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Fix 9461 mutations api endpoint final #9914

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merged 9 commits into from
Mar 14, 2023
Merged

Fix 9461 mutations api endpoint final #9914

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967afbe
fix #9461 - mutations api endpoint
jagnathan May 26, 2022
eeb8f8a
Updated more files for removed fields
jagnathan Oct 12, 2022
3b2f8bb
db changes and renaming the column prefixes from oncotator to mutation
jagnathan Oct 27, 2022
d1a400d
Update SQL statements
jagnathan Nov 11, 2022
871eccd
db changes and renaming the column prefixes from oncotator to mutation
jagnathan Oct 27, 2022
98c892f
Update migration.sql
jagnathan Nov 12, 2022
dec3627
Removed Link columns
jagnathan Dec 2, 2022
89bde61
Update DB version and renaming mutation_event fields
dippindots Mar 8, 2023
9ca0563
Update Mutation model
dippindots Mar 8, 2023
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3 changes: 1 addition & 2 deletions core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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.getMutationProteinPosStart();
for (CosmicMutationFrequency cmf : cmfs) {
String aa = cmf.getAminoAcidChange();
Matcher m = p.matcher(aa);
Expand Down
40 changes: 13 additions & 27 deletions core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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.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;
Expand Down Expand Up @@ -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.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"));
Expand Down Expand Up @@ -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 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<Map<String, Object>> data = new ArrayList<Map<String, Object>>();
Expand Down
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