added buffers to all InputStreams

ocfl-java-core/src/main/java/edu/wisc/library/ocfl/core/db/BaseObjectDetailsDatabase.java

@@ -37,6 +37,7 @@
 import org.slf4j.LoggerFactory;
 
 import javax.sql.DataSource;
+import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -174,7 +175,7 @@ public void updateObjectDetails(Inventory inventory, String inventoryDigest, Pat
         Enforce.notNull(inventoryFile, "inventoryFile cannot be null");
         Enforce.notNull(runnable, "runnable cannot be null");
 
-        try (var inventoryStream = Files.newInputStream(inventoryFile)) {
+        try (var inventoryStream = new BufferedInputStream(Files.newInputStream(inventoryFile))) {
             updateObjectDetailsInternal(inventory, inventoryDigest, inventoryStream, runnable);
         } catch (IOException e) {
             throw new OcflIOException(e);

ocfl-java-core/src/main/java/edu/wisc/library/ocfl/core/storage/cloud/CloudOcflFileRetriever.java

@@ -29,6 +29,8 @@
 import edu.wisc.library.ocfl.api.model.DigestAlgorithm;
 import edu.wisc.library.ocfl.api.util.Enforce;
 
+import java.io.BufferedInputStream;
+
 /**
  * OcflFileRetriever implementation for lazy-loading files from cloud storage.
  */
@@ -71,7 +73,7 @@ public CloudOcflFileRetriever(CloudClient cloudClient, String key, DigestAlgorit
     @Override
     public FixityCheckInputStream retrieveFile() {
         // TODO caching?
-        return new FixityCheckInputStream(cloudClient.downloadStream(key), digestAlgorithm, digestValue);
+        return new FixityCheckInputStream(new BufferedInputStream(cloudClient.downloadStream(key)), digestAlgorithm, digestValue);
     }
 
 }

ocfl-java-core/src/main/java/edu/wisc/library/ocfl/core/storage/cloud/CloudOcflStorage.java

@@ -56,6 +56,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
@@ -272,7 +273,8 @@ public void reconstructObjectVersion(Inventory inventory, VersionNum versionNum,
 
                 UncheckedFiles.createDirectories(destination.getParent());
 
-                try (var stream = new FixityCheckInputStream(cloudClient.downloadStream(srcPath), digestAlgorithm, id)) {
+                try (var stream = new FixityCheckInputStream(new BufferedInputStream(cloudClient.downloadStream(srcPath)),
+                        digestAlgorithm, id)) {
                     Files.copy(stream, destination);
                     stream.checkFixity();
                 } catch (FixityCheckException e) {
@@ -736,7 +738,7 @@ private Inventory downloadAndVerifyInventory(String objectId, String objectRootP
         var expectedDigest = findAndGetDigestFromSidecar(objectRootPath);
         var remotePath = ObjectPaths.inventoryPath(objectRootPath);
 
-        try (var stream = new FixityCheckInputStream(cloudClient.downloadStream(remotePath),
+        try (var stream = new FixityCheckInputStream(new BufferedInputStream(cloudClient.downloadStream(remotePath)),
                 expectedDigest.getKey(), expectedDigest.getValue())) {
             var inventory = inventoryMapper.read(objectRootPath, expectedDigest.getValue(), stream);
 
@@ -758,7 +760,7 @@ private Inventory downloadAndVerifyMutableInventory(String objectId, String obje
         var expectedDigest = findAndGetDigestFromSidecar(ObjectPaths.mutableHeadVersionPath(objectRootPath));
         var remotePath = ObjectPaths.mutableHeadInventoryPath(objectRootPath);
 
-        try (var stream = new FixityCheckInputStream(cloudClient.downloadStream(remotePath),
+        try (var stream = new FixityCheckInputStream(new BufferedInputStream(cloudClient.downloadStream(remotePath)),
                 expectedDigest.getKey(), expectedDigest.getValue())) {
             var revisionNum = identifyLatestRevision(objectRootPath);
             var inventory = inventoryMapper.readMutableHead(objectRootPath, expectedDigest.getValue(), revisionNum, stream);

ocfl-java-core/src/main/java/edu/wisc/library/ocfl/core/storage/filesystem/FileSystemOcflFileRetriever.java

@@ -30,6 +30,7 @@
 import edu.wisc.library.ocfl.api.model.DigestAlgorithm;
 import edu.wisc.library.ocfl.api.util.Enforce;
 
+import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -55,7 +56,7 @@ public FileSystemOcflFileRetriever(Path filePath, DigestAlgorithm digestAlgorith
     @Override
     public FixityCheckInputStream retrieveFile() {
         try {
-            return new FixityCheckInputStream(Files.newInputStream(filePath), digestAlgorithm, digestValue);
+            return new FixityCheckInputStream(new BufferedInputStream(Files.newInputStream(filePath)), digestAlgorithm, digestValue);
         } catch (IOException e) {
             throw new OcflIOException(e);
         }

ocfl-java-core/src/main/java/edu/wisc/library/ocfl/core/storage/filesystem/FileSystemOcflStorage.java

@@ -57,6 +57,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.io.UncheckedIOException;
 import java.nio.file.FileAlreadyExistsException;
@@ -292,7 +293,7 @@ public void reconstructObjectVersion(Inventory inventory, VersionNum versionNum,
 
                 UncheckedFiles.createDirectories(destination.getParent());
 
-                try (var stream = new FixityCheckInputStream(Files.newInputStream(srcPath), digestAlgorithm, id)) {
+                try (var stream = new FixityCheckInputStream(new BufferedInputStream(Files.newInputStream(srcPath)), digestAlgorithm, id)) {
                     Files.copy(stream, destination);
                     stream.checkFixity();
                 } catch (IOException e) {
@@ -642,7 +643,7 @@ private FixityCheckInputStream inventoryVerifyingInputStream(Path inventoryPath)
         var expectedDigest = SidecarMapper.readDigest(sidecarPath);
         var algorithm = SidecarMapper.getDigestAlgorithmFromSidecar(FileUtil.pathToStringStandardSeparator(sidecarPath));
 
-        return new FixityCheckInputStream(Files.newInputStream(inventoryPath), algorithm, expectedDigest);
+        return new FixityCheckInputStream(new BufferedInputStream(Files.newInputStream(inventoryPath)), algorithm, expectedDigest);
     }
 
     private RevisionNum identifyLatestRevision(Path objectRootPath) {

ocfl-java-core/src/main/java/edu/wisc/library/ocfl/core/validation/Validator.java

@@ -48,7 +48,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
@@ -516,7 +515,7 @@ private void fixityCheck(String objectRootPath, SimpleInventory inventory, Manif
                     expectations.putAll(fixityDigests);
                 }
 
-                try (var contentStream = new BufferedInputStream(storage.readFile(storagePath))) {
+                try (var contentStream = storage.readFile(storagePath)) {
                     var wrapped = MultiDigestInputStream.create(contentStream, expectations.keySet());
 
                     while (wrapped.read() != -1) {
@@ -734,7 +733,7 @@ private ParseResult parseInventory(String inventoryPath,
     }
 
     private String computeInventoryDigest(String inventoryPath, DigestAlgorithm algorithm) {
-        try (var stream = new BufferedInputStream(storage.readFile(inventoryPath))) {
+        try (var stream = storage.readFile(inventoryPath)) {
             var wrapped = MultiDigestInputStream.create(stream, List.of(algorithm));
             while (wrapped.read() > 0) {
                 // consume stream

ocfl-java-core/src/main/java/edu/wisc/library/ocfl/core/validation/storage/CloudStorage.java

@@ -30,6 +30,7 @@
 import edu.wisc.library.ocfl.core.storage.cloud.KeyNotFoundException;
 import edu.wisc.library.ocfl.core.storage.cloud.ListResult;
 
+import java.io.BufferedInputStream;
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.List;
@@ -81,7 +82,7 @@ public boolean fileExists(String filePath) {
     @Override
     public InputStream readFile(String filePath) {
         try {
-            return client.downloadStream(filePath);
+            return new BufferedInputStream(client.downloadStream(filePath));
         } catch (KeyNotFoundException e) {
             throw new NotFoundException(String.format("%s was not found", filePath), e);
         }

ocfl-java-core/src/main/java/edu/wisc/library/ocfl/core/validation/storage/FileSystemStorage.java

@@ -29,6 +29,7 @@
 import edu.wisc.library.ocfl.api.util.Enforce;
 import edu.wisc.library.ocfl.core.util.FileUtil;
 
+import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.file.FileVisitResult;
@@ -75,7 +76,7 @@ public boolean fileExists(String filePath) {
     @Override
     public InputStream readFile(String filePath) {
         try {
-            return Files.newInputStream(storageRoot.resolve(filePath));
+            return new BufferedInputStream(Files.newInputStream(storageRoot.resolve(filePath)));
         } catch (NoSuchFileException e) {
             throw new NotFoundException(String.format("%s was not found", filePath), e);
         } catch (IOException e) {

ocfl-java-itest/src/test/java/edu/wisc/library/ocfl/itest/OcflITest.java

@@ -43,6 +43,7 @@
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.io.TempDir;
 
+import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -2299,7 +2300,7 @@ private void assertStream(String expected, OcflObjectVersionFile actual) throws
     }
 
     private void verifyStream(Path expectedFile, OcflObjectVersionFile actual) throws IOException {
-        try (var fileStream = Files.newInputStream(expectedFile)) {
+        try (var fileStream = new BufferedInputStream(Files.newInputStream(expectedFile))) {
             assertStream(TestHelper.inputToString(fileStream), actual);
         }
     }

ocfl-java-test/src/main/java/edu/wisc/library/ocfl/test/TestHelper.java

@@ -24,6 +24,7 @@
 
 package edu.wisc.library.ocfl.test;
 
+import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -40,7 +41,7 @@ private TestHelper() {
     }
 
     public static String fileToString(Path file) {
-        try (var input = Files.newInputStream(file)) {
+        try (var input = new BufferedInputStream(Files.newInputStream(file))) {
             return inputToString(input);
         } catch (IOException e) {
             throw new RuntimeException(e);
@@ -63,7 +64,7 @@ public static InputStream inputStream(String content) {
 
     public static InputStream inputStream(Path path) {
         try {
-            return Files.newInputStream(path);
+            return new BufferedInputStream(Files.newInputStream(path));
         } catch (IOException e) {
             throw new RuntimeException(e);
         }