diff --git a/common/source/java/ch/systemsx/cisd/common/io/ByteArrayBasedContent.java b/common/source/java/ch/systemsx/cisd/common/io/ByteArrayBasedContent.java
index 5e9627f18e79407fbff0870e57ff270bf3e8fe32..9ba45c46f3f27077bf6bd49f30996c0fe2cc8366 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/ByteArrayBasedContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/ByteArrayBasedContent.java
@@ -18,6 +18,10 @@ package ch.systemsx.cisd.common.io;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
+import java.nio.ByteBuffer;
+
+import ch.systemsx.cisd.common.filesystem.ByteBufferRandomAccessFile;
+import ch.systemsx.cisd.common.filesystem.IRandomAccessFile;
/**
* Content based on an array of bytes.
@@ -69,4 +73,9 @@ public class ByteArrayBasedContent implements IContent
{
return new ByteArrayInputStream(byteArray);
}
+
+ public IRandomAccessFile getReadOnlyRandomAccessFile()
+ {
+ return new ByteBufferRandomAccessFile(ByteBuffer.wrap(byteArray));
+ }
}
diff --git a/common/source/java/ch/systemsx/cisd/common/io/ContentProviderBasedContent.java b/common/source/java/ch/systemsx/cisd/common/io/ContentProviderBasedContent.java
index 647e96f9937b250b66e8d249ab2054120ca53e1e..8ff889b3de31b7965db4c554c4ef0c816978b56e 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/ContentProviderBasedContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/ContentProviderBasedContent.java
@@ -18,6 +18,8 @@ package ch.systemsx.cisd.common.io;
import java.io.InputStream;
+import ch.systemsx.cisd.common.filesystem.IRandomAccessFile;
+
/**
* Content based on a {@link IContentProvider}.
*
@@ -56,6 +58,11 @@ public class ContentProviderBasedContent implements IContent
return getContent().getInputStream();
}
+ public IRandomAccessFile getReadOnlyRandomAccessFile()
+ {
+ return getContent().getReadOnlyRandomAccessFile();
+ }
+
private IContent getContent()
{
if (content == null)
@@ -64,5 +71,5 @@ public class ContentProviderBasedContent implements IContent
}
return content;
}
-
+
}
diff --git a/common/source/java/ch/systemsx/cisd/common/io/FileBasedContent.java b/common/source/java/ch/systemsx/cisd/common/io/FileBasedContent.java
index b76e440084379932ec71fe1ae81a6712218f3087..4442ae357fba4f2e815b9733a9e8fada29aed116 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/FileBasedContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/FileBasedContent.java
@@ -20,9 +20,13 @@ import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
+import java.io.IOException;
import java.io.InputStream;
+import java.io.RandomAccessFile;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.filesystem.IRandomAccessFile;
+import ch.systemsx.cisd.common.filesystem.RandomAccessFileImpl;
/**
* File content. Wraps an instance of {@link File}.
@@ -78,4 +82,15 @@ public class FileBasedContent implements IContent
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
}
+
+ public IRandomAccessFile getReadOnlyRandomAccessFile()
+ {
+ try
+ {
+ return new RandomAccessFileImpl(new RandomAccessFile(file, "r"));
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
}
diff --git a/common/source/java/ch/systemsx/cisd/common/io/IContent.java b/common/source/java/ch/systemsx/cisd/common/io/IContent.java
index e2b6037273f64861b0ab2a897d2477e7769710f6..cf4b6b330456233031f4d57ee71f24e4abbd4f53 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/IContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/IContent.java
@@ -18,8 +18,10 @@ package ch.systemsx.cisd.common.io;
import java.io.InputStream;
+import ch.systemsx.cisd.common.filesystem.IRandomAccessFile;
+
/**
- * Abstract of streamable binary content with name and known size.
+ * Abstract of streamable and random-accessible binary content with name and known size.
*
* @author Franz-Josef Elmer
*/
@@ -40,6 +42,11 @@ public interface IContent
*/
public boolean exists();
+ /**
+ * Returns a random access file object for read-only use.
+ */
+ public IRandomAccessFile getReadOnlyRandomAccessFile();
+
/**
* Returns a new instance of an input stream over the complete content. Note that the returned
* {@link InputStream} is expected to have {@link InputStream#markSupported()}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
index 52521107b7437e7f3021674922efaa7e8e8be5e7..9a1f18c3cdeb009c5a69d75b88b0f6394b91a95d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
@@ -37,12 +37,13 @@ import javax.imageio.ImageIO;
import org.apache.commons.io.IOUtils;
-import com.sun.media.jai.codec.FileSeekableStream;
import com.sun.media.jai.codec.ImageCodec;
import com.sun.media.jai.codec.ImageDecoder;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.io.FileBasedContent;
+import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.common.utilities.DataTypeUtil;
/**
@@ -182,9 +183,9 @@ public class ImageUtil
* @throws IllegalArgumentException if the input stream doesn't start with a magic number
* identifying supported image format.
*/
- public static BufferedImage loadImage(InputStream inputStream)
+ public static BufferedImage loadImage(IContent content)
{
- return loadImage(inputStream, 0);
+ return loadImage(content, 0);
}
/**
@@ -195,12 +196,12 @@ public class ImageUtil
* @throws IllegalArgumentException if the input stream doesn't start with a magic number
* identifying supported image format.
*/
- public static BufferedImage loadImage(InputStream inputStream, int page)
+ public static BufferedImage loadImage(IContent content, int page)
{
- InputStream markSupportingInputStream = inputStream;
- if (inputStream.markSupported() == false)
+ InputStream markSupportingInputStream = content.getInputStream();
+ if (markSupportingInputStream.markSupported() == false)
{
- markSupportingInputStream = new BufferedInputStream(inputStream);
+ markSupportingInputStream = new BufferedInputStream(markSupportingInputStream);
}
String fileType = DataTypeUtil.tryToFigureOutFileTypeOf(markSupportingInputStream);
return loadImage(markSupportingInputStream, fileType, page);
@@ -214,7 +215,7 @@ public class ImageUtil
* @throws IllegalArgumentException if the input stream doesn't start with a magic number
* identifying supported image format.
*/
- public static BufferedImage loadImage(InputStream inputStream, String fileType, int page)
+ private static BufferedImage loadImage(InputStream inputStream, String fileType, int page)
{
try
{
@@ -251,15 +252,7 @@ public class ImageUtil
{
throw new IllegalArgumentException("File does not exist: " + file.getAbsolutePath());
}
- try
- {
- FileSeekableStream inStream = new FileSeekableStream(file);
- return loadImage(inStream);
- } catch (IOException ex)
- {
- throw new IllegalArgumentException("Isn't a valid image file: "
- + file.getAbsolutePath() + ". Error: " + ex.getMessage());
- }
+ return loadImage(new FileBasedContent(file));
}
/**
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
index 2d8e8ac588c9c9d1b590b09a24739b803ff6a831..22b9bbcae4b03e6c04c6c1b46e1f8f8af6816efa 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
@@ -18,8 +18,6 @@ package ch.systemsx.cisd.openbis.dss.generic.shared.utils;
import java.awt.image.BufferedImage;
import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
@@ -27,7 +25,9 @@ import org.testng.AssertJUnit;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.filesystem.IRandomAccessFile;
+import ch.systemsx.cisd.common.io.FileBasedContent;
+import ch.systemsx.cisd.common.io.IContent;
/**
*
@@ -36,6 +36,37 @@ import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
*/
public class ImageUtilTest extends AssertJUnit
{
+ private static class MockIContent implements IContent
+ {
+ final MockInputStream is = new MockInputStream();
+
+ public String tryGetName()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ public long getSize()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ public boolean exists()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ public IRandomAccessFile getReadOnlyRandomAccessFile()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ public InputStream getInputStream()
+ {
+ return is;
+ }
+
+ }
+
private static class MockInputStream extends InputStream
{
boolean closeInvoked;
@@ -100,17 +131,17 @@ public class ImageUtilTest extends AssertJUnit
@Test
public void testInputStreamAutomaticallyClosed()
{
- MockInputStream inputStream = new MockInputStream();
+ MockIContent content = new MockIContent();
try
{
- ImageUtil.loadImage(inputStream);
+ ImageUtil.loadImage(content);
fail("IllegalArgumentException expected");
} catch (IllegalArgumentException ex)
{
assertEquals("File type of an image input stream couldn't be determined.", ex.getMessage());
}
- assertEquals(true, inputStream.closeInvoked);
+ assertEquals(true, content.is.closeInvoked);
}
private BufferedImage loadImageByFile(String fileName)
@@ -123,15 +154,7 @@ public class ImageUtilTest extends AssertJUnit
private BufferedImage loadImageByInputStream(String fileName)
{
File file = new File(dir, fileName);
- BufferedImage image;
- try
- {
- image = ImageUtil.loadImage(new FileInputStream(file));
- } catch (FileNotFoundException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- return image;
+ return ImageUtil.loadImage(new FileBasedContent(file));
}
private void assertImageSize(int expectedWith, int expectedHeight, BufferedImage image)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
index 4e4ab5dc8979dc19a9c4139486f7a74937f62d4b..6b22e8228d4fedabb45026766c70e9fe898e3f75 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
@@ -24,7 +24,6 @@ import java.awt.image.RenderedImage;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
-import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
@@ -470,12 +469,11 @@ public class ImageChannelsUtils
private static BufferedImage loadImage(AbsoluteImageReference imageReference)
{
IContent content = imageReference.getContent();
- InputStream inputStream = content.getInputStream();
// extracts the correct page if necessary
int page = (imageReference.tryGetPage() != null) ? imageReference.tryGetPage() : 0;
- BufferedImage image = ImageUtil.loadImage(inputStream, page);
+ BufferedImage image = ImageUtil.loadImage(content, page);
return image;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index ed4cf6cb7ace14b5bad31a26709a98ee11c97856..ad6ef6d49e67738051f1a56c49f464cffad508ed 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -219,7 +219,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
IImagingDatasetLoader imageAccessor)
{
IContent imageFile = getAnyImagePath(imageAccessor, dataset);
- BufferedImage image = ImageUtil.loadImage(imageFile.getInputStream());
+ BufferedImage image = ImageUtil.loadImage(imageFile);
Size imageSize = new Size(image.getWidth(), image.getHeight());
return imageSize;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
index 00b25a1caac2e399b112dabecfac5d45baef6d20..db7cc1938fe1c4c4fc7454668f8314875506ba7b 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
@@ -242,7 +242,7 @@ public class ImageChannelsUtilsTest extends AssertJUnit
private String getImageContentDescription(IContent image)
{
- BufferedImage bufferedImage = ImageUtil.loadImage(image.getInputStream());
+ BufferedImage bufferedImage = ImageUtil.loadImage(image);
return getImageContentDescription(bufferedImage);
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 4abfe1dda2c313b6a4d24746f5182a0de891deb0..2269ffb0c839c7124fe03f59b8a2f5e04ddf878d 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.dss.screening.server;
import java.awt.image.BufferedImage;
-import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
@@ -42,6 +41,7 @@ import ch.systemsx.cisd.base.image.IImageTransformer;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.base.mdarray.MDFloatArray;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.io.ByteArrayBasedContent;
import ch.systemsx.cisd.common.io.ConcatenatedFileOutputStreamWriter;
import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.io.IContent;
@@ -333,7 +333,8 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
{
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
imagesWriter.writeNextBlock(outputStream);
- return ImageUtil.loadImage(new ByteArrayInputStream(outputStream.toByteArray()));
+ return ImageUtil
+ .loadImage(new ByteArrayBasedContent(outputStream.toByteArray(), "UNKNOWN"));
}
@Test
@@ -448,14 +449,14 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
ImgDatasetDTO dataset = createDataset(datasetId);
dataset.setContainerId(containerId);
dataset.setPermId(DATASET_CODE);
-
+
long experimentId = 888;
ImgContainerDTO container = new ImgContainerDTO(null, null, null, experimentId);
container.setId(containerId);
one(dao).tryGetDatasetByPermId(DATASET_CODE);
will(returnValue(dataset));
-
+
allowing(dao).hasDatasetChannels(DATASET_CODE);
will(returnValue(false));
@@ -601,7 +602,8 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
private FeatureVectorDatasetReference createFeatureVectorDatasetReference(String dataSetCode)
{
- return new FeatureVectorDatasetReference(dataSetCode, "", null, null, null, null, null, null);
+ return new FeatureVectorDatasetReference(dataSetCode, "", null, null, null, null, null,
+ null);
}
// Used for the authorization test