Complete CNA table

src/main/java/org/cbioportal/web/StudyViewController.java

@@ -959,15 +959,15 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchGenomicDataCounts(
         @Parameter(required = true, description = "Intercepted Genomic Data Count Filter")
         @Valid @RequestAttribute(required = false, value = "interceptedGenomicDataCountFilter") GenomicDataCountFilter interceptedGenomicDataCountFilter
     ) throws StudyNotFoundException {
-        List<GenomicDataFilter> gdFilters = interceptedGenomicDataCountFilter.getGenomicDataFilters();
+        List<GenomicDataFilter> genomicDataFilters = interceptedGenomicDataCountFilter.getGenomicDataFilters();
         StudyViewFilter studyViewFilter = interceptedGenomicDataCountFilter.getStudyViewFilter();
         // when there is only one filter, it means study view is doing a single chart filter operation
         // remove filter from studyViewFilter to return all data counts
         // the reason we do this is to make sure after chart get filtered, user can still see unselected portion of the chart
-        if (gdFilters.size() == 1) {
+        if (genomicDataFilters.size() == 1) {
             studyViewFilterUtil.removeSelfFromGenomicDataFilter(
-                gdFilters.get(0).getHugoGeneSymbol(), 
-                gdFilters.get(0).getProfileType(), 
+                genomicDataFilters.get(0).getHugoGeneSymbol(), 
+                genomicDataFilters.get(0).getProfileType(), 
                 studyViewFilter);
         }
         List<SampleIdentifier> filteredSampleIdentifiers = studyViewFilterApplier.apply(studyViewFilter);
@@ -983,7 +983,7 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchGenomicDataCounts(
         List<GenomicDataCountItem> result = studyViewService.getCNAAlterationCountsByGeneSpecific(
             studyIds,
             sampleIds,
-            gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).collect(Collectors.toList()));
+            genomicDataFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).collect(Collectors.toList()));
 
         return new ResponseEntity<>(result, HttpStatus.OK);
     }

src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java

@@ -360,6 +360,7 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchGenomicDataCounts(
                     studyViewFilter);
         }
 
+        // This endpoint is CNA specific. The name choice of "genomic data" does not imply it support other genomic data types
         List<GenomicDataCountItem> result = studyViewColumnarService.getCNACountsByGeneSpecific(studyViewFilter, genomicDataFilters);
 
         return new ResponseEntity<>(result, HttpStatus.OK);

src/main/resources/db-scripts/clickhouse/clickhouse.sql

@@ -249,33 +249,38 @@ FROM patient AS p
                          ON (p.internal_id = clinpat.internal_id) AND (clinpat.attr_id = cam.attr_id)
 WHERE cam.patient_attribute = 1;
 
-CREATE TABLE IF NOT EXISTS genetic_alteration_derived
+CREATE TABLE IF NOT EXISTS genetic_alteration_derived_cna
 (
     sample_unique_id String,
     hugo_gene_symbol String,
-    cna_value Int8
+    profile_type String,
+    alteration_value Float32
 )
     ENGINE = MergeTree()
-        ORDER BY (sample_unique_id, hugo_gene_symbol);
+        ORDER BY (sample_unique_id, hugo_gene_symbol, profile_type);
 
-INSERT INTO TABLE genetic_alteration_derived
+INSERT INTO TABLE genetic_alteration_derived_cna
 SELECT
     sample_unique_id,
     hugo_gene_symbol,
-    multiIf(value = '2', 2, value = '1', 1, value = '0', 0, value = '-1', -1, value = '-2', -2, 99) as cna_value
+    profile_type,
+    toFloat32(cna_value) as alteration_value
 FROM
     (SELECT
          sample_id,
          hugo_gene_symbol,
+         profile_type,
          cna_value,
          cancer_study_id
     FROM
         (SELECT
             gp.cancer_study_id AS cancer_study_id,
             g.hugo_gene_symbol AS hugo_gene_symbol,
+            arrayElement(splitByString('_', assumeNotNull(gp.stable_id)), -1) AS profile_type,
             arrayMap(x -> (x = '' ? NULL : x), splitByString(',', assumeNotNull(trim(trailing ',' from ga.values)))) AS cna_value,
             arrayMap(x -> (x = '' ? NULL : toInt64(x)), splitByString(',', assumeNotNull(trim(trailing ',' from gps.ordered_sample_list)))) AS sample_id
-        FROM genetic_profile gp
+        FROM
+            genetic_profile gp
             JOIN genetic_profile_samples gps ON gp.genetic_profile_id = gps.genetic_profile_id
             JOIN genetic_alteration ga ON gp.genetic_profile_id = ga.genetic_profile_id
             JOIN gene g ON ga.genetic_entity_id = g.genetic_entity_id
@@ -292,4 +297,4 @@ OPTIMIZE TABLE gene_panel_to_gene_derived;
 OPTIMIZE TABLE sample_derived;
 OPTIMIZE TABLE genomic_event_derived;
 OPTIMIZE TABLE clinical_data_derived;
-OPTIMIZE TABLE genetic_alteration_derived;
+OPTIMIZE TABLE genetic_alteration_derived_cna;

src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml

@@ -235,17 +235,19 @@
 
     <!-- for /genomic-data-counts/fetch - (returns GenomicDataCountItem objects) -->
     <select id="getCNACounts" resultMap="GenomicDataCountItemResultMap">
+        <bind name="profileType" value="genomicDataFilters[0].profileType" />
         WITH cna_query as (
             SELECT
                 hugo_gene_symbol as hugoGeneSymbol,
-                'cna' as profileType,
+                #{profileType} as profileType,
                 multiIf(cna_value = 2, 'Amplified', cna_value = 1, 'Gained', cna_value = 0, 'Diploid', cna_value = -1,
                 'Heterozygously deleted', cna_value = -2, 'Homozygously deleted', 'NA') as label,
                 toString(cna_value) as value,
                 cast(count(*) as INTEGER) as count
-            FROM genetic_alteration_derived_test
+            FROM genetic_alteration_derived_cna
             <where>
                 sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
+                AND profile_type = #{profileType}
                 <foreach item="genomicDataFilter" collection="genomicDataFilters" open=" AND (" separator=" OR " close=")">
                     hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
                 </foreach>
@@ -265,7 +267,7 @@
         UNION ALL
         SELECT
             hugoGeneSymbol,
-            'cna' as profileType,
+            #{profileType},
             'NA' as label,
             'NA' as value,
             cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - cna_count) as INTEGER) as count
@@ -275,9 +277,9 @@
     <!-- for /mutation-data-counts/fetch (returns GenomicDataCountItem objects) mutation counts pie chart part -->
     <select id="getMutationCounts">
         WITH profiled_count as (
-            SELECT count(distinct stgp.sample_unique_id)
-            FROM sample_to_gene_panel stgp
-                JOIN gene_panel_to_gene gpg ON stgp.gene_panel_id = gpg.gene_panel_id
+            SELECT count(distinct sgp.sample_unique_id)
+            FROM sample_to_gene_panel_derived sgp
+                JOIN gene_panel_to_gene_derived gpg ON sgp.gene_panel_id = gpg.gene_panel_id
             WHERE
                 sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
                 AND gpg.gene = #{genomicDataFilter.hugoGeneSymbol}
@@ -310,7 +312,7 @@
             sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
             AND variant_type = 'mutation'
             <foreach item="genomicDataFilter" collection="genomicDataFilters" open=" AND (" separator=" OR " close=")">
-            hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
+                hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
             </foreach>
         </where>
         GROUP BY