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Rfc80/add na clinical data filtering #11050

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merged 4 commits into from
Oct 8, 2024
Merged

Rfc80/add na clinical data filtering #11050

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06c8b4c
Add Categorical Clinical Attribute NA filtering
haynescd Oct 7, 2024
84304f5
Add Numerical Clinical Data NA Filtering
haynescd Oct 7, 2024
696b2c2
Remove Union
haynescd Oct 8, 2024
7e303fd
Add api tests for clinical data NA filtering
alisman Oct 8, 2024
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96 changes: 83 additions & 13 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -317,6 +317,46 @@
</sql>

<sql id="numericalClinicalDataCountFilter">

<!-- check if 'NA' is selected -->
<bind name="userSelectsNA" value="false" />
<bind name="userSelectsNumericalValue" value="false" />
<foreach item="dataFilterValue" collection="clinicalDataFilter.values">
<choose>
<when test="dataFilterValue.value == 'NA'">
<bind name="userSelectsNA" value="true" />
</when>
<otherwise>
<bind name="userSelectsNumericalValue" value="true" />
</otherwise>
</choose>
</foreach>
(
<!-- if 'NA' is selected, prepare NA samples -->
<if test="userSelectsNA">
SELECT DISTINCT ${unique_id}
FROM sample_derived sd
LEFT JOIN (<include refid="selectAllClinicalDataByAttribute"/>) AS categorical_clinical_data
ON
<choose>
<when test="'${type}' == 'sample'">
sd.sample_unique_id = categorical_clinical_data.sample_unique_id
</when>
<otherwise>
sd.patient_unique_id = categorical_clinical_data.patient_unique_id
</otherwise>
</choose>
WHERE empty(attribute_value)
AND EXISTS (<include refid="selectAllClinicalDataByAttribute"/>)
</if>

<!-- if both 'NA' and non-NA are selected, union them together -->
<if test="userSelectsNA and userSelectsNumericalValue">
UNION ALL
</if>

<!-- if non-NA is selected, prepare non-NA samples -->
<if test="userSelectsNumericalValue">
SELECT ${unique_id}
FROM ${table_name}
WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND
Expand Down Expand Up @@ -368,23 +408,53 @@
</if>
</trim>
</foreach>
</if>
)
</sql>

<sql id="categoricalClinicalDataCountFilter">
SELECT ${unique_id}
FROM ${table_name}
WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND
type='${type}'
<foreach item="dataFilterValue" collection="clinicalDataFilter.values" open=" AND ((" separator=") OR (" close="))">
<trim prefix="" prefixOverrides="AND">
AND (
<include refid="normalizeAttributeValue">
<property name="attribute_value" value="attribute_value"/>
</include>
) ILIKE '${dataFilterValue.value}'
</trim>
<sql id="selectAllClinicalDataByAttribute">
SELECT sample_unique_id, patient_unique_id, attribute_value
FROM clinical_data_derived
WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND type='${type}'
AND cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterHelper.studyViewFilter.studyIds" open="(" separator="," close=")">
#{studyId}

</foreach>
</sql>

<sql id="categoricalClinicalDataCountFilter">
(
SELECT ${unique_id}
FROM sample_derived sd
LEFT JOIN (<include refid="selectAllClinicalDataByAttribute"/>) AS categorical_clinical_data
ON
<choose>
<when test="'${type}' == 'sample'">
sd.sample_unique_id = categorical_clinical_data.sample_unique_id
</when>
<otherwise>
sd.patient_unique_id = categorical_clinical_data.patient_unique_id
</otherwise>
</choose>
WHERE
<foreach item="dataFilterValue" collection="clinicalDataFilter.values" open=" ((" separator=") OR (" close="))">
<choose>
<when test="dataFilterValue.value == 'NA'">
empty(attribute_value)
</when>
<otherwise>
(
<include refid="normalizeAttributeValue">
<property name="attribute_value" value="attribute_value"/>
</include>
) ILIKE '${dataFilterValue.value}'
</otherwise>
</choose>
</foreach>
AND EXISTS (<include refid="selectAllClinicalDataByAttribute"/>)
)
</sql>

<sql id="numericalGenomicDataFilter">
<!-- check if 'NA' is selected -->
Expand Down
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