From ceb89bf8c9e1baae913a5f7993b27ab8b88dadd2 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 25 Oct 2007 12:58:26 +0000
Subject: [PATCH] IDataStructure changed
SVN: 2252
---
.../cisd/bds/AbstractDataStructure.java | 50 +++++++-
.../cisd/bds/DataStructureLoader.java | 4 +-
.../systemsx/cisd/bds/DataStructureV1_0.java | 44 ++++---
.../ch/systemsx/cisd/bds/IDataStructure.java | 27 +++-
.../cisd/bds/DataStructureLoaderTest.java | 5 +-
.../cisd/bds/DataStructureV1_0Test.java | 119 ++++++++++++------
6 files changed, 183 insertions(+), 66 deletions(-)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java b/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
index dca7be2e5bb..939286081f8 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
@@ -27,33 +27,77 @@ import ch.systemsx.cisd.bds.storage.IStorage;
abstract class AbstractDataStructure implements IDataStructure
{
protected final IStorage storage;
- protected final IDirectory root;
+
+ protected IDirectory root;
AbstractDataStructure(IStorage storage)
{
assert storage != null: "Unspecified storage.";
this.storage = storage;
+ }
+
+ private void mountStorage()
+ {
storage.mount();
root = storage.getRoot();
}
+ /**
+ * Asserts that this instance is already opened or created otherwise a {@link IllegalStateException} is thrown.
+ */
+ protected void assertOpenOrCreated()
+ {
+ if (root == null)
+ {
+ throw new IllegalStateException("Data structure should first be opened or created.");
+ }
+ }
+
+ /**
+ * Validates this data structure and throws {@link DataStructureException} if invalid.
+ */
+ protected abstract void assertValid();
+
+ /**
+ * Performs opening specific for the concrete data structure. Will be invoked after the common part of
+ * {@link #open()} but before validation with {@link #assertValid()}.
+ */
+ protected abstract void performOpening();
+
+ /**
+ * Performs closing specific for the concrete data structure. Will be invoked before validation with
+ * {@link #assertValid()}.
+ */
+ protected abstract void performClosing();
+
//
// IDataStructure
//
+
+ public final void create()
+ {
+ mountStorage();
+ }
- public void load()
+ public final void open()
{
+ mountStorage();
+ performOpening();
Version loadedVersion = Version.loadFrom(root);
if (loadedVersion.isBackwardsCompatibleWith(getVersion()) == false)
{
throw new DataStructureException("Version of loaded data structure is " + loadedVersion
+ " which is not backward compatible with " + getVersion());
}
+ assertValid();
}
- public void save()
+ public final void close()
{
+ assertOpenOrCreated();
getVersion().saveTo(root);
+ performClosing();
+ assertValid();
storage.unmount();
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
index 6c23fa41ac0..9f6ddd0e4bd 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
@@ -49,7 +49,9 @@ public class DataStructureLoader
IStorage storage = createStorage(name);
storage.mount();
Version version = Version.loadFrom(storage.getRoot());
- return DataStructureFactory.createDataStructure(storage, version);
+ IDataStructure dataStructure = DataStructureFactory.createDataStructure(storage, version);
+ dataStructure.open();
+ return dataStructure;
}
private IStorage createStorage(String name)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
index 5f678739efc..22702846d0c 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -57,6 +57,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
*/
public IDirectory getOriginalData()
{
+ assertOpenOrCreated();
return Utilities.getOrCreateSubDirectory(getDataDirectory(), DIR_ORIGINAL);
}
@@ -68,6 +69,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
*/
public IFormattedData getFormatedData()
{
+ assertOpenOrCreated();
if (format == null)
{
throw new DataStructureException("Couldn't create formated data because of undefined format.");
@@ -81,6 +83,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
public void setFormat(Format format)
{
assert format != null : "Unspecified format.";
+ assertOpenOrCreated();
this.format = format;
}
@@ -92,6 +95,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
*/
public ExperimentIdentifier getExperimentIdentifier()
{
+ assertOpenOrCreated();
return ExperimentIdentifier.loadFrom(getMetaDataDirectory());
}
@@ -101,6 +105,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
public void setExperimentIdentifier(ExperimentIdentifier id)
{
assert id != null : "Unspecified experiment identifier";
+ assertOpenOrCreated();
id.saveTo(getMetaDataDirectory());
}
@@ -112,6 +117,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
*/
public ProcessingType getProcessingType()
{
+ assertOpenOrCreated();
return ProcessingType.loadFrom(getMetaDataDirectory());
}
@@ -121,34 +127,21 @@ public class DataStructureV1_0 extends AbstractDataStructure
public void setProcessingType(ProcessingType type)
{
assert type != null : "Unspecified processing type.";
+ assertOpenOrCreated();
type.saveTo(getMetaDataDirectory());
}
- /**
- * Loads the data structure from the storage and sets the format.
- */
- @Override
- public void load()
- {
- super.load();
- setFormat(Format.loadFrom(getMetaDataDirectory()));
- }
-
@Override
- public void save()
+ protected void assertValid()
{
if (getOriginalData().iterator().hasNext() == false)
{
throw new DataStructureException("Empty original data directory.");
}
IDirectory metaDataDirectory = getMetaDataDirectory();
- if (metaDataDirectory.tryToGetNode(Format.FORMAT_DIR) == null)
+ if (metaDataDirectory.tryToGetNode(Format.FORMAT_DIR) == null && format == null)
{
- if (format == null)
- {
- throw new DataStructureException("Unspecified format.");
- }
- format.saveTo(metaDataDirectory);
+ throw new DataStructureException("Unspecified format.");
}
if (metaDataDirectory.tryToGetNode(ExperimentIdentifier.FOLDER) == null)
{
@@ -158,7 +151,22 @@ public class DataStructureV1_0 extends AbstractDataStructure
{
throw new DataStructureException("Unspecified processing type.");
}
- super.save();
+ }
+
+ @Override
+ protected void performOpening()
+ {
+ setFormat(Format.loadFrom(getMetaDataDirectory()));
+ }
+
+ @Override
+ protected void performClosing()
+ {
+ IDirectory metaDataDirectory = getMetaDataDirectory();
+ if (metaDataDirectory.tryToGetNode(Format.FORMAT_DIR) == null && format != null)
+ {
+ format.saveTo(metaDataDirectory);
+ }
}
private IDirectory getDataDirectory()
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java b/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java
index c7dbd88c5ca..cfa80e22a7f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java
@@ -18,20 +18,37 @@ package ch.systemsx.cisd.bds;
/**
- * Common interface of all data structures.
+ * Common interface of all data structures. Implementations of this interface provide methods to manipulate a data
+ * structure. These methods are specific for the version of the data structure. For each version there is a concrete
+ * class implementing this interface.
+ * <p>
+ * A data structure must first be created with {@link #create()} or opened with {@link #open()} before any other method
+ * can be invoked. An {@link IllegalStateException} is thrown otherwise. Finally a data structure has to be closed with
+ * {@link #close()} in order to commit all changes made since creation or opening.
*
* @author Franz-Josef Elmer
*/
public interface IDataStructure extends IHasVersion
{
/**
- * Loads the data structure.
+ * Creates a new empty data structure.
*/
- public void load();
+ public void create();
+
+ /**
+ * Opens an existing data structure and validates it.
+ *
+ * @throws DataStructureException if the data structure is invalid.
+ */
+ public void open();
/**
- * Saves the data structure.
+ * Closes the data structure. Before the data structure is closed it will be validated.
+ *
+ * @throws DataStructureException if the data structure is invalid.
+ * @throws IllegalStateException if called before the first invocation of either {@link #create()} or
+ * {@link #open()}.
*/
- public void save();
+ public void close();
}
\ No newline at end of file
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
index f37ebc2fdfd..dad5c33423c 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
@@ -43,17 +43,18 @@ public class DataStructureLoaderTest
}
@Test
- public void testLoad()
+ public void testOpen()
{
File dir = new File(TEST_DIR, "ds");
assert dir.mkdir();
DataStructureV1_0 dataStructure = new DataStructureV1_0(new FileStorage(dir));
+ dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
ExperimentIdentifier experimentIdentifier = new ExperimentIdentifier("g", "p", "e");
dataStructure.setExperimentIdentifier(experimentIdentifier);
dataStructure.setProcessingType(ProcessingType.RAW_DATA);
- dataStructure.save();
+ dataStructure.close();
IDataStructure ds = new DataStructureLoader(TEST_DIR).load("ds");
assertEquals(DataStructureV1_0.class, ds.getClass());
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
index 6e3a03d0c02..deda05911b9 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
@@ -61,6 +61,7 @@ public class DataStructureV1_0Test
@Test
public void testGetOriginalData()
{
+ dataStructure.create();
IDirectory dataFolder = dataStructure.getOriginalData();
assertEquals(DataStructureV1_0.DIR_ORIGINAL, dataFolder.getName());
assertEquals(DataStructureV1_0.DIR_DATA, dataFolder.tryToGetParent().getName());
@@ -69,6 +70,7 @@ public class DataStructureV1_0Test
@Test
public void testGetFormatedData()
{
+ dataStructure.create();
dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
IFormattedData formatedData = dataStructure.getFormatedData();
assertTrue(formatedData instanceof NoFormattedData);
@@ -78,6 +80,7 @@ public class DataStructureV1_0Test
@Test
public void testGetFormatedDataBeforeInvokingSetVersion()
{
+ dataStructure.create();
try
{
dataStructure.getFormatedData();
@@ -91,6 +94,7 @@ public class DataStructureV1_0Test
@Test
public void testSetProcessingType()
{
+ dataStructure.create();
dataStructure.setProcessingType(ProcessingType.COMPUTED_DATA);
IDirectory root = storage.getRoot();
IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
@@ -100,6 +104,7 @@ public class DataStructureV1_0Test
@Test
public void testSetProcessingTypeTwice()
{
+ dataStructure.create();
dataStructure.setProcessingType(ProcessingType.RAW_DATA);
dataStructure.setProcessingType(ProcessingType.COMPUTED_DATA);
IDirectory root = storage.getRoot();
@@ -110,6 +115,7 @@ public class DataStructureV1_0Test
@Test
public void testGetProcessingType()
{
+ dataStructure.create();
dataStructure.setProcessingType(ProcessingType.COMPUTED_DATA);
assertEquals(ProcessingType.COMPUTED_DATA, dataStructure.getProcessingType());
}
@@ -117,6 +123,7 @@ public class DataStructureV1_0Test
@Test
public void testGetUnknownProcessingType()
{
+ dataStructure.create();
dataStructure.setProcessingType(ProcessingType.COMPUTED_DATA);
IDirectory s = Utilities.getSubDirectory(storage.getRoot(), DataStructureV1_0.DIR_METADATA);
s.addKeyValuePair(ProcessingType.PROCESSING_TYPE, "blabla");
@@ -126,6 +133,7 @@ public class DataStructureV1_0Test
@Test
public void testSetExperimentIdentifier()
{
+ dataStructure.create();
ExperimentIdentifier id = new ExperimentIdentifier("g", "p", "e");
dataStructure.setExperimentIdentifier(id);
IDirectory root = storage.getRoot();
@@ -139,6 +147,7 @@ public class DataStructureV1_0Test
@Test
public void testSetExperimentIdentifierTwice()
{
+ dataStructure.create();
dataStructure.setExperimentIdentifier(new ExperimentIdentifier("a", "b", "c"));
ExperimentIdentifier id = new ExperimentIdentifier("g", "p", "e");
dataStructure.setExperimentIdentifier(id);
@@ -153,6 +162,7 @@ public class DataStructureV1_0Test
@Test
public void testGetNonExistingExperimentIdentifier()
{
+ dataStructure.create();
try
{
dataStructure.getExperimentIdentifier();
@@ -166,6 +176,7 @@ public class DataStructureV1_0Test
@Test
public void testGetExperimentIdentifier()
{
+ dataStructure.create();
ExperimentIdentifier id = new ExperimentIdentifier("g", "p", "e");
dataStructure.setExperimentIdentifier(id);
assertEquals(id, dataStructure.getExperimentIdentifier());
@@ -174,15 +185,17 @@ public class DataStructureV1_0Test
@Test
public void testGetVersion()
{
+ dataStructure.create();
assertEquals(new Version(1, 0), dataStructure.getVersion());
}
@Test
- public void testSaveForEmptyData()
+ public void testCloseForEmptyData()
{
+ dataStructure.create();
try
{
- dataStructure.save();
+ dataStructure.close();
fail("DataStructureException expected.");
} catch (DataStructureException e)
{
@@ -191,12 +204,13 @@ public class DataStructureV1_0Test
}
@Test
- public void testSaveIfNoFormat()
+ public void testCloseIfNoFormat()
{
+ dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
try
{
- dataStructure.save();
+ dataStructure.close();
fail("DataStructureException expected.");
} catch (DataStructureException e)
{
@@ -205,13 +219,14 @@ public class DataStructureV1_0Test
}
@Test
- public void testSaveIfNoExperimentID()
+ public void testCloseIfNoExperimentID()
{
+ dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
try
{
- dataStructure.save();
+ dataStructure.close();
fail("DataStructureException expected.");
} catch (DataStructureException e)
{
@@ -220,14 +235,15 @@ public class DataStructureV1_0Test
}
@Test
- public void testSaveIfNoProcessingType()
+ public void testCloseIfNoProcessingType()
{
+ dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
dataStructure.setExperimentIdentifier(new ExperimentIdentifier("g", "p", "e"));
try
{
- dataStructure.save();
+ dataStructure.close();
fail("DataStructureException expected.");
} catch (DataStructureException e)
{
@@ -236,8 +252,9 @@ public class DataStructureV1_0Test
}
@Test
- public void testSave()
+ public void testClose()
{
+ dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
ExperimentIdentifier experimentIdentifier = new ExperimentIdentifier("g", "p", "e");
@@ -245,7 +262,7 @@ public class DataStructureV1_0Test
dataStructure.setProcessingType(ProcessingType.RAW_DATA);
IDirectory root = storage.getRoot();
- dataStructure.save();
+ dataStructure.close();
assertEquals(dataStructure.getVersion(), Version.loadFrom(root));
try
{
@@ -257,7 +274,7 @@ public class DataStructureV1_0Test
}
DataStructureV1_0 reloadedDataStructure = new DataStructureV1_0(storage);
- reloadedDataStructure.load();
+ reloadedDataStructure.open();
assertEquals("42\n", Utilities.getString(reloadedDataStructure.getOriginalData(), "answer"));
assertEquals(UnknownFormat1_0.UNKNOWN_1_0, reloadedDataStructure.getFormatedData().getFormat());
assertEquals(experimentIdentifier, reloadedDataStructure.getExperimentIdentifier());
@@ -265,11 +282,16 @@ public class DataStructureV1_0Test
}
@Test
- public void testLoadIfVersionMissing()
+ public void testOpenIfVersionMissing()
{
+ createExampleDataStructure();
+ storage.mount();
+ IDirectory root = storage.getRoot();
+ root.removeNode(Utilities.getSubDirectory(root, Version.VERSION));
+ storage.unmount();
try
{
- dataStructure.load();
+ dataStructure.open();
fail("DataStructureException expected.");
} catch (DataStructureException e)
{
@@ -278,33 +300,34 @@ public class DataStructureV1_0Test
}
@Test
- public void testLoad()
+ public void testOpen()
{
- IDirectory root = storage.getRoot();
- new Version(1, 0).saveTo(root);
- IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
- UnknownFormat1_0.UNKNOWN_1_0.saveTo(metaData);
- dataStructure.load();
+ createExampleDataStructure();
+ dataStructure.open();
}
@Test
- public void testLoadVersion1_1()
+ public void testOpenVersion1_1()
{
+ createExampleDataStructure();
+ storage.mount();
IDirectory root = storage.getRoot();
new Version(1, 1).saveTo(root);
- IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
- UnknownFormat1_0.UNKNOWN_1_0.saveTo(metaData);
- dataStructure.load();
+ storage.unmount();
+ dataStructure.open();
}
@Test
- public void testLoadVersion2_0()
+ public void testOpenVersion2_0()
{
+ createExampleDataStructure();
+ storage.mount();
IDirectory root = storage.getRoot();
new Version(2, 0).saveTo(root);
+ storage.unmount();
try
{
- dataStructure.load();
+ dataStructure.open();
fail("DataStructureException expected.");
} catch (DataStructureException e)
{
@@ -314,26 +337,30 @@ public class DataStructureV1_0Test
}
@Test
- public void testLoadWithUnknownFormat1_1()
+ public void testOpenWithUnknownFormat1_1()
{
+ createExampleDataStructure();
+ storage.mount();
IDirectory root = storage.getRoot();
- new Version(1, 0).saveTo(root);
- IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
+ IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
new Format(UnknownFormat1_0.UNKNOWN_1_0.getCode(), new Version(1, 1)).saveTo(metaData);
- dataStructure.load();
+ storage.unmount();
+ dataStructure.open();
assertEquals(UnknownFormat1_0.UNKNOWN_1_0, dataStructure.getFormatedData().getFormat());
}
@Test
- public void testLoadWithUnknownFormat2_0()
+ public void testOpenWithUnknownFormat2_0()
{
+ createExampleDataStructure();
+ storage.mount();
IDirectory root = storage.getRoot();
- new Version(1, 0).saveTo(root);
- IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
+ IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
new Format(UnknownFormat1_0.UNKNOWN_1_0.getCode(), new Version(2, 0)).saveTo(metaData);
+ storage.unmount();
try
{
- dataStructure.load();
+ dataStructure.open();
dataStructure.getFormatedData();
fail("DataStructureException expected.");
} catch (DataStructureException e)
@@ -343,14 +370,32 @@ public class DataStructureV1_0Test
}
@Test
- public void testLoadWithAnotherFormat()
+ public void testOpenWithAnotherFormat()
{
+ createExampleDataStructure();
+ storage.mount();
IDirectory root = storage.getRoot();
- new Version(1, 0).saveTo(root);
- IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
+ IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
new Format("another format", new Version(1,1)).saveTo(metaData);
- dataStructure.load();
+ storage.unmount();
+ dataStructure.open();
assertEquals(UnknownFormat1_0.UNKNOWN_1_0, dataStructure.getFormatedData().getFormat());
}
+
+ private void createExampleDataStructure()
+ {
+ storage.mount();
+ IDirectory root = storage.getRoot();
+ new Version(1, 0).saveTo(root);
+ IDirectory data = root.makeDirectory(DataStructureV1_0.DIR_DATA);
+ IDirectory originalDataDir = data.makeDirectory(DataStructureV1_0.DIR_ORIGINAL);
+ originalDataDir.addKeyValuePair("hello", "world");
+ IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
+ new Format(UnknownFormat1_0.UNKNOWN_1_0.getCode(), new Version(2, 0)).saveTo(metaData);
+ new ExperimentIdentifier("g", "p", "e").saveTo(metaData);
+ ProcessingType.COMPUTED_DATA.saveTo(metaData);
+ storage.unmount();
+
+ }
}
--
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