code cleanup

dippindots · Aug 29, 2024 · 61b2b9c · 61b2b9c
1 parent e4fd443
commit 61b2b9c
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Showing 4 changed files with 3 additions and 29 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -66,8 +66,7 @@ public interface StudyViewMapper {
     Map<String, Integer> getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter);
 
     List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
-
-    // TODO: update this with new parameters
+
     List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);
     List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);
 

diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java
@@ -72,10 +72,10 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
         List<ClinicalDataCountItem> filteredClinicalDataCounts;
         Map<String, ClinicalDataType> attributeDatatypeMap;
         switch (dataBinCountFilter) {
+            // TODO: this is to support clinical data, but clinical data is not using this now. We should update controller to use this method later
             case ClinicalDataBinCountFilter clinicalDataBinCountFilter -> {
                 unfilteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(partialFilter, uniqueKeys);
                 filteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(studyViewFilter, uniqueKeys);
-                // TODO: only do this for clinical data, because all genomic data and generic assay data are currently no patient level data
                 attributeDatatypeMap = studyViewColumnarService.getClinicalAttributeDatatypeMap();
             }
             case GenomicDataBinCountFilter genomicDataBinCountFilter -> {

diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java b/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java
@@ -722,34 +722,25 @@ public List<String> getUniqkeyKeys(List<String> studyIds, List<String> caseIds)
 
     public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin> List<U> getDataBins(
         DataBinMethod dataBinMethod, T dataBinCountFilter) {
-        // get data bin filters based on the type of the filter
-        // either Genomic data or Generic Assay data
         List<S> dataBinFilters = fetchDataBinFilters(dataBinCountFilter);
-
         StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter();
 
         if (dataBinFilters.size() == 1) {
             removeSelfFromFilter(dataBinFilters.get(0), studyViewFilter);
         }
 
-        // define result variables
         List<U> resultDataBins;
         List<String> filteredSampleIds = new ArrayList<>();
         List<String> filteredStudyIds = new ArrayList<>();
 
-        // fetchData will fetch data from different services based on the type of the filter
-        // either Genomic data or Generic Assay data
-        // data been fetched and cast as Clinical data, then 
         List<Binnable> filteredData = fetchData(dataBinCountFilter, studyViewFilter, filteredSampleIds,
             filteredStudyIds);
 
         List<String> filteredUniqueSampleKeys = getUniqkeyKeys(filteredStudyIds, filteredSampleIds);
 
-        // data grouped by entity id
         Map<String, List<Binnable>> filteredClinicalDataByAttributeId = filteredData.stream()
             .collect(Collectors.groupingBy(Binnable::getAttrId));
-
-        // Dynamic is the default binning method
+
         if (dataBinMethod == DataBinMethod.STATIC) {
 
             StudyViewFilter filter = studyViewFilter == null ? null : new StudyViewFilter();
@@ -760,8 +751,6 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
 
             List<String> unfilteredSampleIds = new ArrayList<>();
             List<String> unfilteredStudyIds = new ArrayList<>();
-            // get unfiltered data
-            // TODO: maybe we can try to optimize this step
             List<Binnable> unfilteredData = fetchData(dataBinCountFilter, filter, unfilteredSampleIds,
                 unfilteredStudyIds);
 

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -566,16 +566,9 @@
         count(value) as count
         FROM genetic_alteration_derived_gaofei
         <where>
-            --             type='sample' AND
             <include refid="applyStudyViewFilter">
                 <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
             </include>
-            <!--            <if test="filteredAttributeValues != null and !filteredAttributeValues.isEmpty()">-->
-            <!--                AND UPPER(value) NOT IN-->
-            <!--                <foreach item="filteredAttributeValue" collection="filteredAttributeValues" open="(" separator="," close=")">-->
-            <!--                    #{filteredAttributeValue}-->
-            <!--                </foreach>-->
-            <!--            </if>-->
             AND concat(hugo_gene_symbol, profile_type) IN
             <foreach item="attributeId" collection="attributeIds" open="(" separator="," close=")">
                 #{attributeId}
@@ -594,16 +587,9 @@
         count(value) as count
         FROM generic_assay_data_derived_gaofei
         <where>
-            --             type='sample' AND
             <include refid="applyStudyViewFilter">
                 <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
             </include>
-            <!--            <if test="filteredAttributeValues != null and !filteredAttributeValues.isEmpty()">-->
-            <!--                AND UPPER(value) NOT IN-->
-            <!--                <foreach item="filteredAttributeValue" collection="filteredAttributeValues" open="(" separator="," close=")">-->
-            <!--                    #{filteredAttributeValue}-->
-            <!--                </foreach>-->
-            <!--            </if>-->
             AND concat(entity_stable_id, profile_type) IN
             <foreach item="attributeId" collection="attributeIds" open="(" separator="," close=")">
                 #{attributeId}