Merge pull request #9914 from jagnathan/fix-9461-mutations-api-endpoi…

…nt-final Fix 9461 mutations api endpoint final
cBioPortal · Mar 14, 2023 · ec2236f · ec2236f
2 parents d9d1029 + 9ca0563
commit ec2236f
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Showing 22 changed files with 278 additions and 666 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
@@ -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<CosmicMutationFrequency> filterTruncatingCosmicByPosition(
 
         Set<CosmicMutationFrequency> ret = new HashSet<CosmicMutationFrequency>();
         Pattern p = Pattern.compile("[0-9]+");
-        int mutPos = mut.getOncotatorProteinPosStart();
+        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
@@ -145,23 +145,16 @@ public static int addMutationEvent(ExtendedMutation.MutationEvent event) throws
                 event.getTumorSeqAllele(),
                 event.getProteinChange(),
                 event.getMutationType(),
-                event.getFunctionalImpactScore(),
-                Float.toString(event.getFisValue()),
-                event.getLinkXVar(),
-                event.getLinkPdb(),
-                event.getLinkMsa(),
                 event.getNcbiBuild(),
                 event.getStrand(),
                 event.getVariantType(),
                 event.getDbSnpRs(),
                 event.getDbSnpValStatus(),
-                event.getOncotatorDbSnpRs(),
-                event.getOncotatorRefseqMrnaId(),
-                event.getOncotatorCodonChange(),
-                event.getOncotatorUniprotName(),
-                event.getOncotatorUniprotAccession(),
-                Integer.toString(event.getOncotatorProteinPosStart()),
-                Integer.toString(event.getOncotatorProteinPosEnd()),
+                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;
@@ -800,24 +793,17 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet rs)
         event.setEndPosition(rs.getLong("END_POSITION"));
         event.setProteinChange(rs.getString("PROTEIN_CHANGE"));
         event.setMutationType(rs.getString("MUTATION_TYPE"));
-        event.setFunctionalImpactScore(rs.getString("FUNCTIONAL_IMPACT_SCORE"));
-        event.setFisValue(rs.getFloat("FIS_VALUE"));
-        event.setLinkXVar(rs.getString("LINK_XVAR"));
-        event.setLinkPdb(rs.getString("LINK_PDB"));
-        event.setLinkMsa(rs.getString("LINK_MSA"));
         event.setNcbiBuild(rs.getString("NCBI_BUILD"));
         event.setStrand(rs.getString("STRAND"));
         event.setVariantType(rs.getString("VARIANT_TYPE"));
         event.setDbSnpRs(rs.getString("DB_SNP_RS"));
         event.setDbSnpValStatus(rs.getString("DB_SNP_VAL_STATUS"));
         event.setReferenceAllele(rs.getString("REFERENCE_ALLELE"));
-        event.setOncotatorDbSnpRs(rs.getString("ONCOTATOR_DBSNP_RS"));
-        event.setOncotatorRefseqMrnaId(rs.getString("ONCOTATOR_REFSEQ_MRNA_ID"));
-        event.setOncotatorCodonChange(rs.getString("ONCOTATOR_CODON_CHANGE"));
-        event.setOncotatorUniprotName(rs.getString("ONCOTATOR_UNIPROT_ENTRY_NAME"));
-        event.setOncotatorUniprotAccession(rs.getString("ONCOTATOR_UNIPROT_ACCESSION"));
-        event.setOncotatorProteinPosStart(rs.getInt("ONCOTATOR_PROTEIN_POS_START"));
-        event.setOncotatorProteinPosEnd(rs.getInt("ONCOTATOR_PROTEIN_POS_END"));
+        event.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"));
@@ -1391,12 +1377,12 @@ public static Collection<Map<String, Object>> countSamplesWithProteinPosStarts(
         if (geneIdSet.size() == 0 || internalProfileIds.size() == 0) return new ArrayList<Map<String, Object>>(); //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 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, 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<Map<String, Object>> data = new ArrayList<Map<String, Object>>();