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Merge pull request #1085 from josemduarte/miscfixes
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Replacing home-made copy by Files.copy
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@josemduarte
josemduarte committed Mar 6, 2024
2 parents 874ce88 + 7f8f95e commit f94e577
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Showing 4 changed files with 20 additions and 100 deletions.
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

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