diff --git a/build.gradle b/build.gradle index 3d61ec28..7efb24bb 100644 --- a/build.gradle +++ b/build.gradle @@ -11,6 +11,10 @@ repositories { jcenter() } +configurations.all { + exclude group: 'commons-io' +} + java { sourceCompatibility = JavaVersion.VERSION_1_8 targetCompatibility = JavaVersion.VERSION_1_8 @@ -23,7 +27,6 @@ dependencies { api("org.openmicroscopy:omero-common:5.5.0") // Keep from being exposed to child projects - implementation("commons-io:commons-io:2.6") implementation("commons-lang:commons-lang:2.6") } diff --git a/src/main/java/ome/io/bioformats/BfPyramidPixelBuffer.java b/src/main/java/ome/io/bioformats/BfPyramidPixelBuffer.java index 8783a2b7..be4f9232 100644 --- a/src/main/java/ome/io/bioformats/BfPyramidPixelBuffer.java +++ b/src/main/java/ome/io/bioformats/BfPyramidPixelBuffer.java @@ -14,6 +14,7 @@ import java.nio.ByteOrder; import java.nio.channels.FileLock; import java.nio.channels.OverlappingFileLockException; +import java.nio.file.Files; import java.util.List; import loci.formats.FormatException; @@ -37,7 +38,6 @@ import ome.xml.model.enums.EnumerationException; import ome.xml.model.primitives.PositiveInteger; -import org.apache.commons.io.FileUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -440,7 +440,7 @@ protected void closeWriter() throws IOException try { if (writerFile != null) { try { - FileUtils.moveFile(writerFile, readerFile); + Files.move(writerFile.toPath(), readerFile.toPath()); } finally { writerFile = null; } diff --git a/src/main/java/ome/io/nio/AbstractFileSystemService.java b/src/main/java/ome/io/nio/AbstractFileSystemService.java index 246ca8f5..965e4704 100644 --- a/src/main/java/ome/io/nio/AbstractFileSystemService.java +++ b/src/main/java/ome/io/nio/AbstractFileSystemService.java @@ -6,9 +6,9 @@ package ome.io.nio; import java.io.File; +import java.nio.file.Paths; import java.util.Formatter; -import org.apache.commons.io.FilenameUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -79,7 +79,7 @@ protected void createSubpath(String path) { * @return the path relative to the root */ public String getPixelsDirectory() { - return FilenameUtils.concat(root, PIXELS_PATH); + return Paths.get(root, PIXELS_PATH).toString(); } /** @@ -138,6 +138,6 @@ private String getPath(String prefix, Long id) { } } } - return FilenameUtils.concat(root, prefix + suffix + id); + return Paths.get(root, prefix + suffix + id).toString(); } } diff --git a/src/main/java/ome/io/nio/PixelsService.java b/src/main/java/ome/io/nio/PixelsService.java index 92554f7d..cb52c99f 100644 --- a/src/main/java/ome/io/nio/PixelsService.java +++ b/src/main/java/ome/io/nio/PixelsService.java @@ -40,7 +40,6 @@ import ome.model.stats.StatsInfo; import ome.util.PixelData; -import org.apache.commons.io.FileUtils; import org.apache.commons.lang.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -48,6 +47,8 @@ import org.springframework.context.ApplicationEventPublisher; import org.springframework.context.ApplicationEventPublisherAware; +import com.google.common.io.Files; + /** * @author
* Chris Allan     hashDigests) throws FailedTileLoopException { diff --git a/src/test/java/ome/io/nio/utests/BfPixelBufferUnitTest.java b/src/test/java/ome/io/nio/utests/BfPixelBufferUnitTest.java index d87beb7e..faca0c93 100644 --- a/src/test/java/ome/io/nio/utests/BfPixelBufferUnitTest.java +++ b/src/test/java/ome/io/nio/utests/BfPixelBufferUnitTest.java @@ -5,8 +5,8 @@ package ome.io.nio.utests; -import java.io.File; import java.io.IOException; +import java.nio.file.Paths; import ome.io.nio.PixelBuffer; import ome.io.nio.PixelsService; @@ -14,12 +14,13 @@ import ome.model.core.Pixels; import ome.model.enums.PixelsType; -import org.apache.commons.io.FileUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import com.google.common.io.MoreFiles; + /** * Tests the logic for creating {@link BfPixelBuffer} instances. * @since 4.3 @@ -64,7 +65,7 @@ private void setup() { @AfterClass public void tearDown() throws IOException { - FileUtils.deleteDirectory(new File(root)); + MoreFiles.deleteRecursively(Paths.get(root)); } @Test diff --git a/src/test/java/ome/io/nio/utests/HelperUnitTest.java b/src/test/java/ome/io/nio/utests/HelperUnitTest.java index b592cb2e..ac6e4f1e 100644 --- a/src/test/java/ome/io/nio/utests/HelperUnitTest.java +++ b/src/test/java/ome/io/nio/utests/HelperUnitTest.java @@ -6,11 +6,14 @@ import java.io.File; import java.io.IOException; +import java.nio.file.Paths; -import org.apache.commons.io.FileUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.Test; + +import com.google.common.io.MoreFiles; + import ome.io.nio.PixelsService; public class HelperUnitTest { @@ -28,7 +31,7 @@ private String p(String path) { @AfterClass public void tearDown() throws IOException { - FileUtils.deleteDirectory(new File(ROOT)); + MoreFiles.deleteRecursively(Paths.get(ROOT)); } // diff --git a/src/test/java/ome/io/nio/utests/HugePixelBufferUnitTest.java b/src/test/java/ome/io/nio/utests/HugePixelBufferUnitTest.java index 538f21c0..753970bd 100644 --- a/src/test/java/ome/io/nio/utests/HugePixelBufferUnitTest.java +++ b/src/test/java/ome/io/nio/utests/HugePixelBufferUnitTest.java @@ -4,16 +4,16 @@ */ package ome.io.nio.utests; -import java.io.File; import java.io.IOException; +import java.nio.file.Paths; - -import org.apache.commons.io.FileUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import com.google.common.io.MoreFiles; + import ome.io.nio.DimensionsOutOfBoundsException; import ome.io.nio.PixelBuffer; import ome.io.nio.PixelsService; @@ -36,7 +36,7 @@ public class HugePixelBufferUnitTest { @AfterClass public void tearDown() throws IOException { - FileUtils.deleteDirectory(new File(ROOT)); + MoreFiles.deleteRecursively(Paths.get(ROOT)); } @BeforeMethod diff --git a/src/test/java/ome/io/nio/utests/LargePixelBufferUnitTest.java b/src/test/java/ome/io/nio/utests/LargePixelBufferUnitTest.java index a875d52a..a6645778 100644 --- a/src/test/java/ome/io/nio/utests/LargePixelBufferUnitTest.java +++ b/src/test/java/ome/io/nio/utests/LargePixelBufferUnitTest.java @@ -5,15 +5,16 @@ package ome.io.nio.utests; -import java.io.File; import java.io.IOException; +import java.nio.file.Paths; -import org.apache.commons.io.FileUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import com.google.common.io.MoreFiles; + import ome.io.nio.DimensionsOutOfBoundsException; import ome.io.nio.PixelBuffer; import ome.io.nio.PixelsService; @@ -36,7 +37,7 @@ public class LargePixelBufferUnitTest { @AfterClass public void tearDown() throws IOException { - FileUtils.deleteDirectory(new File(ROOT)); + MoreFiles.deleteRecursively(Paths.get(ROOT)); } @BeforeMethod diff --git a/src/test/java/ome/io/nio/utests/NormalPixelBufferUnitTest.java b/src/test/java/ome/io/nio/utests/NormalPixelBufferUnitTest.java index f283d876..0639180c 100644 --- a/src/test/java/ome/io/nio/utests/NormalPixelBufferUnitTest.java +++ b/src/test/java/ome/io/nio/utests/NormalPixelBufferUnitTest.java @@ -5,15 +5,16 @@ package ome.io.nio.utests; -import java.io.File; import java.io.IOException; +import java.nio.file.Paths; -import org.apache.commons.io.FileUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import com.google.common.io.MoreFiles; + import ome.io.nio.DimensionsOutOfBoundsException; import ome.io.nio.PixelBuffer; import ome.io.nio.PixelsService; @@ -36,7 +37,7 @@ public class NormalPixelBufferUnitTest { @AfterClass public void tearDown() throws IOException { - FileUtils.deleteDirectory(new File(ROOT)); + MoreFiles.deleteRecursively(Paths.get(ROOT)); } @BeforeMethod diff --git a/src/test/java/ome/io/nio/utests/OutOfBoundsUnitTest.java b/src/test/java/ome/io/nio/utests/OutOfBoundsUnitTest.java index 86febaca..6e299a11 100644 --- a/src/test/java/ome/io/nio/utests/OutOfBoundsUnitTest.java +++ b/src/test/java/ome/io/nio/utests/OutOfBoundsUnitTest.java @@ -5,8 +5,8 @@ package ome.io.nio.utests; -import java.io.File; import java.io.IOException; +import java.nio.file.Paths; import ome.io.nio.DimensionsOutOfBoundsException; import ome.io.nio.PixelBuffer; @@ -14,12 +14,13 @@ import ome.model.core.Pixels; import ome.model.enums.PixelsType; -import org.apache.commons.io.FileUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import com.google.common.io.MoreFiles; + /** * @author callan * @@ -34,7 +35,7 @@ public class OutOfBoundsUnitTest { @AfterClass public void tearDown() throws IOException { - FileUtils.deleteDirectory(new File(ROOT)); + MoreFiles.deleteRecursively(Paths.get(ROOT)); } @BeforeMethod diff --git a/src/test/java/ome/io/nio/utests/PixelServiceCreatesDirectoryUnitTest.java b/src/test/java/ome/io/nio/utests/PixelServiceCreatesDirectoryUnitTest.java index 2d87140a..9bc25f81 100644 --- a/src/test/java/ome/io/nio/utests/PixelServiceCreatesDirectoryUnitTest.java +++ b/src/test/java/ome/io/nio/utests/PixelServiceCreatesDirectoryUnitTest.java @@ -6,20 +6,21 @@ -import java.io.File; import java.io.IOException; +import java.nio.file.Paths; import ome.io.nio.PixelBuffer; import ome.io.nio.PixelsService; import ome.model.core.Pixels; import ome.model.enums.PixelsType; -import org.apache.commons.io.FileUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import com.google.common.io.MoreFiles; + public class PixelServiceCreatesDirectoryUnitTest { private Pixels pixels; @@ -30,7 +31,7 @@ public class PixelServiceCreatesDirectoryUnitTest { @AfterClass public void tearDown() throws IOException { - FileUtils.deleteDirectory(new File(ROOT)); + MoreFiles.deleteRecursively(Paths.get(ROOT)); } @BeforeMethod