fix 9461 removing Oncotator related properties

fix 9461 removing Oncotator related properties

core/src/main/java/org/mskcc/cbio/maf/MafRecord.java

@@ -103,17 +103,6 @@ public class MafRecord {
  private String maLinkMsa;
  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;
- private int oncotatorProteinPosEnd;
-
  // custom filtering of passenger and driver mutations cols
  private String driverFilter;
  private String driverFilterAnn;
@@ -520,79 +509,7 @@ public String getProteinPosition() {
  public void setProteinPosition(String proteinPosition) {
  this.proteinPosition = proteinPosition;
  }
-
- public String getOncotatorVariantClassification() {
- return oncotatorVariantClassification;
- }
-
- 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;
- }
-
- public void setOncotatorDbSnpValStatus(String oncotatorDbSnpValStatus) {
- this.oncotatorDbSnpValStatus = oncotatorDbSnpValStatus;
- }
-
- public String getOncotatorRefseqMrnaId() {
- return oncotatorRefseqMrnaId;
- }
-
- 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;
- }
-
- public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) {
- this.oncotatorUniprotAccession = oncotatorUniprotAccession;
- }
-
- public String getOncotatorCodonChange() {
- return oncotatorCodonChange;
- }
-
- public void setOncotatorCodonChange(String oncotatorCodonChange) {
- this.oncotatorCodonChange = oncotatorCodonChange;
- }
-
- public int getOncotatorProteinPosStart() {
- return oncotatorProteinPosStart;
- }
-
- public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) {
- this.oncotatorProteinPosStart = oncotatorProteinPosStart;
- }
-
- public int getOncotatorProteinPosEnd() {
- return oncotatorProteinPosEnd;
- }
-
- public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) {
- this.oncotatorProteinPosEnd = oncotatorProteinPosEnd;
- }
-
+
  public String getMaFuncImpact() {
  return maFuncImpact;
  }

core/src/main/java/org/mskcc/cbio/maf/MafUtil.java

@@ -466,17 +466,7 @@ public MafRecord parseRecord(String line) {
  record.setMaLinkVar(TabDelimitedFileUtil.getPartString(maLinkVarIndex, parts));
  record.setMaLinkMsa(TabDelimitedFileUtil.getPartString(maLinkMsaIndex, parts));
  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));
- record.setOncotatorProteinPosEnd(TabDelimitedFileUtil.getPartInt(oncoProteinPosEndIndex, parts));
-
+
  // custom filtering of passenger and driver mutations columns
  record.setDriverFilter(TabDelimitedFileUtil.getPartStringAllowEmptyAndNA(driverIndex, parts));
  record.setDriverFilterAnn(TabDelimitedFileUtil.getPartStringAllowEmpty(driverAnnIndex, parts));

core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java

@@ -116,7 +116,7 @@ private static Set<CosmicMutationFrequency> filterTruncatingCosmicByPosition(
 
  Set<CosmicMutationFrequency> ret = new HashSet<CosmicMutationFrequency>();
  Pattern p = Pattern.compile("[0-9]+");
- int mutPos = mut.getOncotatorProteinPosStart();
+ int mutPos = -1;
  for (CosmicMutationFrequency cmf : cmfs) {
  String aa = cmf.getAminoAcidChange();
  Matcher m = p.matcher(aa);

core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java

@@ -150,12 +150,6 @@ public static int addMutationEvent(ExtendedMutation.MutationEvent event) throws
  event.getVariantType(),
  event.getDbSnpRs(),
  event.getDbSnpValStatus(),
- event.getOncotatorDbSnpRs(),
- event.getOncotatorCodonChange(),
- event.getOncotatorUniprotName(),
- event.getOncotatorUniprotAccession(),
- Integer.toString(event.getOncotatorProteinPosStart()),
- Integer.toString(event.getOncotatorProteinPosEnd()),
  boolToStr(event.isCanonicalTranscript()),
  keyword==null ? "\\N":(event.getGene().getHugoGeneSymbolAllCaps()+" "+keyword));
  return 1;
@@ -800,12 +794,6 @@ 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.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.setCanonicalTranscript(rs.getBoolean("CANONICAL_TRANSCRIPT"));
  event.setTumorSeqAllele(rs.getString("TUMOR_SEQ_ALLELE"));
  event.setKeyword(rs.getString("KEYWORD"));

core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java

@@ -60,12 +60,6 @@ public final static class MutationEvent {
  private String tumorSeqAllele;
  private String dbSnpRs;
  private String dbSnpValStatus;
- private String oncotatorDbSnpRs;
- private String oncotatorUniprotName;
- private String oncotatorUniprotAccession;
- private String oncotatorCodonChange;
- private int oncotatorProteinPosStart;
- private int oncotatorProteinPosEnd;
  private boolean canonicalTranscript;
 
  public long getMutationEventId() {
@@ -189,63 +183,7 @@ public String getDbSnpValStatus() {
  public void setDbSnpValStatus(String dbSnpValStatus) {
  this.dbSnpValStatus = dbSnpValStatus;
  }
-
- public String getOncotatorDbSnpRs() {
- return oncotatorDbSnpRs;
- }
-
- public void setOncotatorDbSnpRs(String oncotatorDbSnpRs) {
- this.oncotatorDbSnpRs = oncotatorDbSnpRs;
- }
-
- 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;
- }
-
- public void setOncotatorUniprotAccession(String oncotatorUniprotAccession) {
- this.oncotatorUniprotAccession = oncotatorUniprotAccession;
- }
-
- public String getOncotatorCodonChange() {
- return oncotatorCodonChange;
- }
-
- public void setOncotatorCodonChange(String oncotatorCodonChange) {
- this.oncotatorCodonChange = oncotatorCodonChange;
- }
-
- public int getOncotatorProteinPosStart() {
- return oncotatorProteinPosStart;
- }
-
- public void setOncotatorProteinPosStart(int oncotatorProteinPosStart) {
- this.oncotatorProteinPosStart = oncotatorProteinPosStart;
- }
-
- public int getOncotatorProteinPosEnd() {
- return oncotatorProteinPosEnd;
- }
-
- public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd) {
- this.oncotatorProteinPosEnd = oncotatorProteinPosEnd;
- }
-
+
  public boolean isCanonicalTranscript() {
  return canonicalTranscript;
  }
@@ -725,73 +663,7 @@ public Integer getNormalRefCount() {
  public void setNormalRefCount(Integer normalRefCount) {
  this.normalRefCount = normalRefCount;
  }
-
- public String getOncotatorDbSnpRs() {
- return event.getOncotatorDbSnpRs();
- }
-
- public void setOncotatorDbSnpRs(String oncotatorDbSnpRs) {
- event.setOncotatorDbSnpRs(oncotatorDbSnpRs);
- }
-
- 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()
- {
- return event.getOncotatorUniprotAccession();
- }
-
- public void setOncotatorUniprotAccession(String oncotatorUniprotAccession)
- {
- event.setOncotatorUniprotAccession(oncotatorUniprotAccession);
- }
-
- public String getOncotatorCodonChange()
- {
- return event.getOncotatorCodonChange();
- }
-
- public void setOncotatorCodonChange(String oncotatorCodonChange)
- {
- event.setOncotatorCodonChange(oncotatorCodonChange);
- }
-
- public int getOncotatorProteinPosStart()
- {
- return event.getOncotatorProteinPosStart();
- }
-
- public void setOncotatorProteinPosStart(int oncotatorProteinPosStart)
- {
- event.setOncotatorProteinPosStart(oncotatorProteinPosStart);
- }
-
- public int getOncotatorProteinPosEnd()
- {
- return event.getOncotatorProteinPosEnd();
- }
-
- public void setOncotatorProteinPosEnd(int oncotatorProteinPosEnd)
- {
- event.setOncotatorProteinPosEnd(oncotatorProteinPosEnd);
- }
-
+
  public boolean isCanonicalTranscript()
  {
  return event.isCanonicalTranscript();

core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java

@@ -364,13 +364,7 @@ public void importData() throws IOException, DaoException {
  mutation.setTumorRefCount(ExtendedMutationUtil.getTumorRefCount(record));
  mutation.setNormalAltCount(ExtendedMutationUtil.getNormalAltCount(record));
  mutation.setNormalRefCount(ExtendedMutationUtil.getNormalRefCount(record));
-
- // TODO rename the oncotator column names (remove "oncotator")
- mutation.setOncotatorCodonChange(codonChange);
- mutation.setOncotatorUniprotAccession(uniprotAccession);
- mutation.setOncotatorProteinPosStart(proteinPosStart);
- mutation.setOncotatorProteinPosEnd(proteinPosEnd);
-
+
  mutation.setDriverFilter(record.getDriverFilter());
  mutation.setDriverFilterAnn(record.getDriverFilterAnn());
  mutation.setDriverTiersFilter(record.getDriverTiersFilter());

core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java

@@ -195,16 +195,7 @@ public static boolean isAcceptableMutation(String mutationType) {
  }
 
  public static String getMutationType(MafRecord record) {
- String mutationType = record.getOncotatorVariantClassification();
-
- if (mutationType == null ||
- mutationType.length() == 0 ||
- mutationType.equals("NULL") ||
- mutationType.equals(TabDelimitedFileUtil.NA_STRING)) {
- mutationType = record.getVariantClassification();
- }
-
- return mutationType;
+ return record.getVariantClassification();
  }
 
  public static Integer getTumorAltCount(MafRecord record) {
@@ -321,12 +312,6 @@ public static ExtendedMutation newMutation() {
  mutation.setTumorRefCount(defaultInt);
  mutation.setNormalAltCount(defaultInt);
  mutation.setNormalRefCount(defaultInt);
- mutation.setOncotatorDbSnpRs(defaultStr);
- mutation.setOncotatorCodonChange(defaultStr);
- mutation.setOncotatorUniprotName(defaultStr);
- mutation.setOncotatorUniprotAccession(defaultStr);
- mutation.setOncotatorProteinPosStart(defaultInt);
- mutation.setOncotatorProteinPosEnd(defaultInt);
  mutation.setCanonicalTranscript(true);
 
  return mutation;

core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java

@@ -127,12 +127,6 @@ 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.setOncotatorUniprotName("CTNB1_HUMAN");
- mutation.setOncotatorUniprotAccession("P35222");
- mutation.setOncotatorProteinPosStart(666);
- mutation.setOncotatorProteinPosEnd(678);
  mutation.setCanonicalTranscript(true);
  mutation.setAnnotationJson(makeMockAnnotationJsonString());
 
@@ -193,12 +187,6 @@ 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("CTNB1_HUMAN", mutation.getOncotatorUniprotName());
- assertEquals("P35222", mutation.getOncotatorUniprotAccession());
- assertEquals(666, mutation.getOncotatorProteinPosStart());
- assertEquals(678, mutation.getOncotatorProteinPosEnd());
  assertEquals(true, mutation.isCanonicalTranscript());
  validateMockAnnotationJson(mutation);