From 967afbeda1a2467f30f7302ebccf2da49be32b32 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 1/9] fix #9461 - mutations api endpoint - modified java files to remove unused properties and changes to tests - db changes, mutationmapper.xml - Update seed_mini.sql roll back changes for refseqMrnaId roll back changes for refseqMrnaId Update ExtendedMutation.java Added required property setOncotatorRefseqMrnaId and getOncotatorRefseqMrnaId --- .../mskcc/cbio/portal/dao/DaoMutation.java | 10 -- .../cbio/portal/model/ExtendedMutation.java | 92 +------------------ .../scripts/ImportExtendedMutationData.java | 30 ------ .../portal/util/ExtendedMutationUtil.java | 5 - .../cbio/portal/web_api/GetMutationData.java | 4 - .../cbio/portal/dao/TestDaoMutation.java | 10 -- core/src/test/resources/seed_mini.sql | 6 +- db-scripts/src/main/resources/cgds.sql | 5 - db-scripts/src/main/resources/migration.sql | 10 ++ .../java/org/cbioportal/model/Mutation.java | 48 +--------- .../persistence/mybatis/MutationMapper.xml | 5 - .../MutationMyBatisRepositoryTest.java | 5 - .../web/MutationControllerTest.java | 80 ---------------- 13 files changed, 18 insertions(+), 292 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..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 @@ -145,11 +145,6 @@ 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(), @@ -800,11 +795,6 @@ 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")); 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..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; @@ -52,12 +53,7 @@ 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; @@ -132,46 +128,6 @@ 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; } @@ -543,47 +499,7 @@ 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; } @@ -837,7 +753,7 @@ 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..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 @@ -206,31 +206,6 @@ public void importData() throws IOException, DaoException { if (record.getEndPosition() < 0) record.setEndPosition(0); - String functionalImpactScore = ""; - // using -1 is not safe, FIS can be a negative value - Float fisValue = Float.MIN_VALUE; - String linkXVar = ""; - String linkMsa = ""; - String linkPdb = ""; - - if (fileHasOMAData) - { -// functionalImpactScore = getField(parts, "MA:FImpact" ); -// fisValue = getField(parts, "MA:FIS"); -// linkXVar = getField(parts, "MA:link.var" ); -// linkMsa = getField(parts, "MA:link.MSA" ); -// linkPdb = getField(parts, "MA:link.PDB" ); - - functionalImpactScore = record.getMaFuncImpact(); - fisValue = record.getMaFIS(); - linkXVar = record.getMaLinkVar(); - linkMsa = record.getMaLinkMsa(); - linkPdb = record.getMaLinkPdb(); - - functionalImpactScore = transformOMAScore(functionalImpactScore); - linkXVar = linkXVar.replace("\"", ""); - } - String mutationType, proteinChange, aaChange, @@ -361,11 +336,6 @@ public void importData() throws IOException, DaoException { mutation.setEndPosition(record.getEndPosition()); mutation.setValidationStatus(record.getValidationStatus()); mutation.setMutationStatus(record.getMutationStatus()); - mutation.setFunctionalImpactScore(functionalImpactScore); - mutation.setFisValue(fisValue); - mutation.setLinkXVar(linkXVar); - mutation.setLinkPdb(linkPdb); - mutation.setLinkMsa(linkMsa); mutation.setNcbiBuild(record.getNcbiBuild()); mutation.setStrand(record.getStrand()); mutation.setVariantType(record.getVariantType()); 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..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 @@ -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); 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..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 @@ -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"); @@ -174,11 +169,6 @@ 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()); diff --git a/core/src/test/resources/seed_mini.sql b/core/src/test/resources/seed_mini.sql index fd98ec7d340..97490696ac6 100644 --- a/core/src/test/resources/seed_mini.sql +++ b/core/src/test/resources/seed_mini.sql @@ -419,9 +419,9 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (21,'TCGA-A1-A0SB-11','Solid Tissues Normal',20); -- mutation_event -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","FUNCTIONAL_IMPACT_SCORE","FIS_VALUE","LINK_XVAR","LINK_PDB","LINK_MSA","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','NA',0,'getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all','NA','NA','37','+','SNP','rs80357223','unknown','rs80357223','NM_007294','c.(2800-2802)CAG>TAG','BRCA1_HUMAN','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","FUNCTIONAL_IMPACT_SCORE","FIS_VALUE","LINK_XVAR","LINK_PDB","LINK_MSA","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','rs28897672','NM_007294','c.(181-183)TGT>GGT','BRCA1_HUMAN','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","FUNCTIONAL_IMPACT_SCORE","FIS_VALUE","LINK_XVAR","LINK_PDB","LINK_MSA","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','c.e2+1','NA','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","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 1871b709a0e..7e3a59c07ee 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -436,11 +436,6 @@ 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), diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index ef820bb95a5..95b2ab91cb2 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -978,6 +978,8 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.12"; ALTER TABLE `sample` MODIFY COLUMN `STABLE_ID` VARCHAR(63) NOT NULL; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.13"; + + ##version: 2.12.14 ALTER TABLE `structural_variant` MODIFY COLUMN `SITE1_ENTREZ_GENE_ID` int(11); ALTER TABLE `structural_variant` ADD COLUMN `SITE1_REGION` varchar(25) AFTER `SITE1_CHROMOSOME`; @@ -1000,3 +1002,11 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.15"; ##version: 2.12.16 ALTER TABLE `structural_variant` ADD COLUMN `ANNOTATION_JSON` JSON AFTER `SV_STATUS`; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16"; + +-- 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`="2.12.16"; diff --git a/model/src/main/java/org/cbioportal/model/Mutation.java b/model/src/main/java/org/cbioportal/model/Mutation.java index 78ee86d4344..1081fb5b81e 100644 --- a/model/src/main/java/org/cbioportal/model/Mutation.java +++ b/model/src/main/java/org/cbioportal/model/Mutation.java @@ -23,11 +23,6 @@ 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; @@ -155,46 +150,6 @@ public void setMutationType(String mutationType) { this.mutationType = mutationType; } - public String getFunctionalImpactScore() { - return functionalImpactScore; - } - - public void setFunctionalImpactScore(String functionalImpactScore) { - this.functionalImpactScore = functionalImpactScore; - } - - public BigDecimal getFisValue() { - return fisValue; - } - - public void setFisValue(BigDecimal fisValue) { - this.fisValue = fisValue; - } - - public String getLinkXvar() { - return linkXvar; - } - - public void setLinkXvar(String linkXvar) { - this.linkXvar = linkXvar; - } - - public String getLinkPdb() { - return linkPdb; - } - - public void setLinkPdb(String linkPdb) { - this.linkPdb = linkPdb; - } - - public String getLinkMsa() { - return linkMsa; - } - - public void setLinkMsa(String linkMsa) { - this.linkMsa = linkMsa; - } - public String getNcbiBuild() { return ncbiBuild; } @@ -210,7 +165,6 @@ public String getVariantType() { public void setVariantType(String variantType) { this.variantType = variantType; } - public String getOncotatorRefseqMrnaId() { return oncotatorRefseqMrnaId; } @@ -218,7 +172,7 @@ public String getOncotatorRefseqMrnaId() { 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..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 @@ -26,11 +26,6 @@ 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, 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..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 @@ -192,11 +192,6 @@ 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()); diff --git a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java index da622a1c6fc..8be4eeefcf1 100644 --- a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java @@ -58,11 +58,6 @@ 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"; @@ -100,11 +95,6 @@ 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"; @@ -195,12 +185,6 @@ 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("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) @@ -231,12 +215,6 @@ public void getMutationsInMolecularProfileBySampleListIdDefaultProjection() thro .andExpect(MockMvcResultMatchers.jsonPath("$[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)) @@ -285,12 +263,6 @@ 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("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) @@ -329,12 +301,6 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr .andExpect(MockMvcResultMatchers.jsonPath("$[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)) @@ -422,12 +388,6 @@ 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("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) @@ -457,12 +417,6 @@ public void fetchMutationsInMultipleMolecularProfiles() throws Exception { .andExpect(MockMvcResultMatchers.jsonPath("$[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)) @@ -517,12 +471,6 @@ 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("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) @@ -552,12 +500,6 @@ public void fetchMutationsInMolecularProfileDefaultProjection() throws Exception .andExpect(MockMvcResultMatchers.jsonPath("$[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)) @@ -613,12 +555,6 @@ 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("$[0].refseqMrnaId").value(TEST_ONCOTATOR_REFSEQ_MRNA_ID_1)) @@ -658,12 +594,6 @@ public void fetchMutationsInMolecularProfileDetailedProjection() throws Exceptio .andExpect(MockMvcResultMatchers.jsonPath("$[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)) @@ -783,11 +713,6 @@ 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); @@ -818,11 +743,6 @@ 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); From eeb8f8a39dcbb092820880355342ffca33ffbc60 Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Wed, 12 Oct 2022 12:07:15 -0400 Subject: [PATCH 2/9] Updated more files for removed fields Updated more files for removed fields Remove unused oncotator fields Remove unused oncotator fields ONCOTATOR_DBSNP_RS ONCOTATOR_UNIPROT_ENTRY_NAME remove fields from sql file ONCOTATOR_DBSNP_RS and ONCOTATOR_UNIPROT_ENTRY_NAME removal from sql file --- .../mskcc/cbio/portal/dao/DaoMutation.java | 4 -- .../cbio/portal/model/ExtendedMutation.java | 54 +------------------ .../portal/util/ExtendedMutationUtil.java | 2 - .../cbio/portal/dao/TestDaoMutation.java | 4 -- core/src/test/resources/seed_mini.sql | 6 +-- db-scripts/src/main/resources/cgds.sql | 2 - db-scripts/src/main/resources/migration.sql | 4 ++ .../java/org/mskcc/cbio/maf/MafRecord.java | 20 +------ .../main/java/org/mskcc/cbio/maf/MafUtil.java | 18 ------- .../src/test/resources/testSql.sql | 12 ++--- 10 files changed, 15 insertions(+), 111 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 bc2fa5a8fa6..24c4eccf6db 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 @@ -150,10 +150,8 @@ public static int addMutationEvent(ExtendedMutation.MutationEvent event) throws event.getVariantType(), event.getDbSnpRs(), event.getDbSnpValStatus(), - event.getOncotatorDbSnpRs(), event.getOncotatorRefseqMrnaId(), event.getOncotatorCodonChange(), - event.getOncotatorUniprotName(), event.getOncotatorUniprotAccession(), Integer.toString(event.getOncotatorProteinPosStart()), Integer.toString(event.getOncotatorProteinPosEnd()), @@ -801,10 +799,8 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet rs) 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")); 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 fb4ee0a7c11..3b14c8dbb0a 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 @@ -61,9 +61,7 @@ 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; @@ -192,14 +190,6 @@ 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; } @@ -207,23 +197,7 @@ public String getOncotatorRefseqMrnaId() { 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; } @@ -736,14 +710,6 @@ 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(); @@ -753,24 +719,6 @@ 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() { 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 67197ab2a47..2e211642d4a 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 @@ -321,10 +321,8 @@ 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); 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 f73ca25e766..f6e9ae6b22f 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 @@ -127,10 +127,8 @@ 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); @@ -194,10 +192,8 @@ 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()); diff --git a/core/src/test/resources/seed_mini.sql b/core/src/test/resources/seed_mini.sql index 97490696ac6..7cb9f6ea6f2 100644 --- a/core/src/test/resources/seed_mini.sql +++ b/core/src/test/resources/seed_mini.sql @@ -419,9 +419,9 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (21,'TCGA-A1-A0SB-11','Solid Tissues Normal',20); -- mutation_event -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","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'); +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_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","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','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","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','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","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','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); -- mutation INSERT INTO "mutation" ("MUTATION_EVENT_ID","GENETIC_PROFILE_ID","SAMPLE_ID","ENTREZ_GENE_ID","CENTER","SEQUENCER","MUTATION_STATUS","VALIDATION_STATUS","TUMOR_SEQ_ALLELE1","TUMOR_SEQ_ALLELE2","MATCHED_NORM_SAMPLE_BARCODE","MATCH_NORM_SEQ_ALLELE1","MATCH_NORM_SEQ_ALLELE2","TUMOR_VALIDATION_ALLELE1","TUMOR_VALIDATION_ALLELE2","MATCH_NORM_VALIDATION_ALLELE1","MATCH_NORM_VALIDATION_ALLELE2","VERIFICATION_STATUS","SEQUENCING_PHASE","SEQUENCE_SOURCE","VALIDATION_METHOD","SCORE","BAM_FILE","TUMOR_ALT_COUNT","TUMOR_REF_COUNT","NORMAL_ALT_COUNT","NORMAL_REF_COUNT") VALUES (2038,6,6,672,'genome.wustl.edu','IlluminaGAIIx','Germline','Unknown','G','A','TCGA-A1-A0SH-10A-03D-A099-09','G','A','NA','NA','NA','NA','Unknown','Phase_IV','Capture','NA','1','dbGAP',-1,-1,-1,-1); diff --git a/db-scripts/src/main/resources/cgds.sql b/db-scripts/src/main/resources/cgds.sql index 7e3a59c07ee..b9e126db350 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -441,10 +441,8 @@ CREATE TABLE `mutation_event` ( `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), diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index 95b2ab91cb2..e7c1c15b160 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -1009,4 +1009,8 @@ ALTER TABLE `mutation_event` DROP COLUMN `FIS_VALUE`; ALTER TABLE `mutation_event` DROP COLUMN `LINK_XVAR`; ALTER TABLE `mutation_event` DROP COLUMN `LINK_PDB`; ALTER TABLE `mutation_event` DROP COLUMN `LINK_MSA`; + +-- changes for issue 9779 +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_DBSNP_RS`; +ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_UNIPROT_ENTRY_NAME`; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16"; diff --git a/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java b/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java index 512372e642c..8b6d57b720b 100644 --- a/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java +++ b/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java @@ -104,11 +104,9 @@ public class MafRecord { 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; @@ -528,15 +526,7 @@ public String getOncotatorVariantClassification() { 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; } @@ -553,14 +543,6 @@ 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; } diff --git a/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java b/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java index 0a33ab68bc4..e1a00484272 100644 --- a/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java +++ b/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java @@ -110,10 +110,8 @@ public class MafUtil { public static final String PROTEIN_POSITION = "Protein_position"; // oncotator column names - public static final String ONCOTATOR_DBSNP_RS = "ONCOTATOR_DBSNP_RS"; public static final String ONCOTATOR_VARIANT_CLASSIFICATION = "ONCOTATOR_VARIANT_CLASSIFICATION"; public static final String ONCOTATOR_REFSEQ_MRNA_ID = "ONCOTATOR_REFSEQ_MRNA_ID"; - public static final String ONCOTATOR_UNIPROT_ENTRY_NAME = "ONCOTATOR_UNIPROT_ENTRY_NAME"; public static final String ONCOTATOR_UNIPROT_ACCESSION = "ONCOTATOR_UNIPROT_ACCESSION"; public static final String ONCOTATOR_CODON_CHANGE = "ONCOTATOR_CODON_CHANGE"; public static final String ONCOTATOR_PROTEIN_POS_START = "ONCOTATOR_PROTEIN_POS_START"; @@ -182,10 +180,8 @@ public class MafUtil { private int normalVafIndex = -1; // default Oncotator column indices - private int oncoDbSnpRsIndex = -1; private int oncoVariantClassificationIndex = -1; private int oncoRefseqMrnaIdIndex = -1; - private int oncoUniprotNameIndex = -1; private int oncoUniprotAccessionIndex = -1; private int oncoCodonChangeIndex = -1; private int oncoProteinPosStartIndex = -1; @@ -304,14 +300,10 @@ public MafUtil(String headerLine, Set namespaces) { scoreIndex = i; } else if(header.equalsIgnoreCase(BAM_FILE)) { bamFileIndex = i; - } else if(header.equalsIgnoreCase(ONCOTATOR_DBSNP_RS)) { - oncoDbSnpRsIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_VARIANT_CLASSIFICATION)) { oncoVariantClassificationIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_REFSEQ_MRNA_ID)) { oncoRefseqMrnaIdIndex = i; - } else if(header.equalsIgnoreCase(ONCOTATOR_UNIPROT_ENTRY_NAME)) { - oncoUniprotNameIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_UNIPROT_ACCESSION)) { oncoUniprotAccessionIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_CODON_CHANGE)) { @@ -446,10 +438,8 @@ public MafRecord parseRecord(String line) { record.setMaLinkPdb(TabDelimitedFileUtil.getPartString(maLinkPdbIndex, parts)); // Oncotator columns - record.setOncotatorDbSnpRs(TabDelimitedFileUtil.getPartString(oncoDbSnpRsIndex, parts)); record.setOncotatorVariantClassification(TabDelimitedFileUtil.getPartString(oncoVariantClassificationIndex, parts)); record.setOncotatorRefseqMrnaId(TabDelimitedFileUtil.getPartString(oncoRefseqMrnaIdIndex, parts)); - record.setOncotatorUniprotName(TabDelimitedFileUtil.getPartString(oncoUniprotNameIndex, parts)); record.setOncotatorUniprotAccession(TabDelimitedFileUtil.getPartString(oncoUniprotAccessionIndex, parts)); record.setOncotatorCodonChange(TabDelimitedFileUtil.getPartString(oncoCodonChangeIndex, parts)); record.setOncotatorProteinPosStart(TabDelimitedFileUtil.getPartInt(oncoProteinPosStartIndex, parts)); @@ -640,10 +630,6 @@ public int getOncoVariantClassificationIndex() { return oncoVariantClassificationIndex; } - public int getOncoDbSnpRsIndex() { - return oncoDbSnpRsIndex; - } - public int getMaFImpactIndex() { return maFImpactIndex; } @@ -668,10 +654,6 @@ public int getOncoRefseqMrnaIdIndex() { return oncoRefseqMrnaIdIndex; } - public int getOncoUniprotNameIndex() { - return oncoUniprotNameIndex; - } - public int getOncoCodonChangeIndex() { return oncoCodonChangeIndex; } diff --git a/persistence/persistence-mybatis/src/test/resources/testSql.sql b/persistence/persistence-mybatis/src/test/resources/testSql.sql index 0a4781ce8e8..26e96e09918 100644 --- a/persistence/persistence-mybatis/src/test/resources/testSql.sql +++ b/persistence/persistence-mybatis/src/test/resources/testSql.sql @@ -124,12 +124,12 @@ INSERT INTO sample (INTERNAL_ID,STABLE_ID,SAMPLE_TYPE,PATIENT_ID) VALUES (18,'TC INSERT INTO sample (INTERNAL_ID,STABLE_ID,SAMPLE_TYPE,PATIENT_ID) VALUES (19,'TCGA-A1-A0SB-01','Primary Solid Tumor',18); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_DBSNP_RS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ENTRY_NAME,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','NA',0,'getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all','NA','NA','37','+','SNP','rs80357223','unknown','rs80357223','NM_007294','c.(2800-2802)CAG>TAG','BRCA1_HUMAN','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_DBSNP_RS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ENTRY_NAME,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','rs28897672','NM_007294','c.(181-183)TGT>GGT','BRCA1_HUMAN','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_DBSNP_RS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ENTRY_NAME,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','c.e2+1','NA','NA',-1,-1,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_DBSNP_RS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ENTRY_NAME,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2040,207,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','NA',0,'getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all','NA','NA','37','+','SNP','rs80357223','unknown','rs80357223','NM_007294','c.(2800-2802)CAG>TAG','BRCA1_HUMAN','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_DBSNP_RS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ENTRY_NAME,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2041,207,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','rs28897672','NM_007294','c.(181-183)TGT>GGT','BRCA1_HUMAN','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_DBSNP_RS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ENTRY_NAME,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2042,208,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','c.e2+1','NA','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,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','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,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','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,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','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2040,207,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','NA',0,'getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all','NA','NA','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2041,207,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2042,208,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (2038,6,6, 'Putative_Driver', 'Pathogenic', 'Tier 1', 'Highly Actionable'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (22604,6,6, 'Putative_Passenger', 'Pathogenic', 'Tier 2', 'Potentially Actionable'); From 3b2f8bb8be56b1459d64246c2995dda203fbf2b3 Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Thu, 27 Oct 2022 11:16:17 -0400 Subject: [PATCH 3/9] db changes and renaming the column prefixes from oncotator to mutation db changes in sql for renaming columns renamed the column prefixes from oncotator to mutation on multiple classes and files --- .../mskcc/cbio/portal/dao/DaoCosmicData.java | 3 +- .../mskcc/cbio/portal/dao/DaoMutation.java | 20 ++-- .../cbio/portal/model/ExtendedMutation.java | 92 +++++++-------- .../scripts/ImportExtendedMutationData.java | 12 +- .../portal/util/ExtendedMutationUtil.java | 12 +- .../cbio/portal/dao/TestDaoMutation.java | 20 ++-- core/src/test/resources/seed_mini.sql | 6 +- db-scripts/src/main/resources/cgds.sql | 10 +- db-scripts/src/main/resources/migration.sql | 6 + .../java/org/mskcc/cbio/maf/MafRecord.java | 72 ++++++------ .../main/java/org/mskcc/cbio/maf/MafUtil.java | 12 +- .../java/org/cbioportal/model/Mutation.java | 30 ++--- .../persistence/mybatis/MutationMapper.xml | 10 +- .../MutationMyBatisRepositoryTest.java | 19 ++- .../src/org/mskcc/portal/model/MafRecord.java | 42 +++---- .../cbioportal/web/mixin/MutationMixin.java | 6 +- .../web/parameter/sort/MutationSortBy.java | 6 +- .../web/MutationControllerTest.java | 109 +++++++++--------- 18 files changed, 245 insertions(+), 242 deletions(-) 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..c084b2bcc9e 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java @@ -39,7 +39,6 @@ import java.util.Collection; import java.util.HashMap; import java.util.HashSet; -import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; @@ -116,7 +115,7 @@ private static Set filterTruncatingCosmicByPosition( Set ret = new HashSet(); Pattern p = Pattern.compile("[0-9]+"); - int mutPos = mut.getOncotatorProteinPosStart(); + int mutPos = mut.getMutationProteinPosStart(); 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 24c4eccf6db..c37fabefd66 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 @@ -150,11 +150,11 @@ public static int addMutationEvent(ExtendedMutation.MutationEvent event) throws event.getVariantType(), event.getDbSnpRs(), event.getDbSnpValStatus(), - event.getOncotatorRefseqMrnaId(), - event.getOncotatorCodonChange(), - event.getOncotatorUniprotAccession(), - Integer.toString(event.getOncotatorProteinPosStart()), - Integer.toString(event.getOncotatorProteinPosEnd()), + event.getMutationRefseqMrnaId(), + event.getMutationCodonChange(), + event.getMutationUniprotAccession(), + Integer.toString(event.getMutationProteinPosStart()), + Integer.toString(event.getMutationProteinPosEnd()), boolToStr(event.isCanonicalTranscript()), keyword==null ? "\\N":(event.getGene().getHugoGeneSymbolAllCaps()+" "+keyword)); return 1; @@ -799,11 +799,11 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet rs) event.setDbSnpRs(rs.getString("DB_SNP_RS")); event.setDbSnpValStatus(rs.getString("DB_SNP_VAL_STATUS")); event.setReferenceAllele(rs.getString("REFERENCE_ALLELE")); - event.setOncotatorRefseqMrnaId(rs.getString("ONCOTATOR_REFSEQ_MRNA_ID")); - event.setOncotatorCodonChange(rs.getString("ONCOTATOR_CODON_CHANGE")); - event.setOncotatorUniprotAccession(rs.getString("ONCOTATOR_UNIPROT_ACCESSION")); - event.setOncotatorProteinPosStart(rs.getInt("ONCOTATOR_PROTEIN_POS_START")); - event.setOncotatorProteinPosEnd(rs.getInt("ONCOTATOR_PROTEIN_POS_END")); + event.setMutationRefseqMrnaId(rs.getString("MUTATION_REFSEQ_MRNA_ID")); + event.setMutationCodonChange(rs.getString("MUTATION_CODON_CHANGE")); + event.setMutationUniprotAccession(rs.getString("MUTATION_UNIPROT_ACCESSION")); + event.setMutationProteinPosStart(rs.getInt("MUTATION_PROTEIN_POS_START")); + event.setMutationProteinPosEnd(rs.getInt("MUTATION_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 3b14c8dbb0a..b969d3874fa 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 @@ -49,7 +49,7 @@ public final static class MutationEvent { private long mutationEventId; private CanonicalGene gene; private String chr; - private long startPosition; + private long startPosition; private long endPosition; private String proteinChange; // amino acid change private String mutationType; // variant classification @@ -61,11 +61,11 @@ public final static class MutationEvent { private String tumorSeqAllele; private String dbSnpRs; private String dbSnpValStatus; - private String oncotatorRefseqMrnaId; - private String oncotatorUniprotAccession; - private String oncotatorCodonChange; - private int oncotatorProteinPosStart; - private int oncotatorProteinPosEnd; + private String mutationRefseqMrnaId; + private String mutationUniprotAccession; + private String mutationCodonChange; + private int mutationProteinPosStart; + private int mutationProteinPosEnd; private boolean canonicalTranscript; public long getMutationEventId() { @@ -190,44 +190,44 @@ public void setDbSnpValStatus(String dbSnpValStatus) { this.dbSnpValStatus = dbSnpValStatus; } - public String getOncotatorRefseqMrnaId() { - return oncotatorRefseqMrnaId; + public String getMutationRefseqMrnaId() { + return mutationRefseqMrnaId; } - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; + public void setMutationRefseqMrnaId(String mutationRefseqMrnaId) { + this.mutationRefseqMrnaId = mutationRefseqMrnaId; } - public String getOncotatorUniprotAccession() { - return oncotatorUniprotAccession; + public String getMutationUniprotAccession() { + return mutationUniprotAccession; } - public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) { - this.oncotatorUniprotAccession = oncotatorUniprotAccession; + public void setMutationUniprotAccession(String mutationUniprotAccession) { + this.mutationUniprotAccession = mutationUniprotAccession; } - public String getOncotatorCodonChange() { - return oncotatorCodonChange; + public String getMutationCodonChange() { + return mutationCodonChange; } - public void setOncotatorCodonChange(String oncotatorCodonChange) { - this.oncotatorCodonChange = oncotatorCodonChange; + public void setMutationCodonChange(String mutationCodonChange) { + this.mutationCodonChange = mutationCodonChange; } - public int getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; + public int getMutationProteinPosStart() { + return mutationProteinPosStart; } - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; + public void setMutationProteinPosStart(int mutationProteinPosStart) { + this.mutationProteinPosStart = mutationProteinPosStart; } - public int getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; + public int getMutationProteinPosEnd() { + return mutationProteinPosEnd; } - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; + public void setMutationProteinPosEnd(int mutationProteinPosEnd) { + this.mutationProteinPosEnd = mutationProteinPosEnd; } public boolean isCanonicalTranscript() { @@ -710,54 +710,54 @@ public void setNormalRefCount(Integer normalRefCount) { this.normalRefCount = normalRefCount; } - public String getOncotatorRefseqMrnaId() + public String getMutationRefseqMrnaId() { - return event.getOncotatorRefseqMrnaId(); + return event.getMutationRefseqMrnaId(); } - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) + public void setMutationRefseqMrnaId(String mutationRefseqMrnaId) { - event.setOncotatorRefseqMrnaId(oncotatorRefseqMrnaId); + event.setMutationRefseqMrnaId(mutationRefseqMrnaId); } - public String getOncotatorUniprotAccession() + public String getMutationUniprotAccession() { - return event.getOncotatorUniprotAccession(); + return event.getMutationUniprotAccession(); } - public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) + public void setMutationUniprotAccession(String mutationUniprotAccession) { - event.setOncotatorUniprotAccession(oncotatorUniprotAccession); + event.setMutationUniprotAccession(mutationUniprotAccession); } - public String getOncotatorCodonChange() + public String getMutationCodonChange() { - return event.getOncotatorCodonChange(); + return event.getMutationCodonChange(); } - public void setOncotatorCodonChange(String oncotatorCodonChange) + public void setMutationCodonChange(String mutationCodonChange) { - event.setOncotatorCodonChange(oncotatorCodonChange); + event.setMutationCodonChange(mutationCodonChange); } - public int getOncotatorProteinPosStart() + public int getMutationProteinPosStart() { - return event.getOncotatorProteinPosStart(); + return event.getMutationProteinPosStart(); } - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) + public void setMutationProteinPosStart(int mutationProteinPosStart) { - event.setOncotatorProteinPosStart(oncotatorProteinPosStart); + event.setMutationProteinPosStart(mutationProteinPosStart); } - public int getOncotatorProteinPosEnd() + public int getMutationProteinPosEnd() { - return event.getOncotatorProteinPosEnd(); + return event.getMutationProteinPosEnd(); } - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) + public void setMutationProteinPosEnd(int mutationProteinPosEnd) { - event.setOncotatorProteinPosEnd(oncotatorProteinPosEnd); + event.setMutationProteinPosEnd(mutationProteinPosEnd); } public boolean isCanonicalTranscript() diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java index 447b9e63575..3b27a91aedf 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 @@ -367,12 +367,12 @@ public void importData() throws IOException, DaoException { mutation.setNormalAltCount(ExtendedMutationUtil.getNormalAltCount(record)); mutation.setNormalRefCount(ExtendedMutationUtil.getNormalRefCount(record)); - // TODO rename the oncotator column names (remove "oncotator") - mutation.setOncotatorCodonChange(codonChange); - mutation.setOncotatorRefseqMrnaId(refseqMrnaId); - mutation.setOncotatorUniprotAccession(uniprotAccession); - mutation.setOncotatorProteinPosStart(proteinPosStart); - mutation.setOncotatorProteinPosEnd(proteinPosEnd); + // renamed the oncotator column names to mutation + mutation.setMutationCodonChange(codonChange); + mutation.setMutationRefseqMrnaId(refseqMrnaId); + mutation.setMutationUniprotAccession(uniprotAccession); + mutation.setMutationProteinPosStart(proteinPosStart); + mutation.setMutationProteinPosEnd(proteinPosEnd); mutation.setDriverFilter(record.getDriverFilter()); mutation.setDriverFilterAnn(record.getDriverFilterAnn()); diff --git a/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java b/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java index 2e211642d4a..58ffeaa73b7 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java +++ b/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java @@ -195,7 +195,7 @@ public static boolean isAcceptableMutation(String mutationType) { } public static String getMutationType(MafRecord record) { - String mutationType = record.getOncotatorVariantClassification(); + String mutationType = record.getMafVariantClassification(); if (mutationType == null || mutationType.length() == 0 || @@ -321,11 +321,11 @@ public static ExtendedMutation newMutation() { mutation.setTumorRefCount(defaultInt); mutation.setNormalAltCount(defaultInt); mutation.setNormalRefCount(defaultInt); - mutation.setOncotatorCodonChange(defaultStr); - mutation.setOncotatorRefseqMrnaId(defaultStr); - mutation.setOncotatorUniprotAccession(defaultStr); - mutation.setOncotatorProteinPosStart(defaultInt); - mutation.setOncotatorProteinPosEnd(defaultInt); + mutation.setMutationCodonChange(defaultStr); + mutation.setMutationRefseqMrnaId(defaultStr); + mutation.setMutationUniprotAccession(defaultStr); + mutation.setMutationProteinPosStart(defaultInt); + mutation.setMutationProteinPosEnd(defaultInt); mutation.setCanonicalTranscript(true); return mutation; 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 f6e9ae6b22f..002e70145a7 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 @@ -127,11 +127,11 @@ private void runTheTest() throws DaoException{ mutation.setTumorRefCount(16); mutation.setNormalAltCount(8); mutation.setNormalRefCount(18); - mutation.setOncotatorCodonChange("c.(133-135)TCT>TTT"); - mutation.setOncotatorRefseqMrnaId("NM_001904"); - mutation.setOncotatorUniprotAccession("P35222"); - mutation.setOncotatorProteinPosStart(666); - mutation.setOncotatorProteinPosEnd(678); + mutation.setMutationCodonChange("c.(133-135)TCT>TTT"); + mutation.setMutationRefseqMrnaId("NM_001904"); + mutation.setMutationUniprotAccession("P35222"); + mutation.setMutationProteinPosStart(666); + mutation.setMutationProteinPosEnd(678); mutation.setCanonicalTranscript(true); mutation.setAnnotationJson(makeMockAnnotationJsonString()); @@ -192,11 +192,11 @@ private void validateMutation(ExtendedMutation mutation) { assertEquals(Integer.valueOf(16), mutation.getTumorRefCount()); assertEquals(Integer.valueOf(8), mutation.getNormalAltCount()); assertEquals(Integer.valueOf(18), mutation.getNormalRefCount()); - assertEquals("c.(133-135)TCT>TTT", mutation.getOncotatorCodonChange()); - assertEquals("NM_001904", mutation.getOncotatorRefseqMrnaId()); - assertEquals("P35222", mutation.getOncotatorUniprotAccession()); - assertEquals(666, mutation.getOncotatorProteinPosStart()); - assertEquals(678, mutation.getOncotatorProteinPosEnd()); + assertEquals("c.(133-135)TCT>TTT", mutation.getMutationCodonChange()); + assertEquals("NM_001904", mutation.getMutationRefseqMrnaId()); + assertEquals("P35222", mutation.getMutationUniprotAccession()); + assertEquals(666, mutation.getMutationProteinPosStart()); + assertEquals(678, mutation.getMutationProteinPosEnd()); assertEquals(true, mutation.isCanonicalTranscript()); validateMockAnnotationJson(mutation); diff --git a/core/src/test/resources/seed_mini.sql b/core/src/test/resources/seed_mini.sql index 7cb9f6ea6f2..dddf5a75a37 100644 --- a/core/src/test/resources/seed_mini.sql +++ b/core/src/test/resources/seed_mini.sql @@ -419,9 +419,9 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (21,'TCGA-A1-A0SB-11','Solid Tissues Normal',20); -- mutation_event -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","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','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","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','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","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','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","MUTATION_REFSEQ_MRNA_ID","MUTATION_CODON_CHANGE","MUTATION_UNIPROT_ACCESSION","MUTATION_PROTEIN_POS_START","MUTATION_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","MUTATION_REFSEQ_MRNA_ID","MUTATION_CODON_CHANGE","MUTATION_UNIPROT_ACCESSION","MUTATION_PROTEIN_POS_START","MUTATION_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","MUTATION_REFSEQ_MRNA_ID","MUTATION_CODON_CHANGE","MUTATION_UNIPROT_ACCESSION","MUTATION_PROTEIN_POS_START","MUTATION_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); -- mutation INSERT INTO "mutation" ("MUTATION_EVENT_ID","GENETIC_PROFILE_ID","SAMPLE_ID","ENTREZ_GENE_ID","CENTER","SEQUENCER","MUTATION_STATUS","VALIDATION_STATUS","TUMOR_SEQ_ALLELE1","TUMOR_SEQ_ALLELE2","MATCHED_NORM_SAMPLE_BARCODE","MATCH_NORM_SEQ_ALLELE1","MATCH_NORM_SEQ_ALLELE2","TUMOR_VALIDATION_ALLELE1","TUMOR_VALIDATION_ALLELE2","MATCH_NORM_VALIDATION_ALLELE1","MATCH_NORM_VALIDATION_ALLELE2","VERIFICATION_STATUS","SEQUENCING_PHASE","SEQUENCE_SOURCE","VALIDATION_METHOD","SCORE","BAM_FILE","TUMOR_ALT_COUNT","TUMOR_REF_COUNT","NORMAL_ALT_COUNT","NORMAL_REF_COUNT") VALUES (2038,6,6,672,'genome.wustl.edu','IlluminaGAIIx','Germline','Unknown','G','A','TCGA-A1-A0SH-10A-03D-A099-09','G','A','NA','NA','NA','NA','Unknown','Phase_IV','Capture','NA','1','dbGAP',-1,-1,-1,-1); diff --git a/db-scripts/src/main/resources/cgds.sql b/db-scripts/src/main/resources/cgds.sql index b9e126db350..c695c632d22 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -441,11 +441,11 @@ CREATE TABLE `mutation_event` ( `VARIANT_TYPE` varchar(15), `DB_SNP_RS` varchar(25), `DB_SNP_VAL_STATUS` varchar(255), - `ONCOTATOR_REFSEQ_MRNA_ID` varchar(64), - `ONCOTATOR_CODON_CHANGE` varchar(255), - `ONCOTATOR_UNIPROT_ACCESSION` varchar(64), - `ONCOTATOR_PROTEIN_POS_START` int(11), - `ONCOTATOR_PROTEIN_POS_END` int(11), + `MUTATION_REFSEQ_MRNA_ID` varchar(64), + `MUTATION_CODON_CHANGE` varchar(255), + `MUTATION_UNIPROT_ACCESSION` varchar(64), + `MUTATION_PROTEIN_POS_START` int(11), + `MUTATION_PROTEIN_POS_END` int(11), `CANONICAL_TRANSCRIPT` boolean, `KEYWORD` varchar(255) DEFAULT NULL COMMENT 'e.g. truncating, V200 Missense, E338del, ', KEY (`KEYWORD`), diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index e7c1c15b160..34ac6dcdae5 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -1013,4 +1013,10 @@ ALTER TABLE `mutation_event` DROP COLUMN `LINK_MSA`; -- changes for issue 9779 ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_DBSNP_RS`; ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_UNIPROT_ENTRY_NAME`; +ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_REFSEQ_MRNA_ID TO MUTATION_REFSEQ_MRNA_ID; +ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_CODON_CHANGE TO MUTATION_CODON_CHANGE; +ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_UNIPROT_ACCESSION TO MUTATION_UNIPROT_ACCESSION; +ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_PROTEIN_POS_START TO MUTATION_PROTEIN_POS_START; +ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_PROTEIN_POS_END TO MUTATION_PROTEIN_POS_END; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16"; + diff --git a/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java b/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java index 8b6d57b720b..673faf0cd3a 100644 --- a/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java +++ b/maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java @@ -103,14 +103,14 @@ public class MafRecord { private String maLinkMsa; private String maLinkPdb; - // Oncotator cols - private String oncotatorDbSnpValStatus; - private String oncotatorVariantClassification; - private String oncotatorRefseqMrnaId; - private String oncotatorUniprotAccession; - private String oncotatorCodonChange; - private int oncotatorProteinPosStart; - private int oncotatorProteinPosEnd; + // Oncotator columns are renamed to maf columns + private String mafDbSnpValStatus; + private String mafVariantClassification; + private String mafRefseqMrnaId; + private String mafUniprotAccession; + private String mafCodonChange; + private int mafProteinPosStart; + private int mafProteinPosEnd; // custom filtering of passenger and driver mutations cols private String driverFilter; @@ -519,60 +519,60 @@ public void setProteinPosition(String proteinPosition) { this.proteinPosition = proteinPosition; } - public String getOncotatorVariantClassification() { - return oncotatorVariantClassification; + public String getMafVariantClassification() { + return mafVariantClassification; } - public void setOncotatorVariantClassification(String oncotatorVariantClassification) { - this.oncotatorVariantClassification = oncotatorVariantClassification; + public void setMafVariantClassification(String mafVariantClassification) { + this.mafVariantClassification = mafVariantClassification; } - public String getOncotatorDbSnpValStatus() { - return oncotatorDbSnpValStatus; + public String getMafDbSnpValStatus() { + return mafDbSnpValStatus; } - public void setOncotatorDbSnpValStatus(String oncotatorDbSnpValStatus) { - this.oncotatorDbSnpValStatus = oncotatorDbSnpValStatus; + public void setMafDbSnpValStatus(String mafDbSnpValStatus) { + this.mafDbSnpValStatus = mafDbSnpValStatus; } - public String getOncotatorRefseqMrnaId() { - return oncotatorRefseqMrnaId; + public String getMafRefseqMrnaId() { + return mafRefseqMrnaId; } - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; + public void setMafRefseqMrnaId(String mafRefseqMrnaId) { + this.mafRefseqMrnaId = mafRefseqMrnaId; } - public String getOncotatorUniprotAccession() { - return oncotatorUniprotAccession; + public String getMafUniprotAccession() { + return mafUniprotAccession; } - public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) { - this.oncotatorUniprotAccession = oncotatorUniprotAccession; + public void setMafUniprotAccession(String mafUniprotAccession) { + this.mafUniprotAccession = mafUniprotAccession; } - public String getOncotatorCodonChange() { - return oncotatorCodonChange; + public String getMafCodonChange() { + return mafCodonChange; } - public void setOncotatorCodonChange(String oncotatorCodonChange) { - this.oncotatorCodonChange = oncotatorCodonChange; + public void setMafCodonChange(String mafCodonChange) { + this.mafCodonChange = mafCodonChange; } - public int getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; + public int getMafProteinPosStart() { + return mafProteinPosStart; } - public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; + public void setMafProteinPosStart(int mafProteinPosStart) { + this.mafProteinPosStart = mafProteinPosStart; } - public int getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; + public int getMafProteinPosEnd() { + return mafProteinPosEnd; } - public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; + public void setMafProteinPosEnd(int mafProteinPosEnd) { + this.mafProteinPosEnd = mafProteinPosEnd; } public String getMaFuncImpact() { diff --git a/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java b/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java index e1a00484272..9505f6ce320 100644 --- a/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java +++ b/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java @@ -438,12 +438,12 @@ public MafRecord parseRecord(String line) { record.setMaLinkPdb(TabDelimitedFileUtil.getPartString(maLinkPdbIndex, parts)); // Oncotator columns - record.setOncotatorVariantClassification(TabDelimitedFileUtil.getPartString(oncoVariantClassificationIndex, parts)); - record.setOncotatorRefseqMrnaId(TabDelimitedFileUtil.getPartString(oncoRefseqMrnaIdIndex, parts)); - record.setOncotatorUniprotAccession(TabDelimitedFileUtil.getPartString(oncoUniprotAccessionIndex, parts)); - record.setOncotatorCodonChange(TabDelimitedFileUtil.getPartString(oncoCodonChangeIndex, parts)); - record.setOncotatorProteinPosStart(TabDelimitedFileUtil.getPartInt(oncoProteinPosStartIndex, parts)); - record.setOncotatorProteinPosEnd(TabDelimitedFileUtil.getPartInt(oncoProteinPosEndIndex, parts)); + record.setMafVariantClassification(TabDelimitedFileUtil.getPartString(oncoVariantClassificationIndex, parts)); + record.setMafRefseqMrnaId(TabDelimitedFileUtil.getPartString(oncoRefseqMrnaIdIndex, parts)); + record.setMafUniprotAccession(TabDelimitedFileUtil.getPartString(oncoUniprotAccessionIndex, parts)); + record.setMafCodonChange(TabDelimitedFileUtil.getPartString(oncoCodonChangeIndex, parts)); + record.setMafProteinPosStart(TabDelimitedFileUtil.getPartInt(oncoProteinPosStartIndex, parts)); + record.setMafProteinPosEnd(TabDelimitedFileUtil.getPartInt(oncoProteinPosEndIndex, parts)); // custom filtering of passenger and driver mutations columns record.setDriverFilter(TabDelimitedFileUtil.getPartStringAllowEmptyAndNA(driverIndex, parts)); diff --git a/model/src/main/java/org/cbioportal/model/Mutation.java b/model/src/main/java/org/cbioportal/model/Mutation.java index 1081fb5b81e..cd3e08ebdc6 100644 --- a/model/src/main/java/org/cbioportal/model/Mutation.java +++ b/model/src/main/java/org/cbioportal/model/Mutation.java @@ -25,9 +25,9 @@ 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 mutationRefseqMrnaId; + private Integer mutationProteinPosStart; + private Integer mutationProteinPosEnd; private String keyword; private AlleleSpecificCopyNumber alleleSpecificCopyNumber; @JsonRawValue @@ -165,28 +165,28 @@ public String getVariantType() { public void setVariantType(String variantType) { this.variantType = variantType; } - public String getOncotatorRefseqMrnaId() { - return oncotatorRefseqMrnaId; + public String getMutationRefseqMrnaId() { + return mutationRefseqMrnaId; } - public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) { - this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId; + public void setMutationRefseqMrnaId(String mutationRefseqMrnaId) { + this.mutationRefseqMrnaId = mutationRefseqMrnaId; } - public Integer getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; + public Integer getMutationProteinPosStart() { + return mutationProteinPosStart; } - public void setOncotatorProteinPosStart(Integer oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; + public void setMutationProteinPosStart(Integer mutationProteinPosStart) { + this.mutationProteinPosStart = mutationProteinPosStart; } - public Integer getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; + public Integer getMutationProteinPosEnd() { + return mutationProteinPosEnd; } - public void setOncotatorProteinPosEnd(Integer oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; + public void setMutationProteinPosEnd(Integer mutationProteinPosEnd) { + this.mutationProteinPosEnd = mutationProteinPosEnd; } public String getKeyword() { diff --git a/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml b/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml index c3944740e87..15186c38bf0 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 @@ -28,9 +28,9 @@ 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.MUTATION_REFSEQ_MRNA_ID AS mutationRefseqMrnaId, + mutation_event.MUTATION_PROTEIN_POS_START AS mutationProteinPosStart, + mutation_event.MUTATION_PROTEIN_POS_END AS mutationProteinPosEnd, mutation_event.KEYWORD AS keyword, mutation.ANNOTATION_JSON as annotationJSON, alteration_driver_annotation.DRIVER_FILTER as driverFilter, @@ -378,7 +378,7 @@ FROM mutation INNER JOIN mutation_event ON mutation.MUTATION_EVENT_ID = mutation_event.MUTATION_EVENT_ID WHERE mutation_event.ENTREZ_GENE_ID = #{entrezGeneId} - AND mutation_event.ONCOTATOR_PROTEIN_POS_START >= #{proteinPosStart} - AND mutation_event.ONCOTATOR_PROTEIN_POS_END #{proteinPosEnd} + AND mutation_event.MUTATION_PROTEIN_POS_START >= #{proteinPosStart} + AND mutation_event.MUTATION_PROTEIN_POS_END #{proteinPosEnd} diff --git a/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java b/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java index e1b971e6f55..2b09851bdeb 100644 --- a/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java +++ b/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java @@ -16,7 +16,6 @@ import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import java.math.BigDecimal; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -117,9 +116,9 @@ public void getMutationsInMolecularProfileBySampleListIdSummaryProjection() thro Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getOncotatorRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getMutationRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -158,9 +157,9 @@ public void getMutationsInMolecularProfileBySampleListIdAndEntrezGeneIdsSummaryP Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getOncotatorRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getMutationRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -195,9 +194,9 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getOncotatorRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getMutationRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); diff --git a/portal/src/org/mskcc/portal/model/MafRecord.java b/portal/src/org/mskcc/portal/model/MafRecord.java index ceaab613ce5..78cef29dfd6 100644 --- a/portal/src/org/mskcc/portal/model/MafRecord.java +++ b/portal/src/org/mskcc/portal/model/MafRecord.java @@ -47,10 +47,10 @@ public class MafRecord { private int normalAltCount; private int normalRefCount; - private String oncotatorProteinChange; - private String oncotatorVariantClassification; - private String oncotatorCosmicOverlapping; - private String oncotatorDbSnpRs; + private String mafProteinChange; + private String mafVariantClassification; + private String mafCosmicOverlapping; + private String mafDbSnpRs; public String getChr() { return chr; @@ -340,37 +340,37 @@ public void setNormalRefCount(int normalRefCount) { this.normalRefCount = normalRefCount; } - public String getOncotatorProteinChange() { - return oncotatorProteinChange; + public String getMafProteinChange() { + return mafProteinChange; } - public void setOncotatorProteinChange(String oncotatorProteinChange) { - this.oncotatorProteinChange = oncotatorProteinChange; + public void setMafProteinChange(String mafProteinChange) { + this.mafProteinChange = mafProteinChange; } - public String getOncotatorVariantClassification() { - return oncotatorVariantClassification; + public String getMafVariantClassification() { + return mafVariantClassification; } - public void setOncotatorVariantClassification( - String oncotatorVariantClassification) { - this.oncotatorVariantClassification = oncotatorVariantClassification; + public void setMafVariantClassification( + String mafVariantClassification) { + this.mafVariantClassification = mafVariantClassification; } - public String getOncotatorCosmicOverlapping() { - return oncotatorCosmicOverlapping; + public String getMafCosmicOverlapping() { + return mafCosmicOverlapping; } - public void setOncotatorCosmicOverlapping(String oncotatorCosmicOverlapping) { - this.oncotatorCosmicOverlapping = oncotatorCosmicOverlapping; + public void setMafCosmicOverlapping(String mafCosmicOverlapping) { + this.mafCosmicOverlapping = mafCosmicOverlapping; } - public String getOncotatorDbSnpRs() { - return oncotatorDbSnpRs; + public String getMafDbSnpRs() { + return mafDbSnpRs; } - public void setOncotatorDbSnpRs(String oncotatorDbSnpRs) { - this.oncotatorDbSnpRs = oncotatorDbSnpRs; + public void setMafDbSnpRs(String mafDbSnpRs) { + this.mafDbSnpRs = mafDbSnpRs; } diff --git a/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java b/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java index 7cee18693fe..9eb90f47e89 100644 --- a/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java +++ b/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java @@ -7,11 +7,11 @@ public class MutationMixin { @JsonProperty("variantAllele") private String tumorSeqAllele; @JsonProperty("refseqMrnaId") - private String oncotatorRefseqMrnaId; + private String mutationRefseqMrnaId; @JsonProperty("proteinPosStart") - private Integer oncotatorProteinPosStart; + private Integer mutationProteinPosStart; @JsonProperty("proteinPosEnd") - private Integer oncotatorProteinPosEnd; + private Integer mutationProteinPosEnd; @JsonProperty("chr") private String chr; @JsonProperty("namespaceColumns") diff --git a/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java b/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java index ff89f1960f8..ad7874ffb8c 100644 --- a/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java +++ b/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java @@ -19,9 +19,9 @@ public enum MutationSortBy { mutationType("mutationType"), ncbiBuild("ncbiBuild"), variantType("variantType"), - refseqMrnaId("oncotatorRefseqMrnaId"), - proteinPosStart("oncotatorProteinPosStart"), - proteinPosEnd("oncotatorProteinPosEnd"), + refseqMrnaId("mutationRefseqMrnaId"), + proteinPosStart("mutationProteinPosStart"), + proteinPosEnd("mutationProteinPosEnd"), 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 8be4eeefcf1..0ecfb3c3770 100644 --- a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java @@ -30,7 +30,6 @@ import org.springframework.test.web.servlet.setup.MockMvcBuilders; import org.springframework.web.context.WebApplicationContext; -import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; @@ -60,9 +59,9 @@ 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_MUTATION_REFSEQ_MRNA_ID_1 = "test_mutation_refseq_mrna_id_1"; + private static final int TEST_MUTATION_PROTEIN_POS_START_1 = 1; + private static final int TEST_MUTATION_PROTEIN_POS_END_1 = 1; private static final String TEST_KEYWORD_1 = "test_keyword_1"; private static final String TEST_HUGO_GENE_SYMBOL_1 = "test_hugo_gene_symbol_1"; private static final String TEST_TYPE_1 = "test_type_1"; @@ -97,9 +96,9 @@ 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_MUTATION_REFSEQ_MRNA_ID_2 = "test_MUTATION_refseq_mrna_id_2"; + private static final int TEST_MUTATION_PROTEIN_POS_START_2 = 2; + private static final int TEST_MUTATION_PROTEIN_POS_END_2 = 2; private static final String TEST_KEYWORD_2 = "test_keyword_2"; private static final String TEST_HUGO_GENE_SYMBOL_2 = "test_hugo_gene_symbol_2"; private static final String TEST_TYPE_2 = "test_type_2"; @@ -187,9 +186,9 @@ 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("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[0].namespaceColumns.columnName.fieldName").value("fieldValue")) @@ -217,9 +216,9 @@ 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("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[1].namespaceColumns.columnName.fieldName").value("fieldValue")); @@ -265,9 +264,9 @@ 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("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_1)) @@ -303,9 +302,9 @@ 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("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_2)) @@ -390,9 +389,9 @@ 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("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[1].molecularProfileId") @@ -419,9 +418,9 @@ 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("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist()); } @@ -473,9 +472,9 @@ public void fetchMutationsInMolecularProfileDefaultProjection() throws Exception .andExpect(MockMvcResultMatchers.jsonPath("$[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].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene").doesNotExist()) .andExpect(MockMvcResultMatchers.jsonPath("$[1].molecularProfileId") @@ -502,9 +501,9 @@ public void fetchMutationsInMolecularProfileDefaultProjection() throws Exception .andExpect(MockMvcResultMatchers.jsonPath("$[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].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene").doesNotExist()); } @@ -557,9 +556,9 @@ 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("$[0].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].keyword").value(TEST_KEYWORD_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_1)) @@ -596,9 +595,9 @@ 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("$[1].refseqMrnaId").value(TEST_MUTATION_REFSEQ_MRNA_ID_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].keyword").value(TEST_KEYWORD_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.entrezGeneId").value(TEST_ENTREZ_GENE_ID_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_2)) @@ -644,14 +643,14 @@ public void fetchMutationCountsByPosition() throws Exception { List mutationCountByPositionList = new ArrayList<>(); MutationCountByPosition mutationCountByPosition1 = new MutationCountByPosition(); mutationCountByPosition1.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1); - mutationCountByPosition1.setProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_1); - mutationCountByPosition1.setProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_1); + mutationCountByPosition1.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_1); + mutationCountByPosition1.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_1); mutationCountByPosition1.setCount(TEST_MUTATION_COUNT_1); mutationCountByPositionList.add(mutationCountByPosition1); MutationCountByPosition mutationCountByPosition2 = new MutationCountByPosition(); mutationCountByPosition2.setEntrezGeneId(TEST_ENTREZ_GENE_ID_2); - mutationCountByPosition2.setProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_2); - mutationCountByPosition2.setProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_2); + mutationCountByPosition2.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_2); + mutationCountByPosition2.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_2); mutationCountByPosition2.setCount(TEST_MUTATION_COUNT_2); mutationCountByPositionList.add(mutationCountByPosition2); @@ -662,13 +661,13 @@ public void fetchMutationCountsByPosition() throws Exception { List mutationPositionIdentifiers = new ArrayList<>(); MutationPositionIdentifier mutationPositionIdentifier1 = new MutationPositionIdentifier(); mutationPositionIdentifier1.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1); - mutationPositionIdentifier1.setProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_1); - mutationPositionIdentifier1.setProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_1); + mutationPositionIdentifier1.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_1); + mutationPositionIdentifier1.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_1); mutationPositionIdentifiers.add(mutationPositionIdentifier1); MutationPositionIdentifier mutationPositionIdentifier2 = new MutationPositionIdentifier(); mutationPositionIdentifier2.setEntrezGeneId(TEST_ENTREZ_GENE_ID_2); - mutationPositionIdentifier2.setProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_2); - mutationPositionIdentifier2.setProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_2); + mutationPositionIdentifier2.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_2); + mutationPositionIdentifier2.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_2); mutationPositionIdentifiers.add(mutationPositionIdentifier2); mockMvc.perform(MockMvcRequestBuilders.post("/mutation-counts-by-position/fetch") @@ -679,12 +678,12 @@ public void fetchMutationCountsByPosition() throws Exception { .andExpect(MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON)) .andExpect(MockMvcResultMatchers.jsonPath("$", Matchers.hasSize(2))) .andExpect(MockMvcResultMatchers.jsonPath("$[0].entrezGeneId").value(TEST_ENTREZ_GENE_ID_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_1)) - .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_1)) + .andExpect(MockMvcResultMatchers.jsonPath("$[0].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[0].count").value(TEST_MUTATION_COUNT_1)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].entrezGeneId").value(TEST_ENTREZ_GENE_ID_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_ONCOTATOR_PROTEIN_POS_START_2)) - .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_ONCOTATOR_PROTEIN_POS_END_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosStart").value(TEST_MUTATION_PROTEIN_POS_START_2)) + .andExpect(MockMvcResultMatchers.jsonPath("$[1].proteinPosEnd").value(TEST_MUTATION_PROTEIN_POS_END_2)) .andExpect(MockMvcResultMatchers.jsonPath("$[1].count").value(TEST_MUTATION_COUNT_2)); } @@ -715,9 +714,9 @@ 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.setMutationRefseqMrnaId(TEST_MUTATION_REFSEQ_MRNA_ID_1); + mutation1.setMutationProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_1); + mutation1.setMutationProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_1); mutation1.setKeyword(TEST_KEYWORD_1); mutation1.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation1); @@ -745,9 +744,9 @@ 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.setMutationRefseqMrnaId(TEST_MUTATION_REFSEQ_MRNA_ID_2); + mutation2.setMutationProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_2); + mutation2.setMutationProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_2); mutation2.setKeyword(TEST_KEYWORD_2); mutation2.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation2); From d1a400d48cf363a9a6cdd2da5c1bae5d7dafa6cb Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Fri, 11 Nov 2022 13:04:46 -0500 Subject: [PATCH 4/9] Update SQL statements Update testSql.sql updating testSql for the name change of columns from ONCOTATOR to MUTATION Update DaoMutation.java The data files still use the old column prefix of ONCOTATOR instead of MUTATION Update DaoMutation.java Update migration.sql Adding quotes around column names --- .../java/org/mskcc/cbio/portal/dao/DaoMutation.java | 6 +++--- db-scripts/src/main/resources/migration.sql | 10 +++++----- .../src/test/resources/testSql.sql | 12 ++++++------ 3 files changed, 14 insertions(+), 14 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 c37fabefd66..8254292e9e4 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 @@ -1377,12 +1377,12 @@ public static Collection> countSamplesWithProteinPosStarts( if (geneIdSet.size() == 0 || internalProfileIds.size() == 0) return new ArrayList>(); //empty IN() clause would be a SQL error below try { con = JdbcUtil.getDbConnection(DaoMutation.class); - String sql = "SELECT ONCOTATOR_PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID, count(DISTINCT SAMPLE_ID) " + + String sql = "SELECT MUTATION_PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID, count(DISTINCT SAMPLE_ID) " + "FROM mutation INNER JOIN mutation_event ON mutation.MUTATION_EVENT_ID=mutation_event.MUTATION_EVENT_ID " + "WHERE mutation.ENTREZ_GENE_ID IN (" + StringUtils.join(geneIdSet, ",") + ") " + "AND GENETIC_PROFILE_ID IN (" + StringUtils.join(internalProfileIds, ",") + ") " + - "AND (mutation.ENTREZ_GENE_ID, ONCOTATOR_PROTEIN_POS_START) IN (" + StringUtils.join(proteinPosStarts, ",") + ") " + - "GROUP BY ONCOTATOR_PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID"; + "AND (mutation.ENTREZ_GENE_ID, MUTATION_PROTEIN_POS_START) IN (" + StringUtils.join(proteinPosStarts, ",") + ") " + + "GROUP BY MUTATION_PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID"; pstmt = con.prepareStatement(sql); rs = pstmt.executeQuery(); Collection> data = new ArrayList>(); diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index 34ac6dcdae5..4302a17e19e 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -1013,10 +1013,10 @@ ALTER TABLE `mutation_event` DROP COLUMN `LINK_MSA`; -- changes for issue 9779 ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_DBSNP_RS`; ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_UNIPROT_ENTRY_NAME`; -ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_REFSEQ_MRNA_ID TO MUTATION_REFSEQ_MRNA_ID; -ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_CODON_CHANGE TO MUTATION_CODON_CHANGE; -ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_UNIPROT_ACCESSION TO MUTATION_UNIPROT_ACCESSION; -ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_PROTEIN_POS_START TO MUTATION_PROTEIN_POS_START; -ALTER TABLE `mutation_event` CHANGE COLUMN ONCOTATOR_PROTEIN_POS_END TO MUTATION_PROTEIN_POS_END; +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_REFSEQ_MRNA_ID` TO `MUTATION_REFSEQ_MRNA_ID`; +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_CODON_CHANGE` TO `MUTATION_CODON_CHANGE`; +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_UNIPROT_ACCESSION` TO `MUTATION_UNIPROT_ACCESSION`; +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_START` TO `MUTATION_PROTEIN_POS_START`; +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_END` TO `MUTATION_PROTEIN_POS_END`; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16"; diff --git a/persistence/persistence-mybatis/src/test/resources/testSql.sql b/persistence/persistence-mybatis/src/test/resources/testSql.sql index 26e96e09918..31c35fa5c4d 100644 --- a/persistence/persistence-mybatis/src/test/resources/testSql.sql +++ b/persistence/persistence-mybatis/src/test/resources/testSql.sql @@ -124,12 +124,12 @@ INSERT INTO sample (INTERNAL_ID,STABLE_ID,SAMPLE_TYPE,PATIENT_ID) VALUES (18,'TC INSERT INTO sample (INTERNAL_ID,STABLE_ID,SAMPLE_TYPE,PATIENT_ID) VALUES (19,'TCGA-A1-A0SB-01','Primary Solid Tumor',18); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,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','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,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','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,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','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2040,207,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','NA',0,'getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all','NA','NA','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2041,207,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,FUNCTIONAL_IMPACT_SCORE,FIS_VALUE,LINK_XVAR,LINK_PDB,LINK_MSA,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,ONCOTATOR_REFSEQ_MRNA_ID,ONCOTATOR_CODON_CHANGE,ONCOTATOR_UNIPROT_ACCESSION,ONCOTATOR_PROTEIN_POS_START,ONCOTATOR_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2042,208,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2040,207,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2041,207,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2042,208,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (2038,6,6, 'Putative_Driver', 'Pathogenic', 'Tier 1', 'Highly Actionable'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (22604,6,6, 'Putative_Passenger', 'Pathogenic', 'Tier 2', 'Potentially Actionable'); From 871eccd6fef87fbb3ee3796c399f28478509ab01 Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Thu, 27 Oct 2022 11:16:17 -0400 Subject: [PATCH 5/9] db changes and renaming the column prefixes from oncotator to mutation db changes in sql for renaming columns renamed the column prefixes from oncotator to mutation on multiple classes and files From 98c892fb67a1d48d15e59b25f7792c7998e3b2eb Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Fri, 11 Nov 2022 21:24:44 -0500 Subject: [PATCH 6/9] Update migration.sql Update migration.sql fix syntax errors in mysql change column Update migration.sql fix syntax errors in mysql change column setting db version setting db version --- db-scripts/src/main/resources/migration.sql | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index 4302a17e19e..3345a6b97e7 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -1013,10 +1013,10 @@ ALTER TABLE `mutation_event` DROP COLUMN `LINK_MSA`; -- changes for issue 9779 ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_DBSNP_RS`; ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_UNIPROT_ENTRY_NAME`; -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_REFSEQ_MRNA_ID` TO `MUTATION_REFSEQ_MRNA_ID`; -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_CODON_CHANGE` TO `MUTATION_CODON_CHANGE`; -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_UNIPROT_ACCESSION` TO `MUTATION_UNIPROT_ACCESSION`; -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_START` TO `MUTATION_PROTEIN_POS_START`; -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_END` TO `MUTATION_PROTEIN_POS_END`; +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_REFSEQ_MRNA_ID` `MUTATION_REFSEQ_MRNA_ID` varchar(64); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_CODON_CHANGE` `MUTATION_CODON_CHANGE` varchar(255); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_UNIPROT_ACCESSION` `MUTATION_UNIPROT_ACCESSION` varchar(64); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_START` `MUTATION_PROTEIN_POS_START` int(11); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_END` `MUTATION_PROTEIN_POS_END` int(11); UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16"; From dec3627cfc6e1237a9eb7faa8a734830bb467140 Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Fri, 2 Dec 2022 13:35:27 -0500 Subject: [PATCH 7/9] Removed Link columns Removed Link columns and modified the documentation --- docs/Imported-MAF-Columns.md | 5 ----- .../main/java/org/mskcc/cbio/maf/MafUtil.java | 19 +------------------ 2 files changed, 1 insertion(+), 23 deletions(-) diff --git a/docs/Imported-MAF-Columns.md b/docs/Imported-MAF-Columns.md index 43ff6bb47d6..da449abf013 100644 --- a/docs/Imported-MAF-Columns.md +++ b/docs/Imported-MAF-Columns.md @@ -69,11 +69,6 @@ Relevant classes: | ONCOTATOR_CODON_CHANGE | ONCOTATOR_CODON_CHANGE | | mutation_event.oncotator_codon_change ** [maps to DB but MAF value never imported] | see ImportExtendedMutation (codonChange = record.getCodons()) / MAF field "Codons" always overrides MAF value ONCOTATOR_CODON_CHANGE // "ONCOTATOR_CODON_CHANGE" never used? / MafRecord (record.getOncotatorCodonChange()) never used | | ONCOTATOR_PROTEIN_POS_START | ONCOTATOR_PROTEIN_POS_START | | mutation_event.oncotator_protein_pos_start ** [maps to DB but MAF value never imported] | see ExtendedMutationUtil.getProteinPosStart() / resolved from record.getProteinPosition() or record.getProteinChange() based on what is avialable / MAF field "ONCOTATOR_PROTEIN_POS_START" never used? | | ONCOTATOR_PROTEIN_POS_END | ONCOTATOR_PROTEIN_POS_END | | mutation_event.oncotator_protein_pos_end ** [maps to DB but MAF value never imported] | see ExtendedMutationUtil.getProteinPosStart() / resolved from record.getProteinPosition() or record.getProteinChange() based on what is avialable / MAF field "ONCOTATOR_PROTEIN_POS_END" never used? | -| MA_FIMPACT | MA:FImpact | | mutation_event.functional_impact_score | | -| MA_FIS | MA:FIS | | mutation_event.fis_value | | -| MA_LINK_VAR | MA:link.var | | mutation_event.link_xvar | | -| MA_LINK_MSA | MA:link.MSA | | mutation_event.link_msa | | -| MA_LINK_PDB | MA:link.PDB | | mutation_event.link_pdb | | | DRIVER_FILTER | cbp_driver | mutation.driver_filter | | | | DRIVER_FILTER_ANNOTATION | cbp_driver_annotation | mutation.driver_filter_annotation | | | | DRIVER_TIERS_FILTER | cbp_driver_tiers | mutation.driver_tiers_filter | | | diff --git a/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java b/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java index 9505f6ce320..003f7fa44ab 100644 --- a/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java +++ b/maf/src/main/java/org/mskcc/cbio/maf/MafUtil.java @@ -116,14 +116,7 @@ public class MafUtil { public static final String ONCOTATOR_CODON_CHANGE = "ONCOTATOR_CODON_CHANGE"; public static final String ONCOTATOR_PROTEIN_POS_START = "ONCOTATOR_PROTEIN_POS_START"; public static final String ONCOTATOR_PROTEIN_POS_END = "ONCOTATOR_PROTEIN_POS_END"; - - // mutation assessor column names - public static final String MA_FIMPACT = "MA:FImpact"; - public static final String MA_FIS = "MA:FIS"; - public static final String MA_LINK_VAR = "MA:link.var"; - public static final String MA_LINK_MSA = "MA:link.MSA"; - public static final String MA_LINK_PDB = "MA:link.PDB"; - + // custom filtering of passenger and driver mutations column names public static final String DRIVER_FILTER = "cbp_driver"; public static final String DRIVER_FILTER_ANNOTATION = "cbp_driver_annotation"; @@ -312,16 +305,6 @@ public MafUtil(String headerLine, Set namespaces) { oncoProteinPosStartIndex = i; } else if(header.equalsIgnoreCase(ONCOTATOR_PROTEIN_POS_END)) { oncoProteinPosEndIndex = i; - } else if(header.equalsIgnoreCase(MA_FIMPACT)) { - maFImpactIndex = i; - } else if(header.equalsIgnoreCase(MA_FIS)) { - maFisIndex = i; - } else if(header.equalsIgnoreCase(MA_LINK_VAR)) { - maLinkVarIndex = i; - } else if(header.equalsIgnoreCase(MA_LINK_MSA)) { - maLinkMsaIndex = i; - } else if(header.equalsIgnoreCase(MA_LINK_PDB)) { - maLinkPdbIndex = i; } else if(header.equalsIgnoreCase(T_REF_COUNT) || header.equalsIgnoreCase(I_T_REF_COUNT) || header.equalsIgnoreCase(AD_REF)) { From 89bde61b4c71cd8bda2c49018f062f5b60829363 Mon Sep 17 00:00:00 2001 From: Gaofei <15748980+dippindots@users.noreply.github.com> Date: Wed, 8 Mar 2023 00:16:04 -0500 Subject: [PATCH 8/9] Update DB version and renaming mutation_event fields --- .../org/mskcc/cbio/portal/dao/DaoMutation.java | 16 ++++++++-------- core/src/test/resources/seed_mini.sql | 6 +++--- db-scripts/src/main/resources/cgds.sql | 12 ++++++------ db-scripts/src/main/resources/migration.sql | 13 +++++++------ .../persistence/mybatis/MutationMapper.xml | 10 +++++----- .../src/test/resources/testSql.sql | 12 ++++++------ pom.xml | 2 +- 7 files changed, 36 insertions(+), 35 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 8254292e9e4..bb0c1e7eea9 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 @@ -799,11 +799,11 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet rs) event.setDbSnpRs(rs.getString("DB_SNP_RS")); event.setDbSnpValStatus(rs.getString("DB_SNP_VAL_STATUS")); event.setReferenceAllele(rs.getString("REFERENCE_ALLELE")); - event.setMutationRefseqMrnaId(rs.getString("MUTATION_REFSEQ_MRNA_ID")); - event.setMutationCodonChange(rs.getString("MUTATION_CODON_CHANGE")); - event.setMutationUniprotAccession(rs.getString("MUTATION_UNIPROT_ACCESSION")); - event.setMutationProteinPosStart(rs.getInt("MUTATION_PROTEIN_POS_START")); - event.setMutationProteinPosEnd(rs.getInt("MUTATION_PROTEIN_POS_END")); + event.setMutationRefseqMrnaId(rs.getString("REFSEQ_MRNA_ID")); + event.setMutationCodonChange(rs.getString("CODON_CHANGE")); + event.setMutationUniprotAccession(rs.getString("UNIPROT_ACCESSION")); + event.setMutationProteinPosStart(rs.getInt("PROTEIN_POS_START")); + event.setMutationProteinPosEnd(rs.getInt("PROTEIN_POS_END")); event.setCanonicalTranscript(rs.getBoolean("CANONICAL_TRANSCRIPT")); event.setTumorSeqAllele(rs.getString("TUMOR_SEQ_ALLELE")); event.setKeyword(rs.getString("KEYWORD")); @@ -1377,12 +1377,12 @@ public static Collection> countSamplesWithProteinPosStarts( if (geneIdSet.size() == 0 || internalProfileIds.size() == 0) return new ArrayList>(); //empty IN() clause would be a SQL error below try { con = JdbcUtil.getDbConnection(DaoMutation.class); - String sql = "SELECT MUTATION_PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID, count(DISTINCT SAMPLE_ID) " + + String sql = "SELECT PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID, count(DISTINCT SAMPLE_ID) " + "FROM mutation INNER JOIN mutation_event ON mutation.MUTATION_EVENT_ID=mutation_event.MUTATION_EVENT_ID " + "WHERE mutation.ENTREZ_GENE_ID IN (" + StringUtils.join(geneIdSet, ",") + ") " + "AND GENETIC_PROFILE_ID IN (" + StringUtils.join(internalProfileIds, ",") + ") " + - "AND (mutation.ENTREZ_GENE_ID, MUTATION_PROTEIN_POS_START) IN (" + StringUtils.join(proteinPosStarts, ",") + ") " + - "GROUP BY MUTATION_PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID"; + "AND (mutation.ENTREZ_GENE_ID, PROTEIN_POS_START) IN (" + StringUtils.join(proteinPosStarts, ",") + ") " + + "GROUP BY PROTEIN_POS_START, GENETIC_PROFILE_ID, mutation.ENTREZ_GENE_ID"; pstmt = con.prepareStatement(sql); rs = pstmt.executeQuery(); Collection> data = new ArrayList>(); diff --git a/core/src/test/resources/seed_mini.sql b/core/src/test/resources/seed_mini.sql index dddf5a75a37..e17819cfb51 100644 --- a/core/src/test/resources/seed_mini.sql +++ b/core/src/test/resources/seed_mini.sql @@ -419,9 +419,9 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (21,'TCGA-A1-A0SB-11','Solid Tissues Normal',20); -- mutation_event -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","MUTATION_REFSEQ_MRNA_ID","MUTATION_CODON_CHANGE","MUTATION_UNIPROT_ACCESSION","MUTATION_PROTEIN_POS_START","MUTATION_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","MUTATION_REFSEQ_MRNA_ID","MUTATION_CODON_CHANGE","MUTATION_UNIPROT_ACCESSION","MUTATION_PROTEIN_POS_START","MUTATION_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","MUTATION_REFSEQ_MRNA_ID","MUTATION_CODON_CHANGE","MUTATION_UNIPROT_ACCESSION","MUTATION_PROTEIN_POS_START","MUTATION_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","REFSEQ_MRNA_ID","CODON_CHANGE","UNIPROT_ACCESSION","PROTEIN_POS_START","PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","REFSEQ_MRNA_ID","CODON_CHANGE","UNIPROT_ACCESSION","PROTEIN_POS_START","PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","REFSEQ_MRNA_ID","CODON_CHANGE","UNIPROT_ACCESSION","PROTEIN_POS_START","PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); -- mutation INSERT INTO "mutation" ("MUTATION_EVENT_ID","GENETIC_PROFILE_ID","SAMPLE_ID","ENTREZ_GENE_ID","CENTER","SEQUENCER","MUTATION_STATUS","VALIDATION_STATUS","TUMOR_SEQ_ALLELE1","TUMOR_SEQ_ALLELE2","MATCHED_NORM_SAMPLE_BARCODE","MATCH_NORM_SEQ_ALLELE1","MATCH_NORM_SEQ_ALLELE2","TUMOR_VALIDATION_ALLELE1","TUMOR_VALIDATION_ALLELE2","MATCH_NORM_VALIDATION_ALLELE1","MATCH_NORM_VALIDATION_ALLELE2","VERIFICATION_STATUS","SEQUENCING_PHASE","SEQUENCE_SOURCE","VALIDATION_METHOD","SCORE","BAM_FILE","TUMOR_ALT_COUNT","TUMOR_REF_COUNT","NORMAL_ALT_COUNT","NORMAL_REF_COUNT") VALUES (2038,6,6,672,'genome.wustl.edu','IlluminaGAIIx','Germline','Unknown','G','A','TCGA-A1-A0SH-10A-03D-A099-09','G','A','NA','NA','NA','NA','Unknown','Phase_IV','Capture','NA','1','dbGAP',-1,-1,-1,-1); diff --git a/db-scripts/src/main/resources/cgds.sql b/db-scripts/src/main/resources/cgds.sql index c695c632d22..c0b20e8b6cd 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -441,11 +441,11 @@ CREATE TABLE `mutation_event` ( `VARIANT_TYPE` varchar(15), `DB_SNP_RS` varchar(25), `DB_SNP_VAL_STATUS` varchar(255), - `MUTATION_REFSEQ_MRNA_ID` varchar(64), - `MUTATION_CODON_CHANGE` varchar(255), - `MUTATION_UNIPROT_ACCESSION` varchar(64), - `MUTATION_PROTEIN_POS_START` int(11), - `MUTATION_PROTEIN_POS_END` int(11), + `REFSEQ_MRNA_ID` varchar(64), + `CODON_CHANGE` varchar(255), + `UNIPROT_ACCESSION` varchar(64), + `PROTEIN_POS_START` int(11), + `PROTEIN_POS_END` int(11), `CANONICAL_TRANSCRIPT` boolean, `KEYWORD` varchar(255) DEFAULT NULL COMMENT 'e.g. truncating, V200 Missense, E338del, ', KEY (`KEYWORD`), @@ -755,5 +755,5 @@ CREATE TABLE `resource_study` ( ); -- THIS MUST BE KEPT IN SYNC WITH db.version PROPERTY IN pom.xml -INSERT INTO info VALUES ('2.12.16', NULL); +INSERT INTO info VALUES ('2.13.0', NULL); diff --git a/db-scripts/src/main/resources/migration.sql b/db-scripts/src/main/resources/migration.sql index 3345a6b97e7..dfec6a97381 100644 --- a/db-scripts/src/main/resources/migration.sql +++ b/db-scripts/src/main/resources/migration.sql @@ -1003,6 +1003,7 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.15"; ALTER TABLE `structural_variant` ADD COLUMN `ANNOTATION_JSON` JSON AFTER `SV_STATUS`; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16"; +##version: 2.13.0 -- changes for issue 9461 ALTER TABLE `mutation_event` DROP COLUMN `FUNCTIONAL_IMPACT_SCORE`; ALTER TABLE `mutation_event` DROP COLUMN `FIS_VALUE`; @@ -1013,10 +1014,10 @@ ALTER TABLE `mutation_event` DROP COLUMN `LINK_MSA`; -- changes for issue 9779 ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_DBSNP_RS`; ALTER TABLE `mutation_event` DROP COLUMN `ONCOTATOR_UNIPROT_ENTRY_NAME`; -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_REFSEQ_MRNA_ID` `MUTATION_REFSEQ_MRNA_ID` varchar(64); -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_CODON_CHANGE` `MUTATION_CODON_CHANGE` varchar(255); -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_UNIPROT_ACCESSION` `MUTATION_UNIPROT_ACCESSION` varchar(64); -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_START` `MUTATION_PROTEIN_POS_START` int(11); -ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_END` `MUTATION_PROTEIN_POS_END` int(11); -UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16"; +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_REFSEQ_MRNA_ID` `REFSEQ_MRNA_ID` varchar(64); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_CODON_CHANGE` `CODON_CHANGE` varchar(255); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_UNIPROT_ACCESSION` `UNIPROT_ACCESSION` varchar(64); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_START` `PROTEIN_POS_START` int(11); +ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_END` `PROTEIN_POS_END` int(11); +UPDATE `info` SET `DB_SCHEMA_VERSION`="2.13.0"; diff --git a/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 15186c38bf0..54708c6631d 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 @@ -28,9 +28,9 @@ mutation_event.MUTATION_TYPE AS mutationType, mutation_event.NCBI_BUILD AS ncbiBuild, mutation_event.VARIANT_TYPE AS variantType, - mutation_event.MUTATION_REFSEQ_MRNA_ID AS mutationRefseqMrnaId, - mutation_event.MUTATION_PROTEIN_POS_START AS mutationProteinPosStart, - mutation_event.MUTATION_PROTEIN_POS_END AS mutationProteinPosEnd, + mutation_event.REFSEQ_MRNA_ID AS mutationRefseqMrnaId, + mutation_event.PROTEIN_POS_START AS mutationProteinPosStart, + mutation_event.PROTEIN_POS_END AS mutationProteinPosEnd, mutation_event.KEYWORD AS keyword, mutation.ANNOTATION_JSON as annotationJSON, alteration_driver_annotation.DRIVER_FILTER as driverFilter, @@ -378,7 +378,7 @@ FROM mutation INNER JOIN mutation_event ON mutation.MUTATION_EVENT_ID = mutation_event.MUTATION_EVENT_ID WHERE mutation_event.ENTREZ_GENE_ID = #{entrezGeneId} - AND mutation_event.MUTATION_PROTEIN_POS_START >= #{proteinPosStart} - AND mutation_event.MUTATION_PROTEIN_POS_END #{proteinPosEnd} + AND mutation_event.PROTEIN_POS_START >= #{proteinPosStart} + AND mutation_event.PROTEIN_POS_END #{proteinPosEnd} diff --git a/persistence/persistence-mybatis/src/test/resources/testSql.sql b/persistence/persistence-mybatis/src/test/resources/testSql.sql index 31c35fa5c4d..03d82e3c833 100644 --- a/persistence/persistence-mybatis/src/test/resources/testSql.sql +++ b/persistence/persistence-mybatis/src/test/resources/testSql.sql @@ -124,12 +124,12 @@ INSERT INTO sample (INTERNAL_ID,STABLE_ID,SAMPLE_TYPE,PATIENT_ID) VALUES (18,'TC INSERT INTO sample (INTERNAL_ID,STABLE_ID,SAMPLE_TYPE,PATIENT_ID) VALUES (19,'TCGA-A1-A0SB-01','Primary Solid Tumor',18); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2040,207,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2041,207,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); -INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,MUTATION_REFSEQ_MRNA_ID,MUTATION_CODON_CHANGE,MUTATION_UNIPROT_ACCESSION,MUTATION_PROTEIN_POS_START,MUTATION_PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2042,208,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2040,207,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','NM_007294','c.(2800-2802)CAG>TAG','P38398',934,934,1,'BRCA1 truncating'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2041,207,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','NM_007294','c.(181-183)TGT>GGT','P38398',61,61,1,'BRCA1 C61 missense'); +INSERT INTO mutation_event (MUTATION_EVENT_ID,ENTREZ_GENE_ID,CHR,START_POSITION,END_POSITION,REFERENCE_ALLELE,TUMOR_SEQ_ALLELE,PROTEIN_CHANGE,MUTATION_TYPE,NCBI_BUILD,STRAND,VARIANT_TYPE,DB_SNP_RS,DB_SNP_VAL_STATUS,REFSEQ_MRNA_ID,CODON_CHANGE,UNIPROT_ACCESSION,PROTEIN_POS_START,PROTEIN_POS_END,CANONICAL_TRANSCRIPT,KEYWORD) VALUES (2042,208,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','NM_007294','c.e2+1','NA',-1,-1,1,'BRCA1 truncating'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (2038,6,6, 'Putative_Driver', 'Pathogenic', 'Tier 1', 'Highly Actionable'); INSERT INTO alteration_driver_annotation (ALTERATION_EVENT_ID,GENETIC_PROFILE_ID,SAMPLE_ID, DRIVER_FILTER, DRIVER_FILTER_ANNOTATION, DRIVER_TIERS_FILTER, DRIVER_TIERS_FILTER_ANNOTATION) VALUES (22604,6,6, 'Putative_Passenger', 'Pathogenic', 'Tier 2', 'Potentially Actionable'); diff --git a/pom.xml b/pom.xml index 349bdb237df..5453d89f434 100644 --- a/pom.xml +++ b/pom.xml @@ -315,7 +315,7 @@ 720 - 2.12.16 + 2.13.0 From 9ca056342e29ab99f4d968dcfa9dea77ba934029 Mon Sep 17 00:00:00 2001 From: Gaofei <15748980+dippindots@users.noreply.github.com> Date: Wed, 8 Mar 2023 01:11:11 -0500 Subject: [PATCH 9/9] Update Mutation model --- .../mskcc/cbio/portal/dao/DaoCosmicData.java | 2 +- .../mskcc/cbio/portal/dao/DaoMutation.java | 20 ++--- .../cbio/portal/model/ExtendedMutation.java | 90 +++++++++---------- .../scripts/ImportExtendedMutationData.java | 10 +-- .../portal/util/ExtendedMutationUtil.java | 10 +-- .../cbio/portal/dao/TestDaoMutation.java | 20 ++--- .../java/org/cbioportal/model/Mutation.java | 30 +++---- .../persistence/mybatis/MutationMapper.xml | 6 +- .../MutationMyBatisRepositoryTest.java | 18 ++-- .../cbioportal/web/mixin/MutationMixin.java | 6 +- .../web/parameter/sort/MutationSortBy.java | 6 +- .../web/MutationControllerTest.java | 12 +-- 12 files changed, 115 insertions(+), 115 deletions(-) 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 c084b2bcc9e..24a8209e64b 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java @@ -115,7 +115,7 @@ private static Set filterTruncatingCosmicByPosition( Set ret = new HashSet(); Pattern p = Pattern.compile("[0-9]+"); - int mutPos = mut.getMutationProteinPosStart(); + int mutPos = mut.getProteinPosStart(); for (CosmicMutationFrequency cmf : cmfs) { String aa = cmf.getAminoAcidChange(); Matcher m = p.matcher(aa); diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java index bb0c1e7eea9..8adbdaddb3f 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java +++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java @@ -150,11 +150,11 @@ public static int addMutationEvent(ExtendedMutation.MutationEvent event) throws event.getVariantType(), event.getDbSnpRs(), event.getDbSnpValStatus(), - event.getMutationRefseqMrnaId(), - event.getMutationCodonChange(), - event.getMutationUniprotAccession(), - Integer.toString(event.getMutationProteinPosStart()), - Integer.toString(event.getMutationProteinPosEnd()), + event.getRefseqMrnaId(), + event.getCodonChange(), + event.getUniprotAccession(), + Integer.toString(event.getProteinPosStart()), + Integer.toString(event.getProteinPosEnd()), boolToStr(event.isCanonicalTranscript()), keyword==null ? "\\N":(event.getGene().getHugoGeneSymbolAllCaps()+" "+keyword)); return 1; @@ -799,11 +799,11 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet rs) event.setDbSnpRs(rs.getString("DB_SNP_RS")); event.setDbSnpValStatus(rs.getString("DB_SNP_VAL_STATUS")); event.setReferenceAllele(rs.getString("REFERENCE_ALLELE")); - event.setMutationRefseqMrnaId(rs.getString("REFSEQ_MRNA_ID")); - event.setMutationCodonChange(rs.getString("CODON_CHANGE")); - event.setMutationUniprotAccession(rs.getString("UNIPROT_ACCESSION")); - event.setMutationProteinPosStart(rs.getInt("PROTEIN_POS_START")); - event.setMutationProteinPosEnd(rs.getInt("PROTEIN_POS_END")); + event.setRefseqMrnaId(rs.getString("REFSEQ_MRNA_ID")); + event.setCodonChange(rs.getString("CODON_CHANGE")); + event.setUniprotAccession(rs.getString("UNIPROT_ACCESSION")); + event.setProteinPosStart(rs.getInt("PROTEIN_POS_START")); + event.setProteinPosEnd(rs.getInt("PROTEIN_POS_END")); event.setCanonicalTranscript(rs.getBoolean("CANONICAL_TRANSCRIPT")); event.setTumorSeqAllele(rs.getString("TUMOR_SEQ_ALLELE")); event.setKeyword(rs.getString("KEYWORD")); 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 b969d3874fa..21c276f225f 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java +++ b/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java @@ -61,11 +61,11 @@ public final static class MutationEvent { private String tumorSeqAllele; private String dbSnpRs; private String dbSnpValStatus; - private String mutationRefseqMrnaId; - private String mutationUniprotAccession; - private String mutationCodonChange; - private int mutationProteinPosStart; - private int mutationProteinPosEnd; + private String refseqMrnaId; + private String uniprotAccession; + private String codonChange; + private int proteinPosStart; + private int proteinPosEnd; private boolean canonicalTranscript; public long getMutationEventId() { @@ -190,44 +190,44 @@ public void setDbSnpValStatus(String dbSnpValStatus) { this.dbSnpValStatus = dbSnpValStatus; } - public String getMutationRefseqMrnaId() { - return mutationRefseqMrnaId; + public String getRefseqMrnaId() { + return refseqMrnaId; } - public void setMutationRefseqMrnaId(String mutationRefseqMrnaId) { - this.mutationRefseqMrnaId = mutationRefseqMrnaId; + public void setRefseqMrnaId(String refseqMrnaId) { + this.refseqMrnaId = refseqMrnaId; } - public String getMutationUniprotAccession() { - return mutationUniprotAccession; + public String getUniprotAccession() { + return uniprotAccession; } - public void setMutationUniprotAccession(String mutationUniprotAccession) { - this.mutationUniprotAccession = mutationUniprotAccession; + public void setUniprotAccession(String uniprotAccession) { + this.uniprotAccession = uniprotAccession; } - public String getMutationCodonChange() { - return mutationCodonChange; + public String getCodonChange() { + return codonChange; } - public void setMutationCodonChange(String mutationCodonChange) { - this.mutationCodonChange = mutationCodonChange; + public void setCodonChange(String codonChange) { + this.codonChange = codonChange; } - public int getMutationProteinPosStart() { - return mutationProteinPosStart; + public int getProteinPosStart() { + return proteinPosStart; } - public void setMutationProteinPosStart(int mutationProteinPosStart) { - this.mutationProteinPosStart = mutationProteinPosStart; + public void setProteinPosStart(int proteinPosStart) { + this.proteinPosStart = proteinPosStart; } - public int getMutationProteinPosEnd() { - return mutationProteinPosEnd; + public int getProteinPosEnd() { + return proteinPosEnd; } - public void setMutationProteinPosEnd(int mutationProteinPosEnd) { - this.mutationProteinPosEnd = mutationProteinPosEnd; + public void setProteinPosEnd(int proteinPosEnd) { + this.proteinPosEnd = proteinPosEnd; } public boolean isCanonicalTranscript() { @@ -710,54 +710,54 @@ public void setNormalRefCount(Integer normalRefCount) { this.normalRefCount = normalRefCount; } - public String getMutationRefseqMrnaId() + public String getRefseqMrnaId() { - return event.getMutationRefseqMrnaId(); + return event.getRefseqMrnaId(); } - public void setMutationRefseqMrnaId(String mutationRefseqMrnaId) + public void setRefseqMrnaId(String refseqMrnaId) { - event.setMutationRefseqMrnaId(mutationRefseqMrnaId); + event.setRefseqMrnaId(refseqMrnaId); } - public String getMutationUniprotAccession() + public String getUniprotAccession() { - return event.getMutationUniprotAccession(); + return event.getUniprotAccession(); } - public void setMutationUniprotAccession(String mutationUniprotAccession) + public void setUniprotAccession(String uniprotAccession) { - event.setMutationUniprotAccession(mutationUniprotAccession); + event.setUniprotAccession(uniprotAccession); } - public String getMutationCodonChange() + public String getCodonChange() { - return event.getMutationCodonChange(); + return event.getCodonChange(); } - public void setMutationCodonChange(String mutationCodonChange) + public void setCodonChange(String codonChange) { - event.setMutationCodonChange(mutationCodonChange); + event.setCodonChange(codonChange); } - public int getMutationProteinPosStart() + public int getProteinPosStart() { - return event.getMutationProteinPosStart(); + return event.getProteinPosStart(); } - public void setMutationProteinPosStart(int mutationProteinPosStart) + public void setProteinPosStart(int proteinPosStart) { - event.setMutationProteinPosStart(mutationProteinPosStart); + event.setProteinPosStart(proteinPosStart); } - public int getMutationProteinPosEnd() + public int getProteinPosEnd() { - return event.getMutationProteinPosEnd(); + return event.getProteinPosEnd(); } - public void setMutationProteinPosEnd(int mutationProteinPosEnd) + public void setProteinPosEnd(int proteinPosEnd) { - event.setMutationProteinPosEnd(mutationProteinPosEnd); + event.setProteinPosEnd(proteinPosEnd); } public boolean isCanonicalTranscript() diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java index 3b27a91aedf..dd230f16af7 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java @@ -368,11 +368,11 @@ public void importData() throws IOException, DaoException { mutation.setNormalRefCount(ExtendedMutationUtil.getNormalRefCount(record)); // renamed the oncotator column names to mutation - mutation.setMutationCodonChange(codonChange); - mutation.setMutationRefseqMrnaId(refseqMrnaId); - mutation.setMutationUniprotAccession(uniprotAccession); - mutation.setMutationProteinPosStart(proteinPosStart); - mutation.setMutationProteinPosEnd(proteinPosEnd); + mutation.setCodonChange(codonChange); + mutation.setRefseqMrnaId(refseqMrnaId); + mutation.setUniprotAccession(uniprotAccession); + mutation.setProteinPosStart(proteinPosStart); + mutation.setProteinPosEnd(proteinPosEnd); mutation.setDriverFilter(record.getDriverFilter()); mutation.setDriverFilterAnn(record.getDriverFilterAnn()); diff --git a/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java b/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java index 58ffeaa73b7..f4f61b59844 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java +++ b/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java @@ -321,11 +321,11 @@ public static ExtendedMutation newMutation() { mutation.setTumorRefCount(defaultInt); mutation.setNormalAltCount(defaultInt); mutation.setNormalRefCount(defaultInt); - mutation.setMutationCodonChange(defaultStr); - mutation.setMutationRefseqMrnaId(defaultStr); - mutation.setMutationUniprotAccession(defaultStr); - mutation.setMutationProteinPosStart(defaultInt); - mutation.setMutationProteinPosEnd(defaultInt); + mutation.setCodonChange(defaultStr); + mutation.setRefseqMrnaId(defaultStr); + mutation.setUniprotAccession(defaultStr); + mutation.setProteinPosStart(defaultInt); + mutation.setProteinPosEnd(defaultInt); mutation.setCanonicalTranscript(true); return mutation; diff --git a/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java b/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java index 002e70145a7..d55b2085cd1 100644 --- a/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java +++ b/core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java @@ -127,11 +127,11 @@ private void runTheTest() throws DaoException{ mutation.setTumorRefCount(16); mutation.setNormalAltCount(8); mutation.setNormalRefCount(18); - mutation.setMutationCodonChange("c.(133-135)TCT>TTT"); - mutation.setMutationRefseqMrnaId("NM_001904"); - mutation.setMutationUniprotAccession("P35222"); - mutation.setMutationProteinPosStart(666); - mutation.setMutationProteinPosEnd(678); + mutation.setCodonChange("c.(133-135)TCT>TTT"); + mutation.setRefseqMrnaId("NM_001904"); + mutation.setUniprotAccession("P35222"); + mutation.setProteinPosStart(666); + mutation.setProteinPosEnd(678); mutation.setCanonicalTranscript(true); mutation.setAnnotationJson(makeMockAnnotationJsonString()); @@ -192,11 +192,11 @@ private void validateMutation(ExtendedMutation mutation) { assertEquals(Integer.valueOf(16), mutation.getTumorRefCount()); assertEquals(Integer.valueOf(8), mutation.getNormalAltCount()); assertEquals(Integer.valueOf(18), mutation.getNormalRefCount()); - assertEquals("c.(133-135)TCT>TTT", mutation.getMutationCodonChange()); - assertEquals("NM_001904", mutation.getMutationRefseqMrnaId()); - assertEquals("P35222", mutation.getMutationUniprotAccession()); - assertEquals(666, mutation.getMutationProteinPosStart()); - assertEquals(678, mutation.getMutationProteinPosEnd()); + assertEquals("c.(133-135)TCT>TTT", mutation.getCodonChange()); + assertEquals("NM_001904", mutation.getRefseqMrnaId()); + assertEquals("P35222", mutation.getUniprotAccession()); + assertEquals(666, mutation.getProteinPosStart()); + assertEquals(678, mutation.getProteinPosEnd()); assertEquals(true, mutation.isCanonicalTranscript()); validateMockAnnotationJson(mutation); diff --git a/model/src/main/java/org/cbioportal/model/Mutation.java b/model/src/main/java/org/cbioportal/model/Mutation.java index cd3e08ebdc6..62fc787e288 100644 --- a/model/src/main/java/org/cbioportal/model/Mutation.java +++ b/model/src/main/java/org/cbioportal/model/Mutation.java @@ -25,9 +25,9 @@ public class Mutation extends Alteration implements Serializable { private String mutationType; private String ncbiBuild; private String variantType; - private String mutationRefseqMrnaId; - private Integer mutationProteinPosStart; - private Integer mutationProteinPosEnd; + private String refseqMrnaId; + private Integer proteinPosStart; + private Integer proteinPosEnd; private String keyword; private AlleleSpecificCopyNumber alleleSpecificCopyNumber; @JsonRawValue @@ -165,28 +165,28 @@ public String getVariantType() { public void setVariantType(String variantType) { this.variantType = variantType; } - public String getMutationRefseqMrnaId() { - return mutationRefseqMrnaId; + public String getRefseqMrnaId() { + return refseqMrnaId; } - public void setMutationRefseqMrnaId(String mutationRefseqMrnaId) { - this.mutationRefseqMrnaId = mutationRefseqMrnaId; + public void setRefseqMrnaId(String refseqMrnaId) { + this.refseqMrnaId = refseqMrnaId; } - public Integer getMutationProteinPosStart() { - return mutationProteinPosStart; + public Integer getProteinPosStart() { + return proteinPosStart; } - public void setMutationProteinPosStart(Integer mutationProteinPosStart) { - this.mutationProteinPosStart = mutationProteinPosStart; + public void setProteinPosStart(Integer proteinPosStart) { + this.proteinPosStart = proteinPosStart; } - public Integer getMutationProteinPosEnd() { - return mutationProteinPosEnd; + public Integer getProteinPosEnd() { + return proteinPosEnd; } - public void setMutationProteinPosEnd(Integer mutationProteinPosEnd) { - this.mutationProteinPosEnd = mutationProteinPosEnd; + public void setProteinPosEnd(Integer proteinPosEnd) { + this.proteinPosEnd = proteinPosEnd; } public String getKeyword() { diff --git a/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml b/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml index 54708c6631d..b780dd0939a 100644 --- a/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml +++ b/persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml @@ -28,9 +28,9 @@ mutation_event.MUTATION_TYPE AS mutationType, mutation_event.NCBI_BUILD AS ncbiBuild, mutation_event.VARIANT_TYPE AS variantType, - mutation_event.REFSEQ_MRNA_ID AS mutationRefseqMrnaId, - mutation_event.PROTEIN_POS_START AS mutationProteinPosStart, - mutation_event.PROTEIN_POS_END AS mutationProteinPosEnd, + mutation_event.REFSEQ_MRNA_ID AS refseqMrnaId, + mutation_event.PROTEIN_POS_START AS proteinPosStart, + mutation_event.PROTEIN_POS_END AS proteinPosEnd, mutation_event.KEYWORD AS keyword, mutation.ANNOTATION_JSON as annotationJSON, alteration_driver_annotation.DRIVER_FILTER as driverFilter, 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 2b09851bdeb..a75b6eb7f5c 100644 --- a/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java +++ b/persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java @@ -116,9 +116,9 @@ public void getMutationsInMolecularProfileBySampleListIdSummaryProjection() thro Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getMutationRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -157,9 +157,9 @@ public void getMutationsInMolecularProfileBySampleListIdAndEntrezGeneIdsSummaryP Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getMutationRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -194,9 +194,9 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getMutationProteinPosStart()); - Assert.assertEquals("NM_007294", mutation.getMutationRefseqMrnaId()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosEnd()); + Assert.assertEquals((Integer) 934, mutation.getProteinPosStart()); + Assert.assertEquals("NM_007294", mutation.getRefseqMrnaId()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); diff --git a/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java b/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java index 9eb90f47e89..86b80142466 100644 --- a/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java +++ b/web/src/main/java/org/cbioportal/web/mixin/MutationMixin.java @@ -7,11 +7,11 @@ public class MutationMixin { @JsonProperty("variantAllele") private String tumorSeqAllele; @JsonProperty("refseqMrnaId") - private String mutationRefseqMrnaId; + private String refseqMrnaId; @JsonProperty("proteinPosStart") - private Integer mutationProteinPosStart; + private Integer proteinPosStart; @JsonProperty("proteinPosEnd") - private Integer mutationProteinPosEnd; + private Integer proteinPosEnd; @JsonProperty("chr") private String chr; @JsonProperty("namespaceColumns") diff --git a/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java b/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java index ad7874ffb8c..ce2caf51cdb 100644 --- a/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java +++ b/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java @@ -19,9 +19,9 @@ public enum MutationSortBy { mutationType("mutationType"), ncbiBuild("ncbiBuild"), variantType("variantType"), - refseqMrnaId("mutationRefseqMrnaId"), - proteinPosStart("mutationProteinPosStart"), - proteinPosEnd("mutationProteinPosEnd"), + refseqMrnaId("refseqMrnaId"), + proteinPosStart("proteinPosStart"), + proteinPosEnd("proteinPosEnd"), keyword("keyword"); private String originalValue; diff --git a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java index 0ecfb3c3770..7f9018d0e85 100644 --- a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java @@ -714,9 +714,9 @@ private List createExampleMutations() { mutation1.setDriverTiersFilterAnnotation(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1); mutation1.setNcbiBuild(TEST_NCBI_BUILD_1); mutation1.setVariantType(TEST_VARIANT_TYPE_1); - mutation1.setMutationRefseqMrnaId(TEST_MUTATION_REFSEQ_MRNA_ID_1); - mutation1.setMutationProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_1); - mutation1.setMutationProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_1); + mutation1.setRefseqMrnaId(TEST_MUTATION_REFSEQ_MRNA_ID_1); + mutation1.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_1); + mutation1.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_1); mutation1.setKeyword(TEST_KEYWORD_1); mutation1.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation1); @@ -744,9 +744,9 @@ private List createExampleMutations() { mutation2.setDriverTiersFilterAnnotation(TEST_DRIVER_TIERS_FILTER_ANNOTATION_2); mutation2.setNcbiBuild(TEST_NCBI_BUILD_2); mutation2.setVariantType(TEST_VARIANT_TYPE_2); - mutation2.setMutationRefseqMrnaId(TEST_MUTATION_REFSEQ_MRNA_ID_2); - mutation2.setMutationProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_2); - mutation2.setMutationProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_2); + mutation2.setRefseqMrnaId(TEST_MUTATION_REFSEQ_MRNA_ID_2); + mutation2.setProteinPosStart(TEST_MUTATION_PROTEIN_POS_START_2); + mutation2.setProteinPosEnd(TEST_MUTATION_PROTEIN_POS_END_2); mutation2.setKeyword(TEST_KEYWORD_2); mutation2.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation2);