Merge branch 'genomic-v2' into ALS-7242

.github/workflows/github-actions-test.yml

@@ -16,4 +16,4 @@ jobs:
       - name: Test with Maven
         run: mvn --update-snapshots test
         env:
-          GITHUB_TOKEN: ${{ github.token }}
+          GITHUB_TOKEN: ${{ github.token }}

.github/workflows/label-checker.yml

@@ -16,6 +16,6 @@ jobs:
     steps:
       - uses: docker://agilepathway/pull-request-label-checker:latest
         with:
-          one_of: breaking-change,enhancement,bug,documentation,ignore-for-release
+          one_of: breaking-change,enhancement,bug,documentation,ignore-for-release,dependencies
           repo_token: ${{ secrets.GITHUB_TOKEN }}
 

client-api/pom.xml

@@ -17,8 +17,6 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <maven.compiler.source>1.7</maven.compiler.source>
-    <maven.compiler.target>1.7</maven.compiler.target>
   </properties>
 
   <dependencies>

data/pom.xml

@@ -11,6 +11,8 @@
 	<artifactId>data</artifactId>
 
 	<name>data</name>
+	<properties>
+	</properties>
 
 	<dependencies>
 		<dependency>

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/InfoColumnMeta.java

@@ -1,16 +1,5 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
 
-import lombok.Builder;
-import lombok.Value;
-import lombok.extern.jackson.Jacksonized;
-
-@Jacksonized
-@Value
-@Builder
-public class InfoColumnMeta {
-
-    String key, description;
-    boolean continuous;
-    Float min, max;
+public record InfoColumnMeta(String key, String description, boolean continuous, Float min, Float max) {
 
 }

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/VariantMetadataIndex.java

@@ -1,11 +1,14 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
 
 import java.io.*;
+import java.nio.file.Files;
 import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.stream.Collectors;
 import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
 
+import com.google.common.base.Joiner;
 import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJavaIndexedStorage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -21,23 +24,23 @@
  * a fast, disk-based backing store.
  */
 public class VariantMetadataIndex implements Serializable {
-	// todo: make this variable
-	public static String VARIANT_METADATA_BIN_FILE = "/opt/local/hpds/all/VariantMetadata.javabin";
+	public static final String VARIANT_METADATA_FILENAME = "VariantMetadata.javabin";
+	public static String VARIANT_METADATA_BIN_FILE = "/opt/local/hpds/all/" + VARIANT_METADATA_FILENAME;
 
 	private static final long serialVersionUID = 5917054606643971537L;
 	private static Logger log = LoggerFactory.getLogger(VariantMetadataIndex.class); 
 
 	// (String) contig  --> (Integer) Bucket -->  (String) variant spec --> INFO column data[].
-	private Map<String,  FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, String[]>> > indexMap = new HashMap<String,  FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, String[]>> >();
+	private final Map<String,  FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, String[]>> > indexMap = new HashMap<>();
 
-	// todo: make this variable
-	private static String fileStoragePrefix = "/opt/local/hpds/all/VariantMetadataStorage";
+	public static final String VARIANT_METADATA_STORAGE_FILE_PREFIX = "VariantMetadataStorage";
+	private static String fileStoragePrefix = "/opt/local/hpds/all/" + VARIANT_METADATA_STORAGE_FILE_PREFIX;
 
 	/**
 	 * This map allows us to load millions of variants without re-writing the fbbis each time (which would blow up the disk space).
 	 * We need to remember to flush() between each contig this gets saved to the fbbis array.
 	 */
-	private transient Map<String,  ConcurrentHashMap<Integer, ConcurrentHashMap<String, String[]>> > loadingMap = new HashMap<String,  ConcurrentHashMap<Integer, ConcurrentHashMap<String, String[]>> >();
+	private transient Map<String,  ConcurrentHashMap<Integer, ConcurrentHashMap<String, String[]>> > loadingMap = new HashMap<>();
 
 	/**
 	 * This constructor should only be used for testing; we expect the files to be in the default locations in production
@@ -60,7 +63,7 @@ public VariantMetadataIndex() throws IOException {
 	 * @param variantSpec
 	 * @return
 	 */
-	public String[] findBySingleVariantSpec(String variantSpec, VariantBucketHolder<String[]> bucketCache) {
+	public Set<String> findBySingleVariantSpec(String variantSpec, VariantBucketHolder<String[]> bucketCache) {
 		try {
 			String[] segments = variantSpec.split(",");
 			if (segments.length < 2) {
@@ -75,7 +78,7 @@ public String[] findBySingleVariantSpec(String variantSpec, VariantBucketHolder<
 					|| chrOffset != bucketCache.lastChunkOffset) {
 				FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, String[]>> ContigFbbis = indexMap.get(contig);
 				if(ContigFbbis == null) {
-					return new String[0];
+					return Set.of();
 				}
 				bucketCache.lastValue = ContigFbbis.get(chrOffset);
 				bucketCache.lastContig = contig;
@@ -85,20 +88,20 @@ public String[] findBySingleVariantSpec(String variantSpec, VariantBucketHolder<
 			if( bucketCache.lastValue != null) {
 				if(bucketCache.lastValue.get(variantSpec) == null) {
 					log.warn("No variant data found for spec " + variantSpec);
-					return new String[0];
+					return Set.of();
 				}
-				return  bucketCache.lastValue.get(variantSpec);
+				return Set.of(bucketCache.lastValue.get(variantSpec));
 			}
 			log.warn("No bucket found for spec " + variantSpec + " in bucket " + chrOffset);
-			return new String[0];
+			return Set.of();
 
 		} catch (UncheckedIOException e) {
 			log.warn("IOException caught looking up variantSpec : " + variantSpec, e);
-			return new String[0];
+			return Set.of();
 		}
 	}
 
-	public Map<String, String[]> findByMultipleVariantSpec(Collection<String> varientSpecList) {
+	public Map<String, Set<String>> findByMultipleVariantSpec(Collection<String> varientSpecList) {
 //		log.debug("SPEC list "  + varientSpecList.size() + " :: " + Arrays.deepToString(varientSpecList.toArray()));
 
 		VariantBucketHolder<String[]> bucketCache = new VariantBucketHolder<String[]>();
@@ -161,7 +164,7 @@ public synchronized void flush() throws IOException {
 			if(contigFbbis == null) {
 				log.info("creating new file for " + contig);
 				String filePath = fileStoragePrefix + "_" + contig + ".bin";
-				contigFbbis = new FileBackedJavaIndexedStorage(Integer.class, (Class<ConcurrentHashMap<String, String[]>>)(Class<?>) ConcurrentHashMap.class, new File(filePath));
+				contigFbbis = new FileBackedJavaIndexedStorage(Integer.class, ConcurrentHashMap.class, new File(filePath));
 				indexMap.put(contig, contigFbbis);
 			}
 
@@ -196,13 +199,57 @@ public void complete() throws IOException {
 
 	public static VariantMetadataIndex createInstance(String metadataIndexPath) {
 		try(ObjectInputStream in = new ObjectInputStream(new GZIPInputStream(
-				new FileInputStream(metadataIndexPath)))){
-			return (VariantMetadataIndex) in.readObject();
+				new FileInputStream(metadataIndexPath + VARIANT_METADATA_FILENAME)))){
+			VariantMetadataIndex variantMetadataIndex = (VariantMetadataIndex) in.readObject();
+			variantMetadataIndex.updateStorageDirectory(new File(metadataIndexPath));
+			return variantMetadataIndex;
 		} catch(Exception e) {
 			// todo: handle exceptions better
 			log.info("No Metadata Index found at " + metadataIndexPath);
-			log.debug("Error loading metadata index:", e);
 			return null;
 		}
 	}
+
+	public static void merge(VariantMetadataIndex variantMetadataIndex1, VariantMetadataIndex variantMetadataIndex2, String outputDirectory) throws IOException {
+		VariantMetadataIndex merged = new VariantMetadataIndex(outputDirectory + VARIANT_METADATA_STORAGE_FILE_PREFIX);
+		if (!variantMetadataIndex1.indexMap.keySet().equals(variantMetadataIndex2.indexMap.keySet())) {
+			log.warn("Merging incompatible variant indexes. Index1 keys: " + Joiner.on(",").join(variantMetadataIndex1.indexMap.keySet()) + ". Index 2 keys: " + Joiner.on(",").join(variantMetadataIndex2.indexMap.keySet()));
+			throw new IllegalStateException("Cannot merge variant metadata index with different contig keys");
+		}
+		for (String contig : variantMetadataIndex1.indexMap.keySet()) {
+			String filePath = outputDirectory + VARIANT_METADATA_STORAGE_FILE_PREFIX + "_" + contig + ".bin";
+			FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, String[]>> mergedFbbis = new FileBackedJavaIndexedStorage(Integer.class, ConcurrentHashMap.class, new File(filePath));
+
+			// Store the merged result here because FileBackedByteIndexedStorage must be written all at once
+			Map<Integer, ConcurrentHashMap<String, String[]>> mergedStagedFbbis = new HashMap<>();
+
+			FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, String[]>> fbbis1 = variantMetadataIndex1.indexMap.get(contig);
+			FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, String[]>> fbbis2 = variantMetadataIndex2.indexMap.get(contig);
+
+			fbbis1.keys().forEach(key -> {
+				mergedStagedFbbis.put(key, fbbis1.get(key));
+			});
+			fbbis2.keys().forEach(key -> {
+				ConcurrentHashMap<String, String[]> metadataMap = mergedStagedFbbis.get(key);
+				if (metadataMap == null) {
+					mergedStagedFbbis.put(key, fbbis2.get(key));
+				} else {
+					metadataMap.putAll(fbbis2.get(key));
+				}
+			});
+
+			mergedStagedFbbis.forEach(mergedFbbis::put);
+			mergedFbbis.complete();
+			merged.indexMap.put(contig, mergedFbbis);
+		}
+
+		try(ObjectOutputStream out = new ObjectOutputStream(new GZIPOutputStream(Files.newOutputStream(new File(outputDirectory + VARIANT_METADATA_FILENAME).toPath())))){
+			out.writeObject(merged);
+			out.flush();
+		}
+	}
+
+	public void updateStorageDirectory(File genomicDataDirectory) {
+		indexMap.values().forEach(value -> value.updateStorageDirectory(genomicDataDirectory));
+	}
 }