Skip to content

Commit

Permalink
unify numerical data filters in one sql
Browse files Browse the repository at this point in the history
  • Loading branch information
@onursumer
onursumer committed Nov 22, 2024
1 parent b186f92 commit d9459f3
Showing 1 changed file with 94 additions and 151 deletions.
245 changes: 94 additions & 151 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -272,6 +272,77 @@
</foreach>
</sql>

<sql id="applyNumericalDataFilter">
<foreach item="dataFilterValue" collection="${data_filter_collection}" open="((" separator=") OR (" close="))">
<trim prefix="" prefixOverrides="AND">
<!-- Special case: NA -->
<if test="dataFilterValue.value eq 'NA'">
AND
<include refid="isAttributeValueNA">
<property name="attribute_value" value="${attribute_value}"/>
</include>
</if>
<!--
Special case: Non-numerical value within numerical filter collection.
Even if the data type is numerical we can still have non-numerical values
such as "UNKNOWN", "NOT COLLECTED", "NOT RELEASED", etc.
-->
<if test="dataFilterValue.value != null">
AND (
<include refid="normalizeAttributeValue">
<property name="attribute_value" value="${attribute_value}"/>
</include>
) ILIKE #{dataFilterValue.value}
</if>
<!--
Special case: Numerical range values such as <18, >=90, etc.
We need to make sure to treat these values as numerical for filtering purposes.
-->
<if test="dataFilterValue.start != null and dataFilterValue.end == null">
AND match(${attribute_value}, '^>?=?[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start == null and dataFilterValue.end != null">
AND match(${attribute_value}, '^&lt;?=?[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start != null and dataFilterValue.end != null">
AND match(${attribute_value}, '^[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<!--
Actual filtering of values that fall within the range of (start, end].
Note that start value is exclusive, but end value is inclusive.
-->
<if test="dataFilterValue.start != null or dataFilterValue.end != null">
<choose>
<when test="dataFilterValue.start == dataFilterValue.end">
AND abs(
minus(
<include refid="castStringValueToFloat">
<property name="attribute_value" value="${attribute_value}"/>
</include>,
cast(#{dataFilterValue.start} as float)
)
) &lt; exp(-11)
</when>
<otherwise>
<if test="dataFilterValue.start != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="${attribute_value}"/>
</include> &gt; cast(#{dataFilterValue.start} as float)
</if>
<if test="dataFilterValue.end != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="${attribute_value}"/>
</include> &lt;= cast(#{dataFilterValue.end} as float)
</if>
</otherwise>
</choose>
</if>
</trim>
</foreach>
</sql>

<sql id="applyClinicalDataCountFilter">
<foreach item="clinicalDataFilter"
collection="studyViewFilterHelper.studyViewFilter.clinicalDataFilters"
Expand All @@ -288,11 +359,11 @@
</include>
</when>
<otherwise>
<include refid="numericalClinicalDataCountFilter">
<property name="unique_id" value="sample_unique_id"/>
<property name="table_name" value="clinical_data_derived"/>
<property name="type" value="sample"/>
</include>
<include refid="numericalClinicalDataCountFilter">
<property name="unique_id" value="sample_unique_id"/>
<property name="table_name" value="clinical_data_derived"/>
<property name="type" value="sample"/>
</include>
</otherwise>
</choose>

Expand Down Expand Up @@ -362,64 +433,15 @@

<!-- if non-NA is selected, prepare non-NA samples -->
<if test="userSelectsNumericalValue">
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">
<if test="dataFilterValue.value eq 'NA'">
AND
<include refid="isAttributeValueNA">
<property name="attribute_value" value="attribute_value"/>
</include>
</if>
<if test="dataFilterValue.value != null">
AND (
<include refid="normalizeAttributeValue">
<property name="attribute_value" value="attribute_value"/>
</include>
) ILIKE #{dataFilterValue.value}
</if>
<if test="dataFilterValue.start != null and dataFilterValue.end == null">
AND match(attribute_value, '^>?=?[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start == null and dataFilterValue.end != null">
AND match(attribute_value, '^&lt;?=?[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start != null and dataFilterValue.end != null">
AND match(attribute_value, '^[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start != null or dataFilterValue.end != null">
<choose>
<when test="dataFilterValue.start == dataFilterValue.end">
AND abs(
minus(
<include refid="castStringValueToFloat">
<property name="attribute_value" value="attribute_value"/>
</include>,
cast(#{dataFilterValue.start} as float)
)
) &lt; exp(-11)
</when>
<otherwise>
<if test="dataFilterValue.start != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="attribute_value"/>
</include> &gt; cast(#{dataFilterValue.start} as float)
</if>
<if test="dataFilterValue.end != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="attribute_value"/>
</include> &lt;= cast(#{dataFilterValue.end} as float)
</if>
</otherwise>
</choose>
</if>
</trim>
</foreach>
SELECT ${unique_id}
FROM ${table_name}
WHERE attribute_name = #{clinicalDataFilter.attributeId} AND
type='${type}'
AND
<include refid="applyNumericalDataFilter">
<property name="attribute_value" value="attribute_value"/>
<property name="data_filter_collection" value="clinicalDataFilter.values"/>
</include>
</if>
)
</sql>
Expand Down Expand Up @@ -501,47 +523,10 @@
SELECT DISTINCT sample_unique_id
FROM (<include refid="selectAllNumericalGeneticAlterations"/>) AS genomic_numerical_query
WHERE
<foreach item="dataFilterValue" collection="genomicDataFilter.values" open="((" separator=") OR (" close="))">
<trim prefix="" prefixOverrides="AND">
<if test="dataFilterValue.start != null and dataFilterValue.end == null">
AND match(alteration_value, '^>?=?[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start == null and dataFilterValue.end != null">
AND match(alteration_value, '^&lt;?=?[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start != null and dataFilterValue.end != null">
AND match(alteration_value, '^[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start != null or dataFilterValue.end != null">
<choose>
<when test="dataFilterValue.start == dataFilterValue.end">
AND abs(
minus(
<include refid="castStringValueToFloat">
<property name="attribute_value" value="alteration_value"/>
</include>,
cast(#{dataFilterValue.start} as float)
)
) &lt; exp(-11)
</when>
<otherwise>
<if test="dataFilterValue.start != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="alteration_value"/>
</include> &gt; cast(#{dataFilterValue.start} as float)
</if>
<if test="dataFilterValue.end != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="alteration_value"/>
</include> &lt;= cast(#{dataFilterValue.end} as float)
</if>
</otherwise>
</choose>
</if>
</trim>
</foreach>
<include refid="applyNumericalDataFilter">
<property name="attribute_value" value="alteration_value"/>
<property name="data_filter_collection" value="genomicDataFilter.values"/>
</include>
</if>
</sql>

Expand Down Expand Up @@ -603,53 +588,11 @@
<include refid="normalizeAttributeValue">
<property name="attribute_value" value="value"/>
</include> != 'NA'
<foreach item="dataFilterValue" collection="genericAssayDataFilter.values" open=" AND ((" separator=") OR (" close="))">
<trim prefix="" prefixOverrides="AND">
<if test="dataFilterValue.value eq 'NA'">
AND
<include refid="isAttributeValueNA">
<property name="attribute_value" value="value"/>
</include>
</if>
<if test="dataFilterValue.start != null and dataFilterValue.end == null">
AND match(value, '^>?=?[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start == null and dataFilterValue.end != null">
AND match(value, '^&lt;?=?[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start != null and dataFilterValue.end != null">
AND match(value, '^[-+]?[0-9]*[.,]?[0-9]+$')
</if>
<if test="dataFilterValue.start != null or dataFilterValue.end != null">
<choose>
<when test="dataFilterValue.start == dataFilterValue.end">
AND abs(
minus(
<include refid="castStringValueToFloat">
<property name="attribute_value" value="value"/>
</include>,
cast(#{dataFilterValue.start} as float)
)
) &lt; exp(-11)
</when>
<otherwise>
<if test="dataFilterValue.start != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="value"/>
</include> &gt; cast(#{dataFilterValue.start} as float)
</if>
<if test="dataFilterValue.end != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="value"/>
</include> &lt;= cast(#{dataFilterValue.end} as float)
</if>
</otherwise>
</choose>
</if>
</trim>
</foreach>
AND
<include refid="applyNumericalDataFilter">
<property name="attribute_value" value="value"/>
<property name="data_filter_collection" value="genericAssayDataFilter.values"/>
</include>
</if>
</sql>

Expand Down

0 comments on commit d9459f3

Please sign in to comment.