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@fuzhaoyuan
fuzhaoyuan committed Sep 27, 2024
1 parent 98ee298 commit dea9647
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Showing 2 changed files with 23 additions and 15 deletions.
36 changes: 21 additions & 15 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 @@ -140,10 +140,12 @@
<if test="studyViewFilterHelper.studyViewFilter.genomicDataFilters != null and !studyViewFilterHelper.studyViewFilter.genomicDataFilters.isEmpty()">
<foreach item="genomicDataFilter" collection="studyViewFilterHelper.studyViewFilter.genomicDataFilters" open="INTERSECT" separator="INTERSECT">
<choose>
<!-- Currently we only handle CNA in categorical genomic data filters. Future categorical profile types will involve updates to this part-->
<when test="genomicDataFilter.profileType == 'cna' or genomicDataFilter.profileType == 'gistic'">
<include refid="categoricalGenomicDataFilter"/>
<include refid="categoricalGenomicDataFilterForCNA"/>
</when>
<otherwise>
<!-- when you make selection in genomic binning chart, it will still send genomic data filter -->
<include refid="numericalGenomicDataFilter"/>
</otherwise>
</choose>
Expand Down Expand Up @@ -386,31 +388,33 @@

<sql id="numericalGenomicDataFilter">
<!-- check if 'NA' is selected -->
<bind name="containsNA" value="false" />
<bind name="containsNumericalValue" value="false" />
<bind name="userSelectsNA" value="false" />
<bind name="userSelectsNumericalValue" value="false" />
<foreach item="dataFilterValue" collection="genomicDataFilter.values">
<choose>
<when test="dataFilterValue.value == 'NA'">
<bind name="containsNA" value="true" />
<bind name="userSelectsNA" value="true" />
</when>
<otherwise>
<bind name="containsNumericalValue" value="true" />
<bind name="userSelectsNumericalValue" value="true" />
</otherwise>
</choose>
</foreach>
<if test="containsNA">
<!-- if 'NA' is selected, prepare NA samples -->
<if test="userSelectsNA">
SELECT DISTINCT sd.sample_unique_id
FROM sample_derived sd
LEFT JOIN (<include refid="selectAllGenomicNumericalSamples"/>) AS sthiswrongagain ON sd.sample_unique_id = sthiswrongagain.sample_unique_id
LEFT JOIN (<include refid="selectAllNumericalGeneticAlterations"/>) AS genomic_numerical_query ON sd.sample_unique_id = genomic_numerical_query.sample_unique_id
WHERE alteration_value IS null
</if>
<if test="containsNA and containsNumericalValue">
<!-- if both 'NA' and non-NA are selected, union them together -->
<if test="userSelectsNA and userSelectsNumericalValue">
UNION ALL
</if>
<if test="containsNumericalValue">
SELECT DISTINCT sd.sample_unique_id
FROM sample_derived sd
INNER JOIN (<include refid="selectAllGenomicNumericalSamples"/>) AS genomic_numerical_query ON sd.sample_unique_id = genomic_numerical_query.sample_unique_id
<!-- if non-NA is selected, prepare non-NA samples -->
<if test="userSelectsNumericalValue">
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">
Expand Down Expand Up @@ -456,9 +460,9 @@
</if>
</sql>

<sql id="selectAllGenomicNumericalSamples">
<sql id="selectAllNumericalGeneticAlterations">
SELECT sample_unique_id, alteration_value
FROM genetic_alteration_derived comeonwhyisitnotworking
FROM genetic_alteration_derived
WHERE profile_type = #{genomicDataFilter.profileType}
AND hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
AND cancer_study_identifier IN
Expand Down Expand Up @@ -603,7 +607,7 @@
</if>
</sql>

<sql id="categoricalGenomicDataFilter">
<sql id="categoricalGenomicDataFilterForCNA">
<!-- filter on study to reduce query size in preparation of the following LEFT JOIN -->
WITH cna_query AS (
SELECT sample_unique_id, alteration_value
Expand All @@ -625,7 +629,9 @@
</foreach>
<foreach item="dataFilterValue" collection="genomicDataFilter.values" open="AND (" separator=" OR " close=")">
<choose>
<!-- NA value samples -->
<when test="dataFilterValue.value == 'NA'">alteration_value IS null</when>
<!-- non-NA value samples -->
<otherwise>alteration_value == #{dataFilterValue.value}</otherwise>
</choose>
</foreach>
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2 changes: 2 additions & 0 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -236,6 +236,7 @@
<!-- for /genomic-data-counts/fetch - (returns GenomicDataCountItem objects) -->
<select id="getCNACounts" resultMap="GenomicDataCountItemResultMap">
<bind name="profileType" value="genomicDataFilters[0].profileType" />
<!-- get all non-NA value samples. A caveat here is that if user select only 'NA', this query will return empty (null) thus we need the 2 coalesce() below to handle this case -->
WITH cna_query as (
SELECT
hugo_gene_symbol as hugoGeneSymbol,
Expand Down Expand Up @@ -579,6 +580,7 @@

<select id="getGenomicDataBinCounts" resultType="org.cbioportal.model.ClinicalDataCount">
<bind name="profileType" value="genomicDataBinFilters[0].profileType" />
<!-- get all non-NA value samples. A caveat here is that if user select only 'NA', this query will return empty (null) thus we need the 2 coalesce() below to handle this case -->
WITH genomic_numerical_query AS (
SELECT
concat(hugo_gene_symbol, profile_type) AS attributeId,
Expand Down

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