ALS-4461: Remove IOExceptions thrown from FBBIS

hms-dbmi · Aug 9, 2023 · df03002 · df03002
1 parent 88ea1c2
commit df03002
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Showing 3 changed files with 27 additions and 39 deletions.
diff --git a/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedByteIndexedStorage.java b/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedByteIndexedStorage.java
@@ -13,7 +13,6 @@ public abstract class FileBackedByteIndexedStorage <K, V extends Serializable> i
 	protected ConcurrentHashMap<K, Long[]> index;
 	protected File storageFile;
 	protected boolean completed = false;
-	protected Long maxStorageSize;  //leave this in to not break serialization
 
 
 	public FileBackedByteIndexedStorage(Class<K> keyClass, Class<V> valueClass, File storageFile) throws FileNotFoundException {
@@ -34,7 +33,7 @@ public Set<K> keys(){
 		return index.keySet();
 	}
 
-	public void put(K key, V value) throws IOException {
+	public void put(K key, V value) {
 		if(completed) {
 			throw new RuntimeException("A completed FileBackedByteIndexedStorage cannot be modified.");
 		}
@@ -47,6 +46,8 @@ public void put(K key, V value) throws IOException {
 				storage.write(out.toByteArray());
 				recordIndex[1] = storage.getFilePointer() - recordIndex[0];
 			}
+		} catch (IOException e) {
+			throw new UncheckedIOException(e);
 		}
 		index.put(key, recordIndex);
 	}
@@ -72,9 +73,6 @@ public void complete() {
 		this.completed = true;
 	}
 
-	public boolean isComplete() {
-		return this.completed;
-	}
 	public V get(K key) {
 		try {
 			if(this.storage==null) {
@@ -109,7 +107,7 @@ public V get(K key) {
 
 	protected abstract ByteArrayOutputStream writeObject(V value) throws IOException;
 
-	public V getOrELse(K key, V defaultValue) throws IOException {
+	public V getOrELse(K key, V defaultValue) {
 		V result = get(key);
 		return result == null ? defaultValue : result;
 	}

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java
@@ -122,14 +122,8 @@ public BucketIndexBySample(VariantStore variantStore, String storageDir) throws
 
 		int[] processedPatients = new int[1];
 		patientIds.parallelStream().forEach((patientId)->{
-			try {
-				BigInteger patientMask = new BigInteger(new String(patientBucketCharMasks[patientIds.indexOf(patientId)]),2);
-				patientBucketMasks.put(patientId, patientMask);
-			}catch(NumberFormatException e) {
-				log.error("NFE caught for " + patientId, e);
-			} catch (IOException e) {
-				throw new UncheckedIOException(e);
-			}
+			BigInteger patientMask = new BigInteger(new String(patientBucketCharMasks[patientIds.indexOf(patientId)]),2);
+			patientBucketMasks.put(patientId, patientMask);
 			processedPatients[0] += 1;
 			int processedPatientsCount = processedPatients[0];
 			if (processedPatientsCount % 1000 == 0) {

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java
@@ -162,7 +162,7 @@ private Map<String, FileBackedByteIndexedInfoStore> loadInfoStores(String direct
                             infoStores.put(filename.replace("_infoStore.javabin", ""), infoStore);
                             ois.close();
                         } catch (IOException | ClassNotFoundException e) {
-                            e.printStackTrace();
+                            throw new RuntimeException(e);
                         }
                     });
         }
@@ -192,34 +192,30 @@ public FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariantMask
 
         FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariantMasks>> merged = new FileBackedStorageVariantMasksImpl(new File(outputDirectory + chromosome + "masks.bin"));
         variantMaskStorage1.keys().forEach(key -> {
-            try {
-                Map<String, VariantMasks> masks1 = variantMaskStorage1.get(key);
-                Map<String, VariantMasks> masks2 = variantMaskStorage2.get(key);
-                if (masks2 == null) {
-                    masks2 = Map.of();
-                }
+            Map<String, VariantMasks> masks1 = variantMaskStorage1.get(key);
+            Map<String, VariantMasks> masks2 = variantMaskStorage2.get(key);
+            if (masks2 == null) {
+                masks2 = Map.of();
+            }
 
-                ConcurrentHashMap<String, VariantMasks> mergedMasks = new ConcurrentHashMap<>();
-                for (Map.Entry<String, VariantMasks> entry : masks1.entrySet()) {
-                    VariantMasks variantMasks2 = masks2.get(entry.getKey());
-                    if (variantMasks2 == null) {
-                        // this will have all null masks, which will result in null when
-                        // appended to a null, or be replaced with an empty bitmask otherwise
-                        variantMasks2 = new VariantMasks();
-                    }
-                    mergedMasks.put(entry.getKey(), append(entry.getValue(), variantMasks2));
+            ConcurrentHashMap<String, VariantMasks> mergedMasks = new ConcurrentHashMap<>();
+            for (Map.Entry<String, VariantMasks> entry : masks1.entrySet()) {
+                VariantMasks variantMasks2 = masks2.get(entry.getKey());
+                if (variantMasks2 == null) {
+                    // this will have all null masks, which will result in null when
+                    // appended to a null, or be replaced with an empty bitmask otherwise
+                    variantMasks2 = new VariantMasks();
                 }
-                // Any entry in the second set that is not in the merged set can be merged with an empty variant mask,
-                // if there were a corresponding entry in set 1, it would have been merged in the previous loop
-                for (Map.Entry<String, VariantMasks> entry : masks2.entrySet()) {
-                    if (!mergedMasks.containsKey(entry.getKey())) {
-                        mergedMasks.put(entry.getKey(), append(new VariantMasks(), entry.getValue()));
-                    }
+                mergedMasks.put(entry.getKey(), append(entry.getValue(), variantMasks2));
+            }
+            // Any entry in the second set that is not in the merged set can be merged with an empty variant mask,
+            // if there were a corresponding entry in set 1, it would have been merged in the previous loop
+            for (Map.Entry<String, VariantMasks> entry : masks2.entrySet()) {
+                if (!mergedMasks.containsKey(entry.getKey())) {
+                    mergedMasks.put(entry.getKey(), append(new VariantMasks(), entry.getValue()));
                 }
-                merged.put(key, mergedMasks);
-            } catch (IOException e) {
-                throw new RuntimeException(e);
             }
+            merged.put(key, mergedMasks);
         });
 
         ConcurrentHashMap<String, VariantMasks> mergedMasks = new ConcurrentHashMap<>();