From eeb85e9354bb7fbc4298e54436b8da9f643e3e70 Mon Sep 17 00:00:00 2001 From: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com> Date: Wed, 24 Aug 2022 13:33:11 -0400 Subject: [PATCH] fix 9461 removing Oncotator related properties fix 9461 removing Oncotator related properties --- .../java/org/mskcc/cbio/maf/MafRecord.java | 85 +---------- .../main/java/org/mskcc/cbio/maf/MafUtil.java | 12 +- .../mskcc/cbio/portal/dao/DaoCosmicData.java | 2 +- .../mskcc/cbio/portal/dao/DaoMutation.java | 12 -- .../cbio/portal/model/ExtendedMutation.java | 132 +----------------- .../scripts/ImportExtendedMutationData.java | 8 +- .../portal/util/ExtendedMutationUtil.java | 17 +-- .../cbio/portal/dao/TestDaoMutation.java | 12 -- .../java/org/cbioportal/model/Mutation.java | 18 --- .../MutationMyBatisRepositoryTest.java | 8 +- .../web/parameter/sort/MutationSortBy.java | 2 - .../web/MutationControllerTest.java | 4 - 12 files changed, 8 insertions(+), 304 deletions(-) diff --git a/core/src/main/java/org/mskcc/cbio/maf/MafRecord.java b/core/src/main/java/org/mskcc/cbio/maf/MafRecord.java index 62db074d7ff..72be1870dfe 100644 --- a/core/src/main/java/org/mskcc/cbio/maf/MafRecord.java +++ b/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; } diff --git a/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java b/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java index ce5132ec121..c8b17e8ab97 100644 --- a/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java +++ b/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)); 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 index b7e0960ad37..f2b3d9d7064 100644 --- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java +++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCosmicData.java @@ -116,7 +116,7 @@ private static Set filterTruncatingCosmicByPosition( Set ret = new HashSet(); 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); 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 ca1527188f7..c5646783928 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 @@ -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")); 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 ab54c4a3713..472801bdb62 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 @@ -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(); 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 144137a4906..893dd0f5c75 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 @@ -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()); 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 2725fb85c78..4d264068dcd 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 @@ -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; 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 07b237b8bf3..80050cc78a9 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 @@ -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); diff --git a/model/src/main/java/org/cbioportal/model/Mutation.java b/model/src/main/java/org/cbioportal/model/Mutation.java index a204b5e10cd..1727381f0f7 100644 --- a/model/src/main/java/org/cbioportal/model/Mutation.java +++ b/model/src/main/java/org/cbioportal/model/Mutation.java @@ -25,8 +25,6 @@ public class Mutation extends Alteration implements Serializable { private String mutationType; private String ncbiBuild; private String variantType; - private Integer oncotatorProteinPosStart; - private Integer oncotatorProteinPosEnd; private String keyword; private AlleleSpecificCopyNumber alleleSpecificCopyNumber; @JsonRawValue @@ -165,22 +163,6 @@ public void setVariantType(String variantType) { this.variantType = variantType; } - public Integer getOncotatorProteinPosStart() { - return oncotatorProteinPosStart; - } - - public void setOncotatorProteinPosStart(Integer oncotatorProteinPosStart) { - this.oncotatorProteinPosStart = oncotatorProteinPosStart; - } - - public Integer getOncotatorProteinPosEnd() { - return oncotatorProteinPosEnd; - } - - public void setOncotatorProteinPosEnd(Integer oncotatorProteinPosEnd) { - this.oncotatorProteinPosEnd = oncotatorProteinPosEnd; - } - public String getKeyword() { return keyword; } 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 5405e77f4b0..f231fe3d803 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 @@ -117,8 +117,6 @@ public void getMutationsInMolecularProfileBySampleListIdSummaryProjection() thro Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); @@ -157,9 +155,7 @@ public void getMutationsInMolecularProfileBySampleListIdAndEntrezGeneIdsSummaryP Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); - Assert.assertEquals("Q934*", mutation.getProteinChange()); + Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); Assert.assertEquals((Integer) (-1), mutation.getTumorAltCount()); @@ -193,8 +189,6 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr Assert.assertEquals("37", mutation.getNcbiBuild()); Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount()); Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosEnd()); - Assert.assertEquals((Integer) 934, mutation.getOncotatorProteinPosStart()); Assert.assertEquals("Q934*", mutation.getProteinChange()); Assert.assertEquals("G", mutation.getReferenceAllele()); Assert.assertEquals((Long) 41244748L, mutation.getStartPosition()); diff --git a/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java b/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java index 539feb4719e..2f3649088bc 100644 --- a/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java +++ b/web/src/main/java/org/cbioportal/web/parameter/sort/MutationSortBy.java @@ -19,8 +19,6 @@ public enum MutationSortBy { mutationType("mutationType"), ncbiBuild("ncbiBuild"), variantType("variantType"), - proteinPosStart("oncotatorProteinPosStart"), - proteinPosEnd("oncotatorProteinPosEnd"), keyword("keyword"); private String originalValue; diff --git a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java index 211c06371c6..4d7798c18bf 100644 --- a/web/src/test/java/org/cbioportal/web/MutationControllerTest.java +++ b/web/src/test/java/org/cbioportal/web/MutationControllerTest.java @@ -703,8 +703,6 @@ private List createExampleMutations() { mutation1.setDriverTiersFilterAnnotation(TEST_DRIVER_TIERS_FILTER_ANNOTATION_1); mutation1.setNcbiBuild(TEST_NCBI_BUILD_1); mutation1.setVariantType(TEST_VARIANT_TYPE_1); - mutation1.setOncotatorProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_1); - mutation1.setOncotatorProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_1); mutation1.setKeyword(TEST_KEYWORD_1); mutation1.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation1); @@ -732,8 +730,6 @@ private List createExampleMutations() { mutation2.setDriverTiersFilterAnnotation(TEST_DRIVER_TIERS_FILTER_ANNOTATION_2); mutation2.setNcbiBuild(TEST_NCBI_BUILD_2); mutation2.setVariantType(TEST_VARIANT_TYPE_2); - mutation2.setOncotatorProteinPosStart(TEST_ONCOTATOR_PROTEIN_POS_START_2); - mutation2.setOncotatorProteinPosEnd(TEST_ONCOTATOR_PROTEIN_POS_END_2); mutation2.setKeyword(TEST_KEYWORD_2); mutation2.setAnnotationJSON(NAME_SPACE_COLUMNS); mutationList.add(mutation2);