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Change mybatis mapper to use uppercase table and column names
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@pvannierop
pvannierop committed Apr 18, 2024
1 parent 8b07d3f commit c267a89
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Showing 32 changed files with 1,250 additions and 1,250 deletions.
252 changes: 126 additions & 126 deletions src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml
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22 changes: 11 additions & 11 deletions src/main/resources/org/cbioportal/persistence/mybatis/AlterationDriverAnnotationMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,19 +5,19 @@

<select id="getAlterationDriverAnnotations" resultType="org.cbioportal.model.AlterationDriverAnnotation">
SELECT
alteration_driver_annotation.ALTERATION_EVENT_ID as alterationEventId,
alteration_driver_annotation.GENETIC_PROFILE_ID as geneticProfileId,
alteration_driver_annotation.SAMPLE_ID as sampleId,
alteration_driver_annotation.DRIVER_FILTER as driverFilter,
alteration_driver_annotation.DRIVER_FILTER_ANNOTATION as driverFilterAnnotation,
alteration_driver_annotation.DRIVER_TIERS_FILTER as driverTiersFilter,
alteration_driver_annotation.DRIVER_TIERS_FILTER_ANNOTATION as driverTiersFilterAnnotation
FROM alteration_driver_annotation
INNER JOIN genetic_profile ON
genetic_profile.GENETIC_PROFILE_ID = alteration_driver_annotation.GENETIC_PROFILE_ID
ALTERATION_DRIVER_ANNOTATION.ALTERATION_EVENT_ID as alterationEventId,
ALTERATION_DRIVER_ANNOTATION.GENETIC_PROFILE_ID as geneticProfileId,
ALTERATION_DRIVER_ANNOTATION.SAMPLE_ID as sampleId,
ALTERATION_DRIVER_ANNOTATION.DRIVER_FILTER as driverFilter,
ALTERATION_DRIVER_ANNOTATION.DRIVER_FILTER_ANNOTATION as driverFilterAnnotation,
ALTERATION_DRIVER_ANNOTATION.DRIVER_TIERS_FILTER as driverTiersFilter,
ALTERATION_DRIVER_ANNOTATION.DRIVER_TIERS_FILTER_ANNOTATION as driverTiersFilterAnnotation
FROM ALTERATION_DRIVER_ANNOTATION
INNER JOIN GENETIC_PROFILE ON
GENETIC_PROFILE.GENETIC_PROFILE_ID = ALTERATION_DRIVER_ANNOTATION.GENETIC_PROFILE_ID
<where>
<if test="molecularProfileIds != null and !molecularProfileIds.isEmpty()">
genetic_profile.STABLE_ID IN
GENETIC_PROFILE.STABLE_ID IN
<foreach item="id" collection="molecularProfileIds" open="(" separator="," close=")">
#{id}
</foreach>
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20 changes: 10 additions & 10 deletions src/main/resources/org/cbioportal/persistence/mybatis/CancerTypeMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,13 @@
<mapper namespace="org.cbioportal.persistence.mybatis.CancerTypeMapper">

<sql id="select">
type_of_cancer.TYPE_OF_CANCER_ID AS "${prefix}typeOfCancerId"
TYPE_OF_CANCER.TYPE_OF_CANCER_ID AS "${prefix}typeOfCancerId"
<if test="projection == 'SUMMARY' || projection == 'DETAILED'">
,
type_of_cancer.NAME AS "${prefix}name",
type_of_cancer.DEDICATED_COLOR AS "${prefix}dedicatedColor",
type_of_cancer.SHORT_NAME AS "${prefix}shortName",
type_of_cancer.PARENT AS "${prefix}parent"
TYPE_OF_CANCER.NAME AS "${prefix}name",
TYPE_OF_CANCER.DEDICATED_COLOR AS "${prefix}dedicatedColor",
TYPE_OF_CANCER.SHORT_NAME AS "${prefix}shortName",
TYPE_OF_CANCER.PARENT AS "${prefix}parent"
</if>
</sql>

Expand All @@ -19,12 +19,12 @@
<include refid="select">
<property name="prefix" value=""/>
</include>
FROM type_of_cancer
FROM TYPE_OF_CANCER
<if test="sortBy != null and projection != 'ID'">
ORDER BY "${sortBy}" ${direction}
</if>
<if test="projection == 'ID'">
ORDER BY type_of_cancer.TYPE_OF_CANCER_ID ASC
ORDER BY TYPE_OF_CANCER.TYPE_OF_CANCER_ID ASC
</if>
<if test="limit != null and limit != 0">
LIMIT #{limit} OFFSET #{offset}
Expand All @@ -34,16 +34,16 @@
<select id="getMetaCancerTypes" resultType="org.cbioportal.model.meta.BaseMeta">
SELECT
COUNT(*) AS "totalCount"
FROM type_of_cancer
FROM TYPE_OF_CANCER
</select>

<select id="getCancerType" resultType="org.cbioportal.model.TypeOfCancer">
SELECT
<include refid="select">
<property name="prefix" value=""/>
</include>
FROM type_of_cancer
WHERE type_of_cancer.TYPE_OF_CANCER_ID = #{cancerTypeId}
FROM TYPE_OF_CANCER
WHERE TYPE_OF_CANCER.TYPE_OF_CANCER_ID = #{cancerTypeId}
</select>

</mapper>
112 changes: 56 additions & 56 deletions src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,46 +4,46 @@
<mapper namespace="org.cbioportal.persistence.mybatis.ClinicalAttributeMapper">

<sql id="select">
clinical_attribute_meta.ATTR_ID AS "${prefix}attrId",
cancer_study.CANCER_STUDY_IDENTIFIER AS "${prefix}cancerStudyIdentifier",
clinical_attribute_meta.CANCER_STUDY_ID AS "${prefix}cancerStudyId",
clinical_attribute_meta.PATIENT_ATTRIBUTE AS "${prefix}patientAttribute",
clinical_attribute_meta.DISPLAY_NAME AS "${prefix}displayName"
CLINICAL_ATTRIBUTE_META.ATTR_ID AS "${prefix}attrId",
CANCER_STUDY.CANCER_STUDY_IDENTIFIER AS "${prefix}cancerStudyIdentifier",
CLINICAL_ATTRIBUTE_META.CANCER_STUDY_ID AS "${prefix}cancerStudyId",
CLINICAL_ATTRIBUTE_META.PATIENT_ATTRIBUTE AS "${prefix}patientAttribute",
CLINICAL_ATTRIBUTE_META.DISPLAY_NAME AS "${prefix}displayName"
<if test="projection == 'SUMMARY' || projection == 'DETAILED'">
,
clinical_attribute_meta.DESCRIPTION AS "${prefix}description",
clinical_attribute_meta.DATATYPE AS "${prefix}datatype",
clinical_attribute_meta.PRIORITY AS "${prefix}priority"
CLINICAL_ATTRIBUTE_META.DESCRIPTION AS "${prefix}description",
CLINICAL_ATTRIBUTE_META.DATATYPE AS "${prefix}datatype",
CLINICAL_ATTRIBUTE_META.PRIORITY AS "${prefix}priority"
</if>
</sql>

<sql id="joinSample">
INNER JOIN sample ON clinical_sample.INTERNAL_ID = sample.INTERNAL_ID
INNER JOIN patient ON sample.PATIENT_ID = patient.INTERNAL_ID
INNER JOIN cancer_study ON patient.CANCER_STUDY_ID = cancer_study.CANCER_STUDY_ID
INNER JOIN SAMPLE ON CLINICAL_SAMPLE.INTERNAL_ID = SAMPLE.INTERNAL_ID
INNER JOIN PATIENT ONSAMPLE.PATIENT_ID = PATIENT.INTERNAL_ID
INNER JOIN CANCER_STUDY ON PATIENT.CANCER_STUDY_ID = CANCER_STUDY.CANCER_STUDY_ID
</sql>

<sql id="joinPatient">
INNER JOIN patient ON clinical_patient.INTERNAL_ID = patient.INTERNAL_ID
INNER JOIN sample ON sample.PATIENT_ID = patient.INTERNAL_ID
INNER JOIN cancer_study ON patient.CANCER_STUDY_ID = cancer_study.CANCER_STUDY_ID
INNER JOIN PATIENT ONCLINICAL_PATIENT.INTERNAL_ID = PATIENT.INTERNAL_ID
INNER JOIN SAMPLE ON SAMPLE.PATIENT_ID = PATIENT.INTERNAL_ID
INNER JOIN CANCER_STUDY ON PATIENT.CANCER_STUDY_ID = CANCER_STUDY.CANCER_STUDY_ID
</sql>

<sql id="whereSample">
<where>
<if test="sampleIds == null">
cancer_study.CANCER_STUDY_IDENTIFIER = #{studyIds[0]}
CANCER_STUDY.CANCER_STUDY_IDENTIFIER = #{studyIds[0]}
</if>
<if test="sampleIds != null">
<if test="@java.util.Arrays@stream(studyIds.toArray()).distinct().count() == 1">
cancer_study.CANCER_STUDY_IDENTIFIER = #{studyIds[0]} AND
sample.STABLE_ID IN
CANCER_STUDY.CANCER_STUDY_IDENTIFIER = #{studyIds[0]} AND
SAMPLE.STABLE_ID IN
<foreach item="item" collection="sampleIds" open="(" separator="," close=")">
#{item}
</foreach>
</if>
<if test="@java.util.Arrays@stream(studyIds.toArray()).distinct().count() > 1">
(cancer_study.CANCER_STUDY_IDENTIFIER, sample.STABLE_ID) IN
(CANCER_STUDY.CANCER_STUDY_IDENTIFIER, SAMPLE.STABLE_ID) IN
<foreach index="i" collection="sampleIds" open="(" separator="," close=")">
(#{studyIds[${i}]}, #{sampleIds[${i}]})
</foreach>
Expand All @@ -54,12 +54,12 @@

<sql id="whereBySampleListId">
<where>
sample.INTERNAL_ID IN
SAMPLE.INTERNAL_ID IN
(
SELECT sample_list_list.SAMPLE_ID FROM sample_list_list
INNER JOIN sample_list ON sample_list_list.LIST_ID = sample_list.LIST_ID
WHERE sample_list.STABLE_ID = #{sampleListId}
AND sample_list_list.SAMPLE_ID = sample.INTERNAL_ID
SELECT SAMPLE_LIST_LIST.SAMPLE_ID FROM SAMPLE_LIST_LIST
INNER JOIN SAMPLE_LIST ON SAMPLE_LIST_LIST.LIST_ID = SAMPLE_LIST.LIST_ID
WHERE SAMPLE_LIST.STABLE_ID = #{sampleListId}
AND SAMPLE_LIST_LIST.SAMPLE_ID = SAMPLE.INTERNAL_ID
)
</where>
</sql>
Expand All @@ -69,11 +69,11 @@
<include refid="select">
<property name="prefix" value=""/>
</include>
FROM clinical_attribute_meta
INNER JOIN cancer_study ON clinical_attribute_meta.CANCER_STUDY_ID = cancer_study.CANCER_STUDY_ID
FROM CLINICAL_ATTRIBUTE_META
INNER JOIN CANCER_STUDY ON CLINICAL_ATTRIBUTE_META.CANCER_STUDY_ID = CANCER_STUDY.CANCER_STUDY_ID
<where>
<if test="studyIds != null and !studyIds.isEmpty()">
cancer_study.CANCER_STUDY_IDENTIFIER IN
CANCER_STUDY.CANCER_STUDY_IDENTIFIER IN
<foreach item="item" collection="studyIds" open="(" separator="," close=")">
#{item}
</foreach>
Expand All @@ -83,7 +83,7 @@
ORDER BY "${sortBy}" ${direction}
</if>
<if test="projection == 'ID'">
ORDER BY clinical_attribute_meta.ATTR_ID ASC
ORDER BY CLINICAL_ATTRIBUTE_META.ATTR_ID ASC
</if>
<if test="limit != null and limit != 0">
LIMIT #{limit} OFFSET #{offset}
Expand All @@ -93,11 +93,11 @@
<select id="getMetaClinicalAttributes" resultType="org.cbioportal.model.meta.BaseMeta">
SELECT
COUNT(*) AS "totalCount"
FROM clinical_attribute_meta
INNER JOIN cancer_study ON clinical_attribute_meta.CANCER_STUDY_ID = cancer_study.CANCER_STUDY_ID
FROM CLINICAL_ATTRIBUTE_META
INNER JOIN CANCER_STUDY ON CLINICAL_ATTRIBUTE_META.CANCER_STUDY_ID = CANCER_STUDY.CANCER_STUDY_ID
<where>
<if test="list != null and !list.isEmpty()">
cancer_study.CANCER_STUDY_IDENTIFIER IN
CANCER_STUDY.CANCER_STUDY_IDENTIFIER IN
<foreach item="item" collection="list" open="(" separator="," close=")">
#{item}
</foreach>
Expand All @@ -110,68 +110,68 @@
<include refid="select">
<property name="prefix" value=""/>
</include>
FROM clinical_attribute_meta
INNER JOIN cancer_study ON clinical_attribute_meta.CANCER_STUDY_ID = cancer_study.CANCER_STUDY_ID
WHERE clinical_attribute_meta.ATTR_ID = #{clinicalAttributeId}
AND cancer_study.CANCER_STUDY_IDENTIFIER = #{studyId}
FROM CLINICAL_ATTRIBUTE_META
INNER JOIN CANCER_STUDY ON CLINICAL_ATTRIBUTE_META.CANCER_STUDY_ID = CANCER_STUDY.CANCER_STUDY_ID
WHERE CLINICAL_ATTRIBUTE_META.ATTR_ID = #{clinicalAttributeId}
AND CANCER_STUDY.CANCER_STUDY_IDENTIFIER = #{studyId}
</select>

<select id="getClinicalAttributeCountsBySampleIds" resultType="org.cbioportal.model.ClinicalAttributeCount">
SELECT count(*) as "count",
clinical_sample.ATTR_ID as "attrId"
FROM clinical_sample
CLINICAL_SAMPLE.ATTR_ID as "attrId"
FROM CLINICAL_SAMPLE
<include refid="joinSample"/>
<include refid="whereSample"/>
GROUP BY clinical_sample.ATTR_ID
GROUP BY CLINICAL_SAMPLE.ATTR_ID

UNION

SELECT count(*) as "count",
clinical_patient.ATTR_ID as "attrId"
FROM clinical_patient
CLINICAL_PATIENT.ATTR_ID as "attrId"
FROM CLINICAL_PATIENT
<include refid="joinPatient"/>
<include refid="whereSample"/>
GROUP BY clinical_patient.ATTR_ID
GROUP BY CLINICAL_PATIENT.ATTR_ID
</select>

<select id="getClinicalAttributeCountsBySampleListId" resultType="org.cbioportal.model.ClinicalAttributeCount">
SELECT count(*) as "count",
clinical_sample.ATTR_ID as "attrId"
FROM clinical_sample
CLINICAL_SAMPLE.ATTR_ID as "attrId"
FROM CLINICAL_SAMPLE
<include refid="joinSample"/>
<include refid="whereBySampleListId"/>
GROUP BY clinical_sample.ATTR_ID
GROUP BY CLINICAL_SAMPLE.ATTR_ID

UNION

SELECT count(*) as "count",
clinical_patient.ATTR_ID as "attrId"
FROM clinical_patient
CLINICAL_PATIENT.ATTR_ID as "attrId"
FROM CLINICAL_PATIENT
<include refid="joinPatient"/>
<include refid="whereBySampleListId"/>
GROUP BY clinical_patient.ATTR_ID
GROUP BY CLINICAL_PATIENT.ATTR_ID
</select>

<select id="getClinicalAttributesByStudyIdsAndAttributeIds" resultType="org.cbioportal.model.ClinicalAttribute">
SELECT
clinical_attribute_meta.ATTR_ID AS "attrId",
cancer_study.CANCER_STUDY_IDENTIFIER AS "cancerStudyIdentifier",
clinical_attribute_meta.CANCER_STUDY_ID AS "cancerStudyId",
clinical_attribute_meta.PATIENT_ATTRIBUTE AS "patientAttribute",
clinical_attribute_meta.DISPLAY_NAME AS "displayName",
clinical_attribute_meta.DATATYPE AS "datatype"
FROM clinical_attribute_meta
INNER JOIN cancer_study ON clinical_attribute_meta.CANCER_STUDY_ID = cancer_study.CANCER_STUDY_ID
CLINICAL_ATTRIBUTE_META.ATTR_ID AS "attrId",
CANCER_STUDY.CANCER_STUDY_IDENTIFIER AS "cancerStudyIdentifier",
CLINICAL_ATTRIBUTE_META.CANCER_STUDY_ID AS "cancerStudyId",
CLINICAL_ATTRIBUTE_META.PATIENT_ATTRIBUTE AS "patientAttribute",
CLINICAL_ATTRIBUTE_META.DISPLAY_NAME AS "displayName",
CLINICAL_ATTRIBUTE_META.DATATYPE AS "datatype"
FROM CLINICAL_ATTRIBUTE_META
INNER JOIN CANCER_STUDY ON CLINICAL_ATTRIBUTE_META.CANCER_STUDY_ID = CANCER_STUDY.CANCER_STUDY_ID
<where>
<if test="studyIds != null and !studyIds.isEmpty()">
cancer_study.CANCER_STUDY_IDENTIFIER IN
CANCER_STUDY.CANCER_STUDY_IDENTIFIER IN
<foreach item="item" collection="studyIds" open="(" separator="," close=")">
#{item}
</foreach>
</if>
<if test="attributeIds != null and !attributeIds.isEmpty()">
AND
clinical_attribute_meta.ATTR_ID IN
CLINICAL_ATTRIBUTE_META.ATTR_ID IN
<foreach item="item" collection="attributeIds" open="(" separator="," close=")">
#{item}
</foreach>
Expand Down
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