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Replacing home-made copy by Files.copy #1085

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merged 4 commits into from Mar 6, 2024
Merged

Replacing home-made copy by Files.copy #1085

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37b5fca
Replacing home-made copy by Files.copy. Other minor fixes
josemduarte Mar 4, 2024
9d59f59
Merge branch 'master' into miscfixes
josemduarte Mar 4, 2024
df2e83d
Merge branch 'master' into miscfixes
josemduarte Mar 4, 2024
7f8f95e
Typo
josemduarte Mar 4, 2024
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73 changes: 15 additions & 58 deletions biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
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Expand Up @@ -22,7 +22,6 @@
package org.biojava.nbio.core.util;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FilenameFilter;
Expand All @@ -34,13 +33,8 @@
import java.net.URL;
import java.net.URLConnection;
import java.nio.channels.Channels;
import java.nio.channels.FileChannel;
import java.nio.channels.ReadableByteChannel;
import java.nio.file.FileVisitResult;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.SimpleFileVisitor;
import java.nio.file.*;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.Scanner;

Expand All @@ -57,39 +51,6 @@ public enum Hash{
MD5, SHA1, SHA256, UNKNOWN
}

/**
* Copy the content of file src to dst TODO since java 1.7 this is provided
* in java.nio.file.Files
*
* @param src
* @param dst
* @throws IOException
*/
@SuppressWarnings("resource")
public static void copy(File src, File dst) throws IOException {

// Took following recipe from
// http://stackoverflow.com/questions/106770/standard-concise-way-to-copy-a-file-in-java
// The nio package seems to be the most efficient way to copy a file
FileChannel source = null;
FileChannel destination = null;

try {
// we need the supress warnings here (the warning that the stream is not closed is harmless)
// see http://stackoverflow.com/questions/12970407/does-filechannel-close-close-the-underlying-stream
source = new FileInputStream(src).getChannel();
destination = new FileOutputStream(dst).getChannel();
destination.transferFrom(source, 0, source.size());
} finally {
if (source != null) {
source.close();
}
if (destination != null) {
destination.close();
}
}
}

/**
* Gets the file extension of a file, excluding '.'.
* If the file name has no extension the file name is returned.
Expand All @@ -100,7 +61,7 @@ public static String getFileExtension(File f) {
String fileName = f.getName();
String ext = "";
int mid = fileName.lastIndexOf(".");
ext = fileName.substring(mid + 1, fileName.length());
ext = fileName.substring(mid + 1);
return ext;
}

Expand Down Expand Up @@ -165,7 +126,7 @@ public static void downloadFile(URL url, File destination) throws IOException {
}

logger.debug("Copying temp file [{}] to final location [{}]", tempFile, destination);
copy(tempFile, destination);
Files.copy(tempFile.toPath(), destination.toPath(), StandardCopyOption.REPLACE_EXISTING);

// delete the tmp file
tempFile.delete();
Expand Down Expand Up @@ -252,24 +213,20 @@ public static void createValidationFiles(URLConnection resourceUrlConnection, Fi
public static boolean validateFile(File localFile) {
File sizeFile = new File(localFile.getParentFile(), localFile.getName() + SIZE_EXT);
if(sizeFile.exists()) {
Scanner scanner = null;
try {
scanner = new Scanner(sizeFile);
long expectedSize = scanner.nextLong();
long actualLSize = localFile.length();
if (expectedSize != actualLSize) {
logger.warn("File [{}] size ({}) does not match expected size ({}).", localFile, actualLSize, expectedSize);
return false;
}
} catch (FileNotFoundException e) {
logger.warn("could not validate size of file [{}] because no size metadata file exists.", localFile);
} finally {
scanner.close();
}
try (Scanner scanner = new Scanner(sizeFile)) {
long expectedSize = scanner.nextLong();
long actualSize = localFile.length();
if (expectedSize != actualSize) {
logger.warn("File [{}] size ({}) does not match expected size ({}).", localFile, actualSize, expectedSize);
return false;
}
} catch (FileNotFoundException e) {
logger.warn("could not validate size of file [{}] because no size metadata file exists.", localFile);
}
}

File[] hashFiles = localFile.getParentFile().listFiles(new FilenameFilter() {
String hashPattern = String.format("%s%s_(%s|%s|%s)", localFile.getName(), HASH_EXT, Hash.MD5, Hash.SHA1, Hash.SHA256);
final String hashPattern = String.format("%s%s_(%s|%s|%s)", localFile.getName(), HASH_EXT, Hash.MD5, Hash.SHA1, Hash.SHA256);
@Override
public boolean accept(File dir, String name) {
return name.matches(hashPattern);
Expand Down Expand Up @@ -401,7 +358,7 @@ public static URLConnection prepareURLConnection(String url, int timeout) throws
public static void deleteDirectory(Path dir) throws IOException {
if(dir == null || !Files.exists(dir))
return;
Files.walkFileTree(dir, new SimpleFileVisitor<Path>() {
Files.walkFileTree(dir, new SimpleFileVisitor<>() {
@Override
public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
Files.delete(file);
Expand Down
39 changes: 0 additions & 39 deletions biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java
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Expand Up @@ -8,8 +8,6 @@
import static org.junit.jupiter.api.Assertions.assertTrue;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintStream;
import java.net.URL;
Expand All @@ -20,43 +18,6 @@

class FileDownloadUtilsTest {

@Nested
class FileCopy {

private File createSrcFile () throws IOException {
byte [] toSave = new byte []{1,2,3,4,5};
File src = Files.createTempFile("test", ".dat").toFile();
try (FileOutputStream fos = new FileOutputStream(src);){
fos.write(toSave);
}
return src;
}

@Test
void copyFile() throws IOException {
File src = createSrcFile();
//sanity check
assertEquals(5, src.length());
File dest = Files.createTempFile("dest", ".dat").toFile();
assertEquals(0, dest.length());
FileDownloadUtils.copy(src, dest);
assertEquals(5, dest.length());

//original is unaffected
assertEquals(5, src.length());

// bytes are identical
try (FileInputStream fis1 = new FileInputStream(src);
FileInputStream fis2 = new FileInputStream(dest)) {
int b = -1;
while (( b = fis1.read()) != -1) {
int b2 = fis2.read();
assertEquals (b, b2);
}
}
}
}

@Nested
class FileExtension {
@Test
Expand Down
3 changes: 2 additions & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
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Expand Up @@ -32,6 +32,7 @@
import java.io.*;
import java.net.URL;
import java.nio.file.Files;
import java.nio.file.StandardCopyOption;
import java.text.DateFormat;
import java.text.DecimalFormat;
import java.text.ParseException;
Expand Down Expand Up @@ -653,7 +654,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
in.close();
out.close();

FileDownloadUtils.copy(tempFile,localFile);
Files.copy(tempFile.toPath(), localFile.toPath(), StandardCopyOption.REPLACE_EXISTING);

// delete the tmp file
tempFile.delete();
Expand Down
5 changes: 3 additions & 2 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
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Expand Up @@ -33,6 +33,7 @@
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
Expand Down Expand Up @@ -390,7 +391,7 @@ public void testEmptyChemComp() throws IOException, StructureException {
Files.createDirectories(testCif.getParent());
URL resource = AtomCacheTest.class.getResource("/atp.cif.gz");
File src = new File(resource.getPath());
FileDownloadUtils.copy(src, testCif.toFile());
Files.copy(src.toPath(), testCif, StandardCopyOption.REPLACE_EXISTING);

// Load structure
Structure s = cache.getStructure("1ABC");
Expand Down Expand Up @@ -453,7 +454,7 @@ public void testEmptyGZChemComp() throws IOException, StructureException {
Files.createDirectories(testCif.getParent());
URL resource = AtomCacheTest.class.getResource("/atp.cif.gz");
File src = new File(resource.getPath());
FileDownloadUtils.copy(src, testCif.toFile());
Files.copy(src.toPath(), testCif, StandardCopyOption.REPLACE_EXISTING);

// Load structure
Structure s = cache.getStructure("1ABC");
Expand Down