deprecate certain methods, and add more comments

src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java

@@ -126,6 +126,12 @@ public static List<ClinicalDataBin> calculateDynamicDataBins(
      * Size of the generated list is equal to 'dataCount.count',
      * and each ClinicalData in the list contains the same value 'dataCount.value'
      * 
+     * This method improves the performance of the data binning because it allows us to fetch only
+     * the clinical data counts data which is a lot more compact and faster to generated than the actual clinical data.
+     * We only need the attribute id and the value of the clinical data to generate data bins.
+     * Constructing the clinical data in memory by using clinical data counts significantly improves the performance,
+     * and it also allows us to use the exact same SQL used by the clinical data counts endpoint. 
+     * 
      * @param dataCount ClinicalDataCount instance containing the count and the value
      * @return  a list of ClinicalData with size 'dataCount.count' and value 'dataCount.value'
      */

src/main/java/org/cbioportal/web/util/DataBinner.java

@@ -31,6 +31,11 @@ public class DataBinner {
     @Autowired
     private LogScaleDataBinner logScaleDataBinner;
 
+    /**
+     * This method should only be invoked by legacy endpoints because it requires sample/patient ids.
+     * 
+     * @deprecated 
+     */
     public <T extends DataBinFilter> List<DataBin> calculateClinicalDataBins(
         T dataBinFilter,
         ClinicalDataType clinicalDataType,
@@ -53,6 +58,9 @@ public <T extends DataBinFilter> List<DataBin> calculateClinicalDataBins(
         List<Binnable> unfilteredClinicalData
     ) {
         // calculate data bins for unfiltered clinical data
+        // we need this additional calculation to know the bins generated for the initial state.
+        // this allows us to keep the number of bins and bin ranges consistent.
+        // we only want to update the counts for each bin, we don't want to regenerate the bins for the filtered data.
         List<DataBin> dataBins = calculateDataBins(
             dataBinFilter,
             unfilteredClinicalData
@@ -66,16 +74,21 @@ public <T extends DataBinFilter> List<DataBin> calculateClinicalDataBins(
         );
     }
 
+    /**
+     * This method should only be invoked by legacy endpoints because it requires sample/patient ids.
+     *
+     * @deprecated
+     */
     public List<DataBin> recalcBinCount(
         List<DataBin> dataBins,
         ClinicalDataType clinicalDataType,
         List<Binnable> clinicalData,
-        List<String> ids
+        List<String> caseIds
     ) {
         return recalcBinCount(
             dataBins,
             clinicalData,
-            countNAs(clinicalData, clinicalDataType, ids)
+            countNAs(clinicalData, clinicalDataType, caseIds)
         );
     }
 
@@ -125,17 +138,22 @@ public List<DataBin> recalcBinCount(
         return dataBins;
     }
 
+    /**
+     * This method should only be invoked by legacy endpoints because it requires sample/patient ids.
+     *
+     * @deprecated
+     */
     public <T extends DataBinFilter> List<DataBin> calculateDataBins(
         T dataBinFilter,
         ClinicalDataType clinicalDataType,
         List<Binnable> clinicalData,
-        List<String> ids
+        List<String> caseIds
     ) {
         return calculateDataBins(
             dataBinFilter,
             clinicalDataType,
             clinicalData,
-            ids,
+            caseIds,
             DEFAULT_DISTINCT_VALUE_THRESHOLD
         );
     }
@@ -161,14 +179,19 @@ public <T extends DataBinFilter> List<DataBin> calculateDataBins(
         return calculateDataBins(dataBinFilter, clinicalData, naDataBin, distinctValueThreshold);
     }
 
+    /**
+     * This method should only be invoked by legacy endpoints because it requires sample/patient ids.
+     *
+     * @deprecated
+     */
     public <T extends DataBinFilter> List<DataBin> calculateDataBins(
         T dataBinFilter,
         ClinicalDataType clinicalDataType,
         List<Binnable> clinicalData,
-        List<String> ids,
+        List<String> caseIds,
         Integer distinctValueThreshold
     ) {
-        DataBin naDataBin = calcNaDataBin(clinicalData, clinicalDataType, ids);
+        DataBin naDataBin = calcNaDataBin(clinicalData, clinicalDataType, caseIds);
 
         return calculateDataBins(dataBinFilter, clinicalData, naDataBin, distinctValueThreshold);
     }
@@ -580,18 +603,21 @@ public List<BigDecimal> adjustCustomBins(
      * NA count is: Number of clinical data marked actually as "NA" + Number of patients/samples without clinical data.
      * Assuming that clinical data is for a single attribute.
      *
+     * This method should only be invoked by legacy endpoints because it requires sample/patient ids.
+     * 
      * @param clinicalData clinical data list for a single attribute
-     * @param ids          sample/patient ids
+     * @param caseIds          sample/patient ids
      *
      * @return 'NA' clinical data count as a DataBin instance
+     * @deprecated
      */
     public DataBin calcNaDataBin(
         List<Binnable> clinicalData,
         ClinicalDataType clinicalDataType,
-        List<String> ids
+        List<String> caseIds
     ) {
         DataBin bin = initNaDataBin();
-        bin.setCount(countNAs(clinicalData, clinicalDataType, ids).intValue());
+        bin.setCount(countNAs(clinicalData, clinicalDataType, caseIds).intValue());
 
         return bin;
     }
@@ -618,7 +644,12 @@ public DataBin initNaDataBin() {
         return bin;
     }
 
-    public Long countNAs(List<Binnable> clinicalData, ClinicalDataType clinicalDataType, List<String> ids) {
+    /**
+     * This method should only be invoked by legacy endpoints because it requires sample/patient ids
+     * 
+     * @deprecated 
+     */
+    public Long countNAs(List<Binnable> clinicalData, ClinicalDataType clinicalDataType, List<String> caseIds) {
         // Calculate the number of clinical data marked actually as "NA", "NAN", or "N/A"
 
         Long count = countNAs(clinicalData);
@@ -637,7 +668,7 @@ public Long countNAs(List<Binnable> clinicalData, ClinicalDataType clinicalDataT
             uniqueClinicalDataIds = Collections.emptySet();
         }
 
-        Set<String> uniqueInputIds = new HashSet<>(ids);
+        Set<String> uniqueInputIds = new HashSet<>(caseIds);
 
         // remove the ids with existing clinical data,
         // size of the difference (of two sets) is the count we need