INSERT INTO "patient" ("INTERNAL_ID","STABLE_ID","CANCER_STUDY_ID") VALUES (15,' INSERT INTO "patient" ("INTERNAL_ID","STABLE_ID","CANCER_STUDY_ID") VALUES (16,'TCGA-XX-0900',1); INSERT INTO "patient" ("INTERNAL_ID","STABLE_ID","CANCER_STUDY_ID") VALUES (17,'TCGA-AA-3664',1); INSERT INTO "patient" ("INTERNAL_ID","STABLE_ID","CANCER_STUDY_ID") VALUES (18,'TCGA-AA-3665',1); +INSERT INTO "patient" ("INTERNAL_ID","STABLE_ID","CANCER_STUDY_ID") VALUES (19,'TCGA-A2-A04U',1); +INSERT INTO "patient" ("INTERNAL_ID","STABLE_ID","CANCER_STUDY_ID") VALUES (20,'TCGA-A1-A0SB',1); -- sample INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (1,'TCGA-A1-A0SB-01','Primary Solid Tumor',1); @@ -409,6 +415,8 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (17,'TCGA-AA-3664-01','Primary Solid Tumor',17); INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (18,'TCGA-AA-3665-01','Primary Solid Tumor',18); INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (19,'TCGA-A1-A0SB-02','Primary Solid Tumor',1); +INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (20,'TCGA-A2-A04U-11','Solid Tissues Normal',19); +INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (21,'TCGA-A1-A0SB-11','Solid Tissues Normal',20); -- mutation_event INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","FUNCTIONAL_IMPACT_SCORE","FIS_VALUE","LINK_XVAR","LINK_PDB","LINK_MSA","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','NA',0,'getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all','NA','NA','37','+','SNP','rs80357223','unknown','rs80357223','NM_007294','c.(2800-2802)CAG>TAG','BRCA1_HUMAN','P38398',934,934,1,'BRCA1 truncating'); @@ -579,3 +587,4 @@ INSERT INTO authorities (EMAIL,AUTHORITY) values ('jami@gmail.com','ROLE_USER'); INSERT INTO authorities (EMAIL,AUTHORITY) values ('Lonnie@openid.org','ROLE_USER'); INSERT INTO authorities (EMAIL,AUTHORITY) values ('Dhorak@yahoo.com','ROLE_USER'); INSERT INTO authorities (EMAIL,AUTHORITY) values ('Dhorak@yahoo.com','ROLE_MANAGER'); + diff --git a/core/src/test/scripts/system_tests_validate_studies.py b/core/src/test/scripts/system_tests_validate_studies.py index 660ba5391f8..24d05dcde21 100755 --- a/core/src/test/scripts/system_tests_validate_studies.py +++ b/core/src/test/scripts/system_tests_validate_studies.py @@ -68,6 +68,22 @@ def test_exit_status_success(self): exit_status = validateStudies.main(args) self.assertEqual(0, exit_status) + def test_exit_status_success_for_legacy_cna_discrete(self): + """study 0 : no errors, expected exit_status = 0. + + Possible exit statuses: + 0: 'VALID', + 1: 'INVALID' + """ + + # Build up arguments and run + print("===study 0") + args = ['--list-of-studies', 'test_data/study_es_0_legacy_cna_discrete/', + '--portal_info_dir', PORTAL_INFO_DIR] + args = validateStudies.interface(args) + exit_status = validateStudies.main(args) + self.assertEqual(0, exit_status) + def test_exit_status_failure(self): """study 1 : errors, expected exit_status = 1.""" 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 9068287db04..741bc2143b3 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 @@ -1,9 +1,6305 @@ -Hugo_Symbol Entrez_Gene_Id TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SF-01 TCGA-A1-A0SG-01 TCGA-A1-A0SH-01 TCGA-A1-A0SI-01 TCGA-A1-A0SJ-01 TCGA-A1-A0SK-01 TCGA-A1-A0SM-01 TCGA-A1-A0SN-01 TCGA-A1-A0SO-01 TCGA-A1-A0SP-01 TCGA-A1-A0SQ-01 TCGA-A2-A04N-01 TCGA-A2-A04P-01 TCGA-A2-A04Q-01 TCGA-A2-A04R-01 TCGA-A2-A04T-01 TCGA-A2-A04U-01 TCGA-A2-A04V-01 TCGA-A2-A04W-01 TCGA-A2-A04X-01 TCGA-A2-A04Y-01 TCGA-A2-A0CL-01 TCGA-A2-A0CM-01 TCGA-A2-A0CP-01 TCGA-A2-A0CQ-01 TCGA-A2-A0CS-01 TCGA-A2-A0CT-01 TCGA-A2-A0CU-01 TCGA-A2-A0CV-01 TCGA-A2-A0CW-01 TCGA-A2-A0CX-01 TCGA-A2-A0D0-01 TCGA-A2-A0D1-01 TCGA-A2-A0D2-01 TCGA-A2-A0D3-01 TCGA-A2-A0D4-01 TCGA-A2-A0EM-01 TCGA-A2-A0EN-01 TCGA-A2-A0EO-01 TCGA-A2-A0EQ-01 TCGA-A2-A0ER-01 TCGA-A2-A0ES-01 TCGA-A2-A0ET-01 TCGA-A2-A0EU-01 TCGA-A2-A0EV-01 TCGA-A2-A0EW-01 TCGA-A2-A0EX-01 TCGA-A2-A0EY-01 TCGA-A2-A0ST-01 TCGA-A2-A0SU-01 TCGA-A2-A0SV-01 TCGA-A2-A0SW-01 TCGA-A2-A0SX-01 TCGA-A2-A0SY-01 TCGA-A2-A0T0-01 TCGA-A2-A0T1-01 TCGA-A2-A0T2-01 TCGA-A2-A0T3-01 TCGA-A2-A0T4-01 TCGA-A2-A0T5-01 TCGA-A2-A0T6-01 TCGA-A2-A0T7-01 TCGA-A2-A0YC-01 TCGA-A2-A0YD-01 TCGA-A2-A0YE-01 TCGA-A2-A0YF-01 TCGA-A2-A0YG-01 TCGA-A2-A0YH-01 TCGA-A2-A0YI-01 TCGA-A2-A0YJ-01 TCGA-A2-A0YK-01 TCGA-A2-A0YL-01 TCGA-A2-A0YM-01 TCGA-A2-A0YT-01 TCGA-A2-A1FV-01 TCGA-A2-A1FW-01 TCGA-A2-A1FX-01 TCGA-A2-A1FZ-01 TCGA-A2-A1G0-01 TCGA-A2-A1G1-01 TCGA-A2-A1G4-01 TCGA-A2-A1G6-01 TCGA-A2-A259-01 TCGA-A2-A25A-01 TCGA-A2-A25B-01 TCGA-A2-A25C-01 TCGA-A2-A25D-01 TCGA-A2-A25E-01 TCGA-A2-A25F-01 TCGA-A7-A0CD-01 TCGA-A7-A0CE-01 TCGA-A7-A0CG-01 TCGA-A7-A0CH-01 TCGA-A7-A0CJ-01 TCGA-A7-A0D9-01 TCGA-A7-A0DA-01 TCGA-A7-A0DB-01 TCGA-A7-A13D-01 TCGA-A7-A13E-01 TCGA-A7-A13F-01 TCGA-A7-A13G-01 TCGA-A7-A26E-01 TCGA-A7-A26F-01 TCGA-A7-A26G-01 TCGA-A7-A26H-01 TCGA-A7-A26I-01 TCGA-A7-A26J-01 TCGA-A8-A06N-01 TCGA-A8-A06O-01 TCGA-A8-A06P-01 TCGA-A8-A06Q-01 TCGA-A8-A06R-01 TCGA-A8-A06T-01 TCGA-A8-A06U-01 TCGA-A8-A06X-01 TCGA-A8-A06Y-01 TCGA-A8-A06Z-01 TCGA-A8-A075-01 TCGA-A8-A076-01 TCGA-A8-A079-01 TCGA-A8-A07B-01 TCGA-A8-A07E-01 TCGA-A8-A07F-01 TCGA-A8-A07G-01 TCGA-A8-A07I-01 TCGA-A8-A07J-01 TCGA-A8-A07L-01 TCGA-A8-A07O-01 TCGA-A8-A07P-01 TCGA-A8-A07R-01 TCGA-A8-A07S-01 TCGA-A8-A07U-01 TCGA-A8-A07W-01 TCGA-A8-A07Z-01 TCGA-A8-A081-01 TCGA-A8-A082-01 TCGA-A8-A083-01 TCGA-A8-A084-01 TCGA-A8-A085-01 TCGA-A8-A086-01 TCGA-A8-A08A-01 TCGA-A8-A08B-01 TCGA-A8-A08C-01 TCGA-A8-A08F-01 TCGA-A8-A08G-01 TCGA-A8-A08H-01 TCGA-A8-A08I-01 TCGA-A8-A08J-01 TCGA-A8-A08L-01 TCGA-A8-A08O-01 TCGA-A8-A08P-01 TCGA-A8-A08R-01 TCGA-A8-A08S-01 TCGA-A8-A08T-01 TCGA-A8-A08X-01 TCGA-A8-A08Z-01 TCGA-A8-A090-01 TCGA-A8-A091-01 TCGA-A8-A092-01 TCGA-A8-A093-01 TCGA-A8-A094-01 TCGA-A8-A095-01 TCGA-A8-A096-01 TCGA-A8-A097-01 TCGA-A8-A099-01 TCGA-A8-A09A-01 TCGA-A8-A09B-01 TCGA-A8-A09C-01 TCGA-A8-A09D-01 TCGA-A8-A09E-01 TCGA-A8-A09G-01 TCGA-A8-A09I-01 TCGA-A8-A09M-01 TCGA-A8-A09N-01 TCGA-A8-A09Q-01 TCGA-A8-A09R-01 TCGA-A8-A09T-01 TCGA-A8-A09V-01 TCGA-A8-A09W-01 TCGA-A8-A09X-01 TCGA-A8-A09Z-01 TCGA-A8-A0A1-01 TCGA-A8-A0A2-01 TCGA-A8-A0A4-01 TCGA-A8-A0A6-01 TCGA-A8-A0A7-01 TCGA-A8-A0A9-01 TCGA-A8-A0AB-01 TCGA-A8-A0AD-01 TEST-A23C-01 TEST-A23E-01 TEST-A23H-01 TEST-A2B8-01 TEST-A2FB-01 TEST-A2FF-01 TEST-A2FG-01 TCGA-AN-A03X-01 TCGA-AN-A03Y-01 TCGA-AN-A041-01 TCGA-AN-A046-01 TCGA-AN-A049-01 TCGA-AN-A04A-01 TCGA-AN-A04C-01 TCGA-AN-A04D-01 TCGA-AN-A0AJ-01 TCGA-AN-A0AK-01 TCGA-AN-A0AL-01 TCGA-AN-A0AM-01 TCGA-AN-A0AR-01 TCGA-AN-A0AS-01 TCGA-AN-A0AT-01 TCGA-AN-A0FD-01 TCGA-AN-A0FF-01 TCGA-AN-A0FJ-01 TCGA-AN-A0FK-01 TCGA-AN-A0FL-01 TCGA-AN-A0FN-01 TCGA-AN-A0FS-01 TCGA-AN-A0FT-01 TCGA-AN-A0FV-01 TCGA-AN-A0FW-01 TCGA-AN-A0FX-01 TCGA-AN-A0FY-01 TCGA-AN-A0FZ-01 TCGA-AN-A0XL-01 TCGA-AN-A0XN-01 TCGA-AN-A0XO-01 TCGA-AN-A0XR-01 TCGA-AN-A0XS-01 TCGA-AN-A0XT-01 TCGA-AN-A0XU-01 TCGA-AN-A0XV-01 TCGA-AN-A0XW-01 TCGA-AO-A03L-01 TCGA-AO-A03M-01 TCGA-AO-A03N-01 TCGA-AO-A03O-01 TCGA-AO-A03P-01 TCGA-AO-A03R-01 TCGA-AO-A03T-01 TCGA-AO-A03U-01 TCGA-AO-A03V-01 TCGA-AO-A0J2-01 TCGA-AO-A0J3-01 TCGA-AO-A0J4-01 TCGA-AO-A0J5-01 TCGA-AO-A0J6-01 TCGA-AO-A0J7-01 TCGA-AO-A0J8-01 TCGA-AO-A0J9-01 TCGA-AO-A0JA-01 TCGA-AO-A0JB-01 TCGA-AO-A0JC-01 TCGA-AO-A0JD-01 TCGA-AO-A0JE-01 TCGA-AO-A0JF-01 TCGA-AO-A0JG-01 TCGA-AO-A0JI-01 TCGA-AO-A0JJ-01 TCGA-AO-A0JL-01 TCGA-AO-A0JM-01 TCGA-AO-A124-01 TCGA-AO-A125-01 TCGA-AO-A126-01 TCGA-AO-A128-01 TCGA-AO-A129-01 TCGA-AO-A12A-01 TCGA-AO-A12B-01 TCGA-AO-A12D-01 TCGA-AO-A12E-01 TCGA-AO-A12F-01 TCGA-AO-A12G-01 TCGA-AO-A12H-01 TCGA-AO-A1KO-01 TCGA-AO-A1KP-01 TCGA-AO-A1KQ-01 TCGA-AO-A1KR-01 TCGA-AO-A1KS-01 TCGA-AO-A1KT-01 TCGA-AQ-A04H-01 TCGA-AQ-A04J-01 TCGA-AQ-A04L-01 TCGA-AQ-A0Y5-01 TCGA-AQ-A1H2-01 TCGA-AQ-A1H3-01 TCGA-AR-A0TP-01 TCGA-AR-A0TQ-01 TCGA-AR-A0TR-01 TCGA-AR-A0TS-01 TCGA-AR-A0TT-01 TCGA-AR-A0TV-01 TCGA-AR-A0TW-01 TCGA-AR-A0TX-01 TCGA-AR-A0TY-01 TCGA-AR-A0TZ-01 TCGA-AR-A0U0-01 TCGA-AR-A0U1-01 TCGA-AR-A0U2-01 TCGA-AR-A0U3-01 TCGA-AR-A0U4-01 TCGA-AR-A1AH-01 TCGA-AR-A1AI-01 TCGA-AR-A1AJ-01 TCGA-AR-A1AK-01 TCGA-AR-A1AL-01 TCGA-AR-A1AN-01 TCGA-AR-A1AO-01 TCGA-AR-A1AP-01 TCGA-AR-A1AQ-01 TCGA-AR-A1AR-01 TCGA-AR-A1AS-01 TCGA-AR-A1AU-01 TCGA-AR-A1AV-01 TCGA-AR-A1AW-01 TCGA-AR-A1AX-01 TCGA-AR-A1AY-01 TCGA-AR-A24H-01 TCGA-AR-A24K-01 TCGA-AR-A24L-01 TCGA-AR-A24M-01 TCGA-AR-A24N-01 TCGA-AR-A24O-01 TCGA-AR-A24P-01 TCGA-AR-A24Q-01 TCGA-AR-A24R-01 TCGA-AR-A24S-01 TCGA-AR-A24T-01 TCGA-AR-A24U-01 TCGA-AR-A24V-01 TCGA-AR-A24W-01 TCGA-AR-A24X-01 TCGA-AR-A24Z-01 TCGA-AR-A250-01 TCGA-AR-A251-01 TCGA-AR-A252-01 TCGA-AR-A254-01 TCGA-AR-A255-01 TCGA-AR-A256-01 TCGA-B6-A0I2-01 TCGA-B6-A0I5-01 TCGA-B6-A0I9-01 TCGA-B6-A0IA-01 TCGA-B6-A0IB-01 TCGA-B6-A0IC-01 TCGA-B6-A0IE-01 TCGA-B6-A0IH-01 TCGA-B6-A0IJ-01 TCGA-B6-A0IK-01 TCGA-B6-A0IM-01 TCGA-B6-A0IN-01 TCGA-B6-A0IO-01 TCGA-B6-A0IP-01 TCGA-B6-A0IQ-01 TCGA-B6-A0RE-01 TCGA-B6-A0RG-01 TCGA-B6-A0RH-01 TCGA-B6-A0RI-01 TCGA-B6-A0RL-01 TCGA-B6-A0RM-01 TCGA-B6-A0RN-01 TCGA-B6-A0RO-01 TCGA-B6-A0RP-01 TCGA-B6-A0RQ-01 TCGA-B6-A0RS-01 TCGA-B6-A0RT-01 TCGA-B6-A0RU-01 TCGA-B6-A0RV-01 TCGA-B6-A0WS-01 TCGA-B6-A0WT-01 TCGA-B6-A0WV-01 TCGA-B6-A0WW-01 TCGA-B6-A0WX-01 TCGA-B6-A0WY-01 TCGA-B6-A0WZ-01 TCGA-B6-A0X0-01 TCGA-B6-A0X1-01 TCGA-B6-A0X4-01 TCGA-B6-A0X5-01 TCGA-B6-A0X7-01 TCGA-B6-A1KC-01 TCGA-B6-A1KF-01 TCGA-B6-A1KI-01 TCGA-B6-A1KN-01 TCGA-BH-A0AU-01 TCGA-BH-A0AV-01 TCGA-BH-A0AW-01 TCGA-BH-A0AY-01 TCGA-BH-A0AZ-01 TCGA-BH-A0B0-01 TCGA-BH-A0B3-01 TCGA-BH-A0B4-01 TCGA-BH-A0B5-01 TCGA-BH-A0B7-01 TCGA-BH-A0B9-01 TCGA-BH-A0BA-01 TCGA-BH-A0BC-01 TCGA-BH-A0BD-01 TCGA-BH-A0BF-01 TCGA-BH-A0BG-01 TCGA-BH-A0BJ-01 TCGA-BH-A0BL-01 TCGA-BH-A0BM-01 TCGA-BH-A0BO-01 TCGA-BH-A0BP-01 TCGA-BH-A0BQ-01 TCGA-BH-A0BR-01 TCGA-BH-A0BS-01 TCGA-BH-A0BT-01 TCGA-BH-A0BV-01 TCGA-BH-A0BW-01 TCGA-BH-A0BZ-01 TCGA-BH-A0C0-01 TCGA-BH-A0C1-01 TCGA-BH-A0C3-01 TCGA-BH-A0C7-01 TCGA-BH-A0DD-01 TCGA-BH-A0DE-01 TCGA-BH-A0DG-01 TCGA-BH-A0DH-01 TCGA-BH-A0DI-01 TCGA-BH-A0DK-01 TCGA-BH-A0DL-01 TCGA-BH-A0DO-01 TCGA-BH-A0DP-01 TCGA-BH-A0DQ-01 TCGA-BH-A0DS-01 TCGA-BH-A0DT-01 TCGA-BH-A0DV-01 TCGA-BH-A0DX-01 TCGA-BH-A0DZ-01 TCGA-BH-A0E0-01 TCGA-BH-A0E1-01 TCGA-BH-A0E2-01 TCGA-BH-A0E6-01 TCGA-BH-A0E7-01 TCGA-BH-A0E9-01 TCGA-BH-A0EA-01 TCGA-BH-A0EB-01 TCGA-BH-A0EE-01 TCGA-BH-A0EI-01 TCGA-BH-A0GY-01 TCGA-BH-A0GZ-01 TCGA-BH-A0H0-01 TCGA-BH-A0H3-01 TCGA-BH-A0H5-01 TCGA-BH-A0H6-01 TCGA-BH-A0H7-01 TCGA-BH-A0H9-01 TCGA-BH-A0HA-01 TCGA-BH-A0HB-01 TCGA-BH-A0HI-01 TCGA-BH-A0HK-01 TCGA-BH-A0HO-01 TCGA-BH-A0HP-01 TCGA-BH-A0HU-01 TCGA-BH-A0HW-01 TCGA-BH-A0HX-01 TCGA-BH-A0RX-01 TCGA-BH-A0W3-01 TCGA-BH-A0W4-01 TCGA-BH-A0W5-01 TCGA-BH-A0W7-01 TCGA-BH-A0WA-01 TCGA-BH-A18F-01 TCGA-BH-A18G-01 TCGA-BH-A18H-01 TCGA-BH-A18I-01 TCGA-BH-A18J-01 TCGA-BH-A18K-01 TCGA-BH-A18L-01 TCGA-BH-A18M-01 TCGA-BH-A18N-01 TCGA-BH-A18P-01 TCGA-BH-A18Q-01 TCGA-BH-A18R-01 TCGA-BH-A18S-01 TCGA-BH-A18T-01 TCGA-BH-A18U-01 TCGA-BH-A18V-01 TCGA-BH-A1EN-01 TCGA-BH-A1EO-01 TCGA-BH-A1ES-01 TCGA-BH-A1ET-01 TCGA-BH-A1EU-01 TCGA-BH-A1EV-01 TCGA-BH-A1EW-01 TCGA-BH-A1EX-01 TCGA-BH-A1EY-01 TCGA-BH-A1F0-01 TCGA-BH-A1F2-01 TCGA-BH-A1F5-01 TCGA-BH-A1F6-01 TCGA-BH-A1F8-01 TCGA-BH-A1FB-01 TCGA-BH-A1FC-01 TCGA-BH-A1FD-01 TCGA-BH-A1FE-01 TCGA-BH-A1FG-01 TCGA-BH-A1FH-01 TCGA-BH-A1FJ-01 TCGA-BH-A1FL-01 TCGA-BH-A1FM-01 TCGA-BH-A1FN-01 TCGA-BH-A1FR-01 TCGA-BH-A1FU-01 TCGA-BH-A201-01 TCGA-BH-A202-01 TCGA-BH-A203-01 TCGA-BH-A204-01 TCGA-BH-A208-01 TCGA-BH-A209-01 TCGA-BH-A28Q-01 TCGA-C8-A12K-01 TCGA-C8-A12L-01 TCGA-C8-A12M-01 TCGA-C8-A12N-01 TCGA-C8-A12P-01 TCGA-C8-A12Q-01 TCGA-C8-A12T-01 TCGA-C8-A12U-01 TCGA-C8-A12V-01 TCGA-C8-A12W-01 TCGA-C8-A12X-01 TCGA-C8-A12Y-01 TCGA-C8-A12Z-01 TCGA-C8-A130-01 TCGA-C8-A131-01 TCGA-C8-A132-01 TCGA-C8-A133-01 TCGA-C8-A134-01 TCGA-C8-A135-01 TCGA-C8-A137-01 TCGA-C8-A138-01 TCGA-C8-A1HE-01 TCGA-C8-A1HF-01 TCGA-C8-A1HG-01 TCGA-C8-A1HI-01 TCGA-C8-A1HJ-01 TCGA-C8-A1HK-01 TCGA-C8-A1HL-01 TCGA-C8-A1HM-01 TCGA-C8-A1HN-01 TCGA-C8-A1HO-01 TCGA-C8-A26V-01 TCGA-C8-A26W-01 TCGA-C8-A26X-01 TCGA-C8-A26Y-01 TCGA-C8-A26Z-01 TCGA-C8-A273-01 TCGA-C8-A274-01 TCGA-C8-A275-01 TCGA-C8-A278-01 TCGA-C8-A27A-01 TCGA-C8-A27B-01 TCGA-D8-A13Y-01 TCGA-D8-A13Z-01 TCGA-D8-A141-01 TCGA-D8-A142-01 TCGA-D8-A143-01 TCGA-D8-A145-01 TCGA-D8-A146-01 TCGA-D8-A147-01 TCGA-D8-A1J8-01 TCGA-D8-A1J9-01 TCGA-D8-A1JA-01 TCGA-D8-A1JB-01 TCGA-D8-A1JC-01 TCGA-D8-A1JD-01 TCGA-D8-A1JE-01 TCGA-D8-A1JF-01 TCGA-D8-A1JG-01 TCGA-D8-A1JH-01 TCGA-D8-A1JI-01 TCGA-D8-A1JJ-01 TCGA-D8-A1JK-01 TCGA-D8-A1JL-01 TCGA-D8-A1JM-01 TCGA-D8-A1JN-01 TCGA-D8-A1JP-01 TCGA-D8-A1JS-01 TCGA-D8-A1JT-01 TCGA-D8-A1JU-01 TCGA-D8-A1X5-01 TCGA-D8-A1X6-01 TCGA-D8-A1X7-01 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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 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TCGA-EW-A1P6-01 0 +AURKAIP1 54998 TCGA-EW-A1P6-01 0 +ERCC5 2073 TCGA-EW-A1P6-01 0 +ACP3 55 TCGA-EW-A1P6-01 0 +ACAP3 116983 TCGA-EW-A1P7-01 0 +AGRN 375790 TCGA-EW-A1P7-01 0 +ATAD3A 55210 TCGA-EW-A1P7-01 0 +ATAD3B 83858 TCGA-EW-A1P7-01 0 +ATAD3C 219293 TCGA-EW-A1P7-01 0 +AURKAIP1 54998 TCGA-EW-A1P7-01 0 +ERCC5 2073 TCGA-EW-A1P7-01 0 +ACP3 55 TCGA-EW-A1P7-01 0 +ACAP3 116983 TCGA-EW-A1P8-01 0 +AGRN 375790 TCGA-EW-A1P8-01 0 +ATAD3A 55210 TCGA-EW-A1P8-01 0 +ATAD3B 83858 TCGA-EW-A1P8-01 0 +ATAD3C 219293 TCGA-EW-A1P8-01 0 +AURKAIP1 54998 TCGA-EW-A1P8-01 0 +ERCC5 2073 TCGA-EW-A1P8-01 0 +ACP3 55 TCGA-EW-A1P8-01 0 +ACAP3 116983 TCGA-EW-A1PA-01 0 +AGRN 375790 TCGA-EW-A1PA-01 0 +ATAD3A 55210 TCGA-EW-A1PA-01 0 +ATAD3B 83858 TCGA-EW-A1PA-01 0 +ATAD3C 219293 TCGA-EW-A1PA-01 0 +AURKAIP1 54998 TCGA-EW-A1PA-01 0 +ERCC5 2073 TCGA-EW-A1PA-01 0 +ACP3 55 TCGA-EW-A1PA-01 0 +ACAP3 116983 TCGA-EW-A1PB-01 0 +AGRN 375790 TCGA-EW-A1PB-01 0 +ATAD3A 55210 TCGA-EW-A1PB-01 0 +ATAD3B 83858 TCGA-EW-A1PB-01 0 +ATAD3C 219293 TCGA-EW-A1PB-01 0 +AURKAIP1 54998 TCGA-EW-A1PB-01 0 +ERCC5 2073 TCGA-EW-A1PB-01 0 +ACP3 55 TCGA-EW-A1PB-01 0 +ACAP3 116983 TCGA-EW-A1PD-01 0 +AGRN 375790 TCGA-EW-A1PD-01 0 +ATAD3A 55210 TCGA-EW-A1PD-01 0 +ATAD3B 83858 TCGA-EW-A1PD-01 0 +ATAD3C 219293 TCGA-EW-A1PD-01 0 +AURKAIP1 54998 TCGA-EW-A1PD-01 0 +ERCC5 2073 TCGA-EW-A1PD-01 0 +ACP3 55 TCGA-EW-A1PD-01 0 +ACAP3 116983 TCGA-EW-A1PE-01 0 +AGRN 375790 TCGA-EW-A1PE-01 0 +ATAD3A 55210 TCGA-EW-A1PE-01 0 +ATAD3B 83858 TCGA-EW-A1PE-01 0 +ATAD3C 219293 TCGA-EW-A1PE-01 0 +AURKAIP1 54998 TCGA-EW-A1PE-01 0 +ERCC5 2073 TCGA-EW-A1PE-01 0 +ACP3 55 TCGA-EW-A1PE-01 0 +ACAP3 116983 TCGA-EW-A1PF-01 -1 +AGRN 375790 TCGA-EW-A1PF-01 -1 +ATAD3A 55210 TCGA-EW-A1PF-01 -1 +ATAD3B 83858 TCGA-EW-A1PF-01 -1 +ATAD3C 219293 TCGA-EW-A1PF-01 -1 +AURKAIP1 54998 TCGA-EW-A1PF-01 -1 +ERCC5 2073 TCGA-EW-A1PF-01 -1 +ACP3 55 TCGA-EW-A1PF-01 0 +ACAP3 116983 TCGA-EW-A1PG-01 0 +AGRN 375790 TCGA-EW-A1PG-01 0 +ATAD3A 55210 TCGA-EW-A1PG-01 0 +ATAD3B 83858 TCGA-EW-A1PG-01 0 +ATAD3C 219293 TCGA-EW-A1PG-01 0 +AURKAIP1 54998 TCGA-EW-A1PG-01 0 +ERCC5 2073 TCGA-EW-A1PG-01 0 +ACP3 55 TCGA-EW-A1PG-01 0 +ACAP3 116983 TCGA-EW-A1PH-01 0 +AGRN 375790 TCGA-EW-A1PH-01 0 +ATAD3A 55210 TCGA-EW-A1PH-01 0 +ATAD3B 83858 TCGA-EW-A1PH-01 0 +ATAD3C 219293 TCGA-EW-A1PH-01 0 +AURKAIP1 54998 TCGA-EW-A1PH-01 0 +ERCC5 2073 TCGA-EW-A1PH-01 0 +ACP3 55 TCGA-EW-A1PH-01 0 +ACAP3 116983 TCGA-EW-A2FS-01 0 +AGRN 375790 TCGA-EW-A2FS-01 0 +ATAD3A 55210 TCGA-EW-A2FS-01 0 +ATAD3B 83858 TCGA-EW-A2FS-01 0 +ATAD3C 219293 TCGA-EW-A2FS-01 0 +AURKAIP1 54998 TCGA-EW-A2FS-01 0 +ERCC5 2073 TCGA-EW-A2FS-01 0 +ACP3 55 TCGA-EW-A2FS-01 0 +ACAP3 116983 TCGA-EW-A2FV-01 0 +AGRN 375790 TCGA-EW-A2FV-01 0 +ATAD3A 55210 TCGA-EW-A2FV-01 0 +ATAD3B 83858 TCGA-EW-A2FV-01 0 +ATAD3C 219293 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 0d5756fcfe7..cfa0fa7acf8 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 @@ -1,9 +1,9 @@ cancer_study_identifier: study_es_0 genetic_alteration_type: COPY_NUMBER_ALTERATION -datatype: DISCRETE +datatype: DISCRETE_LONG stable_id: gistic 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 -pd_annotations_filename: data_cna_pd_annotations.txt +namespaces: CustomNamespace diff --git a/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_clinical_samples.txt b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_clinical_samples.txt new file mode 100644 index 00000000000..82a6dc99fd9 --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_clinical_samples.txt @@ -0,0 +1,850 @@ +#Patient Identifier Sample Identifier Subtype +#Patient identifier Sample identifier Subtype description +#STRING STRING STRING +#1 1 1 +PATIENT_ID SAMPLE_ID SUBTYPE +TCGA-A2-A04P TCGA-A2-A04P-01 basal-like +TCGA-A1-A0SK TCGA-A1-A0SK-01 basal-like +TCGA-A2-A0CM TCGA-A2-A0CM-01 basal-like +TCGA-AR-A1AR TCGA-AR-A1AR-01 basal-like +TCGA-B6-A0WX TCGA-B6-A0WX-01 basal-like +TCGA-BH-A1F0 TCGA-BH-A1F0-01 basal-like +TCGA-B6-A0I6 TCGA-B6-A0I6-01 NA +TCGA-BH-A18V TCGA-BH-A18V-01 basal-like +TCGA-BH-A18Q TCGA-BH-A18Q-01 basal-like +TCGA-BH-A18K TCGA-BH-A18K-01 basal-like +TCGA-BH-A0HL TCGA-BH-A0HL-01 NA +TCGA-BH-A0E0 TCGA-BH-A0E0-01 basal-like +TCGA-BH-A0RX TCGA-BH-A0RX-01 basal-like +TCGA-A7-A13D TCGA-A7-A13D-01 basal-like +TCGA-BH-A0E6 TCGA-BH-A0E6-01 basal-like +TCGA-AO-A0J4 TCGA-AO-A0J4-01 basal-like +TCGA-A7-A0CE TCGA-A7-A0CE-01 basal-like +TCGA-A7-A13E TCGA-A7-A13E-01 +TCGA-A7-A0DA TCGA-A7-A0DA-01 basal-like +TCGA-D8-A142 TCGA-D8-A142-01 basal-like +TCGA-D8-A143 TCGA-D8-A143-01 NA +TCGA-AQ-A04J TCGA-AQ-A04J-01 basal-like +TCGA-BH-A0HN TCGA-BH-A0HN-01 NA +TCGA-A2-A0T0 TCGA-A2-A0T0-01 basal-like +TCGA-A2-A0YE TCGA-A2-A0YE-01 NA +TCGA-A2-A0YJ TCGA-A2-A0YJ-01 NA +TCGA-A2-A0D0 TCGA-A2-A0D0-01 basal-like +TCGA-A2-A04U TCGA-A2-A04U-01 NA +TCGA-AO-A0J6 TCGA-AO-A0J6-01 basal-like +TCGA-A2-A0YM TCGA-A2-A0YM-01 basal-like +TCGA-A2-A0D2 TCGA-A2-A0D2-01 basal-like +TCGA-BH-A0B3 TCGA-BH-A0B3-01 basal-like +TCGA-A2-A04Q TCGA-A2-A04Q-01 basal-like +TCGA-A2-A0SX TCGA-A2-A0SX-01 basal-like +TCGA-AO-A0JL TCGA-AO-A0JL-01 basal-like +TCGA-AO-A12F TCGA-AO-A12F-01 basal-like +TCGA-BH-A0B9 TCGA-BH-A0B9-01 basal-like +TCGA-A2-A04T TCGA-A2-A04T-01 NA +TCGA-B6-A0RT TCGA-B6-A0RT-01 basal-like +TCGA-AO-A128 TCGA-AO-A128-01 NA +TCGA-AO-A129 TCGA-AO-A129-01 basal-like +TCGA-AO-A124 TCGA-AO-A124-01 basal-like +TCGA-B6-A0RU TCGA-B6-A0RU-01 basal-like +TCGA-B6-A0IQ TCGA-B6-A0IQ-01 basal-like +TCGA-B6-A0I2 TCGA-B6-A0I2-01 basal-like +TCGA-B6-A0IJ TCGA-B6-A0IJ-01 basal-like +TCGA-B6-A0X1 TCGA-B6-A0X1-01 NA +TCGA-B6-A0RE TCGA-B6-A0RE-01 basal-like +TCGA-A2-A0ST TCGA-A2-A0ST-01 basal-like +TCGA-AR-A0TP TCGA-AR-A0TP-01 basal-like +TCGA-A1-A0SO TCGA-A1-A0SO-01 basal-like +TCGA-A8-A07C TCGA-A8-A07C-01 basal-like +TCGA-A8-A07O TCGA-A8-A07O-01 basal-like +TCGA-A8-A07R TCGA-A8-A07R-01 basal-like +TCGA-A8-A07U TCGA-A8-A07U-01 basal-like +TCGA-A8-A08H TCGA-A8-A08H-01 basal-like +TCGA-A8-A08R TCGA-A8-A08R-01 basal-like +TCGA-AN-A04D TCGA-AN-A04D-01 basal-like +TCGA-AN-A0AL TCGA-AN-A0AL-01 basal-like +TCGA-AN-A0AR TCGA-AN-A0AR-01 basal-like +TCGA-AN-A0AT TCGA-AN-A0AT-01 NA +TCGA-AN-A0FJ TCGA-AN-A0FJ-01 basal-like +TCGA-AN-A0FL TCGA-AN-A0FL-01 basal-like +TCGA-AN-A0FX TCGA-AN-A0FX-01 basal-like +TCGA-AN-A0G0 TCGA-AN-A0G0-01 NA +TCGA-AN-A0XU TCGA-AN-A0XU-01 basal-like +TCGA-AR-A0TS TCGA-AR-A0TS-01 basal-like +TCGA-AR-A0TU TCGA-AR-A0TU-01 NA +TCGA-AR-A0U0 TCGA-AR-A0U0-01 NA +TCGA-AR-A0U1 TCGA-AR-A0U1-01 basal-like +TCGA-AR-A0U4 TCGA-AR-A0U4-01 basal-like +TCGA-AR-A1AH TCGA-AR-A1AH-01 basal-like +TCGA-AR-A1AI TCGA-AR-A1AI-01 basal-like +TCGA-AR-A1AJ TCGA-AR-A1AJ-01 basal-like +TCGA-AR-A1AQ TCGA-AR-A1AQ-01 basal-like +TCGA-AR-A1AY TCGA-AR-A1AY-01 basal-like +TCGA-BH-A0AV TCGA-BH-A0AV-01 basal-like +TCGA-BH-A0BG TCGA-BH-A0BG-01 basal-like +TCGA-BH-A0BL TCGA-BH-A0BL-01 basal-like +TCGA-BH-A0BW TCGA-BH-A0BW-01 basal-like +TCGA-BH-A0DL TCGA-BH-A0DL-01 basal-like +TCGA-BH-A0WA TCGA-BH-A0WA-01 basal-like +TCGA-BH-A18G TCGA-BH-A18G-01 NA +TCGA-C8-A12K TCGA-C8-A12K-01 basal-like +TCGA-C8-A12V TCGA-C8-A12V-01 basal-like +TCGA-C8-A131 TCGA-C8-A131-01 basal-like +TCGA-C8-A134 TCGA-C8-A134-01 basal-like +TCGA-D8-A147 TCGA-D8-A147-01 basal-like +TCGA-E2-A14N TCGA-E2-A14N-01 basal-like +TCGA-E2-A14R TCGA-E2-A14R-01 basal-like +TCGA-E2-A14X TCGA-E2-A14X-01 basal-like +TCGA-E2-A14Y TCGA-E2-A14Y-01 basal-like +TCGA-E2-A150 TCGA-E2-A150-01 basal-like +TCGA-E2-A158 TCGA-E2-A158-01 basal-like +TCGA-E2-A159 TCGA-E2-A159-01 basal-like +TCGA-E2-A1AZ TCGA-E2-A1AZ-01 NA +TCGA-E2-A1B5 TCGA-E2-A1B5-01 basal-like +TCGA-A8-A08L TCGA-A8-A08L-01 Her2 enriched +TCGA-BH-A1EV TCGA-BH-A1EV-01 Her2 enriched +TCGA-B6-A0I9 TCGA-B6-A0I9-01 Her2 enriched +TCGA-A8-A09X TCGA-A8-A09X-01 Her2 enriched +TCGA-B6-A0IK TCGA-B6-A0IK-01 Her2 enriched +TCGA-BH-A18P TCGA-BH-A18P-01 Her2 enriched +TCGA-A8-A08J TCGA-A8-A08J-01 Her2 enriched +TCGA-BH-A18R TCGA-BH-A18R-01 Her2 enriched +TCGA-AR-A1AT TCGA-AR-A1AT-01 Her2 enriched +TCGA-B6-A0RS TCGA-B6-A0RS-01 Her2 enriched +TCGA-BH-A0DZ TCGA-BH-A0DZ-01 Her2 enriched +TCGA-A2-A0T1 TCGA-A2-A0T1-01 Her2 enriched +TCGA-AO-A0J2 TCGA-AO-A0J2-01 Her2 enriched +TCGA-BH-A0AW TCGA-BH-A0AW-01 Her2 enriched +TCGA-BH-A0EE TCGA-BH-A0EE-01 Her2 enriched +TCGA-A2-A0D1 TCGA-A2-A0D1-01 Her2 enriched +TCGA-AO-A03N TCGA-AO-A03N-01 Her2 enriched +TCGA-A2-A0CY TCGA-A2-A0CY-01 Her2 enriched +TCGA-A2-A04X TCGA-A2-A04X-01 Her2 enriched +TCGA-A2-A0CX TCGA-A2-A0CX-01 Her2 enriched +TCGA-A2-A04W TCGA-A2-A04W-01 Her2 enriched +TCGA-AO-A12D TCGA-AO-A12D-01 Her2 enriched +TCGA-A2-A0CL TCGA-A2-A0CL-01 Her2 enriched +TCGA-AO-A0JE TCGA-AO-A0JE-01 Her2 enriched +TCGA-A2-A0EQ TCGA-A2-A0EQ-01 Her2 enriched +TCGA-AO-A03L TCGA-AO-A03L-01 Her2 enriched +TCGA-B6-A0RH TCGA-B6-A0RH-01 Her2 enriched +TCGA-A8-A075 TCGA-A8-A075-01 Her2 enriched +TCGA-A8-A076 TCGA-A8-A076-01 Her2 enriched +TCGA-A8-A07B TCGA-A8-A07B-01 Her2 enriched +TCGA-A8-A07I TCGA-A8-A07I-01 Her2 enriched +TCGA-A8-A081 TCGA-A8-A081-01 Her2 enriched +TCGA-A8-A08B TCGA-A8-A08B-01 Her2 enriched +TCGA-A8-A08X TCGA-A8-A08X-01 Her2 enriched +TCGA-A8-A092 TCGA-A8-A092-01 Her2 enriched +TCGA-A8-A094 TCGA-A8-A094-01 Her2 enriched +TCGA-A8-A09G TCGA-A8-A09G-01 Her2 enriched +TCGA-A8-A0A7 TCGA-A8-A0A7-01 Her2 enriched +TCGA-AN-A04C TCGA-AN-A04C-01 Her2 enriched +TCGA-AN-A0FV TCGA-AN-A0FV-01 Her2 enriched +TCGA-AR-A0TX TCGA-AR-A0TX-01 Her2 enriched +TCGA-BH-A0B7 TCGA-BH-A0B7-01 Her2 enriched +TCGA-BH-A0HY TCGA-BH-A0HY-01 Her2 enriched +TCGA-C8-A12L TCGA-C8-A12L-01 Her2 enriched +TCGA-C8-A12P TCGA-C8-A12P-01 Her2 enriched +TCGA-C8-A12Q TCGA-C8-A12Q-01 Her2 enriched +TCGA-C8-A12T TCGA-C8-A12T-01 Her2 enriched +TCGA-C8-A12Z TCGA-C8-A12Z-01 Her2 enriched +TCGA-C8-A130 TCGA-C8-A130-01 Her2 enriched +TCGA-C8-A135 TCGA-C8-A135-01 Her2 enriched +TCGA-C8-A137 TCGA-C8-A137-01 Her2 enriched +TCGA-C8-A138 TCGA-C8-A138-01 Her2 enriched +TCGA-C8-A1HF TCGA-C8-A1HF-01 Her2 enriched +TCGA-D8-A13Z TCGA-D8-A13Z-01 Her2 enriched +TCGA-E2-A14P TCGA-E2-A14P-01 Her2 enriched +TCGA-E2-A14V TCGA-E2-A14V-01 Her2 enriched +TCGA-E2-A152 TCGA-E2-A152-01 Her2 enriched +TCGA-E2-A1B0 TCGA-E2-A1B0-01 Her2 enriched +TCGA-A2-A0CU TCGA-A2-A0CU-01 Luminal A +TCGA-AR-A0TR TCGA-AR-A0TR-01 Luminal A +TCGA-BH-A18T TCGA-BH-A18T-01 Luminal A +TCGA-B6-A0I8 TCGA-B6-A0I8-01 Luminal A +TCGA-B6-A0X4 TCGA-B6-A0X4-01 Luminal A +TCGA-A8-A06U TCGA-A8-A06U-01 Luminal A +TCGA-BH-A0EA TCGA-BH-A0EA-01 Luminal A +TCGA-BH-A18N TCGA-BH-A18N-01 Luminal A +TCGA-BH-A1EU TCGA-BH-A1EU-01 Luminal A +TCGA-B6-A0X7 TCGA-B6-A0X7-01 Luminal A +TCGA-A2-A04V TCGA-A2-A04V-01 Luminal A +TCGA-BH-A18S TCGA-BH-A18S-01 Luminal A +TCGA-BH-A18M TCGA-BH-A18M-01 Luminal A +TCGA-B6-A0RM TCGA-B6-A0RM-01 Luminal A +TCGA-BH-A1ET TCGA-BH-A1ET-01 Luminal A +TCGA-B6-A0IN TCGA-B6-A0IN-01 Luminal A +TCGA-BH-A1EO TCGA-BH-A1EO-01 Luminal A +TCGA-B6-A0WS TCGA-B6-A0WS-01 Luminal A +TCGA-B6-A0RP TCGA-B6-A0RP-01 Luminal A +TCGA-B6-A0IH TCGA-B6-A0IH-01 Luminal A +TCGA-B6-A0WY TCGA-B6-A0WY-01 Luminal A +TCGA-BH-A1ES TCGA-BH-A1ES-01 Luminal A +TCGA-B6-A0X0 TCGA-B6-A0X0-01 Luminal A +TCGA-B6-A0RQ TCGA-B6-A0RQ-01 Luminal A +TCGA-B6-A0IG TCGA-B6-A0IG-01 Luminal A +TCGA-BH-A0HO TCGA-BH-A0HO-01 Luminal A +TCGA-BH-A0DS TCGA-BH-A0DS-01 Luminal A +TCGA-BH-A0DQ TCGA-BH-A0DQ-01 Luminal A +TCGA-BH-A0HK TCGA-BH-A0HK-01 Luminal A +TCGA-A7-A0CG TCGA-A7-A0CG-01 Luminal A +TCGA-A7-A0CH TCGA-A7-A0CH-01 Luminal A +TCGA-A7-A0DB TCGA-A7-A0DB-01 Luminal A +TCGA-A7-A0D9 TCGA-A7-A0D9-01 Luminal A +TCGA-AO-A0J8 TCGA-AO-A0J8-01 Luminal A +TCGA-BH-A0GZ TCGA-BH-A0GZ-01 Luminal A +TCGA-AO-A0JA TCGA-AO-A0JA-01 Luminal A +TCGA-AO-A0JF TCGA-AO-A0JF-01 Luminal A +TCGA-A7-A0CD TCGA-A7-A0CD-01 Luminal A +TCGA-D8-A145 TCGA-D8-A145-01 Luminal A +TCGA-BH-A0HP TCGA-BH-A0HP-01 Luminal A +TCGA-BH-A0DK TCGA-BH-A0DK-01 Luminal A +TCGA-BH-A0E2 TCGA-BH-A0E2-01 Luminal A +TCGA-A2-A0YI TCGA-A2-A0YI-01 Luminal A +TCGA-A2-A0YL TCGA-A2-A0YL-01 Luminal A +TCGA-AO-A0JG TCGA-AO-A0JG-01 Luminal A +TCGA-A2-A0YF TCGA-A2-A0YF-01 Luminal A +TCGA-BH-A0DP TCGA-BH-A0DP-01 Luminal A +TCGA-BH-A0E1 TCGA-BH-A0E1-01 Luminal A +TCGA-A2-A0T5 TCGA-A2-A0T5-01 Luminal A +TCGA-A2-A0T6 TCGA-A2-A0T6-01 Luminal A +TCGA-BH-A0HI TCGA-BH-A0HI-01 Luminal A +TCGA-A2-A0T7 TCGA-A2-A0T7-01 Luminal A +TCGA-BH-A0BJ TCGA-BH-A0BJ-01 Luminal A +TCGA-BH-A0H7 TCGA-BH-A0H7-01 Luminal A +TCGA-BH-A0HF TCGA-BH-A0HF-01 Luminal A +TCGA-BH-A0EB TCGA-BH-A0EB-01 Luminal A +TCGA-BH-A0H6 TCGA-BH-A0H6-01 Luminal A +TCGA-A2-A0YD TCGA-A2-A0YD-01 Luminal A +TCGA-BH-A0HB TCGA-BH-A0HB-01 Luminal A +TCGA-BH-A0HX TCGA-BH-A0HX-01 Luminal A +TCGA-AO-A12H TCGA-AO-A12H-01 Luminal A +TCGA-E2-A10E TCGA-E2-A10E-01 Luminal A +TCGA-A2-A0D3 TCGA-A2-A0D3-01 Luminal A +TCGA-E2-A10F TCGA-E2-A10F-01 Luminal A +TCGA-AO-A03V TCGA-AO-A03V-01 Luminal A +TCGA-A2-A0EW TCGA-A2-A0EW-01 Luminal A +TCGA-BH-A0GY TCGA-BH-A0GY-01 Luminal A +TCGA-A2-A0EV TCGA-A2-A0EV-01 Luminal A +TCGA-BH-A0BC TCGA-BH-A0BC-01 Luminal A +TCGA-A2-A0YC TCGA-A2-A0YC-01 Luminal A +TCGA-A2-A0EU TCGA-A2-A0EU-01 Luminal A +TCGA-A2-A0ET TCGA-A2-A0ET-01 Luminal A +TCGA-A2-A04Y TCGA-A2-A04Y-01 Luminal A +TCGA-BH-A0HQ TCGA-BH-A0HQ-01 Luminal A +TCGA-A2-A0ES TCGA-A2-A0ES-01 Luminal A +TCGA-BH-A0BA TCGA-BH-A0BA-01 Luminal A +TCGA-E2-A10B TCGA-E2-A10B-01 Luminal A +TCGA-BH-A0B1 TCGA-BH-A0B1-01 Luminal A +TCGA-BH-A0DH TCGA-BH-A0DH-01 Luminal A +TCGA-BH-A0B4 TCGA-BH-A0B4-01 Luminal A +TCGA-BH-A0H9 TCGA-BH-A0H9-01 Luminal A +TCGA-AO-A0J9 TCGA-AO-A0J9-01 Luminal A +TCGA-AO-A12G TCGA-AO-A12G-01 Luminal A +TCGA-A2-A0SY TCGA-A2-A0SY-01 Luminal A +TCGA-BH-A0E7 TCGA-BH-A0E7-01 Luminal A +TCGA-AO-A03M TCGA-AO-A03M-01 Luminal A +TCGA-BH-A0BV TCGA-BH-A0BV-01 Luminal A +TCGA-BH-A0B8 TCGA-BH-A0B8-01 Luminal A +TCGA-A2-A0CZ TCGA-A2-A0CZ-01 Luminal A +TCGA-A2-A0SU TCGA-A2-A0SU-01 Luminal A +TCGA-AO-A12E TCGA-AO-A12E-01 Luminal A +TCGA-E2-A106 TCGA-E2-A106-01 Luminal A +TCGA-A2-A0CV TCGA-A2-A0CV-01 Luminal A +TCGA-AO-A12C TCGA-AO-A12C-01 Luminal A +TCGA-B6-A0RG TCGA-B6-A0RG-01 Luminal A +TCGA-A2-A0CS TCGA-A2-A0CS-01 Luminal A +TCGA-A2-A0EO TCGA-A2-A0EO-01 Luminal A +TCGA-A2-A0CQ TCGA-A2-A0CQ-01 Luminal A +TCGA-A2-A0EN TCGA-A2-A0EN-01 Luminal A +TCGA-AO-A12A TCGA-AO-A12A-01 Luminal A +TCGA-A2-A0CP TCGA-A2-A0CP-01 Luminal A +TCGA-AO-A126 TCGA-AO-A126-01 Luminal A +TCGA-AO-A125 TCGA-AO-A125-01 Luminal A +TCGA-A2-A0EM TCGA-A2-A0EM-01 Luminal A +TCGA-A2-A04N TCGA-A2-A04N-01 Luminal A +TCGA-AQ-A04L TCGA-AQ-A04L-01 Luminal A +TCGA-B6-A0IO TCGA-B6-A0IO-01 Luminal A +TCGA-B6-A0IP TCGA-B6-A0IP-01 Luminal A +TCGA-B6-A0WZ TCGA-B6-A0WZ-01 Luminal A +TCGA-B6-A0I5 TCGA-B6-A0I5-01 Luminal A +TCGA-B6-A0RV TCGA-B6-A0RV-01 Luminal A +TCGA-B6-A0RO TCGA-B6-A0RO-01 Luminal A +TCGA-B6-A0RN TCGA-B6-A0RN-01 Luminal A +TCGA-B6-A0WT TCGA-B6-A0WT-01 Luminal A +TCGA-B6-A0IA TCGA-B6-A0IA-01 Luminal A +TCGA-B6-A0RI TCGA-B6-A0RI-01 Luminal A +TCGA-A1-A0SE TCGA-A1-A0SE-01 Luminal A +TCGA-A2-A0EX TCGA-A2-A0EX-01 Luminal A +TCGA-AO-A0JJ TCGA-AO-A0JJ-01 Luminal A +TCGA-E2-A105 TCGA-E2-A105-01 Luminal A +TCGA-A1-A0SD TCGA-A1-A0SD-01 Luminal A +TCGA-A1-A0SH TCGA-A1-A0SH-01 Luminal A +TCGA-A1-A0SJ TCGA-A1-A0SJ-01 Luminal A +TCGA-A8-A06P TCGA-A8-A06P-01 Luminal A +TCGA-A8-A06T TCGA-A8-A06T-01 Luminal A +TCGA-A8-A06Y TCGA-A8-A06Y-01 Luminal A +TCGA-A8-A07E TCGA-A8-A07E-01 Luminal A +TCGA-A8-A07F TCGA-A8-A07F-01 Luminal A +TCGA-A8-A07G TCGA-A8-A07G-01 Luminal A +TCGA-A8-A07J TCGA-A8-A07J-01 Luminal A +TCGA-A8-A07P TCGA-A8-A07P-01 Luminal A +TCGA-A8-A083 TCGA-A8-A083-01 Luminal A +TCGA-A8-A086 TCGA-A8-A086-01 Luminal A +TCGA-A8-A08A TCGA-A8-A08A-01 Luminal A +TCGA-A8-A08C TCGA-A8-A08C-01 Luminal A +TCGA-A8-A08O TCGA-A8-A08O-01 Luminal A +TCGA-A8-A08T TCGA-A8-A08T-01 Luminal A +TCGA-A8-A08Z TCGA-A8-A08Z-01 Luminal A +TCGA-A8-A090 TCGA-A8-A090-01 Luminal A +TCGA-A8-A091 TCGA-A8-A091-01 Luminal A +TCGA-A8-A093 TCGA-A8-A093-01 Luminal A +TCGA-A8-A099 TCGA-A8-A099-01 Luminal A +TCGA-A8-A09A TCGA-A8-A09A-01 Luminal A +TCGA-A8-A09B TCGA-A8-A09B-01 Luminal A +TCGA-A8-A09T TCGA-A8-A09T-01 Luminal A +TCGA-A8-A09V TCGA-A8-A09V-01 Luminal A +TCGA-A8-A0A1 TCGA-A8-A0A1-01 Luminal A +TCGA-A8-A0A2 TCGA-A8-A0A2-01 Luminal A +TCGA-A8-A0A4 TCGA-A8-A0A4-01 Luminal A +TCGA-A8-A0A6 TCGA-A8-A0A6-01 Luminal A +TCGA-A8-A0AD TCGA-A8-A0AD-01 Luminal A +TCGA-AN-A03X TCGA-AN-A03X-01 Luminal A +TCGA-AN-A046 TCGA-AN-A046-01 Luminal A +TCGA-AN-A04A TCGA-AN-A04A-01 Luminal A +TCGA-AN-A0FD TCGA-AN-A0FD-01 Luminal A +TCGA-AN-A0FN TCGA-AN-A0FN-01 Luminal A +TCGA-AN-A0FS TCGA-AN-A0FS-01 Luminal A +TCGA-AN-A0FT TCGA-AN-A0FT-01 Luminal A +TCGA-AN-A0FW TCGA-AN-A0FW-01 Luminal A +TCGA-AN-A0FZ TCGA-AN-A0FZ-01 Luminal A +TCGA-AN-A0XL TCGA-AN-A0XL-01 Luminal A +TCGA-AN-A0XN TCGA-AN-A0XN-01 Luminal A +TCGA-AN-A0XO TCGA-AN-A0XO-01 Luminal A +TCGA-AN-A0XP TCGA-AN-A0XP-01 Luminal A +TCGA-AN-A0XS TCGA-AN-A0XS-01 Luminal A +TCGA-AN-A0XT TCGA-AN-A0XT-01 Luminal A +TCGA-AN-A0XV TCGA-AN-A0XV-01 Luminal A +TCGA-AR-A0TW TCGA-AR-A0TW-01 Luminal A +TCGA-AR-A1AK TCGA-AR-A1AK-01 Luminal A +TCGA-AR-A1AL TCGA-AR-A1AL-01 Luminal A +TCGA-AR-A1AN TCGA-AR-A1AN-01 Luminal A +TCGA-AR-A1AP TCGA-AR-A1AP-01 Luminal A +TCGA-AR-A1AS TCGA-AR-A1AS-01 Luminal A +TCGA-AR-A1AU TCGA-AR-A1AU-01 Luminal A +TCGA-AR-A1AW TCGA-AR-A1AW-01 Luminal A +TCGA-AR-A1AX TCGA-AR-A1AX-01 Luminal A +TCGA-BH-A0AZ TCGA-BH-A0AZ-01 Luminal A +TCGA-BH-A0B0 TCGA-BH-A0B0-01 Luminal A +TCGA-BH-A0BM TCGA-BH-A0BM-01 Luminal A +TCGA-BH-A0BO TCGA-BH-A0BO-01 Luminal A +TCGA-BH-A0BP TCGA-BH-A0BP-01 Luminal A +TCGA-BH-A0BQ TCGA-BH-A0BQ-01 Luminal A +TCGA-BH-A0BR TCGA-BH-A0BR-01 Luminal A +TCGA-BH-A0BS TCGA-BH-A0BS-01 Luminal A +TCGA-BH-A0BT TCGA-BH-A0BT-01 Luminal A +TCGA-BH-A0C1 TCGA-BH-A0C1-01 Luminal A +TCGA-BH-A0DE TCGA-BH-A0DE-01 Luminal A +TCGA-BH-A0DG TCGA-BH-A0DG-01 Luminal A +TCGA-BH-A0DI TCGA-BH-A0DI-01 Luminal A +TCGA-BH-A0DO TCGA-BH-A0DO-01 Luminal A +TCGA-BH-A0DT TCGA-BH-A0DT-01 Luminal A +TCGA-BH-A0DX TCGA-BH-A0DX-01 Luminal A +TCGA-BH-A0E9 TCGA-BH-A0E9-01 Luminal A +TCGA-BH-A0EI TCGA-BH-A0EI-01 Luminal A +TCGA-BH-A0H3 TCGA-BH-A0H3-01 Luminal A +TCGA-BH-A0H5 TCGA-BH-A0H5-01 Luminal A +TCGA-BH-A0HA TCGA-BH-A0HA-01 Luminal A +TCGA-BH-A0W4 TCGA-BH-A0W4-01 Luminal A +TCGA-BH-A0W5 TCGA-BH-A0W5-01 Luminal A +TCGA-BH-A0W7 TCGA-BH-A0W7-01 Luminal A +TCGA-BH-A18H TCGA-BH-A18H-01 Luminal A +TCGA-BH-A18I TCGA-BH-A18I-01 Luminal A +TCGA-C8-A12N TCGA-C8-A12N-01 Luminal A +TCGA-C8-A12O TCGA-C8-A12O-01 Luminal A +TCGA-C8-A12Y TCGA-C8-A12Y-01 Luminal A +TCGA-C8-A132 TCGA-C8-A132-01 Luminal A +TCGA-C8-A133 TCGA-C8-A133-01 Luminal A +TCGA-C8-A1HI TCGA-C8-A1HI-01 Luminal A +TCGA-D8-A141 TCGA-D8-A141-01 Luminal A +TCGA-E2-A14Q TCGA-E2-A14Q-01 Luminal A +TCGA-E2-A14T TCGA-E2-A14T-01 Luminal A +TCGA-E2-A14Z TCGA-E2-A14Z-01 Luminal A +TCGA-E2-A153 TCGA-E2-A153-01 Luminal A +TCGA-E2-A154 TCGA-E2-A154-01 Luminal A +TCGA-E2-A156 TCGA-E2-A156-01 Luminal A +TCGA-E2-A15C TCGA-E2-A15C-01 Luminal A +TCGA-E2-A15D TCGA-E2-A15D-01 Luminal A +TCGA-E2-A15E TCGA-E2-A15E-01 Luminal A +TCGA-E2-A15F TCGA-E2-A15F-01 Luminal A +TCGA-E2-A15G TCGA-E2-A15G-01 Luminal A +TCGA-E2-A15H TCGA-E2-A15H-01 Luminal A +TCGA-E2-A15I TCGA-E2-A15I-01 Luminal A +TCGA-E2-A15J TCGA-E2-A15J-01 Luminal A +TCGA-E2-A15O TCGA-E2-A15O-01 Luminal A +TCGA-E2-A15P TCGA-E2-A15P-01 Luminal A +TCGA-E2-A15R TCGA-E2-A15R-01 Luminal A +TCGA-E2-A1B1 TCGA-E2-A1B1-01 Luminal A +TCGA-E2-A1B4 TCGA-E2-A1B4-01 Luminal A +TCGA-E2-A1B6 TCGA-E2-A1B6-01 Luminal A +TCGA-E2-A1BC TCGA-E2-A1BC-01 Luminal A +TCGA-E2-A1BD TCGA-E2-A1BD-01 Luminal A +TCGA-A2-A0SV TCGA-A2-A0SV-01 Luminal B +TCGA-AO-A03O TCGA-AO-A03O-01 Luminal B +TCGA-A2-A0SW TCGA-A2-A0SW-01 Luminal B +TCGA-B6-A0WW TCGA-B6-A0WW-01 Luminal B +TCGA-BH-A18J TCGA-BH-A18J-01 Luminal B +TCGA-BH-A18L TCGA-BH-A18L-01 Luminal B +TCGA-A8-A06X TCGA-A8-A06X-01 Luminal B +TCGA-B6-A0IC TCGA-B6-A0IC-01 Luminal B +TCGA-BH-A18U TCGA-BH-A18U-01 Luminal B +TCGA-BH-A1EW TCGA-BH-A1EW-01 Luminal B +TCGA-AR-A0TY TCGA-AR-A0TY-01 Luminal B +TCGA-B6-A0X5 TCGA-B6-A0X5-01 Luminal B +TCGA-B6-A0WV TCGA-B6-A0WV-01 Luminal B +TCGA-B6-A0RL TCGA-B6-A0RL-01 Luminal B +TCGA-AR-A0U2 TCGA-AR-A0U2-01 Luminal B +TCGA-B6-A0IB TCGA-B6-A0IB-01 Luminal B +TCGA-AO-A0J7 TCGA-AO-A0J7-01 Luminal B +TCGA-AO-A0J3 TCGA-AO-A0J3-01 Luminal B +TCGA-D8-A13Y TCGA-D8-A13Y-01 Luminal B +TCGA-A7-A13F TCGA-A7-A13F-01 Luminal B +TCGA-BH-A0HU TCGA-BH-A0HU-01 Luminal B +TCGA-D8-A140 TCGA-D8-A140-01 Luminal B +TCGA-A7-A0CJ TCGA-A7-A0CJ-01 Luminal B +TCGA-AQ-A04H TCGA-AQ-A04H-01 Luminal B +TCGA-BH-A0H0 TCGA-BH-A0H0-01 Luminal B +TCGA-BH-A0BD TCGA-BH-A0BD-01 Luminal B +TCGA-A2-A0T3 TCGA-A2-A0T3-01 Luminal B +TCGA-A2-A0T4 TCGA-A2-A0T4-01 Luminal B +TCGA-A2-A0YH TCGA-A2-A0YH-01 Luminal B +TCGA-A2-A0YG TCGA-A2-A0YG-01 Luminal B +TCGA-A2-A0EY TCGA-A2-A0EY-01 Luminal B +TCGA-A2-A0D4 TCGA-A2-A0D4-01 Luminal B +TCGA-BH-A0AY TCGA-BH-A0AY-01 Luminal B +TCGA-E2-A107 TCGA-E2-A107-01 Luminal B +TCGA-AO-A0JI TCGA-AO-A0JI-01 Luminal B +TCGA-E2-A10C TCGA-E2-A10C-01 Luminal B +TCGA-E2-A10A TCGA-E2-A10A-01 Luminal B +TCGA-BH-A0C0 TCGA-BH-A0C0-01 Luminal B +TCGA-E2-A109 TCGA-E2-A109-01 Luminal B +TCGA-AO-A0JC TCGA-AO-A0JC-01 Luminal B +TCGA-BH-A0HW TCGA-BH-A0HW-01 Luminal B +TCGA-AO-A0JD TCGA-AO-A0JD-01 Luminal B +TCGA-AO-A0JM TCGA-AO-A0JM-01 Luminal B +TCGA-A2-A0CW TCGA-A2-A0CW-01 Luminal B +TCGA-A2-A0ER TCGA-A2-A0ER-01 Luminal B +TCGA-A2-A0CT TCGA-A2-A0CT-01 Luminal B +TCGA-AO-A12B TCGA-AO-A12B-01 Luminal B +TCGA-A2-A04R TCGA-A2-A04R-01 Luminal B +TCGA-B6-A0IM TCGA-B6-A0IM-01 Luminal B +TCGA-AO-A03P TCGA-AO-A03P-01 Luminal B +TCGA-A1-A0SM TCGA-A1-A0SM-01 Luminal B +TCGA-A8-A06N TCGA-A8-A06N-01 Luminal B +TCGA-A8-A06O TCGA-A8-A06O-01 Luminal B +TCGA-A8-A06Q TCGA-A8-A06Q-01 Luminal B +TCGA-A8-A06R TCGA-A8-A06R-01 Luminal B +TCGA-A8-A06Z TCGA-A8-A06Z-01 Luminal B +TCGA-A8-A079 TCGA-A8-A079-01 Luminal B +TCGA-A8-A07L TCGA-A8-A07L-01 Luminal B +TCGA-A8-A07S TCGA-A8-A07S-01 Luminal B +TCGA-A8-A07W TCGA-A8-A07W-01 Luminal B +TCGA-A8-A07Z TCGA-A8-A07Z-01 Luminal B +TCGA-A8-A082 TCGA-A8-A082-01 Luminal B +TCGA-A8-A084 TCGA-A8-A084-01 Luminal B +TCGA-A8-A085 TCGA-A8-A085-01 Luminal B +TCGA-A8-A08F TCGA-A8-A08F-01 Luminal B +TCGA-A8-A08G TCGA-A8-A08G-01 Luminal B +TCGA-A8-A08I TCGA-A8-A08I-01 Luminal B +TCGA-A8-A08P TCGA-A8-A08P-01 Luminal B +TCGA-A8-A095 TCGA-A8-A095-01 Luminal B +TCGA-A8-A096 TCGA-A8-A096-01 Luminal B +TCGA-A8-A097 TCGA-A8-A097-01 Luminal B +TCGA-A8-A09C TCGA-A8-A09C-01 Luminal B +TCGA-A8-A09D TCGA-A8-A09D-01 Luminal B +TCGA-A8-A09I TCGA-A8-A09I-01 Luminal B +TCGA-A8-A09M TCGA-A8-A09M-01 Luminal B +TCGA-A8-A09N TCGA-A8-A09N-01 Luminal B +TCGA-A8-A09Q TCGA-A8-A09Q-01 Luminal B +TCGA-A8-A09R TCGA-A8-A09R-01 Luminal B +TCGA-A8-A09W TCGA-A8-A09W-01 Luminal B +TCGA-A8-A09Z TCGA-A8-A09Z-01 Luminal B +TCGA-A8-A0A9 TCGA-A8-A0A9-01 Luminal B +TCGA-A8-A0AB TCGA-A8-A0AB-01 Luminal B +TCGA-AN-A03Y TCGA-AN-A03Y-01 Luminal B +TCGA-AN-A041 TCGA-AN-A041-01 Luminal B +TCGA-AN-A049 TCGA-AN-A049-01 Luminal B +TCGA-AN-A0AJ TCGA-AN-A0AJ-01 Luminal B +TCGA-AN-A0AK TCGA-AN-A0AK-01 Luminal B +TCGA-AN-A0AM TCGA-AN-A0AM-01 Luminal B +TCGA-AN-A0AS TCGA-AN-A0AS-01 Luminal B +TCGA-AN-A0FF TCGA-AN-A0FF-01 Luminal B +TCGA-AN-A0FK TCGA-AN-A0FK-01 Luminal B +TCGA-AN-A0FY TCGA-AN-A0FY-01 Luminal B +TCGA-AN-A0XR TCGA-AN-A0XR-01 Luminal B +TCGA-AN-A0XW TCGA-AN-A0XW-01 Luminal B +TCGA-AR-A0TQ TCGA-AR-A0TQ-01 Luminal B +TCGA-AR-A0TT TCGA-AR-A0TT-01 Luminal B +TCGA-AR-A0TV TCGA-AR-A0TV-01 Luminal B +TCGA-AR-A0TZ TCGA-AR-A0TZ-01 Luminal B +TCGA-AR-A0U3 TCGA-AR-A0U3-01 Luminal B +TCGA-AR-A1AV TCGA-AR-A1AV-01 Luminal B +TCGA-BH-A0AU TCGA-BH-A0AU-01 Luminal B +TCGA-BH-A0B5 TCGA-BH-A0B5-01 Luminal B +TCGA-BH-A0BF TCGA-BH-A0BF-01 Luminal B +TCGA-BH-A0BZ TCGA-BH-A0BZ-01 Luminal B +TCGA-BH-A0C3 TCGA-BH-A0C3-01 Luminal B +TCGA-BH-A0C7 TCGA-BH-A0C7-01 Luminal B +TCGA-BH-A0DD TCGA-BH-A0DD-01 Luminal B +TCGA-BH-A0W3 TCGA-BH-A0W3-01 Luminal B +TCGA-BH-A18F TCGA-BH-A18F-01 Luminal B +TCGA-C8-A12M TCGA-C8-A12M-01 Luminal B +TCGA-C8-A12U TCGA-C8-A12U-01 Luminal B +TCGA-C8-A12W TCGA-C8-A12W-01 Luminal B +TCGA-C8-A12X TCGA-C8-A12X-01 Luminal B +TCGA-C8-A1HG TCGA-C8-A1HG-01 Luminal B +TCGA-C8-A1HL TCGA-C8-A1HL-01 Luminal B +TCGA-C8-A1HM TCGA-C8-A1HM-01 Luminal B +TCGA-C8-A1HN TCGA-C8-A1HN-01 Luminal B +TCGA-E2-A14O TCGA-E2-A14O-01 Luminal B +TCGA-E2-A14S TCGA-E2-A14S-01 Luminal B +TCGA-E2-A14W TCGA-E2-A14W-01 Luminal B +TCGA-E2-A155 TCGA-E2-A155-01 Luminal B +TCGA-E2-A15A TCGA-E2-A15A-01 Luminal B +TCGA-E2-A15K TCGA-E2-A15K-01 Luminal B +TCGA-E2-A15L TCGA-E2-A15L-01 Luminal B +TCGA-E2-A15M TCGA-E2-A15M-01 Luminal B +TCGA-E2-A15S TCGA-E2-A15S-01 Luminal B +TCGA-E2-A15T TCGA-E2-A15T-01 Luminal B +TCGA-AO-A03U TCGA-AO-A03U-01 NA +TCGA-B6-A0IE TCGA-B6-A0IE-01 NA +TCGA-A2-A0YK TCGA-A2-A0YK-01 NA +TCGA-E2-A108 TCGA-E2-A108-01 Claudin low +TCGA-AO-A0JB TCGA-AO-A0JB-01 NA +TCGA-AO-A03R TCGA-AO-A03R-01 NA +TCGA-AO-A03T TCGA-AO-A03T-01 NA +TCGA-AR-A1AO TCGA-AR-A1AO-01 Claudin low +TCGA-A2-A0YT TCGA-A2-A0YT-01 Luminal B +TCGA-AQ-A0Y5 TCGA-AQ-A0Y5-01 NA +TCGA-EW-A1P8 TCGA-EW-A1P8-01 NA +TCGA-E2-A1LK TCGA-E2-A1LK-01 NA +TCGA-BH-A1EY TCGA-BH-A1EY-01 NA +TCGA-BH-A1F8 TCGA-BH-A1F8-01 NA +TCGA-BH-A1F2 TCGA-BH-A1F2-01 NA +TCGA-BH-A1FD TCGA-BH-A1FD-01 NA +TCGA-BH-A1FH TCGA-BH-A1FH-01 NA +TCGA-BH-A203 TCGA-BH-A203-01 NA +TCGA-BH-A1FM TCGA-BH-A1FM-01 NA +TCGA-BH-A1EX TCGA-BH-A1EX-01 NA +TCGA-BH-A1FL TCGA-BH-A1FL-01 NA +TCGA-BH-A208 TCGA-BH-A208-01 NA +TCGA-GM-A2D9 TCGA-GM-A2D9-01 NA +TCGA-BH-A1FJ TCGA-BH-A1FJ-01 NA +TCGA-BH-A1EN TCGA-BH-A1EN-01 NA +TCGA-BH-A1FN TCGA-BH-A1FN-01 NA +TCGA-BH-A1FU TCGA-BH-A1FU-01 NA +TCGA-BH-A1FE TCGA-BH-A1FE-01 NA +TCGA-BH-A204 TCGA-BH-A204-01 NA +TCGA-BH-A1F5 TCGA-BH-A1F5-01 NA +TCGA-AR-A256 TCGA-AR-A256-01 NA +TCGA-BH-A1F6 TCGA-BH-A1F6-01 NA +TCGA-BH-A1FC TCGA-BH-A1FC-01 NA +TCGA-BH-A1FB TCGA-BH-A1FB-01 NA +TCGA-BH-A1FG TCGA-BH-A1FG-01 NA +TCGA-BH-A209 TCGA-BH-A209-01 NA +TCGA-BH-A1FR TCGA-BH-A1FR-01 NA +TCGA-AO-A1KS TCGA-AO-A1KS-01 NA +TCGA-A7-A13G TCGA-A7-A13G-01 NA +TCGA-D8-A1JS TCGA-D8-A1JS-01 NA +TCGA-A7-A0DC TCGA-A7-A0DC-01 Luminal A +TCGA-D8-A1JT TCGA-D8-A1JT-01 NA +TCGA-A7-A26E TCGA-A7-A26E-01 NA +TCGA-D8-A1JH TCGA-D8-A1JH-01 NA +TCGA-D8-A1JU TCGA-D8-A1JU-01 NA +TCGA-AO-A1KO TCGA-AO-A1KO-01 NA +TCGA-AO-A1KT TCGA-AO-A1KT-01 NA +TCGA-AO-A0J5 TCGA-AO-A0J5-01 Luminal A +TCGA-B6-A1KC TCGA-B6-A1KC-01 NA +TCGA-AO-A1KQ TCGA-AO-A1KQ-01 NA +TCGA-B6-A1KI TCGA-B6-A1KI-01 NA +TCGA-AO-A1KP TCGA-AO-A1KP-01 NA +TCGA-B6-A1KF TCGA-B6-A1KF-01 NA +TCGA-B6-A1KN TCGA-B6-A1KN-01 NA +TCGA-D8-A1XO TCGA-D8-A1XO-01 NA +TCGA-D8-A1XT TCGA-D8-A1XT-01 NA +TCGA-A1-A0SP TCGA-A1-A0SP-01 NA +TCGA-D8-A1J8 TCGA-D8-A1J8-01 NA +TCGA-D8-A1JF TCGA-D8-A1JF-01 NA +TCGA-D8-A1JG TCGA-D8-A1JG-01 NA +TCGA-D8-A1XS TCGA-D8-A1XS-01 NA +TCGA-A1-A0SB TCGA-A1-A0SB-01 NA +TCGA-A1-A0SB TCGA-A1-A0SB-02 NA +TCGA-A1-A0SF TCGA-A1-A0SF-01 NA +TCGA-A1-A0SG TCGA-A1-A0SG-01 NA +TCGA-A1-A0SI TCGA-A1-A0SI-01 NA +TCGA-A1-A0SN TCGA-A1-A0SN-01 NA +TCGA-A1-A0SQ TCGA-A1-A0SQ-01 NA +TCGA-A2-A1FV TCGA-A2-A1FV-01 NA +TCGA-A2-A1FW TCGA-A2-A1FW-01 NA +TCGA-A2-A1FX TCGA-A2-A1FX-01 NA +TCGA-A2-A1FZ TCGA-A2-A1FZ-01 NA +TCGA-A2-A1G0 TCGA-A2-A1G0-01 NA +TCGA-A2-A1G1 TCGA-A2-A1G1-01 NA +TCGA-A2-A1G4 TCGA-A2-A1G4-01 NA +TCGA-A2-A1G6 TCGA-A2-A1G6-01 NA +TCGA-A2-A259 TCGA-A2-A259-01 NA +TCGA-A2-A25A TCGA-A2-A25A-01 NA +TCGA-A2-A25B TCGA-A2-A25B-01 NA +TCGA-A2-A25C TCGA-A2-A25C-01 NA +TCGA-A2-A25D TCGA-A2-A25D-01 NA +TCGA-A2-A25E TCGA-A2-A25E-01 NA +TCGA-A2-A25F TCGA-A2-A25F-01 NA +TCGA-A7-A26F TCGA-A7-A26F-01 NA +TCGA-A7-A26G TCGA-A7-A26G-01 NA +TCGA-A7-A26H TCGA-A7-A26H-01 NA +TCGA-A7-A26I TCGA-A7-A26I-01 NA +TCGA-A7-A26J TCGA-A7-A26J-01 NA +TCGA-A8-A08S TCGA-A8-A08S-01 Luminal B +TCGA-A8-A09E TCGA-A8-A09E-01 Luminal B +TCGA-A8-A09K TCGA-A8-A09K-01 Luminal B +TEST-A23C TEST-A23C-01 NA +TEST-A23E TEST-A23E-01 NA +TEST-A23H TEST-A23H-01 NA +TCGA-AO-A1KR TCGA-AO-A1KR-01 NA +TCGA-AQ-A1H2 TCGA-AQ-A1H2-01 NA +TCGA-AQ-A1H3 TCGA-AQ-A1H3-01 NA +TCGA-AR-A24H TCGA-AR-A24H-01 NA +TCGA-AR-A24K TCGA-AR-A24K-01 NA +TCGA-AR-A24L TCGA-AR-A24L-01 NA +TCGA-AR-A24M TCGA-AR-A24M-01 NA +TCGA-AR-A24N TCGA-AR-A24N-01 NA 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+TCGA-A2-A0T2 TCGA-A2-A0T2-01 NA +TEST_PATIENT_1 TEST_SAMPLE_1 NA +TEST_PATIENT_2 TEST_SAMPLE_2 NA +TEST_PATIENT_3 TEST_SAMPLE_3 NA +TEST_PATIENT_4 TEST_SAMPLE_4 NA +TEST_PATIENT_5 TEST_SAMPLE_5 NA +TEST_PATIENT_6 TEST_SAMPLE_6 NA +TEST_PATIENT_7 TEST_SAMPLE_7 NA +TEST_PATIENT_8 TEST_SAMPLE_8 NA +TEST_PATIENT_9 TEST_SAMPLE_9 NA +TEST_PATIENT_10 TEST_SAMPLE_10 NA +TEST_PATIENT_11 TEST_SAMPLE_11 NA +TEST_PATIENT_12 TEST_SAMPLE_12 NA +TEST_PATIENT_13 TEST_SAMPLE_13 NA +TEST_PATIENT_14 TEST_SAMPLE_14 NA +TEST_PATIENT_15 TEST_SAMPLE_15 NA +TEST_PATIENT_NAMESPACE TEST_SAMPLE_SOMATIC_HOMOZYGOUS NA +TEST_PATIENT_NAMESPACE TEST_SAMPLE_SOMATIC_HETEROZYGOUS NA +TEST_PATIENT_NAMESPACE TEST_SAMPLE_SOMATIC_UNDEFINED NA diff --git a/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_cna_discrete.txt b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_cna_discrete.txt new file mode 100644 index 00000000000..9068287db04 --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_cna_discrete.txt @@ -0,0 +1,9 @@ +Hugo_Symbol Entrez_Gene_Id TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SF-01 TCGA-A1-A0SG-01 TCGA-A1-A0SH-01 TCGA-A1-A0SI-01 TCGA-A1-A0SJ-01 TCGA-A1-A0SK-01 TCGA-A1-A0SM-01 TCGA-A1-A0SN-01 TCGA-A1-A0SO-01 TCGA-A1-A0SP-01 TCGA-A1-A0SQ-01 TCGA-A2-A04N-01 TCGA-A2-A04P-01 TCGA-A2-A04Q-01 TCGA-A2-A04R-01 TCGA-A2-A04T-01 TCGA-A2-A04U-01 TCGA-A2-A04V-01 TCGA-A2-A04W-01 TCGA-A2-A04X-01 TCGA-A2-A04Y-01 TCGA-A2-A0CL-01 TCGA-A2-A0CM-01 TCGA-A2-A0CP-01 TCGA-A2-A0CQ-01 TCGA-A2-A0CS-01 TCGA-A2-A0CT-01 TCGA-A2-A0CU-01 TCGA-A2-A0CV-01 TCGA-A2-A0CW-01 TCGA-A2-A0CX-01 TCGA-A2-A0D0-01 TCGA-A2-A0D1-01 TCGA-A2-A0D2-01 TCGA-A2-A0D3-01 TCGA-A2-A0D4-01 TCGA-A2-A0EM-01 TCGA-A2-A0EN-01 TCGA-A2-A0EO-01 TCGA-A2-A0EQ-01 TCGA-A2-A0ER-01 TCGA-A2-A0ES-01 TCGA-A2-A0ET-01 TCGA-A2-A0EU-01 TCGA-A2-A0EV-01 TCGA-A2-A0EW-01 TCGA-A2-A0EX-01 TCGA-A2-A0EY-01 TCGA-A2-A0ST-01 TCGA-A2-A0SU-01 TCGA-A2-A0SV-01 TCGA-A2-A0SW-01 TCGA-A2-A0SX-01 TCGA-A2-A0SY-01 TCGA-A2-A0T0-01 TCGA-A2-A0T1-01 TCGA-A2-A0T2-01 TCGA-A2-A0T3-01 TCGA-A2-A0T4-01 TCGA-A2-A0T5-01 TCGA-A2-A0T6-01 TCGA-A2-A0T7-01 TCGA-A2-A0YC-01 TCGA-A2-A0YD-01 TCGA-A2-A0YE-01 TCGA-A2-A0YF-01 TCGA-A2-A0YG-01 TCGA-A2-A0YH-01 TCGA-A2-A0YI-01 TCGA-A2-A0YJ-01 TCGA-A2-A0YK-01 TCGA-A2-A0YL-01 TCGA-A2-A0YM-01 TCGA-A2-A0YT-01 TCGA-A2-A1FV-01 TCGA-A2-A1FW-01 TCGA-A2-A1FX-01 TCGA-A2-A1FZ-01 TCGA-A2-A1G0-01 TCGA-A2-A1G1-01 TCGA-A2-A1G4-01 TCGA-A2-A1G6-01 TCGA-A2-A259-01 TCGA-A2-A25A-01 TCGA-A2-A25B-01 TCGA-A2-A25C-01 TCGA-A2-A25D-01 TCGA-A2-A25E-01 TCGA-A2-A25F-01 TCGA-A7-A0CD-01 TCGA-A7-A0CE-01 TCGA-A7-A0CG-01 TCGA-A7-A0CH-01 TCGA-A7-A0CJ-01 TCGA-A7-A0D9-01 TCGA-A7-A0DA-01 TCGA-A7-A0DB-01 TCGA-A7-A13D-01 TCGA-A7-A13E-01 TCGA-A7-A13F-01 TCGA-A7-A13G-01 TCGA-A7-A26E-01 TCGA-A7-A26F-01 TCGA-A7-A26G-01 TCGA-A7-A26H-01 TCGA-A7-A26I-01 TCGA-A7-A26J-01 TCGA-A8-A06N-01 TCGA-A8-A06O-01 TCGA-A8-A06P-01 TCGA-A8-A06Q-01 TCGA-A8-A06R-01 TCGA-A8-A06T-01 TCGA-A8-A06U-01 TCGA-A8-A06X-01 TCGA-A8-A06Y-01 TCGA-A8-A06Z-01 TCGA-A8-A075-01 TCGA-A8-A076-01 TCGA-A8-A079-01 TCGA-A8-A07B-01 TCGA-A8-A07E-01 TCGA-A8-A07F-01 TCGA-A8-A07G-01 TCGA-A8-A07I-01 TCGA-A8-A07J-01 TCGA-A8-A07L-01 TCGA-A8-A07O-01 TCGA-A8-A07P-01 TCGA-A8-A07R-01 TCGA-A8-A07S-01 TCGA-A8-A07U-01 TCGA-A8-A07W-01 TCGA-A8-A07Z-01 TCGA-A8-A081-01 TCGA-A8-A082-01 TCGA-A8-A083-01 TCGA-A8-A084-01 TCGA-A8-A085-01 TCGA-A8-A086-01 TCGA-A8-A08A-01 TCGA-A8-A08B-01 TCGA-A8-A08C-01 TCGA-A8-A08F-01 TCGA-A8-A08G-01 TCGA-A8-A08H-01 TCGA-A8-A08I-01 TCGA-A8-A08J-01 TCGA-A8-A08L-01 TCGA-A8-A08O-01 TCGA-A8-A08P-01 TCGA-A8-A08R-01 TCGA-A8-A08S-01 TCGA-A8-A08T-01 TCGA-A8-A08X-01 TCGA-A8-A08Z-01 TCGA-A8-A090-01 TCGA-A8-A091-01 TCGA-A8-A092-01 TCGA-A8-A093-01 TCGA-A8-A094-01 TCGA-A8-A095-01 TCGA-A8-A096-01 TCGA-A8-A097-01 TCGA-A8-A099-01 TCGA-A8-A09A-01 TCGA-A8-A09B-01 TCGA-A8-A09C-01 TCGA-A8-A09D-01 TCGA-A8-A09E-01 TCGA-A8-A09G-01 TCGA-A8-A09I-01 TCGA-A8-A09M-01 TCGA-A8-A09N-01 TCGA-A8-A09Q-01 TCGA-A8-A09R-01 TCGA-A8-A09T-01 TCGA-A8-A09V-01 TCGA-A8-A09W-01 TCGA-A8-A09X-01 TCGA-A8-A09Z-01 TCGA-A8-A0A1-01 TCGA-A8-A0A2-01 TCGA-A8-A0A4-01 TCGA-A8-A0A6-01 TCGA-A8-A0A7-01 TCGA-A8-A0A9-01 TCGA-A8-A0AB-01 TCGA-A8-A0AD-01 TEST-A23C-01 TEST-A23E-01 TEST-A23H-01 TEST-A2B8-01 TEST-A2FB-01 TEST-A2FF-01 TEST-A2FG-01 TCGA-AN-A03X-01 TCGA-AN-A03Y-01 TCGA-AN-A041-01 TCGA-AN-A046-01 TCGA-AN-A049-01 TCGA-AN-A04A-01 TCGA-AN-A04C-01 TCGA-AN-A04D-01 TCGA-AN-A0AJ-01 TCGA-AN-A0AK-01 TCGA-AN-A0AL-01 TCGA-AN-A0AM-01 TCGA-AN-A0AR-01 TCGA-AN-A0AS-01 TCGA-AN-A0AT-01 TCGA-AN-A0FD-01 TCGA-AN-A0FF-01 TCGA-AN-A0FJ-01 TCGA-AN-A0FK-01 TCGA-AN-A0FL-01 TCGA-AN-A0FN-01 TCGA-AN-A0FS-01 TCGA-AN-A0FT-01 TCGA-AN-A0FV-01 TCGA-AN-A0FW-01 TCGA-AN-A0FX-01 TCGA-AN-A0FY-01 TCGA-AN-A0FZ-01 TCGA-AN-A0XL-01 TCGA-AN-A0XN-01 TCGA-AN-A0XO-01 TCGA-AN-A0XR-01 TCGA-AN-A0XS-01 TCGA-AN-A0XT-01 TCGA-AN-A0XU-01 TCGA-AN-A0XV-01 TCGA-AN-A0XW-01 TCGA-AO-A03L-01 TCGA-AO-A03M-01 TCGA-AO-A03N-01 TCGA-AO-A03O-01 TCGA-AO-A03P-01 TCGA-AO-A03R-01 TCGA-AO-A03T-01 TCGA-AO-A03U-01 TCGA-AO-A03V-01 TCGA-AO-A0J2-01 TCGA-AO-A0J3-01 TCGA-AO-A0J4-01 TCGA-AO-A0J5-01 TCGA-AO-A0J6-01 TCGA-AO-A0J7-01 TCGA-AO-A0J8-01 TCGA-AO-A0J9-01 TCGA-AO-A0JA-01 TCGA-AO-A0JB-01 TCGA-AO-A0JC-01 TCGA-AO-A0JD-01 TCGA-AO-A0JE-01 TCGA-AO-A0JF-01 TCGA-AO-A0JG-01 TCGA-AO-A0JI-01 TCGA-AO-A0JJ-01 TCGA-AO-A0JL-01 TCGA-AO-A0JM-01 TCGA-AO-A124-01 TCGA-AO-A125-01 TCGA-AO-A126-01 TCGA-AO-A128-01 TCGA-AO-A129-01 TCGA-AO-A12A-01 TCGA-AO-A12B-01 TCGA-AO-A12D-01 TCGA-AO-A12E-01 TCGA-AO-A12F-01 TCGA-AO-A12G-01 TCGA-AO-A12H-01 TCGA-AO-A1KO-01 TCGA-AO-A1KP-01 TCGA-AO-A1KQ-01 TCGA-AO-A1KR-01 TCGA-AO-A1KS-01 TCGA-AO-A1KT-01 TCGA-AQ-A04H-01 TCGA-AQ-A04J-01 TCGA-AQ-A04L-01 TCGA-AQ-A0Y5-01 TCGA-AQ-A1H2-01 TCGA-AQ-A1H3-01 TCGA-AR-A0TP-01 TCGA-AR-A0TQ-01 TCGA-AR-A0TR-01 TCGA-AR-A0TS-01 TCGA-AR-A0TT-01 TCGA-AR-A0TV-01 TCGA-AR-A0TW-01 TCGA-AR-A0TX-01 TCGA-AR-A0TY-01 TCGA-AR-A0TZ-01 TCGA-AR-A0U0-01 TCGA-AR-A0U1-01 TCGA-AR-A0U2-01 TCGA-AR-A0U3-01 TCGA-AR-A0U4-01 TCGA-AR-A1AH-01 TCGA-AR-A1AI-01 TCGA-AR-A1AJ-01 TCGA-AR-A1AK-01 TCGA-AR-A1AL-01 TCGA-AR-A1AN-01 TCGA-AR-A1AO-01 TCGA-AR-A1AP-01 TCGA-AR-A1AQ-01 TCGA-AR-A1AR-01 TCGA-AR-A1AS-01 TCGA-AR-A1AU-01 TCGA-AR-A1AV-01 TCGA-AR-A1AW-01 TCGA-AR-A1AX-01 TCGA-AR-A1AY-01 TCGA-AR-A24H-01 TCGA-AR-A24K-01 TCGA-AR-A24L-01 TCGA-AR-A24M-01 TCGA-AR-A24N-01 TCGA-AR-A24O-01 TCGA-AR-A24P-01 TCGA-AR-A24Q-01 TCGA-AR-A24R-01 TCGA-AR-A24S-01 TCGA-AR-A24T-01 TCGA-AR-A24U-01 TCGA-AR-A24V-01 TCGA-AR-A24W-01 TCGA-AR-A24X-01 TCGA-AR-A24Z-01 TCGA-AR-A250-01 TCGA-AR-A251-01 TCGA-AR-A252-01 TCGA-AR-A254-01 TCGA-AR-A255-01 TCGA-AR-A256-01 TCGA-B6-A0I2-01 TCGA-B6-A0I5-01 TCGA-B6-A0I9-01 TCGA-B6-A0IA-01 TCGA-B6-A0IB-01 TCGA-B6-A0IC-01 TCGA-B6-A0IE-01 TCGA-B6-A0IH-01 TCGA-B6-A0IJ-01 TCGA-B6-A0IK-01 TCGA-B6-A0IM-01 TCGA-B6-A0IN-01 TCGA-B6-A0IO-01 TCGA-B6-A0IP-01 TCGA-B6-A0IQ-01 TCGA-B6-A0RE-01 TCGA-B6-A0RG-01 TCGA-B6-A0RH-01 TCGA-B6-A0RI-01 TCGA-B6-A0RL-01 TCGA-B6-A0RM-01 TCGA-B6-A0RN-01 TCGA-B6-A0RO-01 TCGA-B6-A0RP-01 TCGA-B6-A0RQ-01 TCGA-B6-A0RS-01 TCGA-B6-A0RT-01 TCGA-B6-A0RU-01 TCGA-B6-A0RV-01 TCGA-B6-A0WS-01 TCGA-B6-A0WT-01 TCGA-B6-A0WV-01 TCGA-B6-A0WW-01 TCGA-B6-A0WX-01 TCGA-B6-A0WY-01 TCGA-B6-A0WZ-01 TCGA-B6-A0X0-01 TCGA-B6-A0X1-01 TCGA-B6-A0X4-01 TCGA-B6-A0X5-01 TCGA-B6-A0X7-01 TCGA-B6-A1KC-01 TCGA-B6-A1KF-01 TCGA-B6-A1KI-01 TCGA-B6-A1KN-01 TCGA-BH-A0AU-01 TCGA-BH-A0AV-01 TCGA-BH-A0AW-01 TCGA-BH-A0AY-01 TCGA-BH-A0AZ-01 TCGA-BH-A0B0-01 TCGA-BH-A0B3-01 TCGA-BH-A0B4-01 TCGA-BH-A0B5-01 TCGA-BH-A0B7-01 TCGA-BH-A0B9-01 TCGA-BH-A0BA-01 TCGA-BH-A0BC-01 TCGA-BH-A0BD-01 TCGA-BH-A0BF-01 TCGA-BH-A0BG-01 TCGA-BH-A0BJ-01 TCGA-BH-A0BL-01 TCGA-BH-A0BM-01 TCGA-BH-A0BO-01 TCGA-BH-A0BP-01 TCGA-BH-A0BQ-01 TCGA-BH-A0BR-01 TCGA-BH-A0BS-01 TCGA-BH-A0BT-01 TCGA-BH-A0BV-01 TCGA-BH-A0BW-01 TCGA-BH-A0BZ-01 TCGA-BH-A0C0-01 TCGA-BH-A0C1-01 TCGA-BH-A0C3-01 TCGA-BH-A0C7-01 TCGA-BH-A0DD-01 TCGA-BH-A0DE-01 TCGA-BH-A0DG-01 TCGA-BH-A0DH-01 TCGA-BH-A0DI-01 TCGA-BH-A0DK-01 TCGA-BH-A0DL-01 TCGA-BH-A0DO-01 TCGA-BH-A0DP-01 TCGA-BH-A0DQ-01 TCGA-BH-A0DS-01 TCGA-BH-A0DT-01 TCGA-BH-A0DV-01 TCGA-BH-A0DX-01 TCGA-BH-A0DZ-01 TCGA-BH-A0E0-01 TCGA-BH-A0E1-01 TCGA-BH-A0E2-01 TCGA-BH-A0E6-01 TCGA-BH-A0E7-01 TCGA-BH-A0E9-01 TCGA-BH-A0EA-01 TCGA-BH-A0EB-01 TCGA-BH-A0EE-01 TCGA-BH-A0EI-01 TCGA-BH-A0GY-01 TCGA-BH-A0GZ-01 TCGA-BH-A0H0-01 TCGA-BH-A0H3-01 TCGA-BH-A0H5-01 TCGA-BH-A0H6-01 TCGA-BH-A0H7-01 TCGA-BH-A0H9-01 TCGA-BH-A0HA-01 TCGA-BH-A0HB-01 TCGA-BH-A0HI-01 TCGA-BH-A0HK-01 TCGA-BH-A0HO-01 TCGA-BH-A0HP-01 TCGA-BH-A0HU-01 TCGA-BH-A0HW-01 TCGA-BH-A0HX-01 TCGA-BH-A0RX-01 TCGA-BH-A0W3-01 TCGA-BH-A0W4-01 TCGA-BH-A0W5-01 TCGA-BH-A0W7-01 TCGA-BH-A0WA-01 TCGA-BH-A18F-01 TCGA-BH-A18G-01 TCGA-BH-A18H-01 TCGA-BH-A18I-01 TCGA-BH-A18J-01 TCGA-BH-A18K-01 TCGA-BH-A18L-01 TCGA-BH-A18M-01 TCGA-BH-A18N-01 TCGA-BH-A18P-01 TCGA-BH-A18Q-01 TCGA-BH-A18R-01 TCGA-BH-A18S-01 TCGA-BH-A18T-01 TCGA-BH-A18U-01 TCGA-BH-A18V-01 TCGA-BH-A1EN-01 TCGA-BH-A1EO-01 TCGA-BH-A1ES-01 TCGA-BH-A1ET-01 TCGA-BH-A1EU-01 TCGA-BH-A1EV-01 TCGA-BH-A1EW-01 TCGA-BH-A1EX-01 TCGA-BH-A1EY-01 TCGA-BH-A1F0-01 TCGA-BH-A1F2-01 TCGA-BH-A1F5-01 TCGA-BH-A1F6-01 TCGA-BH-A1F8-01 TCGA-BH-A1FB-01 TCGA-BH-A1FC-01 TCGA-BH-A1FD-01 TCGA-BH-A1FE-01 TCGA-BH-A1FG-01 TCGA-BH-A1FH-01 TCGA-BH-A1FJ-01 TCGA-BH-A1FL-01 TCGA-BH-A1FM-01 TCGA-BH-A1FN-01 TCGA-BH-A1FR-01 TCGA-BH-A1FU-01 TCGA-BH-A201-01 TCGA-BH-A202-01 TCGA-BH-A203-01 TCGA-BH-A204-01 TCGA-BH-A208-01 TCGA-BH-A209-01 TCGA-BH-A28Q-01 TCGA-C8-A12K-01 TCGA-C8-A12L-01 TCGA-C8-A12M-01 TCGA-C8-A12N-01 TCGA-C8-A12P-01 TCGA-C8-A12Q-01 TCGA-C8-A12T-01 TCGA-C8-A12U-01 TCGA-C8-A12V-01 TCGA-C8-A12W-01 TCGA-C8-A12X-01 TCGA-C8-A12Y-01 TCGA-C8-A12Z-01 TCGA-C8-A130-01 TCGA-C8-A131-01 TCGA-C8-A132-01 TCGA-C8-A133-01 TCGA-C8-A134-01 TCGA-C8-A135-01 TCGA-C8-A137-01 TCGA-C8-A138-01 TCGA-C8-A1HE-01 TCGA-C8-A1HF-01 TCGA-C8-A1HG-01 TCGA-C8-A1HI-01 TCGA-C8-A1HJ-01 TCGA-C8-A1HK-01 TCGA-C8-A1HL-01 TCGA-C8-A1HM-01 TCGA-C8-A1HN-01 TCGA-C8-A1HO-01 TCGA-C8-A26V-01 TCGA-C8-A26W-01 TCGA-C8-A26X-01 TCGA-C8-A26Y-01 TCGA-C8-A26Z-01 TCGA-C8-A273-01 TCGA-C8-A274-01 TCGA-C8-A275-01 TCGA-C8-A278-01 TCGA-C8-A27A-01 TCGA-C8-A27B-01 TCGA-D8-A13Y-01 TCGA-D8-A13Z-01 TCGA-D8-A141-01 TCGA-D8-A142-01 TCGA-D8-A143-01 TCGA-D8-A145-01 TCGA-D8-A146-01 TCGA-D8-A147-01 TCGA-D8-A1J8-01 TCGA-D8-A1J9-01 TCGA-D8-A1JA-01 TCGA-D8-A1JB-01 TCGA-D8-A1JC-01 TCGA-D8-A1JD-01 TCGA-D8-A1JE-01 TCGA-D8-A1JF-01 TCGA-D8-A1JG-01 TCGA-D8-A1JH-01 TCGA-D8-A1JI-01 TCGA-D8-A1JJ-01 TCGA-D8-A1JK-01 TCGA-D8-A1JL-01 TCGA-D8-A1JM-01 TCGA-D8-A1JN-01 TCGA-D8-A1JP-01 TCGA-D8-A1JS-01 TCGA-D8-A1JT-01 TCGA-D8-A1JU-01 TCGA-D8-A1X5-01 TCGA-D8-A1X6-01 TCGA-D8-A1X7-01 TCGA-D8-A1X8-01 TCGA-D8-A1X9-01 TCGA-D8-A1XA-01 TCGA-D8-A1XB-01 TCGA-D8-A1XC-01 TCGA-D8-A1XD-01 TCGA-D8-A1XF-01 TCGA-D8-A1XG-01 TCGA-D8-A1XJ-01 TCGA-D8-A1XK-01 TCGA-D8-A1XL-01 TCGA-D8-A1XM-01 TCGA-D8-A1XO-01 TCGA-D8-A1XQ-01 TCGA-D8-A1XR-01 TCGA-D8-A1XS-01 TCGA-D8-A1XT-01 TCGA-D8-A1XU-01 TCGA-D8-A1XV-01 TCGA-D8-A1XW-01 TCGA-D8-A1XY-01 TCGA-D8-A1XZ-01 TCGA-D8-A1Y0-01 TCGA-D8-A1Y1-01 TCGA-D8-A1Y2-01 TCGA-D8-A1Y3-01 TCGA-D8-A27E-01 TCGA-D8-A27F-01 TCGA-D8-A27G-01 TCGA-D8-A27H-01 TCGA-D8-A27I-01 TCGA-D8-A27K-01 TCGA-D8-A27L-01 TCGA-D8-A27M-01 TCGA-D8-A27N-01 TCGA-D8-A27P-01 TCGA-D8-A27R-01 TCGA-D8-A27T-01 TCGA-D8-A27V-01 TCGA-D8-A27W-01 TCGA-E2-A105-01 TCGA-E2-A107-01 TCGA-E2-A108-01 TCGA-E2-A109-01 TCGA-E2-A10A-01 TCGA-E2-A10B-01 TCGA-E2-A10C-01 TCGA-E2-A10E-01 TCGA-E2-A10F-01 TCGA-E2-A14N-01 TCGA-E2-A14O-01 TCGA-E2-A14P-01 TCGA-E2-A14Q-01 TCGA-E2-A14R-01 TCGA-E2-A14S-01 TCGA-E2-A14V-01 TCGA-E2-A14W-01 TCGA-E2-A14X-01 TCGA-E2-A14Y-01 TCGA-E2-A14Z-01 TCGA-E2-A150-01 TCGA-E2-A152-01 TCGA-E2-A153-01 TCGA-E2-A154-01 TCGA-E2-A155-01 TCGA-E2-A156-01 TCGA-E2-A158-01 TCGA-E2-A159-01 TCGA-E2-A15C-01 TCGA-E2-A15G-01 TCGA-E2-A15H-01 TCGA-E2-A15I-01 TCGA-E2-A15J-01 TCGA-E2-A15L-01 TCGA-E2-A15M-01 TCGA-E2-A15O-01 TCGA-E2-A15P-01 TCGA-E2-A15R-01 TCGA-E2-A1AZ-01 TCGA-E2-A1B0-01 TCGA-E2-A1B1-01 TCGA-E2-A1B4-01 TCGA-E2-A1B5-01 TCGA-E2-A1B6-01 TCGA-E2-A1BC-01 TCGA-E2-A1BD-01 TCGA-E2-A1IE-01 TCGA-E2-A1IF-01 TCGA-E2-A1IG-01 TCGA-E2-A1IH-01 TCGA-E2-A1II-01 TCGA-E2-A1IJ-01 TCGA-E2-A1IK-01 TCGA-E2-A1IL-01 TCGA-E2-A1IN-01 TCGA-E2-A1IO-01 TCGA-E2-A1IU-01 TCGA-E2-A1L6-01 TCGA-E2-A1L7-01 TCGA-E2-A1L8-01 TCGA-E2-A1L9-01 TCGA-E2-A1LA-01 TCGA-E2-A1LB-01 TCGA-E2-A1LG-01 TCGA-E2-A1LH-01 TCGA-E2-A1LI-01 TCGA-E2-A1LK-01 TCGA-E2-A1LL-01 TCGA-E9-A1N3-01 TCGA-E9-A1N4-01 TCGA-E9-A1N5-01 TCGA-E9-A1N6-01 TCGA-E9-A1N8-01 TCGA-E9-A1N9-01 TCGA-E9-A1NA-01 TCGA-E9-A1NC-01 TCGA-E9-A1ND-01 TCGA-E9-A1NE-01 TCGA-E9-A1NF-01 TCGA-E9-A1NG-01 TCGA-E9-A1NH-01 TCGA-E9-A1NI-01 TCGA-E9-A1QZ-01 TCGA-E9-A1R0-01 TCGA-E9-A1R2-01 TCGA-E9-A1R3-01 TCGA-E9-A1R4-01 TCGA-E9-A1R5-01 TCGA-E9-A1R6-01 TCGA-E9-A1R7-01 TCGA-E9-A1RA-01 TCGA-E9-A1RB-01 TCGA-E9-A1RC-01 TCGA-E9-A1RD-01 TCGA-E9-A1RE-01 TCGA-E9-A1RF-01 TCGA-E9-A1RG-01 TCGA-E9-A1RH-01 TCGA-E9-A1RI-01 TCGA-E9-A226-01 TCGA-E9-A227-01 TCGA-E9-A228-01 TCGA-E9-A229-01 TCGA-E9-A22A-01 TCGA-E9-A22B-01 TCGA-E9-A22D-01 TCGA-E9-A22E-01 TCGA-E9-A22G-01 TCGA-E9-A22H-01 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0 0 0 0 0 0 0 0 0 0 \ No newline at end of file diff --git a/core/src/test/scripts/test_data/study_es_0/data_cna_pd_annotations.txt b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_cna_pd_annotations.txt similarity index 92% rename from core/src/test/scripts/test_data/study_es_0/data_cna_pd_annotations.txt rename to core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_cna_pd_annotations.txt index 08051332f83..3c91408382e 100644 --- a/core/src/test/scripts/test_data/study_es_0/data_cna_pd_annotations.txt +++ b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_cna_pd_annotations.txt @@ -5,4 +5,4 @@ TCGA-A2-A04U-01 219293 Putative_Passenger Test passenger TCGA-A2-A04U-01 2073 Putative_Driver Test driver TCGA-A7-A26F-01 55210 Class 2 Class annotation TCGA-A7-A26F-01 83858 Class 1 Class annotation -TCGA-A7-A26F-01 2073 Putative_Driver +TCGA-A7-A26F-01 2073 Putative_Driver \ No newline at end of file diff --git a/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_mutations_extended.maf b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_mutations_extended.maf new file mode 100644 index 00000000000..1aacfd5dc88 --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/data_mutations_extended.maf @@ -0,0 +1,3 @@ +#version 2.4 +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer MA:FImpact MA:FIS Amino_Acid_Change MA:link.MSA MA:link.PDB MA:link.var Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO chromosome_name_wu start_wu stop_wu reference_wu variant_wu type_wu gene_name_wu transcript_name_wu transcript_species_wu transcript_source_wu transcript_version_wu strand_wu transcript_status_wu trv_type_wu c_position_wu amino_acid_change_wu ucsc_cons_wu domain_wu all_domains_wu deletion_substructures_wu transcript_error_wu default_gene_name_wu gene_name_source_wu ensembl_gene_id normal_ref_reads normal_var_reads normal_vaf tumor_ref_reads tumors_var_reads tumor_vaf evs_ea evs_aa evs_all chromosome_name_WU start_WU stop_WU reference_WU variant_WU type_WU gene_name_WU transcript_name_WU transcript_species_WU transcript_source_WU transcript_version_WU strand_WU transcript_status_WU trv_type_WU c_position_WU amino_acid_change_WU ucsc_cons_WU domain_WU all_domains_WU deletion_substructures_WU transcript_error_WU default_gene_name_WU gene_name_source_WU EVS_EA EVS_AA EVS_All cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation Zygosity.name Zygosity.code +OR11H1 genome.wustl.edu GRCh37 22 16449539 16449539 -1 Missense_Mutation SNP A A G TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx low 1.49 V89A getma.org/?cm=msa&ty=f&p=O11H1_HUMAN&rb=1&re=154&var=V89A getma.org/?cm=var&var=hg19,22,16449539,A,G&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.266T>C p.Val89Ala p.V89A ENST00000252835 1/1 0 0 OR11H1,missense_variant,p.Val89Ala,ENST00000252835,NM_001005239.1; G ENSG00000130538 ENST00000252835 Transcript missense_variant 267/982 266/981 89/326 V/A gTc/gCc rs199856986,COSM1484040 1 OR11H1 HGNC 15404 protein_coding YES CCDS33594.1 ENSP00000252835 O11H1_HUMAN UPI000004B1CF NM_001005239.1 deleterious(0.02) possibly_damaging(0.589) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF201,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 22 16449539 16449539 A G SNP OR11H1 ENST00000252835 human ensembl 69_37n -1 known missense c.266 p.V89A 234 pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn - no_errors OR11H1 HGNC ENSG00000130538 65 0 0 38 6 13.64 - - - 22 16449539 16449539 A G SNP OR11H1 ENST00000252835 human ensembl 69_37n -1 known missense c.266 p.V89A 234 pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn - no_errors OR11H1 HGNC - - - Putative_Driver Test driver diff --git a/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_clinical_samples.txt b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_clinical_samples.txt new file mode 100644 index 00000000000..7e4f674161b --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_clinical_samples.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: study_es_0 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_samples.txt diff --git a/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_cna_discrete.txt b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_cna_discrete.txt new file mode 100644 index 00000000000..f6ea8bea46c --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_cna_discrete.txt @@ -0,0 +1,10 @@ +cancer_study_identifier: study_es_0 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +stable_id: gistic +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 +pd_annotations_filename: data_cna_pd_annotations.txt +namespaces: CustomNamespace diff --git a/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_mutations_extended.txt b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_mutations_extended.txt new file mode 100644 index 00000000000..94df92aa5d9 --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_mutations_extended.txt @@ -0,0 +1,10 @@ +cancer_study_identifier: study_es_0 +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data from whole exome sequencing. +profile_name: Mutations +data_filename: data_mutations_extended.maf +swissprot_identifier: name +namespaces: Zygosity diff --git a/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_study.txt b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_study.txt new file mode 100644 index 00000000000..c0a01d2480a --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/meta_study.txt @@ -0,0 +1,10 @@ +type_of_cancer: brca-es0 +cancer_study_identifier: study_es_0 +name: Test study es_0 +description: Test study es_0 +citation: Cell 2018 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050 +groups: PUBLIC;GDAC;SU2C-PI3K +add_global_case_list: true +tags_file: study_tags.yml +reference_genome: hg19 diff --git a/docs/Testing.md b/docs/Testing.md index 6eb0d441d5c..503ef43d21f 100644 --- a/docs/Testing.md +++ b/docs/Testing.md @@ -32,7 +32,7 @@ mysql -u root -p SET GLOBAL local_infile=1; CREATE DATABASE cgds_test; CREATE USER 'cbio_user'@'localhost' IDENTIFIED BY 'somepassword'; -GRANT ALL ON cgds_test.* TO 'cbio_user'@'localhost'"; +GRANT ALL ON cgds_test.* TO 'cbio_user'@'localhost'; FLUSH PRIVILEGES; SET default_storage_engine=InnoDB; SET SESSION sql_mode = 'ANSI_QUOTES'; @@ -78,6 +78,7 @@ SET SESSION sql_mode = 'ANSI_QUOTES'; -v /cgds-test.sql:/docker-entrypoint-initdb.d/second_file.sql \ -v /seed_mini.sql:/docker-entrypoint-initdb.d/third_file.sql \ -p 3306:3306 mysql:5.7 + --ssl=0 ``` #### Notes @@ -92,7 +93,7 @@ SET SESSION sql_mode = 'ANSI_QUOTES'; 2. Run integration tests with ``` -mvn integration-test -Ddb.test.username=cbio -Ddb.test.password= +mvn integration-test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword ``` This will create the tables in `cgds_test` and populate your schema with test data. @@ -100,7 +101,7 @@ This will create the tables in `cgds_test` and populate your schema with test da 3. you can run all other tests with ``` -mvn test -Ddb.test.username=cbio -Ddb.test.password= +mvn test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword ``` 4. you can run a specific test with diff --git a/web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java b/web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java index ed339f9e40b..0bf7adbfa65 100644 --- a/web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java @@ -4,7 +4,6 @@ import org.cbioportal.model.CopyNumberCount; import org.cbioportal.model.DiscreteCopyNumberData; import org.cbioportal.model.Gene; -import org.cbioportal.model.ReferenceGenomeGene; import org.cbioportal.model.meta.BaseMeta; import org.cbioportal.service.DiscreteCopyNumberService; import org.cbioportal.web.parameter.CopyNumberCountIdentifier; From a0f749d1e4a91e5477746be88c36743e2c23a64d Mon Sep 17 00:00:00 2001 From: Bas Leenknegt Date: Wed, 16 Nov 2022 11:13:13 +0100 Subject: [PATCH 2/3] Fix validation of long format --- .../scripts/importer/cbioportal_common.py | 1 + .../scripts/system_tests_validate_studies.py | 2 +- .../study_es_0/meta_cna_discrete.txt | 1 - .../test_data/study_es_0/result_report.html | 167 ++++++------------ .../case_lists/cases_cna.txt | 5 + .../case_lists/cases_cnaseq.txt | 5 + .../case_lists/cases_custom.txt | 5 + .../case_lists/cases_sequenced.txt | 5 + .../case_lists/cases_test.txt | 5 + .../meta_study.txt | 1 - 10 files changed, 82 insertions(+), 115 deletions(-) create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cna.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cnaseq.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_custom.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_sequenced.txt create mode 100644 core/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_test.txt diff --git a/core/src/main/scripts/importer/cbioportal_common.py b/core/src/main/scripts/importer/cbioportal_common.py index 699b0532cfd..14eab6ab9a0 100644 --- a/core/src/main/scripts/importer/cbioportal_common.py +++ b/core/src/main/scripts/importer/cbioportal_common.py @@ -356,6 +356,7 @@ class MetaFileTypes(object): MetaFileTypes.SAMPLE_ATTRIBUTES: "org.mskcc.cbio.portal.scripts.ImportClinicalData", MetaFileTypes.PATIENT_ATTRIBUTES: "org.mskcc.cbio.portal.scripts.ImportClinicalData", MetaFileTypes.CNA_DISCRETE: "org.mskcc.cbio.portal.scripts.ImportProfileData", + MetaFileTypes.CNA_DISCRETE_LONG: "org.mskcc.cbio.portal.scripts.ImportProfileData", MetaFileTypes.CNA_LOG2: "org.mskcc.cbio.portal.scripts.ImportProfileData", MetaFileTypes.CNA_CONTINUOUS: "org.mskcc.cbio.portal.scripts.ImportProfileData", MetaFileTypes.SEG: "org.mskcc.cbio.portal.scripts.ImportCopyNumberSegmentData", diff --git a/core/src/test/scripts/system_tests_validate_studies.py b/core/src/test/scripts/system_tests_validate_studies.py index 24d05dcde21..714754ac8dd 100755 --- a/core/src/test/scripts/system_tests_validate_studies.py +++ b/core/src/test/scripts/system_tests_validate_studies.py @@ -77,7 +77,7 @@ def test_exit_status_success_for_legacy_cna_discrete(self): """ # Build up arguments and run - print("===study 0") + print("===study 0 legacy") args = ['--list-of-studies', 'test_data/study_es_0_legacy_cna_discrete/', '--portal_info_dir', PORTAL_INFO_DIR] args = validateStudies.interface(args) 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 cfa0fa7acf8..8bcc1727d1f 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 @@ -6,4 +6,3 @@ 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: CustomNamespace diff --git a/core/src/test/scripts/test_data/study_es_0/result_report.html b/core/src/test/scripts/test_data/study_es_0/result_report.html index d7edca50f3f..00133e553f9 100644 --- a/core/src/test/scripts/test_data/study_es_0/result_report.html +++ b/core/src/test/scripts/test_data/study_es_0/result_report.html @@ -616,7 +616,7 @@

    data_clinical_samples.txt

    - 3 + 4

    data_cna_discrete.txt

     @@ -644,6 +644,59 @@

    data_cna_discrete.txt

    – + + Info + 154, 155, 844… + 6 + Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint + Class 2, Class 1 + + See all 4 values + + + Info – @@ -656,7 +709,7 @@

    data_cna_discrete.txt

    Info – – - Read 9 lines. Lines with warning: 0. Lines with error: 0 + Read 6305 lines. Lines with warning: 0. Lines with error: 0 – @@ -780,116 +833,6 @@

    data_cna_log2.txt

    -
    - -
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    Line NumberColumn NumberMessageValue Encountered
    Debug––Starting validation of file–
    Info2, 3, 6…4Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the OncoprintClass 2, Class 1 - See all 4 values - -
    Info––Validation of file complete–
    Info––Read 8 lines. Lines with warning: 0. Lines with error: 0–
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