Speed up CnaEvent lookup during import

src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java

@@ -45,7 +45,7 @@ public class ImportCnaDiscreteLongData {
     private String genePanel;
     private final DaoGeneOptimized daoGene;
     private CnaUtil cnaUtil;
-    private Set<CnaEvent.Event> existingCnaEvents = new HashSet<>();
+    private Map<CnaEvent.Event, CnaEvent.Event> existingCnaEvents = new HashMap<>();
     private int samplesSkipped = 0;
     private Set<String> namespaces;
 
@@ -84,7 +84,9 @@ public void importData() throws Exception {
             && geneticProfile.showProfileInAnalysisTab();
 
         if (isDiscretizedCnaProfile) {
-            existingCnaEvents.addAll(DaoCnaEvent.getAllCnaEvents());
+            for (CnaEvent.Event event : DaoCnaEvent.getAllCnaEvents()) {
+                existingCnaEvents.put(event, event);
+            }
             MySQLbulkLoader.bulkLoadOn();
         }
 

src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java

@@ -265,9 +265,11 @@ public void importData(int numLines) throws IOException, DaoException {
             DaoGeneticAlteration daoGeneticAlteration = DaoGeneticAlteration.getInstance();
 
             //cache for data found in  cna_event' table:
-            Set<CnaEvent.Event> existingCnaEvents = new HashSet<>();
+            Map<CnaEvent.Event, CnaEvent.Event> existingCnaEvents = new HashMap<>();
             if (isDiscretizedCnaProfile) {
-                existingCnaEvents.addAll(DaoCnaEvent.getAllCnaEvents());
+                for (CnaEvent.Event event : DaoCnaEvent.getAllCnaEvents()) {
+                    existingCnaEvents.put(event, event);
+                }
                 MySQLbulkLoader.bulkLoadOn();
             }
 
@@ -502,7 +504,7 @@ private boolean parseLine(String line, int nrColumns, int sampleStartIndex,
                               boolean isRppaProfile, boolean isDiscretizedCnaProfile,
                               DaoGeneOptimized daoGene,
                               List<Integer> filteredSampleIndices, List<Integer> orderedSampleList,
-                              Set<CnaEvent.Event> existingCnaEvents
+                              Map<CnaEvent.Event, CnaEvent.Event> existingCnaEvents
     ) throws DaoException {
 
         //TODO: refactor this entire function - split functionality into smaller units / subroutines

src/main/java/org/mskcc/cbio/portal/util/CnaUtil.java

@@ -46,33 +46,36 @@ public CnaUtil(String[] headerParts, Set<String> namespaces) {
     }
 
     public static void storeCnaEvents(
-        Set<CnaEvent.Event> existingCnaEvents,
+        Map<CnaEvent.Event,CnaEvent.Event> existingCnaEvents,
         List<CnaEvent> cnaEventsToAdd
     ) throws DaoException {
         for (CnaEvent cnaEvent : cnaEventsToAdd) {
             if (!CNA.AMP.equals(cnaEvent.getAlteration()) && !CNA.HOMDEL.equals(cnaEvent.getAlteration())) {
                 continue;
             }
-
-            // Revert PR https://github.com/cBioPortal/cbioportal-core/pull/1 breaks importer
-            Optional<CnaEvent.Event> existingCnaEvent = existingCnaEvents
-                    .stream()
-                    .filter(e -> e.equals(cnaEvent.getEvent()))
-                    .findFirst();
-            if (existingCnaEvent.isPresent()) {
-                cnaEvent.setEventId(existingCnaEvent.get().getEventId());
+            CnaEvent.Event event = cnaEvent.getEvent();
+            CnaEvent.Event existingEvent = existingCnaEvents.get(event);
+            // Caution :
+            // existingEvent (if found) was retrieved from the database and has a populated event_id field.
+            // event is constructed while parsing the CNA file and does not have a populated event_id field.
+            // The type CnaEvent.Event, and contained types, have overridden hashCode() and equals() functions
+            // which allow successful comparison so that an Event with a non-populated event_id field will
+            // match an Event with a populated / discrepant event_id field. That is to allow this hashmap lookup
+            // of the previously existing event from the database in order to obtain the event_id (see below).
+            if (existingEvent != null) {
+                cnaEvent.setEventId(existingEvent.getEventId());
                 DaoCnaEvent.addCaseCnaEvent(cnaEvent, false);
             } else {
                 DaoCnaEvent.addCaseCnaEvent(cnaEvent, true);
-                existingCnaEvents.add(cnaEvent.getEvent());
+                existingCnaEvents.put(event, event);
             }
         }
     }
 
     public CnaEvent createEvent(
         GeneticProfile geneticProfile,
         int sampleId,
-        long entrezId, 
+        long entrezId,
         String[] parts
     ) throws IOException {
         int cnaProfileId = geneticProfile.getGeneticProfileId();
@@ -88,11 +91,11 @@ public CnaEvent createEvent(
         );
         return cna;
     }
-    
+
     private String convertMapToJsonString(Map<String, Map<String, Object>> map) throws JsonProcessingException {
         return this.objectMapper.writeValueAsString(map);
     }
-    
+
     public long getEntrezSymbol(String[] parts) {
         String entrezAsString = TabDelimitedFileUtil.getPartString(getColumnIndex(CnaUtil.ENTREZ_GENE_ID), parts);
         if (entrezAsString.isEmpty()) {
@@ -123,7 +126,7 @@ private short createAlteration(String[] parts) {
      */
     public int getColumnIndex(String colName) {
         return this.columnIndexMap.getOrDefault(
-            colName.toLowerCase(), 
+            colName.toLowerCase(),
             -1
         );
     }