fix cBioPortal#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

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"));

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();

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());

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);

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);

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());

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);

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),

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";

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;
     }
@@ -210,15 +165,14 @@ public String getVariantType() {
     public void setVariantType(String variantType) {
         this.variantType = variantType;
     }
-
     public String getOncotatorRefseqMrnaId() {
         return oncotatorRefseqMrnaId;
     }
 
     public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) {
         this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId;
     }
-
+    
     public Integer getOncotatorProteinPosStart() {
         return oncotatorProteinPosStart;
     }

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,

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());