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gblaihBryan Lai
authored and
alisman
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add back clinical data mapper queries for clinical table (#11700)
Co-authored-by: Bryan Lai <[email protected]>
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‎src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalDataMapper.xml‎

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@@ -273,4 +273,127 @@
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ON clinical_sample.internal_id = sample_id_subquery.internal_id
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</sql>
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<select id="getVisibleSampleInternalIdsForClinicalTable" resultType="Integer">
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<bind name="doSearch" value="_parameter.containsKey('searchTerm') and searchTerm != null and not searchTerm.isBlank()" />
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<bind name="doSort" value="_parameter.containsKey('sortAttrId') and sortAttrId != null" />
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<bind name="doPaginate" value="_parameter.containsKey('limit') and limit != null and limit != 0" />
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<bind name="sortBySampleId" value="sortAttrId == 'sampleId'" />
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<bind name="sortByPatientId" value="sortAttrId == 'patientId'" />
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<bind name="sortByAttribute" value="sortAttrId != 'sampleId' and sortAttrId != 'patientId'" />
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SELECT sample.internal_id FROM sample
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INNER JOIN patient ON sample.patient_id = patient.internal_id
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INNER JOIN cancer_study ON patient.cancer_study_id = cancer_study.cancer_study_id
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<if test="doSort">
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LEFT JOIN (<include refid="sortAttributeData"/>) as sortData
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ON sample.internal_id = sortData.sampleInternalId
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</if>
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<if test="doSearch">
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INNER JOIN (<include refid="searchedAttributeData"/>) as searchData
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ON sample.internal_id = searchData.sampleInternalId
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</if>
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<include refid="whereSample"/>
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<if test="doSort">
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<choose>
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<when test="sortBySampleId">
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ORDER BY sample.stable_id ${direction}
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</when>
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<when test="sortByPatientId">
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ORDER BY patient.stable_id ${direction}
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</when>
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<when test="sortByAttribute">
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<choose>
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<when test="_databaseId == 'mysql'">
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ORDER BY ISNULL(sortData.sortAttrValue), sortData.sortAttrValue ${direction}
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</when>
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<when test="_databaseId == 'h2'">
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ORDER BY sortData.sortAttrValue ${direction} NULLS LAST
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</when>
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</choose>
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</when>
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<otherwise></otherwise>
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</choose>
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</if>
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<if test="doPaginate">
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LIMIT #{limit} OFFSET #{offset}
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</if>
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</select>
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<sql id="searchedAttributeData">
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SELECT
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DISTINCT sample.internal_id sampleInternalId
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FROM sample
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INNER JOIN patient ON patient.internal_id = sample.patient_id
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INNER JOIN cancer_study ON patient.cancer_study_id = cancer_study.cancer_study_id
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INNER JOIN clinical_sample cs on sample.internal_id = cs.internal_id
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INNER JOIN clinical_patient cp on patient.internal_id = cp.internal_id
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<include refid="whereSample"/>
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AND (
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cs.ATTR_VALUE LIKE CONCAT('%', #{searchTerm}, '%')
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OR cp.ATTR_VALUE LIKE CONCAT('%', #{searchTerm}, '%')
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OR sample.STABLE_ID LIKE CONCAT('%', #{searchTerm}, '%')
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OR patient.STABLE_ID LIKE CONCAT('%', #{searchTerm}, '%')
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)
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</sql>
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<sql id="sortAttributeData">
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<choose>
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<when test="sortIsPatientAttr">
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SELECT sample.internal_id sampleInternalId, sample.stable_id sampleId, patient.stable_id patientId, clinical_patient.attr_id sortAttrId,
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<choose>
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<when test="sortAttrIsNumber">CONVERT(clinical_patient.attr_value, DECIMAL) sortAttrValue
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</when>
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<otherwise>
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clinical_patient.attr_value sortAttrValue
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</otherwise>
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</choose>
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FROM sample
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INNER JOIN patient ON sample.patient_id = patient.internal_id
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INNER JOIN cancer_study ON patient.cancer_study_id = cancer_study.cancer_study_id
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LEFT JOIN clinical_patient ON patient.internal_id = clinical_patient.internal_id AND clinical_patient.attr_id = #{sortAttrId}
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</when>
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<otherwise>
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SELECT sample.internal_id sampleInternalId, sample.stable_id sampleId, patient.stable_id patientId, clinical_sample.attr_id sortAttrId,
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<choose>
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<when test="sortAttrIsNumber">
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CONVERT(clinical_sample.attr_value, DECIMAL) sortAttrValue
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</when>
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<otherwise>
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clinical_sample.attr_value sortAttrValue
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</otherwise>
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</choose>
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FROM clinical_sample
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INNER JOIN sample ON clinical_sample.internal_id = sample.internal_id
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INNER JOIN patient ON sample.patient_id = patient.internal_id
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INNER JOIN cancer_study ON patient.cancer_study_id = cancer_study.cancer_study_id
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WHERE clinical_sample.attr_id = #{sortAttrId}
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</otherwise>
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</choose>
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</sql>
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<select id="getSampleClinicalDataBySampleInternalIds" resultType="org.cbioportal.legacy.model.ClinicalData">
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<!-- Always 'SUMMARY' projection. 'DETAILED' not implemented. -->
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SELECT sample.internal_id internalId, sample.stable_id sampleId, patient.stable_id patientId, cancer_study.cancer_study_identifier studyId, clinical_sample.attr_id attrId, clinical_sample.attr_value attrValue
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FROM clinical_sample
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INNER JOIN sample ON clinical_sample.internal_id = sample.internal_id
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INNER JOIN patient ON sample.patient_id = patient.internal_id
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INNER JOIN cancer_study ON patient.cancer_study_id = cancer_study.cancer_study_id
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WHERE sample.internal_id IN
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<foreach item="item" collection="sampleInternalIds" open="(" separator="," close=")">
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#{item}
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</foreach>
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</select>
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<select id="getPatientClinicalDataBySampleInternalIds" resultType="org.cbioportal.legacy.model.ClinicalData">
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<!-- Always 'SUMMARY' projection. 'DETAILED' not implemented. -->
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SELECT sample.internal_id internalId, sample.stable_id sampleId, patient.stable_id patientId, cancer_study.cancer_study_identifier studyId, clinical_patient.attr_id attrId, clinical_patient.attr_value attrValue
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FROM clinical_patient
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INNER JOIN patient ON clinical_patient.internal_id = patient.internal_id
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INNER JOIN sample ON patient.internal_id = sample.patient_id
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INNER JOIN cancer_study ON patient.cancer_study_id = cancer_study.cancer_study_id
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WHERE sample.internal_id IN
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<foreach item="item" collection="sampleInternalIds" open="(" separator="," close=")">
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#{item}
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</foreach>
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</select>
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</mapper>

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