ALS-6330: (WIP) Integration test refactor, variant explorer fixes.

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java

@@ -97,8 +97,6 @@ public BucketIndexBySample(VariantStore variantStore, String storageDir) throws
 							});
 
 							// For each patient set the patientBucketCharMask entry to 0 or 1 if they have a variant in the bucket.
-
-							// todo: implement for variant explorer
 							int indexOfBucket = Collections.binarySearch(bucketList, bucketKey) + 2; //patientBucketCharMasks has bookend bits
 							for(int x = 0; x < patientIds.size(); x++) {
 								if(patientMaskForBucket[0].testBit(x)) {

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMask.java

@@ -33,4 +33,6 @@ static VariantMask emptyInstance() {
     }
 
     Set<Integer> patientMaskToPatientIdSet(List<String> patientIds);
+
+    boolean isEmpty();
 }

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskBitmaskImpl.java

@@ -1,6 +1,7 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import com.fasterxml.jackson.databind.ser.std.ToStringSerializer;
@@ -75,6 +76,13 @@ public Set<Integer> patientMaskToPatientIdSet(List<String> patientIds) {
         return ids;
     }
 
+    @Override
+    @JsonIgnore
+    public boolean isEmpty() {
+        // because the bitmasks are padded with 11 on each end
+        return bitmask.bitCount() <= 4;
+    }
+
     private VariantMask union(VariantMaskBitmaskImpl variantMaskBitmask) {
         return new VariantMaskBitmaskImpl(variantMaskBitmask.bitmask.or(this.bitmask));
     }

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskSparseImpl.java

@@ -1,5 +1,6 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import java.math.BigInteger;
@@ -59,6 +60,12 @@ public Set<Integer> patientMaskToPatientIdSet(List<String> patientIds) {
                 .collect(Collectors.toSet());
     }
 
+    @Override
+    @JsonIgnore
+    public boolean isEmpty() {
+        return this.patientIndexes.isEmpty();
+    }
+
     private VariantMask union(VariantMaskSparseImpl variantMask) {
         HashSet<Integer> union = new HashSet<>(variantMask.patientIndexes);
         union.addAll(this.patientIndexes);

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java

@@ -144,6 +144,32 @@ public Optional<VariableVariantMasks> getMasks(String variant, VariantBucketHold
 		}
 		return bucketCache.lastValue == null ? Optional.empty() : Optional.ofNullable(bucketCache.lastValue.get(variant));
 	}
+	public List<VariableVariantMasks> getMasksForDbSnpSpec(String variant) {
+		String[] segments = variant.split(",");
+		if (segments.length < 2) {
+			log.error("Less than 2 segments found in this variant : " + variant);
+		}
+
+		int chrOffset = Integer.parseInt(segments[1]) / BUCKET_SIZE;
+		String contig = segments[0];
+
+//		if (Level.DEBUG.equals(log.getEffectiveLevel())) {
+//			log.debug("Getting masks for variant " + variant + "  Same bucket test: " + (bucketCache.lastValue != null
+//					&& contig.contentEquals(bucketCache.lastContig) && chrOffset == bucketCache.lastChunkOffset));
+//		}
+
+		// todo: don't bother doing a lookup if this node does not have the chromosome specified
+		FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVariantMasks>> indexedStorage = variantMaskStorage.get(contig);
+		if (indexedStorage == null) {
+			return List.of();
+		} else {
+			ConcurrentHashMap<String, VariableVariantMasks> specToMaskMap = indexedStorage.get(chrOffset);
+			return specToMaskMap.entrySet().stream()
+					.filter(entry -> entry.getKey().startsWith(variant))
+					.map(Map.Entry::getValue)
+					.collect(Collectors.toList());
+		}
+	}
 
 	public String[] getHeaders() {
 		return vcfHeaders;

etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantMetadataLoader.java

@@ -38,7 +38,7 @@ public class VariantMetadataLoader {
 	GZIP_FLAG_COLUMN=3,
 	FILE_COLUMN = 0;	
 
-	public static void main(String[] args) throws Exception{  
+	public static void main(String[] args) throws IOException {
 		File vcfIndexFile;
 
 		log.info(new File(".").getAbsolutePath());

integration-test/pom.xml

@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
+        <artifactId>pic-sure-hpds</artifactId>
+        <version>3.0.0-SNAPSHOT</version>
+    </parent>
+
+    <artifactId>integration-test</artifactId>
+
+    <properties>
+        <maven.compiler.source>21</maven.compiler.source>
+        <maven.compiler.target>21</maven.compiler.target>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
+            <artifactId>etl</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
+            <artifactId>data</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
+            <artifactId>service</artifactId>
+        </dependency>
+    </dependencies>
+
+</project>

integration-test/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/test/Main.java

@@ -0,0 +1,7 @@
+package edu.harvard.hms.dbmi.avillach.hpds.test;
+
+public class Main {
+    public static void main(String[] args) {
+        System.out.println("Hello world!");
+    }
+}