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i-am-lesliei-am-leslie
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Wrote the sql for getMetaMutation use case. Starting with getMutation method
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‎src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnMutationController.java‎

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Original file line numberDiff line numberDiff line change
@@ -42,8 +42,8 @@ public class ColumnMutationController {
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/**
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* Constructs a new {@link ColumnMutationController} with the specified use case.
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*
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* @param getMutationUseCases the use case responsible for retrieving cancer study
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* metadata.
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* @param getMutationUseCases the use case responsible for retrieving Mutation metadata or Mutation
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*
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*/
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public ColumnMutationController(GetMutationUseCases getMutationUseCases) {
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this.getMutationUseCases = getMutationUseCases;

‎src/main/resources/mappers/clickhouse/mutation/ClickhouseMutationDataMapper.xml‎

Lines changed: 100 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,5 +2,104 @@
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<!DOCTYPE mapper PUBLIC "-//mybatis.org//DTD Mapper 3.0//EN" "http://mybatis.org/dtd/mybatis-3-mapper.dtd">
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<mapper namespace="org.cbioportal.infrastructure.repository.clickhouse.mutation.ClickhouseMutationDataMapper">
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<!-- <sql id="select">-->
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<!-- genomic_event_derived.genetic_profile_stable_id AS "molecularProfileId",-->
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<!-- genomic_event_derived.sample_unique_id AS "sampleId",-->
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<!-- genomic_event_derived.patient_unique_id AS "patientId",-->
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<!-- genomic_event_derived.entrez_gene_id AS "entrezGeneId",-->
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<!-- genomic_event_derived.cancer_study_identifier AS "studyId"-->
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<!-- <if test="projection == 'SUMMARY' || projection == 'DETAILED'">-->
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<!-- ,-->
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<!-- mutation.CENTER AS "center",-->
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<!-- genomic_event_derived.mutation_status AS "mutationStatus",-->
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<!-- mutation.VALIDATION_STATUS AS "validationStatus",-->
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<!-- mutation.TUMOR_ALT_COUNT AS "tumorAltCount",-->
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<!-- mutation.TUMOR_REF_COUNT AS "tumorRefCount",-->
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<!-- mutation.NORMAL_ALT_COUNT AS "normalAltCount",-->
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<!-- mutation.NORMAL_REF_COUNT AS "normalRefCount",-->
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<!-- mutation.AMINO_ACID_CHANGE AS "aminoAcidChange",-->
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<!-- mutation_event.CHR AS "chr",-->
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<!-- mutation_event.START_POSITION AS "startPosition",-->
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<!-- mutation_event.END_POSITION AS "endPosition",-->
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<!-- mutation_event.REFERENCE_ALLELE AS "referenceAllele",-->
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<!-- mutation_event.TUMOR_SEQ_ALLELE AS "tumorSeqAllele",-->
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<!-- mutation_event.PROTEIN_CHANGE AS "proteinChange",-->
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<!-- genomic_event_derived.mutation_type AS "mutationType",-->
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<!-- mutation_event.NCBI_BUILD AS "ncbiBuild",-->
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<!-- genomic_event_derived.mutation_variant AS "variantType",-->
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<!-- mutation_event.REFSEQ_MRNA_ID AS "refseqMrnaId",-->
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<!-- mutation_event.PROTEIN_POS_START AS "proteinPosStart",-->
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<!-- mutation_event.PROTEIN_POS_END AS "proteinPosEnd",-->
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<!-- mutation_event.KEYWORD AS "keyword",-->
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<!-- mutation.ANNOTATION_JSON AS "annotationJSON",-->
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<!-- genomic_event_derived.driver_filter AS "driverFilter",-->
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<!-- alteration_driver_annotation.DRIVER_FILTER_ANNOTATION AS "driverFilterAnnotation",-->
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<!-- genomic_event_derived.driver_tiers_filter AS "driverTiersFilter",-->
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<!-- alteration_driver_annotation.DRIVER_TIERS_FILTER_ANNOTATION as "driverTiersFilterAnnotation"-->
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<!-- -->
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<!-- </if>-->
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<!-- <if test="projection == 'DETAILED'">-->
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<!-- ,-->
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<!-- <include refid="org.cbioportal.legacy.persistence.mybatis.GeneMapper.select">-->
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<!-- <property name="prefix" value="gene."/>-->
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<!-- </include>-->
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<!-- ,-->
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<!-- <include refid="getAlleleSpecificCopyNumber">-->
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<!-- <property name="prefix" value="alleleSpecificCopyNumber."/>-->
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<!-- </include>-->
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<!-- </if>-->
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<!-- </sql>-->
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<sql id="projectionAndLimitFilter">
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<if test="sortBy != null and projection != 'ID'">
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ORDER BY "${sortBy}" ${direction}
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</if>
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<if test="projection == 'ID'">
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ORDER BY genomic_event_derived.genetic_profile_stable_id ASC,
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genomic_event_derived.sample_unique_id ASC,
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genomic_event_derived.entrez_gene_id ASC
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</if>
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<if test="limit != null and limit != 0">
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LIMIT #{limit} OFFSET #{offset}
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</if>
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</sql>
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<sql id="derivedTableWhereFilter">
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<where>
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<if test="molecularProfileIds != null and !molecularProfileIds.isEmpty()">
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genetic_profile_stable_id IN
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<foreach item="item" collection="molecularProfileIds" open="(" separator="," close=")">
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#{item}
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</foreach>
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</if>
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<if test="sampleIds != null and !sampleIds.isEmpty()">
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AND sample_unique_id IN
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<foreach item="item" collection="sampleIds" open="(" separator="," close=")">
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#{item}
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</foreach>
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</if>
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<if test="entrezGeneIds != null and !entrezGeneIds.isEmpty()">
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AND entrez_gene_id IN
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<foreach item="item" collection="entrezGeneIds" open="(" separator="," close=")">
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#{item}
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</foreach>
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</if>
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</where>
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</sql>
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<select id="getMetaMutationsInMultipleMolecularProfiles"
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resultType="org.cbioportal.legacy.model.meta.MutationMeta">
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SELECT
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COUNT(*) AS "totalCount",
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COUNT(DISTINCT sample_unique_id) AS "sampleCount"
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FROM genomic_event_derived
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<include refid="derivedTableWhereFilter"/>
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</select>
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</mapper>

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