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restore accidentally deleted ClinicalEventMapper SQL
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‎src/main/resources/org/cbioportal/legacy/persistence/mybatis/ClinicalEventMapper.xml‎

Lines changed: 106 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -172,4 +172,110 @@
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GROUP BY clinical_event.event_type, patient.stable_id
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</select>
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<select id="getTimelineEvents" resultType="org.cbioportal.legacy.model.ClinicalEvent">
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SELECT
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ANY_VALUE(patient.stable_id) AS patientId,
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cancer_study.cancer_study_identifier AS studyId,
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MIN(clinical_event.start_date) AS startDate,
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GREATEST(MAX(clinical_event.start_date), COALESCE(MAX(clinical_event.stop_date),0)) AS stopDate
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FROM clinical_event
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INNER JOIN patient ON clinical_event.patient_id = patient.internal_id
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INNER JOIN clinical_event_data ON clinical_event.clinical_event_id = clinical_event_data.clinical_event_id
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INNER JOIN cancer_study ON patient.cancer_study_id = cancer_study.cancer_study_id
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<where>
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<if test="patientIds == null and studyIds != null">
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cancer_study.cancer_study_identifier IN
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<if test="studyIds.isEmpty()">(NULL)</if>
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<if test="!studyIds.isEmpty()"><foreach item="item" collection="studyIds" open="(" separator="," close=")">#{item}</foreach></if>
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</if>
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<if test="patientIds != null">
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<if test="@java.util.Arrays@stream(patientIds.toArray()).distinct().count() == 1">
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<bind name="patientArray" value="@org.cbioportal.legacy.persistence.mybatis.util.SqlUtils@listToArray(patientIds)" />
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cancer_study.cancer_study_identifier = #{studyIds[0]} AND
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patient.stable_id IN (
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#{patientArray, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
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)
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</if>
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<if test="@java.util.Arrays@stream(patientIds.toArray()).distinct().count() > 1">
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<bind name="patientUniqueKeys" value="@org.cbioportal.legacy.persistence.mybatis.util.SqlUtils@combineStudyAndPatientIds(studyIds, patientIds)" />
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CONCAT(cancer_study.cancer_study_identifier, ':', patient.stable_id) IN (
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#{patientUniqueKeys, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
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)
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</if>
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</if>
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<if test="!clinicalEvents.isEmpty()">
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AND
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<foreach item="element" collection="clinicalEvents" open="(" separator="OR " close=")">
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<if test="element.attributes == null || element.attributes.isEmpty()">
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clinical_event.event_type = #{element.eventType}
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</if>
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<if test="element.attributes != null and !element.attributes.isEmpty()">
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(CONCAT(clinical_event.event_type, '_', clinical_event_data.key, '_', clinical_event_data.value)) IN
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<foreach item="attribute" collection="element.attributes" open="(" separator="," close=")">
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CONCAT(#{element.eventType}, '_', #{attribute.key}, '_', #{attribute.value})
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</foreach>
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</if>
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</foreach>
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</if>
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</where>
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GROUP BY
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clinical_event.patient_id, cancer_study.cancer_study_identifier;
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</select>
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<resultMap id="clinicalEventsResultMap" type="org.cbioportal.legacy.model.ClinicalEvent">
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<result property="eventType" column="eventType"/>
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<collection property="attributes" ofType="org.cbioportal.legacy.model.ClinicalEventData">
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<result property="key" column="key"/>
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<result property="value" column="value"/>
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</collection>
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</resultMap>
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<select id="getClinicalEventsMeta" resultMap="clinicalEventsResultMap">
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SELECT
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LOWER(clinical_event.event_type) AS eventType,
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LOWER(clinical_event_data.key) AS "key",
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LOWER(clinical_event_data.value) AS value
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FROM clinical_event
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INNER JOIN patient ON clinical_event.patient_id = patient.internal_id
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INNER JOIN clinical_event_data ON clinical_event.clinical_event_id = clinical_event_data.clinical_event_id
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INNER JOIN cancer_study ON patient.cancer_study_id = cancer_study.cancer_study_id
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<where>
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<if test="patientIds == null and studyIds != null">
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cancer_study.cancer_study_identifier IN
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<if test="studyIds.isEmpty()">(NULL)</if>
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<if test="!studyIds.isEmpty()"><foreach item="item" collection="studyIds" open="(" separator="," close=")">#{item}</foreach></if>
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</if>
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<if test="patientIds != null">
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<if test="@java.util.Arrays@stream(patientIds.toArray()).distinct().count() == 1">
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<bind name="patientArray" value="@org.cbioportal.legacy.persistence.mybatis.util.SqlUtils@listToArray(patientIds)" />
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cancer_study.cancer_study_identifier = #{studyIds[0]} AND
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patient.stable_id IN (
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#{patientArray, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
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)
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</if>
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<if test="@java.util.Arrays@stream(patientIds.toArray()).distinct().count() > 1">
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<bind name="patientUniqueKeys" value="@org.cbioportal.legacy.persistence.mybatis.util.SqlUtils@combineStudyAndPatientIds(studyIds, patientIds)" />
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CONCAT(cancer_study.cancer_study_identifier, ':', patient.stable_id) IN (
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#{patientUniqueKeys, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
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)
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</if>
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</if>
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<if test="!clinicalEvents.isEmpty()">
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AND
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<foreach item="element" collection="clinicalEvents" open="(" separator="OR " close=")">
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<if test="element.attributes == null || element.attributes.isEmpty()">
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clinical_event.event_type = #{element.eventType}
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</if>
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<if test="element.attributes != null and !element.attributes.isEmpty()">
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(CONCAT(clinical_event.event_type, '_', clinical_event_data.key)) IN
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<foreach item="attribute" collection="element.attributes" open="(" separator="," close=")">
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CONCAT(#{element.eventType}, '_', #{attribute.key})
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</foreach>
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</if>
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</foreach>
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</if>
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</where>
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GROUP BY clinical_event.event_type , clinical_event_data.key, clinical_event_data.value;
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</select>
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</mapper>

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