diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java index b7e0960ad37..24a8209e64b 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java @@ -39,7 +39,6 @@ import java.util.Collection; import java.util.HashMap; import java.util.HashSet; -import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; @@ -116,7 +115,7 @@ private static Set filterTruncatingCosmicByPosition( Set ret = new HashSet(); Pattern p = Pattern.compile("[0-9]+"); - int mutPos = mut.getOncotatorProteinPosStart(); + int mutPos = mut.getProteinPosStart(); for (CosmicMutationFrequency cmf : cmfs) { String aa = cmf.getAminoAcidChange(); Matcher m = p.matcher(aa); diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java index b3296569615..8adbdaddb3f 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java +++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java @@ -145,23 +145,16 @@ public static int addMutationEvent(ExtendedMutation.MutationEvent event) throws event.getTumorSeqAllele(), event.getProteinChange(), event.getMutationType(), - event.getFunctionalImpactScore(), - Float.toString(event.getFisValue()), - event.getLinkXVar(), - event.getLinkPdb(), - event.getLinkMsa(), event.getNcbiBuild(), event.getStrand(), event.getVariantType(), event.getDbSnpRs(), event.getDbSnpValStatus(), - event.getOncotatorDbSnpRs(), - event.getOncotatorRefseqMrnaId(), - event.getOncotatorCodonChange(), - event.getOncotatorUniprotName(), - event.getOncotatorUniprotAccession(), - Integer.toString(event.getOncotatorProteinPosStart()), - Integer.toString(event.getOncotatorProteinPosEnd()), + event.getRefseqMrnaId(), + event.getCodonChange(), + event.getUniprotAccession(), + Integer.toString(event.getProteinPosStart()), + Integer.toString(event.getProteinPosEnd()), boolToStr(event.isCanonicalTranscript()), keyword==null ? "\\N":(event.getGene().getHugoGeneSymbolAllCaps()+" "+keyword)); return 1; @@ -800,24 +793,17 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet rs) event.setEndPosition(rs.getLong("END_POSITION")); event.setProteinChange(rs.getString("PROTEIN_CHANGE")); event.setMutationType(rs.getString("MUTATION_TYPE")); - event.setFunctionalImpactScore(rs.getString("FUNCTIONAL_IMPACT_SCORE")); - event.setFisValue(rs.getFloat("FIS_VALUE")); - event.setLinkXVar(rs.getString("LINK_XVAR")); - event.setLinkPdb(rs.getString("LINK_PDB")); - event.setLinkMsa(rs.getString("LINK_MSA")); event.setNcbiBuild(rs.getString("NCBI_BUILD")); event.setStrand(rs.getString("STRAND")); event.setVariantType(rs.getString("VARIANT_TYPE")); event.setDbSnpRs(rs.getString("DB_SNP_RS")); event.setDbSnpValStatus(rs.getString("DB_SNP_VAL_STATUS")); event.setReferenceAllele(rs.getString("REFERENCE_ALLELE")); - event.setOncotatorDbSnpRs(rs.getString("ONCOTATOR_DBSNP_RS")); - event.setOncotatorRefseqMrnaId(rs.getString("ONCOTATOR_REFSEQ_MRNA_ID")); - event.setOncotatorCodonChange(rs.getString("ONCOTATOR_CODON_CHANGE")); - event.setOncotatorUniprotName(rs.getString("ONCOTATOR_UNIPROT_ENTRY_NAME")); - event.setOncotatorUniprotAccession(rs.getString("ONCOTATOR_UNIPROT_ACCESSION")); - event.setOncotatorProteinPosStart(rs.getInt("ONCOTATOR_PROTEIN_POS_START")); - event.setOncotatorProteinPosEnd(rs.getInt("ONCOTATOR_PROTEIN_POS_END")); + event.setRefseqMrnaId(rs.getString("REFSEQ_MRNA_ID")); + event.setCodonChange(rs.getString("CODON_CHANGE")); + event.setUniprotAccession(rs.getString("UNIPROT_ACCESSION")); + event.setProteinPosStart(rs.getInt("PROTEIN_POS_START")); + event.setProteinPosEnd(rs.getInt("PROTEIN_POS_END")); event.setCanonicalTranscript(rs.getBoolean("CANONICAL_TRANSCRIPT")); event.setTumorSeqAllele(rs.getString("TUMOR_SEQ_ALLELE")); event.setKeyword(rs.getString("KEYWORD")); @@ -1391,12 +1377,12 @@ public static Collection> countSamplesWithProteinPosStarts( if (geneIdSet.size() == 0 || internalProfileIds.size() == 0) return new ArrayList>(); //empty IN() clause would be a SQL error below try { con = JdbcUtil.getDbConnection(DaoMutation.class); - String sql = "SELECT ONCOTATOR_PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID, count(DISTINCT SAMPLE_ID) " + + String sql = "SELECT PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID, count(DISTINCT SAMPLE_ID) " + "FROM mutation INNER JOIN mutation_event ON mutation.MUTATION_EVENT_ID=mutation_event.MUTATION_EVENT_ID " + "WHERE mutation.ENTREZ_GENE_ID IN (" + StringUtils.join(geneIdSet, ",") + ") " + "AND GENETIC_PROFILE_ID IN (" + StringUtils.join(internalProfileIds, ",") + ") " + - "AND (mutation.ENTREZ_GENE_ID, ONCOTATOR_PROTEIN_POS_START) IN (" + StringUtils.join(proteinPosStarts, ",") + ") " + - "GROUP BY ONCOTATOR_PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID"; + "AND (mutation.ENTREZ_GENE_ID, PROTEIN_POS_START) IN (" + StringUtils.join(proteinPosStarts, ",") + ") " + + "GROUP BY PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID"; pstmt = con.prepareStatement(sql); rs = pstmt.executeQuery(); Collection> data = new ArrayList>(); diff --git a/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java b/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java index 59aa4e44309..21c276f225f 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java +++ b/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java @@ -44,20 +44,16 @@ */ public final class ExtendedMutation { + public final static class MutationEvent { private long mutationEventId; private CanonicalGene gene; private String chr; - private long startPosition; + private long startPosition; private long endPosition; private String proteinChange; // amino acid change private String mutationType; // variant classification - private String functionalImpactScore; - private float fisValue; - private String linkXVar; - private String linkPdb; - private String linkMsa; - private String keyword; + private String keyword; private String ncbiBuild; private String strand; private String variantType; @@ -65,13 +61,11 @@ public final static class MutationEvent { private String tumorSeqAllele; private String dbSnpRs; private String dbSnpValStatus; - private String oncotatorDbSnpRs; - private String oncotatorRefseqMrnaId; - private String oncotatorUniprotName; - private String oncotatorUniprotAccession; - private String oncotatorCodonChange; - private int oncotatorProteinPosStart; - private int oncotatorProteinPosEnd; + private String refseqMrnaId; + private String uniprotAccession; + private String codonChange; + private int proteinPosStart; + private int proteinPosEnd; private boolean canonicalTranscript; public long getMutationEventId() { @@ -132,46 +126,6 @@ public void setMutationType(String mutationType) { this.mutationType = mutationType; } - public String getFunctionalImpactScore() { - return functionalImpactScore; - } - - public void setFunctionalImpactScore(String functionalImpactScore) { - this.functionalImpactScore = functionalImpactScore; - } - - public float getFisValue() { - return fisValue; - } - - public void setFisValue(float fisValue) { - this.fisValue = fisValue; - } - - public String getLinkXVar() { - return linkXVar; - } - - public void setLinkXVar(String linkXVar) { - this.linkXVar = linkXVar; - } - - public String getLinkPdb() { - return linkPdb; - } - - public void setLinkPdb(String linkPdb) { - this.linkPdb = linkPdb; - } - - public String getLinkMsa() { - return linkMsa; - } - - public void setLinkMsa(String linkMsa) { - this.linkMsa = linkMsa; - } - public String getKeyword() { return keyword; } @@ -236,68 +190,44 @@ public void setDbSnpValStatus(String dbSnpValStatus) { this.dbSnpValStatus = dbSnpValStatus; } - public String getOncotatorDbSnpRs() { - return oncotatorDbSnpRs; - } - - public void setOncotatorDbSnpRs(String oncotatorDbSnpRs) { - this.oncotatorDbSnpRs = oncotatorDbSnpRs; - } - - public String getOncotatorRefseqMrnaId() { - return oncotatorRefseqMrnaId; + public String getRefseqMrnaId() { + return refseqMrnaId; } - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; + public void setRefseqMrnaId(String refseqMrnaId) { + this.refseqMrnaId = refseqMrnaId; } - - public String getOncotatorUniprotName() { - return oncotatorUniprotName; - } - - /** - * Set the UniprotKB name (formerly known as ID) of the protein record. - * - * @param oncotatorUniprotName the UniprotKB name - * @deprecated set the accession with - * {@link #setOncotatorUniprotAccession(String)} instead - */ - @Deprecated - public void setOncotatorUniprotName(String oncotatorUniprotName) { - this.oncotatorUniprotName = oncotatorUniprotName; - } - - public String getOncotatorUniprotAccession() { - return oncotatorUniprotAccession; + + public String getUniprotAccession() { + return uniprotAccession; } - public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) { - this.oncotatorUniprotAccession = oncotatorUniprotAccession; + public void setUniprotAccession(String uniprotAccession) { + this.uniprotAccession = uniprotAccession; } - public String getOncotatorCodonChange() { - return oncotatorCodonChange; + public String getCodonChange() { + return codonChange; } - public void setOncotatorCodonChange(String oncotatorCodonChange) { - this.oncotatorCodonChange = oncotatorCodonChange; + public void setCodonChange(String codonChange) { + this.codonChange = codonChange; } - public int getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; + public int getProteinPosStart() { + return proteinPosStart; } - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; + public void setProteinPosStart(int proteinPosStart) { + this.proteinPosStart = proteinPosStart; } - public int getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; + public int getProteinPosEnd() { + return proteinPosEnd; } - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; + public void setProteinPosEnd(int proteinPosEnd) { + this.proteinPosEnd = proteinPosEnd; } public boolean isCanonicalTranscript() { @@ -543,47 +473,7 @@ public void setAminoAcidChange(String aminoAcidChange) { this.aminoAcidChange = aminoAcidChange; } - - public String getFunctionalImpactScore() { - return event.getFunctionalImpactScore(); - } - - public void setFunctionalImpactScore(String fImpact) { - event.setFunctionalImpactScore(fImpact); - } - - public float getFisValue() { - return event.getFisValue(); - } - - public void setFisValue(Float fisValue) { - event.setFisValue(fisValue); - } - - public String getLinkXVar() { - return event.getLinkXVar(); - } - - public void setLinkXVar(String linkXVar) { - event.setLinkXVar(linkXVar); - } - - public String getLinkPdb() { - return event.getLinkPdb(); - } - - public void setLinkPdb(String linkPdb) { - event.setLinkPdb(linkPdb); - } - - public String getLinkMsa() { - return event.getLinkMsa(); - } - - public void setLinkMsa(String linkMsa) { - event.setLinkMsa(linkMsa); - } - + public String getSequencer() { return sequencer; } @@ -820,80 +710,54 @@ public void setNormalRefCount(Integer normalRefCount) { this.normalRefCount = normalRefCount; } - public String getOncotatorDbSnpRs() { - return event.getOncotatorDbSnpRs(); - } - - public void setOncotatorDbSnpRs(String oncotatorDbSnpRs) { - event.setOncotatorDbSnpRs(oncotatorDbSnpRs); - } - - public String getOncotatorRefseqMrnaId() - { - return event.getOncotatorRefseqMrnaId(); - } - - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) - { - event.setOncotatorRefseqMrnaId(oncotatorRefseqMrnaId); - } - - public String getOncotatorUniprotName() + public String getRefseqMrnaId() { - return event.getOncotatorUniprotName(); + return event.getRefseqMrnaId(); } - /** - * Set the UniprotKB name (formerly known as ID) of the protein record. - * - * @param oncotatorUniprotName the UniprotKB name - * @deprecated set the accession with - * {@link #setOncotatorUniprotAccession(String)} instead - */ - @Deprecated - public void setOncotatorUniprotName(String oncotatorUniprotName) + public void setRefseqMrnaId(String refseqMrnaId) { - event.setOncotatorUniprotName(oncotatorUniprotName); + event.setRefseqMrnaId(refseqMrnaId); } - public String getOncotatorUniprotAccession() + public String getUniprotAccession() { - return event.getOncotatorUniprotAccession(); + return event.getUniprotAccession(); } - public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) + public void setUniprotAccession(String uniprotAccession) { - event.setOncotatorUniprotAccession(oncotatorUniprotAccession); + event.setUniprotAccession(uniprotAccession); } - public String getOncotatorCodonChange() + public String getCodonChange() { - return event.getOncotatorCodonChange(); + return event.getCodonChange(); } - public void setOncotatorCodonChange(String oncotatorCodonChange) + public void setCodonChange(String codonChange) { - event.setOncotatorCodonChange(oncotatorCodonChange); + event.setCodonChange(codonChange); } - public int getOncotatorProteinPosStart() + public int getProteinPosStart() { - return event.getOncotatorProteinPosStart(); + return event.getProteinPosStart(); } - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) + public void setProteinPosStart(int proteinPosStart) { - event.setOncotatorProteinPosStart(oncotatorProteinPosStart); + event.setProteinPosStart(proteinPosStart); } - public int getOncotatorProteinPosEnd() + public int getProteinPosEnd() { - return event.getOncotatorProteinPosEnd(); + return event.getProteinPosEnd(); } - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) + public void setProteinPosEnd(int proteinPosEnd) { - event.setOncotatorProteinPosEnd(oncotatorProteinPosEnd); + event.setProteinPosEnd(proteinPosEnd); } public boolean isCanonicalTranscript() diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java index a444d72edff..dd230f16af7 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java @@ -206,31 +206,6 @@ public void importData() throws IOException, DaoException { if (record.getEndPosition() < 0) record.setEndPosition(0); - String functionalImpactScore = ""; - // using -1 is not safe, FIS can be a negative value - Float fisValue = Float.MIN_VALUE; - String linkXVar = ""; - String linkMsa = ""; - String linkPdb = ""; - - if (fileHasOMAData) - { -// functionalImpactScore = getField(parts, "MA:FImpact" ); -// fisValue = getField(parts, "MA:FIS"); -// linkXVar = getField(parts, "MA:link.var" ); -// linkMsa = getField(parts, "MA:link.MSA" ); -// linkPdb = getField(parts, "MA:link.PDB" ); - - functionalImpactScore = record.getMaFuncImpact(); - fisValue = record.getMaFIS(); - linkXVar = record.getMaLinkVar(); - linkMsa = record.getMaLinkMsa(); - linkPdb = record.getMaLinkPdb(); - - functionalImpactScore = transformOMAScore(functionalImpactScore); - linkXVar = linkXVar.replace("\"", ""); - } - String mutationType, proteinChange, aaChange, @@ -361,11 +336,6 @@ public void importData() throws IOException, DaoException { mutation.setEndPosition(record.getEndPosition()); mutation.setValidationStatus(record.getValidationStatus()); mutation.setMutationStatus(record.getMutationStatus()); - mutation.setFunctionalImpactScore(functionalImpactScore); - mutation.setFisValue(fisValue); - mutation.setLinkXVar(linkXVar); - mutation.setLinkPdb(linkPdb); - mutation.setLinkMsa(linkMsa); mutation.setNcbiBuild(record.getNcbiBuild()); mutation.setStrand(record.getStrand()); mutation.setVariantType(record.getVariantType()); @@ -397,12 +367,12 @@ public void importData() throws IOException, DaoException { mutation.setNormalAltCount(ExtendedMutationUtil.getNormalAltCount(record)); mutation.setNormalRefCount(ExtendedMutationUtil.getNormalRefCount(record)); - // TODO rename the oncotator column names (remove "oncotator") - mutation.setOncotatorCodonChange(codonChange); - mutation.setOncotatorRefseqMrnaId(refseqMrnaId); - mutation.setOncotatorUniprotAccession(uniprotAccession); - mutation.setOncotatorProteinPosStart(proteinPosStart); - mutation.setOncotatorProteinPosEnd(proteinPosEnd); + // renamed the oncotator column names to mutation + mutation.setCodonChange(codonChange); + mutation.setRefseqMrnaId(refseqMrnaId); + mutation.setUniprotAccession(uniprotAccession); + mutation.setProteinPosStart(proteinPosStart); + mutation.setProteinPosEnd(proteinPosEnd); mutation.setDriverFilter(record.getDriverFilter()); mutation.setDriverFilterAnn(record.getDriverFilterAnn()); diff --git a/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java b/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java index de4c77af7a7..f4f61b59844 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java +++ b/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java @@ -195,7 +195,7 @@ public static boolean isAcceptableMutation(String mutationType) { } public static String getMutationType(MafRecord record) { - String mutationType = record.getOncotatorVariantClassification(); + String mutationType = record.getMafVariantClassification(); if (mutationType == null || mutationType.length() == 0 || @@ -298,11 +298,6 @@ public static ExtendedMutation newMutation() { mutation.setEndPosition(defaultLong); mutation.setValidationStatus(defaultStr); mutation.setMutationStatus(defaultStr); - mutation.setFunctionalImpactScore(defaultStr); - mutation.setFisValue(defaultFloat); - mutation.setLinkXVar(defaultStr); - mutation.setLinkPdb(defaultStr); - mutation.setLinkMsa(defaultStr); mutation.setNcbiBuild(defaultStr); mutation.setStrand(defaultStr); mutation.setVariantType(defaultStr); @@ -326,13 +321,11 @@ public static ExtendedMutation newMutation() { mutation.setTumorRefCount(defaultInt); mutation.setNormalAltCount(defaultInt); mutation.setNormalRefCount(defaultInt); - mutation.setOncotatorDbSnpRs(defaultStr); - mutation.setOncotatorCodonChange(defaultStr); - mutation.setOncotatorRefseqMrnaId(defaultStr); - mutation.setOncotatorUniprotName(defaultStr); - mutation.setOncotatorUniprotAccession(defaultStr); - mutation.setOncotatorProteinPosStart(defaultInt); - mutation.setOncotatorProteinPosEnd(defaultInt); + mutation.setCodonChange(defaultStr); + mutation.setRefseqMrnaId(defaultStr); + mutation.setUniprotAccession(defaultStr); + mutation.setProteinPosStart(defaultInt); + mutation.setProteinPosEnd(defaultInt); mutation.setCanonicalTranscript(true); return mutation; diff --git a/core/src/main/java/org/mskcc/cbio/portal/web_api/GetMutationData.java b/core/src/main/java/org/mskcc/cbio/portal/web_api/GetMutationData.java index 17920e6e4af..d0653071f7c 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/web_api/GetMutationData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/web_api/GetMutationData.java @@ -182,10 +182,6 @@ public static String getProfileData(String geneticProfileId, buf.append(mutation.getMutationType()).append(TAB); buf.append(mutation.getValidationStatus()).append(TAB); buf.append(mutation.getProteinChange()).append(TAB); - buf.append(mutation.getFunctionalImpactScore()).append(TAB); - buf.append(mutation.getLinkXVar()).append(TAB); - buf.append(mutation.getLinkPdb()).append(TAB); - buf.append(mutation.getLinkMsa()).append(TAB); buf.append(mutation.getChr()).append(TAB); buf.append(mutation.getStartPosition()).append(TAB); buf.append(mutation.getEndPosition()).append(TAB); diff --git a/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java b/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java index 4072ecbe144..d55b2085cd1 100644 --- a/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java +++ b/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java @@ -101,11 +101,6 @@ private void runTheTest() throws DaoException{ mutation.setSequencingCenter("Broad"); mutation.setSequencer("SOLiD"); mutation.setProteinChange("BRCA1_123"); - mutation.setFunctionalImpactScore("H"); - mutation.setFisValue(Float.MIN_VALUE); - mutation.setLinkXVar("link1"); - mutation.setLinkPdb("link2"); - mutation.setLinkMsa("link3"); mutation.setNcbiBuild("37/hg19"); mutation.setStrand("+"); mutation.setVariantType("Consolidated"); @@ -132,13 +127,11 @@ private void runTheTest() throws DaoException{ mutation.setTumorRefCount(16); mutation.setNormalAltCount(8); mutation.setNormalRefCount(18); - mutation.setOncotatorDbSnpRs("rs149680468"); - mutation.setOncotatorCodonChange("c.(133-135)TCT>TTT"); - mutation.setOncotatorRefseqMrnaId("NM_001904"); - mutation.setOncotatorUniprotName("CTNB1_HUMAN"); - mutation.setOncotatorUniprotAccession("P35222"); - mutation.setOncotatorProteinPosStart(666); - mutation.setOncotatorProteinPosEnd(678); + mutation.setCodonChange("c.(133-135)TCT>TTT"); + mutation.setRefseqMrnaId("NM_001904"); + mutation.setUniprotAccession("P35222"); + mutation.setProteinPosStart(666); + mutation.setProteinPosEnd(678); mutation.setCanonicalTranscript(true); mutation.setAnnotationJson(makeMockAnnotationJsonString()); @@ -174,11 +167,6 @@ private void validateMutation(ExtendedMutation mutation) { assertEquals("Broad", mutation.getSequencingCenter()); assertEquals("SOLiD", mutation.getSequencer()); assertEquals("BRCA1_123", mutation.getProteinChange()); - assertEquals("H", mutation.getFunctionalImpactScore()); - assertEquals(Float.MIN_VALUE, mutation.getFisValue(), 1E-30); - assertEquals("link1", mutation.getLinkXVar()); - assertEquals("link2", mutation.getLinkPdb()); - assertEquals("link3", mutation.getLinkMsa()); assertEquals("37/hg19", mutation.getNcbiBuild()); assertEquals("+", mutation.getStrand()); assertEquals("Consolidated", mutation.getVariantType()); @@ -204,13 +192,11 @@ private void validateMutation(ExtendedMutation mutation) { assertEquals(Integer.valueOf(16), mutation.getTumorRefCount()); assertEquals(Integer.valueOf(8), mutation.getNormalAltCount()); assertEquals(Integer.valueOf(18), mutation.getNormalRefCount()); - assertEquals("rs149680468", mutation.getOncotatorDbSnpRs()); - assertEquals("c.(133-135)TCT>TTT", mutation.getOncotatorCodonChange()); - assertEquals("NM_001904", mutation.getOncotatorRefseqMrnaId()); - assertEquals("CTNB1_HUMAN", mutation.getOncotatorUniprotName()); - assertEquals("P35222", mutation.getOncotatorUniprotAccession()); - assertEquals(666, mutation.getOncotatorProteinPosStart()); - assertEquals(678, mutation.getOncotatorProteinPosEnd()); + assertEquals("c.(133-135)TCT>TTT", mutation.getCodonChange()); + assertEquals("NM_001904", mutation.getRefseqMrnaId()); + assertEquals("P35222", mutation.getUniprotAccession()); + assertEquals(666, mutation.getProteinPosStart()); + assertEquals(678, mutation.getProteinPosEnd()); assertEquals(true, mutation.isCanonicalTranscript()); validateMockAnnotationJson(mutation); diff --git a/core/src/test/resources/seed_mini.sql b/core/src/test/resources/seed_mini.sql index fd98ec7d340..e17819cfb51 100644 --- a/core/src/test/resources/seed_mini.sql +++ b/core/src/test/resources/seed_mini.sql @@ -419,9 +419,9 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU 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'); -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 (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','rs28897672','NM_007294','c.(181-183)TGT>GGT','BRCA1_HUMAN','P38398',61,61,1,'BRCA1 C61 missense'); -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 (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','c.e2+1','NA','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","REFSEQ_MRNA_ID","CODON_CHANGE","UNIPROT_ACCESSION","PROTEIN_POS_START","PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","REFSEQ_MRNA_ID","CODON_CHANGE","UNIPROT_ACCESSION","PROTEIN_POS_START","PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","REFSEQ_MRNA_ID","CODON_CHANGE","UNIPROT_ACCESSION","PROTEIN_POS_START","PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); -- mutation INSERT INTO "mutation" ("MUTATION_EVENT_ID","GENETIC_PROFILE_ID","SAMPLE_ID","ENTREZ_GENE_ID","CENTER","SEQUENCER","MUTATION_STATUS","VALIDATION_STATUS","TUMOR_SEQ_ALLELE1","TUMOR_SEQ_ALLELE2","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","SEQUENCING_PHASE","SEQUENCE_SOURCE","VALIDATION_METHOD","SCORE","BAM_FILE","TUMOR_ALT_COUNT","TUMOR_REF_COUNT","NORMAL_ALT_COUNT","NORMAL_REF_COUNT") VALUES (2038,6,6,672,'genome.wustl.edu','IlluminaGAIIx','Germline','Unknown','G','A','TCGA-A1-A0SH-10A-03D-A099-09','G','A','NA','NA','NA','NA','Unknown','Phase_IV','Capture','NA','1','dbGAP',-1,-1,-1,-1); diff --git a/db-scripts/src/main/resources/cgds.sql b/db-scripts/src/main/resources/cgds.sql index 1871b709a0e..c0b20e8b6cd 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -436,23 +436,16 @@ CREATE TABLE `mutation_event` ( `TUMOR_SEQ_ALLELE` text, `PROTEIN_CHANGE` varchar(255), `MUTATION_TYPE` varchar(255) COMMENT 'e.g. Missense, Nonsence, etc.', - `FUNCTIONAL_IMPACT_SCORE` varchar(50) COMMENT 'Result from OMA/XVAR.', - `FIS_VALUE` float, - `LINK_XVAR` varchar(500) COMMENT 'Link to OMA/XVAR Landing Page for the specific mutation.', - `LINK_PDB` varchar(500), - `LINK_MSA` varchar(500), `NCBI_BUILD` varchar(10), `STRAND` varchar(2), `VARIANT_TYPE` varchar(15), `DB_SNP_RS` varchar(25), `DB_SNP_VAL_STATUS` varchar(255), - `ONCOTATOR_DBSNP_RS` varchar(255), - `ONCOTATOR_REFSEQ_MRNA_ID` varchar(64), - `ONCOTATOR_CODON_CHANGE` varchar(255), - `ONCOTATOR_UNIPROT_ENTRY_NAME` varchar(64), - `ONCOTATOR_UNIPROT_ACCESSION` varchar(64), - `ONCOTATOR_PROTEIN_POS_START` int(11), - `ONCOTATOR_PROTEIN_POS_END` int(11), + `REFSEQ_MRNA_ID` varchar(64), + `CODON_CHANGE` varchar(255), + `UNIPROT_ACCESSION` varchar(64), + `PROTEIN_POS_START` int(11), + `PROTEIN_POS_END` int(11), `CANONICAL_TRANSCRIPT` boolean, `KEYWORD` varchar(255) DEFAULT NULL COMMENT 'e.g. truncating, V200 Missense, E338del, ', KEY (`KEYWORD`), @@ -762,5 +755,5 @@ CREATE TABLE `resource_study` ( ); -- THIS MUST BE KEPT IN SYNC WITH db.version PROPERTY IN pom.xml -INSERT INTO info VALUES ('2.12.16', NULL); +INSERT INTO info VALUES ('2.13.0', NULL); diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index ef820bb95a5..dfec6a97381 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -978,6 +978,8 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.12"; ALTER TABLE `sample` MODIFY COLUMN `STABLE_ID` VARCHAR(63) NOT NULL; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.13"; + + ##version: 2.12.14 ALTER TABLE `structural_variant` MODIFY COLUMN `SITE1_ENTREZ_GENE_ID` int(11); ALTER TABLE `structural_variant` ADD COLUMN `SITE1_REGION` varchar(25) AFTER `SITE1_CHROMOSOME`; @@ -1000,3 +1002,22 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.15"; ##version: 2.12.16 ALTER TABLE `structural_variant` ADD COLUMN `ANNOTATION_JSON` JSON AFTER `SV_STATUS`; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16"; + +##version: 2.13.0 +-- changes for issue 9461 +ALTER TABLE `mutation_event` DROP COLUMN `FUNCTIONAL_IMPACT_SCORE`; +ALTER TABLE `mutation_event` DROP COLUMN `FIS_VALUE`; +ALTER TABLE `mutation_event` DROP COLUMN `LINK_XVAR`; +ALTER TABLE `mutation_event` DROP COLUMN `LINK_PDB`; +ALTER TABLE `mutation_event` DROP COLUMN `LINK_MSA`; + +-- changes for issue 9779 +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_DBSNP_RS`; +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_UNIPROT_ENTRY_NAME`; +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_REFSEQ_MRNA_ID` `REFSEQ_MRNA_ID` varchar(64); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_CODON_CHANGE` `CODON_CHANGE` varchar(255); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_UNIPROT_ACCESSION` `UNIPROT_ACCESSION` varchar(64); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_START` `PROTEIN_POS_START` int(11); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_END` `PROTEIN_POS_END` int(11); +UPDATE `info` SET `DB_SCHEMA_VERSION`="2.13.0"; + diff --git a/docs/Imported-MAF-Columns.md b/docs/Imported-MAF-Columns.md index 43ff6bb47d6..da449abf013 100644 --- a/docs/Imported-MAF-Columns.md +++ b/docs/Imported-MAF-Columns.md @@ -69,11 +69,6 @@ Relevant classes: | ONCOTATOR_CODON_CHANGE | ONCOTATOR_CODON_CHANGE | | mutation_event.oncotator_codon_change ** [maps to DB but MAF value never imported] | see ImportExtendedMutation (codonChange = record.getCodons()) / MAF field "Codons" always overrides MAF value ONCOTATOR_CODON_CHANGE // "ONCOTATOR_CODON_CHANGE" never used? / MafRecord (record.getOncotatorCodonChange()) never used | | ONCOTATOR_PROTEIN_POS_START | ONCOTATOR_PROTEIN_POS_START | | mutation_event.oncotator_protein_pos_start ** [maps to DB but MAF value never imported] | see ExtendedMutationUtil.getProteinPosStart() / resolved from record.getProteinPosition() or record.getProteinChange() based on what is avialable / MAF field "ONCOTATOR_PROTEIN_POS_START" never used? | | ONCOTATOR_PROTEIN_POS_END | ONCOTATOR_PROTEIN_POS_END | | mutation_event.oncotator_protein_pos_end ** [maps to DB but MAF value never imported] | see ExtendedMutationUtil.getProteinPosStart() / resolved from record.getProteinPosition() or record.getProteinChange() based on what is avialable / MAF field "ONCOTATOR_PROTEIN_POS_END" never used? | -| MA_FIMPACT | MA:FImpact | | mutation_event.functional_impact_score | | -| MA_FIS | MA:FIS | | mutation_event.fis_value | | -| MA_LINK_VAR | MA:link.var | | mutation_event.link_xvar | | -| MA_LINK_MSA | MA:link.MSA | | mutation_event.link_msa | | -| MA_LINK_PDB | MA:link.PDB | | mutation_event.link_pdb | | | DRIVER_FILTER | cbp_driver | mutation.driver_filter | | | | DRIVER_FILTER_ANNOTATION | cbp_driver_annotation | mutation.driver_filter_annotation | | | | DRIVER_TIERS_FILTER | cbp_driver_tiers | mutation.driver_tiers_filter | | | diff --git a/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java b/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java index 512372e642c..673faf0cd3a 100644 --- a/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java +++ b/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java @@ -103,16 +103,14 @@ public class MafRecord { private String maLinkMsa; private String maLinkPdb; - // Oncotator cols - private String oncotatorDbSnpRs; - private String oncotatorDbSnpValStatus; - private String oncotatorVariantClassification; - private String oncotatorRefseqMrnaId; - private String oncotatorUniprotName; - private String oncotatorUniprotAccession; - private String oncotatorCodonChange; - private int oncotatorProteinPosStart; - private int oncotatorProteinPosEnd; + // Oncotator columns are renamed to maf columns + private String mafDbSnpValStatus; + private String mafVariantClassification; + private String mafRefseqMrnaId; + private String mafUniprotAccession; + private String mafCodonChange; + private int mafProteinPosStart; + private int mafProteinPosEnd; // custom filtering of passenger and driver mutations cols private String driverFilter; @@ -521,76 +519,60 @@ public void setProteinPosition(String proteinPosition) { this.proteinPosition = proteinPosition; } - public String getOncotatorVariantClassification() { - return oncotatorVariantClassification; + public String getMafVariantClassification() { + return mafVariantClassification; } - public void setOncotatorVariantClassification(String oncotatorVariantClassification) { - this.oncotatorVariantClassification = oncotatorVariantClassification; + public void setMafVariantClassification(String mafVariantClassification) { + this.mafVariantClassification = mafVariantClassification; } - - public String getOncotatorDbSnpRs() { - return oncotatorDbSnpRs; - } - - public void setOncotatorDbSnpRs(String oncotatorDbSnpRs) { - this.oncotatorDbSnpRs = oncotatorDbSnpRs; - } - - public String getOncotatorDbSnpValStatus() { - return oncotatorDbSnpValStatus; - } - - public void setOncotatorDbSnpValStatus(String oncotatorDbSnpValStatus) { - this.oncotatorDbSnpValStatus = oncotatorDbSnpValStatus; - } - - public String getOncotatorRefseqMrnaId() { - return oncotatorRefseqMrnaId; + + public String getMafDbSnpValStatus() { + return mafDbSnpValStatus; } - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; + public void setMafDbSnpValStatus(String mafDbSnpValStatus) { + this.mafDbSnpValStatus = mafDbSnpValStatus; } - public String getOncotatorUniprotName() { - return oncotatorUniprotName; + public String getMafRefseqMrnaId() { + return mafRefseqMrnaId; } - public void setOncotatorUniprotName(String oncotatorUniprotName) { - this.oncotatorUniprotName = oncotatorUniprotName; + public void setMafRefseqMrnaId(String mafRefseqMrnaId) { + this.mafRefseqMrnaId = mafRefseqMrnaId; } - public String getOncotatorUniprotAccession() { - return oncotatorUniprotAccession; + public String getMafUniprotAccession() { + return mafUniprotAccession; } - public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) { - this.oncotatorUniprotAccession = oncotatorUniprotAccession; + public void setMafUniprotAccession(String mafUniprotAccession) { + this.mafUniprotAccession = mafUniprotAccession; } - public String getOncotatorCodonChange() { - return oncotatorCodonChange; + public String getMafCodonChange() { + return mafCodonChange; } - public void setOncotatorCodonChange(String oncotatorCodonChange) { - this.oncotatorCodonChange = oncotatorCodonChange; + public void setMafCodonChange(String mafCodonChange) { + this.mafCodonChange = mafCodonChange; } - public int getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; + public int getMafProteinPosStart() { + return mafProteinPosStart; } - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; + public void setMafProteinPosStart(int mafProteinPosStart) { + this.mafProteinPosStart = mafProteinPosStart; } - public int getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; + public int getMafProteinPosEnd() { + return mafProteinPosEnd; } - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; + public void setMafProteinPosEnd(int mafProteinPosEnd) { + this.mafProteinPosEnd = mafProteinPosEnd; } public String getMaFuncImpact() { diff --git a/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java b/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java index 0a33ab68bc4..003f7fa44ab 100644 --- a/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java +++ b/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java @@ -110,22 +110,13 @@ public class MafUtil { public static final String PROTEIN_POSITION = "Protein_position"; // oncotator column names - public static final String ONCOTATOR_DBSNP_RS = "ONCOTATOR_DBSNP_RS"; public static final String ONCOTATOR_VARIANT_CLASSIFICATION = "ONCOTATOR_VARIANT_CLASSIFICATION"; public static final String ONCOTATOR_REFSEQ_MRNA_ID = "ONCOTATOR_REFSEQ_MRNA_ID"; - public static final String ONCOTATOR_UNIPROT_ENTRY_NAME = "ONCOTATOR_UNIPROT_ENTRY_NAME"; public static final String ONCOTATOR_UNIPROT_ACCESSION = "ONCOTATOR_UNIPROT_ACCESSION"; public static final String ONCOTATOR_CODON_CHANGE = "ONCOTATOR_CODON_CHANGE"; public static final String ONCOTATOR_PROTEIN_POS_START = "ONCOTATOR_PROTEIN_POS_START"; public static final String ONCOTATOR_PROTEIN_POS_END = "ONCOTATOR_PROTEIN_POS_END"; - - // mutation assessor column names - public static final String MA_FIMPACT = "MA:FImpact"; - public static final String MA_FIS = "MA:FIS"; - public static final String MA_LINK_VAR = "MA:link.var"; - public static final String MA_LINK_MSA = "MA:link.MSA"; - public static final String MA_LINK_PDB = "MA:link.PDB"; - + // custom filtering of passenger and driver mutations column names public static final String DRIVER_FILTER = "cbp_driver"; public static final String DRIVER_FILTER_ANNOTATION = "cbp_driver_annotation"; @@ -182,10 +173,8 @@ public class MafUtil { private int normalVafIndex = -1; // default Oncotator column indices - private int oncoDbSnpRsIndex = -1; private int oncoVariantClassificationIndex = -1; private int oncoRefseqMrnaIdIndex = -1; - private int oncoUniprotNameIndex = -1; private int oncoUniprotAccessionIndex = -1; private int oncoCodonChangeIndex = -1; private int oncoProteinPosStartIndex = -1; @@ -304,14 +293,10 @@ public MafUtil(String headerLine, Set namespaces) { scoreIndex = i; } else if(header.equalsIgnoreCase(BAM_FILE)) { bamFileIndex = i; - } else if(header.equalsIgnoreCase(ONCOTATOR_DBSNP_RS)) { - oncoDbSnpRsIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_VARIANT_CLASSIFICATION)) { oncoVariantClassificationIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_REFSEQ_MRNA_ID)) { oncoRefseqMrnaIdIndex = i; - } else if(header.equalsIgnoreCase(ONCOTATOR_UNIPROT_ENTRY_NAME)) { - oncoUniprotNameIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_UNIPROT_ACCESSION)) { oncoUniprotAccessionIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_CODON_CHANGE)) { @@ -320,16 +305,6 @@ public MafUtil(String headerLine, Set namespaces) { oncoProteinPosStartIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_PROTEIN_POS_END)) { oncoProteinPosEndIndex = i; - } else if(header.equalsIgnoreCase(MA_FIMPACT)) { - maFImpactIndex = i; - } else if(header.equalsIgnoreCase(MA_FIS)) { - maFisIndex = i; - } else if(header.equalsIgnoreCase(MA_LINK_VAR)) { - maLinkVarIndex = i; - } else if(header.equalsIgnoreCase(MA_LINK_MSA)) { - maLinkMsaIndex = i; - } else if(header.equalsIgnoreCase(MA_LINK_PDB)) { - maLinkPdbIndex = i; } else if(header.equalsIgnoreCase(T_REF_COUNT) || header.equalsIgnoreCase(I_T_REF_COUNT) || header.equalsIgnoreCase(AD_REF)) { @@ -446,14 +421,12 @@ public MafRecord parseRecord(String line) { record.setMaLinkPdb(TabDelimitedFileUtil.getPartString(maLinkPdbIndex, parts)); // Oncotator columns - record.setOncotatorDbSnpRs(TabDelimitedFileUtil.getPartString(oncoDbSnpRsIndex, parts)); - record.setOncotatorVariantClassification(TabDelimitedFileUtil.getPartString(oncoVariantClassificationIndex, parts)); - record.setOncotatorRefseqMrnaId(TabDelimitedFileUtil.getPartString(oncoRefseqMrnaIdIndex, parts)); - record.setOncotatorUniprotName(TabDelimitedFileUtil.getPartString(oncoUniprotNameIndex, parts)); - record.setOncotatorUniprotAccession(TabDelimitedFileUtil.getPartString(oncoUniprotAccessionIndex, parts)); - record.setOncotatorCodonChange(TabDelimitedFileUtil.getPartString(oncoCodonChangeIndex, parts)); - record.setOncotatorProteinPosStart(TabDelimitedFileUtil.getPartInt(oncoProteinPosStartIndex, parts)); - record.setOncotatorProteinPosEnd(TabDelimitedFileUtil.getPartInt(oncoProteinPosEndIndex, parts)); + record.setMafVariantClassification(TabDelimitedFileUtil.getPartString(oncoVariantClassificationIndex, parts)); + record.setMafRefseqMrnaId(TabDelimitedFileUtil.getPartString(oncoRefseqMrnaIdIndex, parts)); + record.setMafUniprotAccession(TabDelimitedFileUtil.getPartString(oncoUniprotAccessionIndex, parts)); + record.setMafCodonChange(TabDelimitedFileUtil.getPartString(oncoCodonChangeIndex, parts)); + record.setMafProteinPosStart(TabDelimitedFileUtil.getPartInt(oncoProteinPosStartIndex, parts)); + record.setMafProteinPosEnd(TabDelimitedFileUtil.getPartInt(oncoProteinPosEndIndex, parts)); // custom filtering of passenger and driver mutations columns record.setDriverFilter(TabDelimitedFileUtil.getPartStringAllowEmptyAndNA(driverIndex, parts)); @@ -640,10 +613,6 @@ public int getOncoVariantClassificationIndex() { return oncoVariantClassificationIndex; } - public int getOncoDbSnpRsIndex() { - return oncoDbSnpRsIndex; - } - public int getMaFImpactIndex() { return maFImpactIndex; } @@ -668,10 +637,6 @@ public int getOncoRefseqMrnaIdIndex() { return oncoRefseqMrnaIdIndex; } - public int getOncoUniprotNameIndex() { - return oncoUniprotNameIndex; - } - public int getOncoCodonChangeIndex() { return oncoCodonChangeIndex; } diff --git a/model/src/main/java/org/cbioportal/model/Mutation.java b/model/src/main/java/org/cbioportal/model/Mutation.java index 78ee86d4344..62fc787e288 100644 --- a/model/src/main/java/org/cbioportal/model/Mutation.java +++ b/model/src/main/java/org/cbioportal/model/Mutation.java @@ -23,16 +23,11 @@ public class Mutation extends Alteration implements Serializable { private String tumorSeqAllele; private String proteinChange; private String mutationType; - private String functionalImpactScore; - private BigDecimal fisValue; - private String linkXvar; - private String linkPdb; - private String linkMsa; private String ncbiBuild; private String variantType; - private String oncotatorRefseqMrnaId; - private Integer oncotatorProteinPosStart; - private Integer oncotatorProteinPosEnd; + private String refseqMrnaId; + private Integer proteinPosStart; + private Integer proteinPosEnd; private String keyword; private AlleleSpecificCopyNumber alleleSpecificCopyNumber; @JsonRawValue @@ -155,46 +150,6 @@ public void setMutationType(String mutationType) { this.mutationType = mutationType; } - public String getFunctionalImpactScore() { - return functionalImpactScore; - } - - public void setFunctionalImpactScore(String functionalImpactScore) { - this.functionalImpactScore = functionalImpactScore; - } - - public BigDecimal getFisValue() { - return fisValue; - } - - public void setFisValue(BigDecimal fisValue) { - this.fisValue = fisValue; - } - - public String getLinkXvar() { - return linkXvar; - } - - public void setLinkXvar(String linkXvar) { - this.linkXvar = linkXvar; - } - - public String getLinkPdb() { - return linkPdb; - } - - public void setLinkPdb(String linkPdb) { - this.linkPdb = linkPdb; - } - - public String getLinkMsa() { - return linkMsa; - } - - public void setLinkMsa(String linkMsa) { - this.linkMsa = linkMsa; - } - public String getNcbiBuild() { return ncbiBuild; } @@ -210,29 +165,28 @@ public String getVariantType() { public void setVariantType(String variantType) { this.variantType = variantType; } - - public String getOncotatorRefseqMrnaId() { - return oncotatorRefseqMrnaId; + public String getRefseqMrnaId() { + return refseqMrnaId; } - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; + public void setRefseqMrnaId(String refseqMrnaId) { + this.refseqMrnaId = refseqMrnaId; } - - public Integer getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; + + public Integer getProteinPosStart() { + return proteinPosStart; } - public void setOncotatorProteinPosStart(Integer oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; + public void setProteinPosStart(Integer proteinPosStart) { + this.proteinPosStart = proteinPosStart; } - public Integer getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; + public Integer getProteinPosEnd() { + return proteinPosEnd; } - public void setOncotatorProteinPosEnd(Integer oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; + public void setProteinPosEnd(Integer proteinPosEnd) { + this.proteinPosEnd = proteinPosEnd; } public String getKeyword() { diff --git a/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml b/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml index 4d31d0a4413..b780dd0939a 100644 --- a/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml +++ b/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml @@ -26,16 +26,11 @@ mutation_event.TUMOR_SEQ_ALLELE AS tumorSeqAllele, mutation_event.PROTEIN_CHANGE AS proteinChange, mutation_event.MUTATION_TYPE AS mutationType, - mutation_event.FUNCTIONAL_IMPACT_SCORE AS functionalImpactScore, - mutation_event.FIS_VALUE AS fisValue, - mutation_event.LINK_XVAR AS linkXvar, - mutation_event.LINK_PDB AS linkPdb, - mutation_event.LINK_MSA AS linkMsa, mutation_event.NCBI_BUILD AS ncbiBuild, mutation_event.VARIANT_TYPE AS variantType, - mutation_event.ONCOTATOR_REFSEQ_MRNA_ID AS oncotatorRefseqMrnaId, - mutation_event.ONCOTATOR_PROTEIN_POS_START AS oncotatorProteinPosStart, - mutation_event.ONCOTATOR_PROTEIN_POS_END AS oncotatorProteinPosEnd, + mutation_event.REFSEQ_MRNA_ID AS refseqMrnaId, + mutation_event.PROTEIN_POS_START AS proteinPosStart, + mutation_event.PROTEIN_POS_END AS proteinPosEnd, mutation_event.KEYWORD AS keyword, mutation.ANNOTATION_JSON as annotationJSON, alteration_driver_annotation.DRIVER_FILTER as driverFilter, @@ -383,7 +378,7 @@ FROM mutation INNER JOIN mutation_event ON mutation.MUTATION_EVENT_ID = mutation_event.MUTATION_EVENT_ID WHERE mutation_event.ENTREZ_GENE_ID = #{entrezGeneId} - AND mutation_event.ONCOTATOR_PROTEIN_POS_START >= #{proteinPosStart} - AND mutation_event.ONCOTATOR_PROTEIN_POS_END #{proteinPosEnd} + AND mutation_event.PROTEIN_POS_START >= #{proteinPosStart} + AND mutation_event.PROTEIN_POS_END #{proteinPosEnd} diff --git a/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java b/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java index b84fa1a32a6..a75b6eb7f5c 100644 --- a/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java +++ b/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java @@ -16,7 +16,6 @@ import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import java.math.BigDecimal; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -117,9 +116,9 @@ public void getMutationsInMolecularProfileBySampleListIdSummaryProjection() thro Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getOncotatorRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -158,9 +157,9 @@ public void getMutationsInMolecularProfileBySampleListIdAndEntrezGeneIdsSummaryP Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getOncotatorRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -192,17 +191,12 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr Assert.assertEquals("BRCA1 truncating", mutation.getKeyword()); Assert.assertEquals("Germline", mutation.getMutationStatus()); Assert.assertEquals("Nonsense_Mutation", mutation.getMutationType()); - Assert.assertEquals("NA", mutation.getFunctionalImpactScore()); - Assert.assertEquals(new BigDecimal("0.0"), mutation.getFisValue()); - Assert.assertEquals("getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all", mutation.getLinkXvar()); - Assert.assertEquals("NA", mutation.getLinkPdb()); - Assert.assertEquals("NA", mutation.getLinkMsa()); Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getOncotatorRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); diff --git a/persistence/persistence-mybatis/src/test/resources/testSql.sql b/persistence/persistence-mybatis/src/test/resources/testSql.sql index 0a4781ce8e8..03d82e3c833 100644 --- a/persistence/persistence-mybatis/src/test/resources/testSql.sql +++ b/persistence/persistence-mybatis/src/test/resources/testSql.sql @@ -124,12 +124,12 @@ INSERT INTO sample (INTERNAL_ID,STABLE_ID,SAMPLE_TYPE,PATIENT_ID) VALUES (18,'TC INSERT INTO sample (INTERNAL_ID,STABLE_ID,SAMPLE_TYPE,PATIENT_ID) VALUES (19,'TCGA-A1-A0SB-01','Primary Solid Tumor',18); -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'); -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 (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','rs28897672','NM_007294','c.(181-183)TGT>GGT','BRCA1_HUMAN','P38398',61,61,1,'BRCA1 C61 missense'); -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 (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','c.e2+1','NA','NA',-1,-1,1,'BRCA1 truncating'); -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 (2040,207,'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'); -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 (2041,207,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','rs28897672','NM_007294','c.(181-183)TGT>GGT','BRCA1_HUMAN','P38398',61,61,1,'BRCA1 C61 missense'); -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 (2042,208,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','c.e2+1','NA','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2040,207,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2041,207,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2042,208,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (2038,6,6, 'Putative_Driver', 'Pathogenic', 'Tier 1', 'Highly Actionable'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (22604,6,6, 'Putative_Passenger', 'Pathogenic', 'Tier 2', 'Potentially Actionable'); diff --git a/pom.xml b/pom.xml index 349bdb237df..5453d89f434 100644 --- a/pom.xml +++ b/pom.xml @@ -315,7 +315,7 @@ 720 - 2.12.16 + 2.13.0 diff --git a/portal/src/org/mskcc/portal/model/MafRecord.java b/portal/src/org/mskcc/portal/model/MafRecord.java index ceaab613ce5..78cef29dfd6 100644 --- a/portal/src/org/mskcc/portal/model/MafRecord.java +++ b/portal/src/org/mskcc/portal/model/MafRecord.java @@ -47,10 +47,10 @@ public class MafRecord { private int normalAltCount; private int normalRefCount; - private String oncotatorProteinChange; - private String oncotatorVariantClassification; - private String oncotatorCosmicOverlapping; - private String oncotatorDbSnpRs; + private String mafProteinChange; + private String mafVariantClassification; + private String mafCosmicOverlapping; + private String mafDbSnpRs; public String getChr() { return chr; @@ -340,37 +340,37 @@ public void setNormalRefCount(int normalRefCount) { this.normalRefCount = normalRefCount; } - public String getOncotatorProteinChange() { - return oncotatorProteinChange; + public String getMafProteinChange() { + return mafProteinChange; } - public void setOncotatorProteinChange(String oncotatorProteinChange) { - this.oncotatorProteinChange = oncotatorProteinChange; + public void setMafProteinChange(String mafProteinChange) { + this.mafProteinChange = mafProteinChange; } - public String getOncotatorVariantClassification() { - return oncotatorVariantClassification; + public String getMafVariantClassification() { + return mafVariantClassification; } - public void setOncotatorVariantClassification( - String oncotatorVariantClassification) { - this.oncotatorVariantClassification = oncotatorVariantClassification; + public void setMafVariantClassification( + String mafVariantClassification) { + this.mafVariantClassification = mafVariantClassification; } - public String getOncotatorCosmicOverlapping() { - return oncotatorCosmicOverlapping; + public String getMafCosmicOverlapping() { + return mafCosmicOverlapping; } - public void setOncotatorCosmicOverlapping(String oncotatorCosmicOverlapping) { - this.oncotatorCosmicOverlapping = oncotatorCosmicOverlapping; + public void setMafCosmicOverlapping(String mafCosmicOverlapping) { + this.mafCosmicOverlapping = mafCosmicOverlapping; } - public String getOncotatorDbSnpRs() { - return oncotatorDbSnpRs; + public String getMafDbSnpRs() { + return mafDbSnpRs; } - public void setOncotatorDbSnpRs(String oncotatorDbSnpRs) { - this.oncotatorDbSnpRs = oncotatorDbSnpRs; + public void setMafDbSnpRs(String mafDbSnpRs) { + this.mafDbSnpRs = mafDbSnpRs; } diff --git a/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java b/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java index 7cee18693fe..86b80142466 100644 --- a/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java +++ b/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java @@ -7,11 +7,11 @@ public class MutationMixin { @JsonProperty("variantAllele") private String tumorSeqAllele; @JsonProperty("refseqMrnaId") - private String oncotatorRefseqMrnaId; + private String refseqMrnaId; @JsonProperty("proteinPosStart") - private Integer oncotatorProteinPosStart; + private Integer proteinPosStart; @JsonProperty("proteinPosEnd") - private Integer oncotatorProteinPosEnd; + private Integer proteinPosEnd; @JsonProperty("chr") private String chr; @JsonProperty("namespaceColumns") diff --git a/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java b/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java index ff89f1960f8..ce2caf51cdb 100644 --- a/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java +++ b/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java @@ -19,9 +19,9 @@ public enum MutationSortBy { mutationType("mutationType"), ncbiBuild("ncbiBuild"), variantType("variantType"), - refseqMrnaId("oncotatorRefseqMrnaId"), - proteinPosStart("oncotatorProteinPosStart"), - proteinPosEnd("oncotatorProteinPosEnd"), + refseqMrnaId("refseqMrnaId"), + proteinPosStart("proteinPosStart"), + proteinPosEnd("proteinPosEnd"), keyword("keyword"); private String originalValue; diff --git a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java index da622a1c6fc..7f9018d0e85 100644 --- a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java @@ -30,7 +30,6 @@ import org.springframework.test.web.servlet.setup.MockMvcBuilders; import org.springframework.web.context.WebApplicationContext; -import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; @@ -58,16 +57,11 @@ public class MutationControllerTest { private static final String TEST_TUMOR_SEQ_ALLELE_1 = "test_tumor_seq_allele_1"; private static final String TEST_PROTEIN_CHANGE_1 = "test_protein_change_1"; private static final String TEST_MUTATION_TYPE_1 = "test_mutation_type_1"; - private static final String TEST_FUNCTIONAL_IMPACT_SCORE_1 = "test_functional_impact_score_1"; - private static final BigDecimal TEST_FIS_VALUE_1 = new BigDecimal(0.1); - private static final String TEST_LINK_XVAR_1 = "test_link_xvar_1"; - private static final String TEST_LINK_PDB_1 = "test_link_pdb_1"; - private static final String TEST_LINK_MSA_1 = "test_link_msa_1"; private static final String TEST_NCBI_BUILD_1 = "test_ncbi_build_1"; private static final String TEST_VARIANT_TYPE_1 = "test_variant_type_1"; - private static final String TEST_ONCOTATOR_REFSEQ_MRNA_ID_1 = "test_oncotator_refseq_mrna_id_1"; - private static final int TEST_ONCOTATOR_PROTEIN_POS_START_1 = 1; - private static final int TEST_ONCOTATOR_PROTEIN_POS_END_1 = 1; + private static final String TEST_MUTATION_REFSEQ_MRNA_ID_1 = "test_mutation_refseq_mrna_id_1"; + private static final int TEST_MUTATION_PROTEIN_POS_START_1 = 1; + private static final int TEST_MUTATION_PROTEIN_POS_END_1 = 1; private static final String TEST_KEYWORD_1 = "test_keyword_1"; private static final String TEST_HUGO_GENE_SYMBOL_1 = "test_hugo_gene_symbol_1"; private static final String TEST_TYPE_1 = "test_type_1"; @@ -100,16 +94,11 @@ public class MutationControllerTest { private static final String TEST_TUMOR_SEQ_ALLELE_2 = "test_tumor_seq_allele_2"; private static final String TEST_PROTEIN_CHANGE_2 = "test_protein_change_2"; private static final String TEST_MUTATION_TYPE_2 = "test_mutation_type_2"; - private static final String TEST_FUNCTIONAL_IMPACT_SCORE_2 = "test_functional_impact_score_2"; - private static final BigDecimal TEST_FIS_VALUE_2 = new BigDecimal(0.2); - private static final String TEST_LINK_XVAR_2 = "test_link_xvar_2"; - private static final String TEST_LINK_PDB_2 = "test_link_pdb_2"; - private static final String TEST_LINK_MSA_2 = "test_link_msa_2"; private static final String TEST_NCBI_BUILD_2 = "test_ncbi_build_2"; private static final String TEST_VARIANT_TYPE_2 = "test_variant_type_2"; - private static final String TEST_ONCOTATOR_REFSEQ_MRNA_ID_2 = "test_oncotator_refseq_mrna_id_2"; - private static final int TEST_ONCOTATOR_PROTEIN_POS_START_2 = 2; - private static final int TEST_ONCOTATOR_PROTEIN_POS_END_2 = 2; + private static final String TEST_MUTATION_REFSEQ_MRNA_ID_2 = "test_MUTATION_refseq_mrna_id_2"; + private static final int TEST_MUTATION_PROTEIN_POS_START_2 = 2; + private static final int TEST_MUTATION_PROTEIN_POS_END_2 = 2; private static final String TEST_KEYWORD_2 = "test_keyword_2"; private static final String TEST_HUGO_GENE_SYMBOL_2 = "test_hugo_gene_symbol_2"; private static final String TEST_TYPE_2 = "test_type_2"; @@ -195,17 +184,11 @@ public void getMutationsInMolecularProfileBySampleListIdDefaultProjection() thro .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].fisValue").value(TEST_FIS_VALUE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkXvar").value(TEST_LINK_XVAR_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkPdb").value(TEST_LINK_PDB_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkMsa").value(TEST_LINK_MSA_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].ncbiBuild").value(TEST_NCBI_BUILD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].variantType").value(TEST_VARIANT_TYPE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[0].namespaceColumns.columnName.fieldName").value("fieldValue")) @@ -231,17 +214,11 @@ public void getMutationsInMolecularProfileBySampleListIdDefaultProjection() thro .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].fisValue").value(TEST_FIS_VALUE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkXvar").value(TEST_LINK_XVAR_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkPdb").value(TEST_LINK_PDB_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkMsa").value(TEST_LINK_MSA_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].ncbiBuild").value(TEST_NCBI_BUILD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].variantType").value(TEST_VARIANT_TYPE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[1].namespaceColumns.columnName.fieldName").value("fieldValue")); @@ -285,17 +262,11 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].fisValue").value(TEST_FIS_VALUE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkXvar").value(TEST_LINK_XVAR_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkPdb").value(TEST_LINK_PDB_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkMsa").value(TEST_LINK_MSA_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].ncbiBuild").value(TEST_NCBI_BUILD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].variantType").value(TEST_VARIANT_TYPE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_1)) @@ -329,17 +300,11 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].fisValue").value(TEST_FIS_VALUE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkXvar").value(TEST_LINK_XVAR_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkPdb").value(TEST_LINK_PDB_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkMsa").value(TEST_LINK_MSA_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].ncbiBuild").value(TEST_NCBI_BUILD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].variantType").value(TEST_VARIANT_TYPE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_2)) @@ -422,17 +387,11 @@ public void fetchMutationsInMultipleMolecularProfiles() throws Exception { .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].fisValue").value(TEST_FIS_VALUE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkXvar").value(TEST_LINK_XVAR_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkPdb").value(TEST_LINK_PDB_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkMsa").value(TEST_LINK_MSA_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].ncbiBuild").value(TEST_NCBI_BUILD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].variantType").value(TEST_VARIANT_TYPE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[1].molecularProfileId") @@ -457,17 +416,11 @@ public void fetchMutationsInMultipleMolecularProfiles() throws Exception { .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].fisValue").value(TEST_FIS_VALUE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkXvar").value(TEST_LINK_XVAR_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkPdb").value(TEST_LINK_PDB_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkMsa").value(TEST_LINK_MSA_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].ncbiBuild").value(TEST_NCBI_BUILD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].variantType").value(TEST_VARIANT_TYPE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist()); } @@ -517,17 +470,11 @@ public void fetchMutationsInMolecularProfileDefaultProjection() throws Exception .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].fisValue").value(TEST_FIS_VALUE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkXvar").value(TEST_LINK_XVAR_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkPdb").value(TEST_LINK_PDB_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkMsa").value(TEST_LINK_MSA_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].ncbiBuild").value(TEST_NCBI_BUILD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].variantType").value(TEST_VARIANT_TYPE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[1].molecularProfileId") @@ -552,17 +499,11 @@ public void fetchMutationsInMolecularProfileDefaultProjection() throws Exception .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].fisValue").value(TEST_FIS_VALUE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkXvar").value(TEST_LINK_XVAR_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkPdb").value(TEST_LINK_PDB_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkMsa").value(TEST_LINK_MSA_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].ncbiBuild").value(TEST_NCBI_BUILD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].variantType").value(TEST_VARIANT_TYPE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist()); } @@ -613,17 +554,11 @@ public void fetchMutationsInMolecularProfileDetailedProjection() throws Exceptio .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].fisValue").value(TEST_FIS_VALUE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkXvar").value(TEST_LINK_XVAR_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkPdb").value(TEST_LINK_PDB_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].linkMsa").value(TEST_LINK_MSA_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].ncbiBuild").value(TEST_NCBI_BUILD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].variantType").value(TEST_VARIANT_TYPE_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_1)) @@ -658,17 +593,11 @@ public void fetchMutationsInMolecularProfileDetailedProjection() throws Exceptio .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverFilterAnnotation").value(TEST_DRIVER_FILTER_ANNOTATION_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilter").value(TEST_DRIVER_TIERS_FILTER_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].functionalImpactScore") - .value(TEST_FUNCTIONAL_IMPACT_SCORE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].fisValue").value(TEST_FIS_VALUE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkXvar").value(TEST_LINK_XVAR_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkPdb").value(TEST_LINK_PDB_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].linkMsa").value(TEST_LINK_MSA_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].ncbiBuild").value(TEST_NCBI_BUILD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].variantType").value(TEST_VARIANT_TYPE_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_2)) @@ -714,14 +643,14 @@ public void fetchMutationCountsByPosition() throws Exception { List mutationCountByPositionList = new ArrayList<>(); MutationCountByPosition mutationCountByPosition1 = new MutationCountByPosition(); mutationCountByPosition1.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1); - mutationCountByPosition1.setProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_1); - mutationCountByPosition1.setProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_1); + mutationCountByPosition1.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_1); + mutationCountByPosition1.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_1); mutationCountByPosition1.setCount(TEST_MUTATION_COUNT_1); mutationCountByPositionList.add(mutationCountByPosition1); MutationCountByPosition mutationCountByPosition2 = new MutationCountByPosition(); mutationCountByPosition2.setEntrezGeneId(TEST_ENTREZ_GENE_ID_2); - mutationCountByPosition2.setProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_2); - mutationCountByPosition2.setProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_2); + mutationCountByPosition2.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_2); + mutationCountByPosition2.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_2); mutationCountByPosition2.setCount(TEST_MUTATION_COUNT_2); mutationCountByPositionList.add(mutationCountByPosition2); @@ -732,13 +661,13 @@ public void fetchMutationCountsByPosition() throws Exception { List mutationPositionIdentifiers = new ArrayList<>(); MutationPositionIdentifier mutationPositionIdentifier1 = new MutationPositionIdentifier(); mutationPositionIdentifier1.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1); - mutationPositionIdentifier1.setProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_1); - mutationPositionIdentifier1.setProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_1); + mutationPositionIdentifier1.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_1); + mutationPositionIdentifier1.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_1); mutationPositionIdentifiers.add(mutationPositionIdentifier1); MutationPositionIdentifier mutationPositionIdentifier2 = new MutationPositionIdentifier(); mutationPositionIdentifier2.setEntrezGeneId(TEST_ENTREZ_GENE_ID_2); - mutationPositionIdentifier2.setProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_2); - mutationPositionIdentifier2.setProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_2); + mutationPositionIdentifier2.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_2); + mutationPositionIdentifier2.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_2); mutationPositionIdentifiers.add(mutationPositionIdentifier2); mockMvc.perform(MockMvcRequestBuilders.post("/mutation-counts-by-position/fetch") @@ -749,12 +678,12 @@ public void fetchMutationCountsByPosition() throws Exception { .andExpect(MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON)) .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2))) .andExpect(MockMvcResultMatchers.jsonPath("$[0].entrezGeneId").value(TEST_ENTREZ_GENE_ID_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].count").value(TEST_MUTATION_COUNT_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].entrezGeneId").value(TEST_ENTREZ_GENE_ID_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].count").value(TEST_MUTATION_COUNT_2)); } @@ -783,16 +712,11 @@ private List createExampleMutations() { mutation1.setDriverFilterAnnotation(TEST_DRIVER_FILTER_ANNOTATION_1); mutation1.setDriverTiersFilter(TEST_DRIVER_TIERS_FILTER_1); mutation1.setDriverTiersFilterAnnotation(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1); - mutation1.setFunctionalImpactScore(TEST_FUNCTIONAL_IMPACT_SCORE_1); - mutation1.setFisValue(TEST_FIS_VALUE_1); - mutation1.setLinkXvar(TEST_LINK_XVAR_1); - mutation1.setLinkPdb(TEST_LINK_PDB_1); - mutation1.setLinkMsa(TEST_LINK_MSA_1); mutation1.setNcbiBuild(TEST_NCBI_BUILD_1); mutation1.setVariantType(TEST_VARIANT_TYPE_1); - mutation1.setOncotatorRefseqMrnaId(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1); - mutation1.setOncotatorProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_1); - mutation1.setOncotatorProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_1); + mutation1.setRefseqMrnaId(TEST_MUTATION_REFSEQ_MRNA_ID_1); + mutation1.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_1); + mutation1.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_1); mutation1.setKeyword(TEST_KEYWORD_1); mutation1.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation1); @@ -818,16 +742,11 @@ private List createExampleMutations() { mutation2.setDriverFilterAnnotation(TEST_DRIVER_FILTER_ANNOTATION_2); mutation2.setDriverTiersFilter(TEST_DRIVER_TIERS_FILTER_2); mutation2.setDriverTiersFilterAnnotation(TEST_DRIVER_TIERS_FILTER_ANNOTATION_2); - mutation2.setFunctionalImpactScore(TEST_FUNCTIONAL_IMPACT_SCORE_2); - mutation2.setFisValue(TEST_FIS_VALUE_2); - mutation2.setLinkXvar(TEST_LINK_XVAR_2); - mutation2.setLinkPdb(TEST_LINK_PDB_2); - mutation2.setLinkMsa(TEST_LINK_MSA_2); mutation2.setNcbiBuild(TEST_NCBI_BUILD_2); mutation2.setVariantType(TEST_VARIANT_TYPE_2); - mutation2.setOncotatorRefseqMrnaId(TEST_ONCOTATOR_REFSEQ_MRNA_ID_2); - mutation2.setOncotatorProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_2); - mutation2.setOncotatorProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_2); + mutation2.setRefseqMrnaId(TEST_MUTATION_REFSEQ_MRNA_ID_2); + mutation2.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_2); + mutation2.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_2); mutation2.setKeyword(TEST_KEYWORD_2); mutation2.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation2);