From f1ab780ba76861b1785028cd63385597131e60a2 Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Thu, 26 May 2022 14:23:25 -0400 Subject: [PATCH 1/3] fix #9461 - mutations api endpoint - modified java files to remove unused properties and changes to tests - db changes, mutationmapper.xml - Update seed_mini.sql --- .../mskcc/cbio/portal/dao/DaoMutation.java | 12 -- .../cbio/portal/model/ExtendedMutation.java | 108 +----------------- .../scripts/ImportExtendedMutationData.java | 33 ------ .../portal/util/ExtendedMutationUtil.java | 6 - .../cbio/portal/web_api/GetMutationData.java | 4 - .../cbio/portal/dao/TestDaoMutation.java | 12 -- core/src/test/resources/seed_mini.sql | 6 +- db-scripts/src/main/resources/cgds.sql | 6 - db-scripts/src/main/resources/migration.sql | 11 ++ .../java/org/cbioportal/model/Mutation.java | 54 --------- .../persistence/mybatis/MutationMapper.xml | 6 - .../MutationMyBatisRepositoryTest.java | 8 -- .../cbioportal/web/mixin/MutationMixin.java | 2 - .../web/parameter/sort/MutationSortBy.java | 1 - .../web/MutationControllerTest.java | 94 --------------- 15 files changed, 16 insertions(+), 347 deletions(-) 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..ca1527188f7 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 @@ -145,18 +145,12 @@ 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(), @@ -800,11 +794,6 @@ 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")); @@ -812,7 +801,6 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet 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")); 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..ab54c4a3713 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; @@ -66,7 +61,6 @@ public final static class MutationEvent { private String dbSnpRs; private String dbSnpValStatus; private String oncotatorDbSnpRs; - private String oncotatorRefseqMrnaId; private String oncotatorUniprotName; private String oncotatorUniprotAccession; private String oncotatorCodonChange; @@ -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; } @@ -244,14 +198,6 @@ 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; } @@ -543,47 +489,7 @@ 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; } @@ -828,16 +734,6 @@ 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(); 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..144137a4906 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()); @@ -399,7 +367,6 @@ public void importData() throws IOException, DaoException { // TODO rename the oncotator column names (remove "oncotator") mutation.setOncotatorCodonChange(codonChange); - mutation.setOncotatorRefseqMrnaId(refseqMrnaId); mutation.setOncotatorUniprotAccession(uniprotAccession); mutation.setOncotatorProteinPosStart(proteinPosStart); mutation.setOncotatorProteinPosEnd(proteinPosEnd); 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..2725fb85c78 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 @@ -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); @@ -328,7 +323,6 @@ public static ExtendedMutation newMutation() { mutation.setNormalRefCount(defaultInt); mutation.setOncotatorDbSnpRs(defaultStr); mutation.setOncotatorCodonChange(defaultStr); - mutation.setOncotatorRefseqMrnaId(defaultStr); mutation.setOncotatorUniprotName(defaultStr); mutation.setOncotatorUniprotAccession(defaultStr); mutation.setOncotatorProteinPosStart(defaultInt); 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..07b237b8bf3 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"); @@ -134,7 +129,6 @@ private void runTheTest() throws DaoException{ 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); @@ -174,11 +168,6 @@ 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()); @@ -206,7 +195,6 @@ private void validateMutation(ExtendedMutation mutation) { 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()); 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..a0cc4fda643 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -435,18 +435,12 @@ 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), diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index c3c4fa5a069..702114aad47 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -978,6 +978,17 @@ 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`; +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..a204b5e10cd 100644 --- a/model/src/main/java/org/cbioportal/model/Mutation.java +++ b/model/src/main/java/org/cbioportal/model/Mutation.java @@ -23,14 +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; @@ -155,46 +149,6 @@ 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; } @@ -211,14 +165,6 @@ 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; } 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..5405e77f4b0 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 @@ -119,7 +119,6 @@ public void getMutationsInMolecularProfileBySampleListIdSummaryProjection() thro 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()); @@ -160,7 +159,6 @@ public void getMutationsInMolecularProfileBySampleListIdAndEntrezGeneIdsSummaryP 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 +190,11 @@ 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..539feb4719e 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 @@ -19,7 +19,6 @@ public enum MutationSortBy { mutationType("mutationType"), ncbiBuild("ncbiBuild"), variantType("variantType"), - refseqMrnaId("oncotatorRefseqMrnaId"), proteinPosStart("oncotatorProteinPosStart"), proteinPosEnd("oncotatorProteinPosEnd"), keyword("keyword"); diff --git a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java index da622a1c6fc..211c06371c6 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)) @@ -783,14 +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); @@ -818,14 +730,8 @@ 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); From 4922133132f51688f21431a6d62db67cc33ae28f Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Thu, 22 Sep 2022 23:26:31 -0400 Subject: [PATCH 2/3] roll back changes for refseqMrnaId roll back changes for refseqMrnaId --- .../org/mskcc/cbio/portal/dao/DaoMutation.java | 2 ++ .../cbio/portal/model/ExtendedMutation.java | 9 +++++++++ .../scripts/ImportExtendedMutationData.java | 3 +++ .../cbio/portal/util/ExtendedMutationUtil.java | 1 + .../mskcc/cbio/portal/dao/TestDaoMutation.java | 2 ++ core/src/test/resources/seed_mini.sql | 6 +++--- db-scripts/src/main/resources/cgds.sql | 1 + db-scripts/src/main/resources/migration.sql | 18 +++++++++--------- .../java/org/cbioportal/model/Mutation.java | 8 ++++++++ .../persistence/mybatis/MutationMapper.xml | 1 + .../mybatis/MutationMyBatisRepositoryTest.java | 3 +++ .../cbioportal/web/mixin/MutationMixin.java | 2 ++ .../web/parameter/sort/MutationSortBy.java | 1 + .../cbioportal/web/MutationControllerTest.java | 14 ++++++++++++++ 14 files changed, 59 insertions(+), 12 deletions(-) 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 ca1527188f7..bc2fa5a8fa6 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 @@ -151,6 +151,7 @@ public static int addMutationEvent(ExtendedMutation.MutationEvent event) throws event.getDbSnpRs(), event.getDbSnpValStatus(), event.getOncotatorDbSnpRs(), + event.getOncotatorRefseqMrnaId(), event.getOncotatorCodonChange(), event.getOncotatorUniprotName(), event.getOncotatorUniprotAccession(), @@ -801,6 +802,7 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet 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")); 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 ab54c4a3713..b31879c7be2 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 @@ -61,6 +61,7 @@ public final static class MutationEvent { private String dbSnpRs; private String dbSnpValStatus; private String oncotatorDbSnpRs; + private String oncotatorRefseqMrnaId; private String oncotatorUniprotName; private String oncotatorUniprotAccession; private String oncotatorCodonChange; @@ -198,6 +199,14 @@ 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; } 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 144137a4906..447b9e63575 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 @@ -210,6 +210,7 @@ public void importData() throws IOException, DaoException { proteinChange, aaChange, codonChange, + refseqMrnaId, uniprotAccession; int proteinPosStart, @@ -240,6 +241,7 @@ public void importData() throws IOException, DaoException { //proteinChange = record.getProteinChange(); aaChange = record.getAminoAcidChange(); codonChange = record.getCodons(); + refseqMrnaId = record.getRefSeq(); //always uniprot accession uniprotAccession = record.getSwissprot(); @@ -367,6 +369,7 @@ public void importData() throws IOException, DaoException { // TODO rename the oncotator column names (remove "oncotator") mutation.setOncotatorCodonChange(codonChange); + mutation.setOncotatorRefseqMrnaId(refseqMrnaId); mutation.setOncotatorUniprotAccession(uniprotAccession); mutation.setOncotatorProteinPosStart(proteinPosStart); mutation.setOncotatorProteinPosEnd(proteinPosEnd); 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 2725fb85c78..67197ab2a47 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 @@ -323,6 +323,7 @@ public static ExtendedMutation newMutation() { mutation.setNormalRefCount(defaultInt); mutation.setOncotatorDbSnpRs(defaultStr); mutation.setOncotatorCodonChange(defaultStr); + mutation.setOncotatorRefseqMrnaId(defaultStr); mutation.setOncotatorUniprotName(defaultStr); mutation.setOncotatorUniprotAccession(defaultStr); mutation.setOncotatorProteinPosStart(defaultInt); 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 07b237b8bf3..f73ca25e766 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 @@ -129,6 +129,7 @@ private void runTheTest() throws DaoException{ 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); @@ -195,6 +196,7 @@ private void validateMutation(ExtendedMutation mutation) { 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()); diff --git a/core/src/test/resources/seed_mini.sql b/core/src/test/resources/seed_mini.sql index 79eb2c23c54..6c0537abe5f 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","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'); +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_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','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","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','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","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','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','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 a0cc4fda643..c591b5bb616 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -441,6 +441,7 @@ CREATE TABLE `mutation_event` ( `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), diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index 702114aad47..777b45d840a 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -978,15 +978,6 @@ 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`; -UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.13"; ##version: 2.12.14 @@ -1003,3 +994,12 @@ ALTER TABLE `structural_variant` DROP COLUMN `SITE2_EXON`; ALTER TABLE `structural_variant` DROP COLUMN `CENTER`; ALTER TABLE `structural_variant` DROP COLUMN `EXTERNAL_ANNOTATION`; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.14"; + + +-- 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`; +UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.14"; diff --git a/model/src/main/java/org/cbioportal/model/Mutation.java b/model/src/main/java/org/cbioportal/model/Mutation.java index a204b5e10cd..1081fb5b81e 100644 --- a/model/src/main/java/org/cbioportal/model/Mutation.java +++ b/model/src/main/java/org/cbioportal/model/Mutation.java @@ -25,6 +25,7 @@ public class Mutation extends Alteration implements Serializable { private String mutationType; private String ncbiBuild; private String variantType; + private String oncotatorRefseqMrnaId; private Integer oncotatorProteinPosStart; private Integer oncotatorProteinPosEnd; private String keyword; @@ -164,7 +165,14 @@ public String getVariantType() { 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; } 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 75b6e1f325b..c3944740e87 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 @@ -28,6 +28,7 @@ mutation_event.MUTATION_TYPE AS mutationType, 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 5405e77f4b0..e1b971e6f55 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 @@ -119,6 +119,7 @@ public void getMutationsInMolecularProfileBySampleListIdSummaryProjection() thro 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()); @@ -159,6 +160,7 @@ public void getMutationsInMolecularProfileBySampleListIdAndEntrezGeneIdsSummaryP 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()); @@ -195,6 +197,7 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr 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 d0f418bda75..7cee18693fe 100644 --- a/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java +++ b/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java @@ -6,6 +6,8 @@ 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 539feb4719e..ff89f1960f8 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 @@ -19,6 +19,7 @@ public enum MutationSortBy { mutationType("mutationType"), ncbiBuild("ncbiBuild"), variantType("variantType"), + refseqMrnaId("oncotatorRefseqMrnaId"), proteinPosStart("oncotatorProteinPosStart"), proteinPosEnd("oncotatorProteinPosEnd"), keyword("keyword"); diff --git a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java index 211c06371c6..8be4eeefcf1 100644 --- a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java @@ -60,6 +60,7 @@ public class MutationControllerTest { private static final String TEST_MUTATION_TYPE_1 = "test_mutation_type_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"; @@ -96,6 +97,7 @@ public class MutationControllerTest { private static final String TEST_MUTATION_TYPE_2 = "test_mutation_type_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"; @@ -185,6 +187,7 @@ public void getMutationsInMolecularProfileBySampleListIdDefaultProjection() thro .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[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("$[0].keyword").value(TEST_KEYWORD_1)) @@ -214,6 +217,7 @@ public void getMutationsInMolecularProfileBySampleListIdDefaultProjection() thro .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_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)) @@ -261,6 +265,7 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[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("$[0].keyword").value(TEST_KEYWORD_1)) @@ -298,6 +303,7 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_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)) @@ -384,6 +390,7 @@ public void fetchMutationsInMultipleMolecularProfiles() throws Exception { .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[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("$[0].keyword").value(TEST_KEYWORD_1)) @@ -412,6 +419,7 @@ public void fetchMutationsInMultipleMolecularProfiles() throws Exception { .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_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)) @@ -465,6 +473,7 @@ public void fetchMutationsInMolecularProfileDefaultProjection() throws Exception .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[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("$[0].keyword").value(TEST_KEYWORD_1)) @@ -493,6 +502,7 @@ public void fetchMutationsInMolecularProfileDefaultProjection() throws Exception .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_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)) @@ -547,6 +557,7 @@ public void fetchMutationsInMolecularProfileDetailedProjection() throws Exceptio .andExpect(MockMvcResultMatchers.jsonPath("$[0].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[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("$[0].keyword").value(TEST_KEYWORD_1)) @@ -585,6 +596,7 @@ public void fetchMutationsInMolecularProfileDetailedProjection() throws Exceptio .andExpect(MockMvcResultMatchers.jsonPath("$[1].driverTiersFilterAnnotation").value(TEST_DRIVER_TIERS_FILTER_ANNOTATION_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)) @@ -703,6 +715,7 @@ private List createExampleMutations() { mutation1.setDriverTiersFilterAnnotation(TEST_DRIVER_TIERS_FILTER_ANNOTATION_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); @@ -732,6 +745,7 @@ private List createExampleMutations() { mutation2.setDriverTiersFilterAnnotation(TEST_DRIVER_TIERS_FILTER_ANNOTATION_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); From 18c282547366b11534bd5f421d49d8543c8a698d Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Fri, 23 Sep 2022 00:03:14 -0400 Subject: [PATCH 3/3] Update ExtendedMutation.java Added required property setOncotatorRefseqMrnaId and getOncotatorRefseqMrnaId --- .../org/mskcc/cbio/portal/model/ExtendedMutation.java | 11 +++++++++++ 1 file changed, 11 insertions(+) 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 b31879c7be2..fb4ee0a7c11 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 @@ -44,6 +44,7 @@ */ public final class ExtendedMutation { + public final static class MutationEvent { private long mutationEventId; private CanonicalGene gene; @@ -743,6 +744,16 @@ 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();