ALS-4978: Fix config issue

hms-dbmi · Oct 16, 2023 · ce53d37 · ce53d37
1 parent 3fc4b64
commit ce53d37
Show file tree

Hide file tree

Showing 2 changed files with 15 additions and 3 deletions.
diff --git a/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java b/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java
@@ -224,11 +224,24 @@ protected Set<Integer> idSetsForEachFilter(Query query) {
 
         if (distributableQuery.hasFilters()) {
             BigInteger patientMaskForVariantInfoFilters = genomicProcessor.getPatientMaskForVariantInfoFilters(distributableQuery);
+			return patientMaskToPatientIdSet(patientMaskForVariantInfoFilters);
         }
 
 		return phenotypicPatientSet;
 	}
 
+	public Set<Integer> patientMaskToPatientIdSet(BigInteger patientMask) {
+		Set<Integer> ids = new HashSet<>();
+		String bitmaskString = patientMask.toString(2);
+		for(int x = 2;x < bitmaskString.length()-2;x++) {
+			if('1'==bitmaskString.charAt(x)) {
+				String patientId = variantService.getPatientIds()[x-2].trim();
+				ids.add(Integer.parseInt(patientId));
+			}
+		}
+		return ids;
+	}
+
 	/**
 	 * Process each filter in the query and return a list of patient ids that should be included in the
 	 * result.

diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessor.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessor.java
@@ -33,9 +33,8 @@ public class GenomicProcessor {
     private final VariantService variantService;
 
     @Autowired
-    public GenomicProcessor(PatientVariantJoinHandler patientVariantJoinHandler, VariantIndexCache variantIndexCache, VariantService variantService) {
+    public GenomicProcessor(PatientVariantJoinHandler patientVariantJoinHandler, VariantService variantService) {
         this.patientVariantJoinHandler = patientVariantJoinHandler;
-        this.variantIndexCache = variantIndexCache;
         this.variantService = variantService;
 
         genomicDataDirectory = System.getProperty("HPDS_GENOMIC_DATA_DIRECTORY", "/opt/local/hpds/all/");
@@ -97,7 +96,7 @@ protected BigInteger getPatientMaskForVariantInfoFilters(DistributableQuery dist
     }
 
     public Set<Integer> patientMaskToPatientIdSet(BigInteger patientMask) {
-        Set<Integer> ids = new TreeSet<Integer>();
+        Set<Integer> ids = new HashSet<>();
         String bitmaskString = patientMask.toString(2);
         for(int x = 2;x < bitmaskString.length()-2;x++) {
             if('1'==bitmaskString.charAt(x)) {