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 e1bfcca4ef8..6c0537abe5f 100644 --- a/core/src/test/resources/seed_mini.sql +++ b/core/src/test/resources/seed_mini.sql @@ -411,9 +411,9 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (19,'TCGA-A1-A0SB-02','Primary Solid Tumor',1); -- mutation_event -INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","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 f28432e323d..c591b5bb616 100644 --- a/db-scripts/src/main/resources/cgds.sql +++ b/db-scripts/src/main/resources/cgds.sql @@ -435,11 +435,6 @@ 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 c3c4fa5a069..777b45d840a 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`; @@ -992,3 +994,12 @@ ALTER TABLE `structural_variant` DROP COLUMN `SITE2_EXON`; ALTER TABLE `structural_variant` DROP COLUMN `CENTER`; ALTER TABLE `structural_variant` DROP COLUMN `EXTERNAL_ANNOTATION`; UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.14"; + + +-- changes for issue 9461 +ALTER TABLE `mutation_event` DROP COLUMN `FUNCTIONAL_IMPACT_SCORE`; +ALTER TABLE `mutation_event` DROP COLUMN `FIS_VALUE`; +ALTER TABLE `mutation_event` DROP COLUMN `LINK_XVAR`; +ALTER TABLE `mutation_event` DROP COLUMN `LINK_PDB`; +ALTER TABLE `mutation_event` DROP COLUMN `LINK_MSA`; +UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.14"; diff --git a/model/src/main/java/org/cbioportal/model/Mutation.java b/model/src/main/java/org/cbioportal/model/Mutation.java index 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);