diff --git a/core/src/main/java/org/mskcc/cbio/maf/MafRecord.java b/core/src/main/java/org/mskcc/cbio/maf/MafRecord.java index 62db074d7ff..72be1870dfe 100644 --- a/core/src/main/java/org/mskcc/cbio/maf/MafRecord.java +++ b/core/src/main/java/org/mskcc/cbio/maf/MafRecord.java @@ -103,17 +103,6 @@ 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; - // custom filtering of passenger and driver mutations cols private String driverFilter; private String driverFilterAnn; @@ -520,79 +509,7 @@ public String getProteinPosition() { public void setProteinPosition(String proteinPosition) { this.proteinPosition = proteinPosition; } - - public String getOncotatorVariantClassification() { - return oncotatorVariantClassification; - } - - public void setOncotatorVariantClassification(String oncotatorVariantClassification) { - this.oncotatorVariantClassification = oncotatorVariantClassification; - } - - 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 void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; - } - - public String getOncotatorUniprotName() { - return oncotatorUniprotName; - } - - public void setOncotatorUniprotName(String oncotatorUniprotName) { - this.oncotatorUniprotName = oncotatorUniprotName; - } - - public String getOncotatorUniprotAccession() { - return oncotatorUniprotAccession; - } - - public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) { - this.oncotatorUniprotAccession = oncotatorUniprotAccession; - } - - public String getOncotatorCodonChange() { - return oncotatorCodonChange; - } - - public void setOncotatorCodonChange(String oncotatorCodonChange) { - this.oncotatorCodonChange = oncotatorCodonChange; - } - - public int getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; - } - - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; - } - - public int getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; - } - - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; - } - + public String getMaFuncImpact() { return maFuncImpact; } diff --git a/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java b/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java index ce5132ec121..e16c6885d31 100644 --- a/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java +++ b/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java @@ -115,13 +115,6 @@ public class MafUtil { public static final String REFSEQ = "RefSeq"; 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"; @@ -187,13 +180,6 @@ public class MafUtil { private int normalDepthIndex = -1; 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; private int oncoProteinPosEndIndex = -1; @@ -310,18 +296,6 @@ 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)) { - oncoCodonChangeIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_PROTEIN_POS_START)) { oncoProteinPosStartIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_PROTEIN_POS_END)) { @@ -466,17 +440,7 @@ public MafRecord parseRecord(String line) { record.setMaLinkVar(TabDelimitedFileUtil.getPartString(maLinkVarIndex, parts)); record.setMaLinkMsa(TabDelimitedFileUtil.getPartString(maLinkMsaIndex, parts)); 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)); - + // custom filtering of passenger and driver mutations columns record.setDriverFilter(TabDelimitedFileUtil.getPartStringAllowEmptyAndNA(driverIndex, parts)); record.setDriverFilterAnn(TabDelimitedFileUtil.getPartStringAllowEmpty(driverAnnIndex, parts)); @@ -672,15 +636,7 @@ public int getTumorTotCovIndex() { public int getTumorVarCovIndex() { return tVarCovIndex; } - - public int getOncoVariantClassificationIndex() { - return oncoVariantClassificationIndex; - } - - public int getOncoDbSnpRsIndex() { - return oncoDbSnpRsIndex; - } - + public int getMaFImpactIndex() { return maFImpactIndex; } @@ -700,23 +656,7 @@ public int getMaLinkMsaIndex() { public int getMaLinkPdbIndex() { return maLinkPdbIndex; } - - public int getOncoRefseqMrnaIdIndex() { - return oncoRefseqMrnaIdIndex; - } - - public int getOncoUniprotNameIndex() { - return oncoUniprotNameIndex; - } - - public int getOncoCodonChangeIndex() { - return oncoCodonChangeIndex; - } - - public int getOncoUniprotAccessionIndex() { - return oncoUniprotAccessionIndex; - } - + public int getOncoProteinPosStartIndex() { return oncoProteinPosStartIndex; } 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..ec90a05dfa6 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 @@ -116,7 +116,7 @@ private static Set filterTruncatingCosmicByPosition( Set ret = new HashSet(); Pattern p = Pattern.compile("[0-9]+"); - int mutPos = mut.getOncotatorProteinPosStart(); + int mutPos = 0; 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..c5646783928 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 +145,11 @@ 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()), boolToStr(event.isCanonicalTranscript()), keyword==null ? "\\N":(event.getGene().getHugoGeneSymbolAllCaps()+" "+keyword)); return 1; @@ -800,24 +788,12 @@ 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.setCanonicalTranscript(rs.getBoolean("CANONICAL_TRANSCRIPT")); event.setTumorSeqAllele(rs.getString("TUMOR_SEQ_ALLELE")); event.setKeyword(rs.getString("KEYWORD")); 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..472801bdb62 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 @@ -52,12 +52,7 @@ public final static class MutationEvent { 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 +60,6 @@ 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 boolean canonicalTranscript; public long getMutationEventId() { @@ -132,46 +120,6 @@ 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; } @@ -235,71 +183,7 @@ public String getDbSnpValStatus() { 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 void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; - } - - 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 void setOncotatorUniprotAccession(String oncotatorUniprotAccession) { - this.oncotatorUniprotAccession = oncotatorUniprotAccession; - } - - public String getOncotatorCodonChange() { - return oncotatorCodonChange; - } - - public void setOncotatorCodonChange(String oncotatorCodonChange) { - this.oncotatorCodonChange = oncotatorCodonChange; - } - - public int getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; - } - - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; - } - - public int getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; - } - - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; - } - + public boolean isCanonicalTranscript() { return canonicalTranscript; } @@ -543,47 +427,7 @@ 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; } @@ -819,83 +663,7 @@ public Integer getNormalRefCount() { 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() - { - return event.getOncotatorUniprotName(); - } - - /** - * 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) - { - event.setOncotatorUniprotName(oncotatorUniprotName); - } - - public String getOncotatorUniprotAccession() - { - return event.getOncotatorUniprotAccession(); - } - - public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) - { - event.setOncotatorUniprotAccession(oncotatorUniprotAccession); - } - - public String getOncotatorCodonChange() - { - return event.getOncotatorCodonChange(); - } - - public void setOncotatorCodonChange(String oncotatorCodonChange) - { - event.setOncotatorCodonChange(oncotatorCodonChange); - } - - public int getOncotatorProteinPosStart() - { - return event.getOncotatorProteinPosStart(); - } - - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) - { - event.setOncotatorProteinPosStart(oncotatorProteinPosStart); - } - - public int getOncotatorProteinPosEnd() - { - return event.getOncotatorProteinPosEnd(); - } - - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) - { - event.setOncotatorProteinPosEnd(oncotatorProteinPosEnd); - } - + public boolean isCanonicalTranscript() { return event.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..893dd0f5c75 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 @@ -206,36 +206,10 @@ 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, codonChange, - refseqMrnaId, uniprotAccession; int proteinPosStart, @@ -266,7 +240,6 @@ public void importData() throws IOException, DaoException { //proteinChange = record.getProteinChange(); aaChange = record.getAminoAcidChange(); codonChange = record.getCodons(); - refseqMrnaId = record.getRefSeq(); //always uniprot accession uniprotAccession = record.getSwissprot(); @@ -361,11 +334,6 @@ 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()); @@ -396,14 +364,7 @@ public void importData() throws IOException, DaoException { mutation.setTumorRefCount(ExtendedMutationUtil.getTumorRefCount(record)); 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); - + mutation.setDriverFilter(record.getDriverFilter()); mutation.setDriverFilterAnn(record.getDriverFilterAnn()); mutation.setDriverTiersFilter(record.getDriverTiersFilter()); 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..4d264068dcd 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 @@ -195,16 +195,7 @@ public static boolean isAcceptableMutation(String mutationType) { } public static String getMutationType(MafRecord record) { - String mutationType = record.getOncotatorVariantClassification(); - - if (mutationType == null || - mutationType.length() == 0 || - mutationType.equals("NULL") || - mutationType.equals(TabDelimitedFileUtil.NA_STRING)) { - mutationType = record.getVariantClassification(); - } - - return mutationType; + return record.getVariantClassification(); } public static Integer getTumorAltCount(MafRecord record) { @@ -298,11 +289,6 @@ 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 +312,6 @@ 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.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..80050cc78a9 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 +127,6 @@ 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.setCanonicalTranscript(true); mutation.setAnnotationJson(makeMockAnnotationJsonString()); @@ -174,11 +162,6 @@ 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 +187,6 @@ 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(true, mutation.isCanonicalTranscript()); validateMockAnnotationJson(mutation); diff --git a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java index 06615c5169a..70cd9c6ff23 100644 --- a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java +++ b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java @@ -138,14 +138,7 @@ public void testImportExtendedMutationDataOncotated() throws IOException, DaoExc // assert table size; 3 silent mutations should be rejected assertEquals(17, mutationList.size()); - - // assert data for oncotator columns - //assertEquals("FAM90A1", mutationList.get(0).getGeneSymbol()); - //assertEquals("Missense_Mutation", mutationList.get(1).getOncotatorVariantClassification()); - //assertEquals("p.R131H", mutationList.get(4).getOncotatorProteinChange()); - //assertEquals("rs76360727;rs33980232", mutationList.get(9).getOncotatorDbSnpRs()); - //assertEquals("p.E366_Q409del(13)|p.Q367R(1)|p.E366_K477del(1)", - //mutationList.get(15).getOncotatorCosmicOverlapping()); + } /** * Tests custom filtering mutation types option (filtering for missense and nonsensemutations). diff --git a/core/src/test/resources/seed_mini.sql b/core/src/test/resources/seed_mini.sql index e1bfcca4ef8..79eb2c23c54 100644 --- a/core/src/test/resources/seed_mini.sql +++ b/core/src/test/resources/seed_mini.sql @@ -411,9 +411,9 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (19,'TCGA-A1-A0SB-02','Primary Solid Tumor',1); -- 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","ONCOTATOR_DBSNP_RS","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','37','+','SNP','rs80357223','unknown','rs80357223','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","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","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','37','+','SNP','rs28897672','byCluster','rs28897672','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","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","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','37','+','SNP','rs80358010','byCluster','rs80358010','c.e2+1','NA','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 f28432e323d..79158895d4a 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -435,21 +435,11 @@ 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), `CANONICAL_TRANSCRIPT` boolean, diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index c3c4fa5a069..986b5665f26 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -978,6 +978,22 @@ 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: 2.12.13 +-- 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`; +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_REFSEQ_MRNA_ID`; +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_DBSNP_RS`; +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_CODON_CHANGE`; +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_UNIPROT_ENTRY_NAME`; +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_UNIPROT_ACCESSION`; + +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`; diff --git a/model/src/main/java/org/cbioportal/model/Mutation.java b/model/src/main/java/org/cbioportal/model/Mutation.java index 78ee86d4344..1727381f0f7 100644 --- a/model/src/main/java/org/cbioportal/model/Mutation.java +++ b/model/src/main/java/org/cbioportal/model/Mutation.java @@ -23,16 +23,8 @@ 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 keyword; private AlleleSpecificCopyNumber alleleSpecificCopyNumber; @JsonRawValue @@ -155,46 +147,6 @@ 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; } @@ -211,30 +163,6 @@ public void setVariantType(String variantType) { this.variantType = variantType; } - public String getOncotatorRefseqMrnaId() { - return oncotatorRefseqMrnaId; - } - - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; - } - - public Integer getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; - } - - public void setOncotatorProteinPosStart(Integer oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; - } - - public Integer getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; - } - - public void setOncotatorProteinPosEnd(Integer oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; - } - public String getKeyword() { return keyword; } 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..75b6e1f325b 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 @@ -26,14 +26,8 @@ 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.KEYWORD AS keyword, 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..217ab3aac87 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 @@ -117,9 +117,6 @@ 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("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -158,9 +155,6 @@ 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("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -192,17 +186,9 @@ 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("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); 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..d0f418bda75 100644 --- a/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java +++ b/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java @@ -6,8 +6,6 @@ public class MutationMixin { @JsonProperty("variantAllele") private String tumorSeqAllele; - @JsonProperty("refseqMrnaId") - private String oncotatorRefseqMrnaId; @JsonProperty("proteinPosStart") private Integer oncotatorProteinPosStart; @JsonProperty("proteinPosEnd") 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..2f3649088bc 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 +19,6 @@ public enum MutationSortBy { mutationType("mutationType"), ncbiBuild("ncbiBuild"), variantType("variantType"), - refseqMrnaId("oncotatorRefseqMrnaId"), - proteinPosStart("oncotatorProteinPosStart"), - proteinPosEnd("oncotatorProteinPosEnd"), 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..4d7798c18bf 100644 --- a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java @@ -58,14 +58,8 @@ 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_KEYWORD_1 = "test_keyword_1"; @@ -100,14 +94,8 @@ 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_KEYWORD_2 = "test_keyword_2"; @@ -195,15 +183,8 @@ 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].keyword").value(TEST_KEYWORD_1)) @@ -231,15 +212,8 @@ 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].keyword").value(TEST_KEYWORD_2)) @@ -285,15 +259,8 @@ 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].keyword").value(TEST_KEYWORD_1)) @@ -329,15 +296,8 @@ 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].keyword").value(TEST_KEYWORD_2)) @@ -422,15 +382,8 @@ 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].keyword").value(TEST_KEYWORD_1)) @@ -457,15 +410,8 @@ 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].keyword").value(TEST_KEYWORD_2)) @@ -517,15 +463,8 @@ 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].keyword").value(TEST_KEYWORD_1)) @@ -552,15 +491,8 @@ 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].keyword").value(TEST_KEYWORD_2)) @@ -613,15 +545,8 @@ 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].keyword").value(TEST_KEYWORD_1)) @@ -658,15 +583,8 @@ 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].keyword").value(TEST_KEYWORD_2)) @@ -783,16 +701,8 @@ 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.setKeyword(TEST_KEYWORD_1); mutation1.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation1); @@ -818,16 +728,8 @@ 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.setKeyword(TEST_KEYWORD_2); mutation2.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation2);