ALS-7882: Checkmarx related cleanup

hms-dbmi · Dec 6, 2024 · 4bc56c4 · 4bc56c4
1 parent 5365a09
commit 4bc56c4
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Showing 10 changed files with 53 additions and 49 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
@@ -50,22 +50,29 @@ public void put(K key, V value) {
 		index.put(key, recordIndex);
 	}
 
-	public void load(Iterable<V> values, Function<V, K> mapper) throws IOException {
+	public void load(Iterable<V> values, Function<V, K> mapper) {
 		//make sure we start fresh
 		if(this.storageFile.exists()) {
 			this.storageFile.delete();
 		}
-		this.storage = new RandomAccessFile(storageFile, "rw");
-		for(V value : values) {
-			put(mapper.apply(value), value);
-		}
-		this.storage.close();
-		complete();
-	}
+		try (RandomAccessFile storage = new RandomAccessFile(storageFile, "rw");) {
+			this.storage = storage;
+			for(V value : values) {
+				put(mapper.apply(value), value);
+			}
+			complete();
+		} catch (IOException e) {
+            throw new UncheckedIOException(e);
+        }
+    }
 
-	public void open() throws FileNotFoundException {
-		this.storage = new RandomAccessFile(this.storageFile, "rwd");
-	}
+	public void open() {
+        try {
+            this.storage = new RandomAccessFile(this.storageFile, "rwd");
+        } catch (FileNotFoundException e) {
+            throw new UncheckedIOException(e);
+        }
+    }
 
 	public void complete() {
 		this.completed = true;

diff --git a/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJavaIndexedStorage.java b/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJavaIndexedStorage.java
@@ -11,10 +11,11 @@ public FileBackedJavaIndexedStorage(Class<K> keyClass, Class<V> valueClass, File
 
     protected ByteArrayOutputStream writeObject(V value) throws IOException {
         ByteArrayOutputStream out = new ByteArrayOutputStream();
-        ObjectOutputStream oos = new ObjectOutputStream(new GZIPOutputStream(out));
-        oos.writeObject(value);
-        oos.flush();
-        oos.close();
+        try (GZIPOutputStream gzipOutputStream = new GZIPOutputStream(out);
+             ObjectOutputStream oos = new ObjectOutputStream(gzipOutputStream)) {
+            oos.writeObject(value);
+            oos.flush();
+        }
         return out;
     }
 

diff --git a/.../src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJsonIndexStorage.java b/.../src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJsonIndexStorage.java
@@ -23,8 +23,8 @@ protected ByteArrayOutputStream writeObject(V value) throws IOException {
     }
 
     protected V readObject(byte[] buffer) {
-        try {
-            return objectMapper.readValue(new GZIPInputStream(new ByteArrayInputStream(buffer)), getTypeReference());
+        try (GZIPInputStream gzipInputStream = new GZIPInputStream(new ByteArrayInputStream(buffer))) {
+            return objectMapper.readValue(gzipInputStream, getTypeReference());
         } catch (IOException e) {
             throw new RuntimeException(e);
         }

diff --git a/...java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/FileBackedByteIndexedInfoStore.java b/...java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/FileBackedByteIndexedInfoStore.java
@@ -36,8 +36,8 @@ public List<String> search(String term) {
 			return new ArrayList<String>();
 		}else {
 			return allValues.keys().stream().filter((value)->{
-				String lowerTerm = term.toLowerCase();
-				return value.toLowerCase().contains(lowerTerm);
+				String lowerTerm = term.toLowerCase(Locale.ENGLISH);
+				return value.toLowerCase(Locale.ENGLISH).contains(lowerTerm);
 			}).collect(Collectors.toList());
 		}
 	}

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoStore.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoStore.java
@@ -3,6 +3,7 @@
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentHashMap.KeySetView;
 import java.util.concurrent.ConcurrentSkipListSet;
@@ -22,8 +23,8 @@ public List<String> search(String term) {
 			return new ArrayList<String>();
 		}else {
 			return allValues.keySet().stream().filter((value)->{
-				String lowerTerm = term.toLowerCase();
-				return value.toLowerCase().contains(lowerTerm);
+				String lowerTerm = term.toLowerCase(Locale.ENGLISH);
+				return value.toLowerCase(Locale.ENGLISH).contains(lowerTerm);
 			}).collect(Collectors.toList());			
 		}
 	}

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java
@@ -44,15 +44,17 @@ public void setVariantSpecIndex(String[] variantSpecIndex) {
 	}
 
 	public static VariantStore readInstance(String genomicDataDirectory) throws IOException, ClassNotFoundException {
-		ObjectInputStream ois = new ObjectInputStream(new GZIPInputStream(new FileInputStream(genomicDataDirectory + VARIANT_STORE_JAVABIN_FILENAME)));
-		VariantStore variantStore = (VariantStore) ois.readObject();
-		ois.close();
-		variantStore.getVariantMaskStorage().values().forEach(store -> {
-			store.updateStorageDirectory(new File(genomicDataDirectory));
-		});
-		variantStore.open();
-		variantStore.setVariantSpecIndex(loadVariantIndexFromFile(genomicDataDirectory));
-		return variantStore;
+		try (GZIPInputStream gzipInputStream = new GZIPInputStream(new FileInputStream(genomicDataDirectory + VARIANT_STORE_JAVABIN_FILENAME));
+			 ObjectInputStream ois = new ObjectInputStream(gzipInputStream)) {
+			VariantStore variantStore = (VariantStore) ois.readObject();
+			ois.close();
+			variantStore.getVariantMaskStorage().values().forEach(store -> {
+				store.updateStorageDirectory(new File(genomicDataDirectory));
+			});
+			variantStore.open();
+			variantStore.setVariantSpecIndex(loadVariantIndexFromFile(genomicDataDirectory));
+			return variantStore;
+		}
 	}
 
 	public void writeInstance(String genomicDirectory) {
@@ -125,11 +127,7 @@ public List<VariableVariantMasks> getMasksForDbSnpSpec(String variant) {
 	public void open() {
 		variantMaskStorage.values().stream().forEach((fbbis -> {
 			if (fbbis != null) {
-				try {
-					fbbis.open();
-				} catch (FileNotFoundException e) {
-					throw new UncheckedIOException(e);
-				}
+				fbbis.open();
 			}
 		}));
 	}

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/SequentialLoader.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/SequentialLoader.java
@@ -75,9 +75,9 @@ public static void main(String[] args) throws IOException, ClassNotFoundExceptio
 		//load each into observation store
 		for(String filename : inputFiles) {
 			log.info("Loading file " + filename);
-			if(filename.toLowerCase().endsWith("sql")) {
+			if(filename.toLowerCase(Locale.ENGLISH).endsWith("sql")) {
 				loadSqlFile(filename);
-			} else if(filename.toLowerCase().endsWith("csv")){
+			} else if(filename.toLowerCase(Locale.ENGLISH).endsWith("csv")){
 				loadCsvFile(filename);
 			}
 		}

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
@@ -336,10 +336,9 @@ public PhenoCube<?> load(String key) throws Exception {
 										byte[] buffer = new byte[length];
 										allObservationsStore.read(buffer);
 										allObservationsStore.close();
-										ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(buffer)));
-										PhenoCube<?> ret = (PhenoCube<?>)inStream.readObject();
-										inStream.close();
-										return ret;
+										try (ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(buffer)))) {
+											return (PhenoCube<?>)inStream.readObject();
+										}
 									}else {
 										log.warn("ColumnMeta not found for : [{}]", key);
 										return null;

diff --git a/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java b/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java
@@ -143,8 +143,8 @@ public SearchResults search(@RequestBody QueryRequest searchJson) {
 
 		// Phenotype Values
 		Object phenotypeResults = searchJson.getQuery() != null ? allColumns.stream().filter((entry) -> {
-			String lowerCaseSearchTerm = searchJson.getQuery().toString().toLowerCase();
-			return entry.getKey().toLowerCase().contains(lowerCaseSearchTerm)
+			String lowerCaseSearchTerm = searchJson.getQuery().toString().toLowerCase(Locale.ENGLISH);
+			return entry.getKey().toLowerCase(Locale.ENGLISH).contains(lowerCaseSearchTerm)
 					|| (entry.getValue().isCategorical() && entry.getValue().getCategoryValues().stream()
 							.map(String::toLowerCase).collect(Collectors.toList()).contains(lowerCaseSearchTerm));
 		}).collect(Collectors.toMap(Entry::getKey, Entry::getValue)) : allColumns;
@@ -154,10 +154,10 @@ public SearchResults search(@RequestBody QueryRequest searchJson) {
 		abstractProcessor.getInfoStoreMeta().stream().forEach(infoColumnMeta -> {
 			//FileBackedByteIndexedInfoStore store = abstractProcessor.getInfoStore(infoColumn);
 			String query = searchJson.getQuery().toString();
-			String lowerCase = query.toLowerCase();
+			String lowerCase = query.toLowerCase(Locale.ENGLISH);
 			boolean storeIsNumeric = infoColumnMeta.continuous();
-			if (infoColumnMeta.description().toLowerCase().contains(lowerCase)
-					|| infoColumnMeta.key().toLowerCase().contains(lowerCase)) {
+			if (infoColumnMeta.description().toLowerCase(Locale.ENGLISH).contains(lowerCase)
+					|| infoColumnMeta.key().toLowerCase(Locale.ENGLISH).contains(lowerCase)) {
 				infoResults.put(infoColumnMeta.key(),
 						ImmutableMap.of("description", infoColumnMeta.description(), "values",
 								storeIsNumeric ? new ArrayList<String>() : abstractProcessor.searchInfoConceptValues(infoColumnMeta.key(), ""), "continuous",

diff --git a/...st/java/edu/harvard/hms/dbmi/avillach/hpds/test/util/BuildIntegrationTestEnvironment.java b/...st/java/edu/harvard/hms/dbmi/avillach/hpds/test/util/BuildIntegrationTestEnvironment.java
@@ -25,9 +25,7 @@ public enum BuildIntegrationTestEnvironment {
             VariantMetadataLoader.main(new String[] {"./src/test/resources/test_vcfIndex.tsv", binFile, "target/VariantMetadataStorage.bin"});
             VariantStore variantStore = VariantStore.readInstance(STORAGE_DIR);
             BucketIndexBySample bucketIndexBySample = new BucketIndexBySample(variantStore, STORAGE_DIR);
-        } catch (IOException e) {
-            throw new RuntimeException(e);
-        } catch (ClassNotFoundException e) {
+        } catch (IOException | ClassNotFoundException e) {
             throw new RuntimeException(e);
         }