diff --git a/bds/source/java/ch/systemsx/cisd/bds/Channel.java b/bds/source/java/ch/systemsx/cisd/bds/Channel.java
new file mode 100644
index 0000000000000000000000000000000000000000..72b6d170c5555e48eac990c13437e307c6da0108
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/Channel.java
@@ -0,0 +1,110 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
+/**
+ * A channel is composed of only one child: <code>wavelength</code>.
+ * <p>
+ * Each channel has its <code>counter</code> which uniquely identifies it.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class Channel implements IStorable
+{
+
+ static final String CHANNEL = "channel";
+
+ static final String WAVELENGTH = "wavelength";
+
+ private final int counter;
+
+ private final int wavelength;
+
+ public Channel(final int counter, final int wavelength)
+ {
+ assert counter > 0 : "Given counter must be > 0.";
+ this.counter = counter;
+ this.wavelength = wavelength;
+ }
+
+ public final int getWavelength()
+ {
+ return wavelength;
+ }
+
+ final static Channel loadFrom(final IDirectory directory)
+ {
+ final String name = directory.getName();
+ assert name.startsWith(CHANNEL);
+ return new Channel(parseCounter(name), Utilities.getNumber(directory, WAVELENGTH));
+ }
+
+ private static int parseCounter(final String name)
+ {
+ try
+ {
+ return Integer.parseInt(name.substring(CHANNEL.length()));
+ } catch (NumberFormatException ex)
+ {
+ throw new DataStructureException(String.format("Could not parse the channel number in '%s'", name), ex);
+ }
+ }
+
+ //
+ // IStorable
+ //
+
+ public final void saveTo(final IDirectory directory)
+ {
+ final IDirectory channelDirectory = directory.makeDirectory(CHANNEL + counter);
+ channelDirectory.addKeyValuePair(WAVELENGTH, getWavelength() + "");
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Channel == false)
+ {
+ return false;
+ }
+ final Channel channel = (Channel) obj;
+ return channel.counter == counter;
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ return 17 * 37 + counter;
+ }
+
+ @Override
+ public final String toString()
+ {
+ return CHANNEL + counter + "[" + wavelength + "=" + getWavelength() + "]";
+ }
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ChannelList.java b/bds/source/java/ch/systemsx/cisd/bds/ChannelList.java
new file mode 100644
index 0000000000000000000000000000000000000000..e13741a1d9fed616630d3d973e2ee2f833424422
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/ChannelList.java
@@ -0,0 +1,80 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.INode;
+
+/**
+ * The list of encapsulated <code>Channels</code> available here.
+ *
+ * @author Christian Ribeaud
+ */
+public final class ChannelList implements IStorable
+{
+ static final String NUMBER_OF_CHANNELS = "number_of_channels";
+
+ private final List<Channel> channels;
+
+ public ChannelList(final List<Channel> channels)
+ {
+ assert channels.size() > 0 : "At least one channel must be specified.";
+ this.channels = channels;
+ }
+
+ /**
+ * Loads all <code>Channels</code> from the specified directory.
+ *
+ * @throws DataStructureException if the <code>Channels</code> could be loaded.
+ */
+ final static ChannelList loadFrom(final IDirectory directory)
+ {
+ final List<Channel> channels = new ArrayList<Channel>();
+ for (INode node : directory)
+ {
+ if (node.getName().startsWith(Channel.CHANNEL))
+ {
+ assert node instanceof IDirectory : "Must be an IDirectory";
+ channels.add(Channel.loadFrom((IDirectory) node));
+ }
+ }
+ return new ChannelList(channels);
+ }
+
+ /** Returns an unmodifiable list of <code>Channel</code>. */
+ public final List<Channel> getChannels()
+ {
+ return Collections.unmodifiableList(channels);
+ }
+
+ //
+ // IStorable
+ //
+
+ public final void saveTo(final IDirectory directory)
+ {
+ directory.addKeyValuePair(NUMBER_OF_CHANNELS, channels.size() + "");
+ for (Channel channel : channels)
+ {
+ channel.saveTo(directory);
+ }
+ }
+}
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 8b55dc2b65020e23f722a869f995af609ef438ec..1447c1b2330cbf13ce52c0c5ffde3c56651afd04 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -42,19 +42,21 @@ public class DataStructureV1_0 extends AbstractDataStructure
static final String CHECKSUM_DIRECTORY = "md5sum";
static final String DIR_METADATA = "metadata";
-
+
static final String DIR_PARAMETERS = "parameters";
static final String DIR_DATA = "data";
static final String DIR_ORIGINAL = "original";
-
+
static final String MAPPING_FILE = "standard_original_mapping";
private static final Version VERSION = new Version(1, 0);
-
+
private final ChecksumBuilder checksumBuilder = new ChecksumBuilder(new MD5ChecksumCalculator());
+
private final Map<String, Reference> standardOriginalMapping = new LinkedHashMap<String, Reference>();
+
private final FormatParameters formatParameters = new FormatParameters();
private Format format;
@@ -121,7 +123,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
assert formatParameter != null : "Unspecified format parameter.";
formatParameters.addParameter(formatParameter);
}
-
+
/**
* Returns the experiment identifier.
*
@@ -143,7 +145,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
assertOpenOrCreated();
id.saveTo(getMetaDataDirectory());
}
-
+
/**
* Returns the date of registration of the experiment.
*
@@ -155,7 +157,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
assertOpenOrCreated();
return ExperimentRegistratorDate.loadFrom(getMetaDataDirectory());
}
-
+
/**
* Sets the date of registration of the experiment.
*/
@@ -176,14 +178,14 @@ public class DataStructureV1_0 extends AbstractDataStructure
assertOpenOrCreated();
return ExperimentRegistrator.loadFrom(getMetaDataDirectory());
}
-
+
public void setExperimentRegistrator(ExperimentRegistrator registrator)
{
assert registrator != null : "Unspecified experiment registrator.";
assertOpenOrCreated();
registrator.saveTo(getMetaDataDirectory());
}
-
+
/**
* Returns the measurement entity.
*
@@ -217,7 +219,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
assertOpenOrCreated();
return ProcessingType.loadFrom(getMetaDataDirectory());
}
-
+
/**
* Sets the processing type. Overwrites an already set or loaded value.
*/
@@ -227,7 +229,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
assertOpenOrCreated();
type.saveTo(getMetaDataDirectory());
}
-
+
/**
* Returns the standard-original mapping.
*
@@ -237,7 +239,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
{
return Collections.unmodifiableMap(standardOriginalMapping);
}
-
+
/**
* Adds a reference to the standard-original mapping.
*
@@ -254,7 +256,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
}
standardOriginalMapping.put(path, reference);
}
-
+
@Override
protected void assertValid()
{
@@ -335,7 +337,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
standardOriginalMapping.put(path, new Reference(path, referenceDefinition.substring(i2 + 1), type));
}
}
-
+
@Override
protected void performClosing()
{
@@ -343,9 +345,9 @@ public class DataStructureV1_0 extends AbstractDataStructure
IDirectory checksumDirectory = metaDataDirectory.makeDirectory(CHECKSUM_DIRECTORY);
String checksumsOfOriginal = checksumBuilder.buildChecksumsForAllFilesIn(getOriginalData());
checksumDirectory.addKeyValuePair(DIR_ORIGINAL, checksumsOfOriginal);
-
+
formatParameters.saveTo(getParametersDirectory());
-
+
StringWriter writer = new StringWriter();
PrintWriter printWriter = new PrintWriter(writer, true);
Collection<Reference> values = standardOriginalMapping.values();
@@ -358,7 +360,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
}
printWriter.close();
metaDataDirectory.addKeyValuePair(MAPPING_FILE, writer.toString());
-
+
if (metaDataDirectory.tryToGetNode(Format.FORMAT_DIR) == null && format != null)
{
format.saveTo(metaDataDirectory);
@@ -374,10 +376,10 @@ public class DataStructureV1_0 extends AbstractDataStructure
{
return Utilities.getOrCreateSubDirectory(root, DIR_METADATA);
}
-
+
private IDirectory getParametersDirectory()
{
return Utilities.getOrCreateSubDirectory(getMetaDataDirectory(), DIR_PARAMETERS);
}
-
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
index 5a66b75bca27e01502d594867dbe0ffff4a46d11..3540ac25f61b14017addaf82947e470fb631eead 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
@@ -20,17 +20,20 @@ import ch.systemsx.cisd.bds.storage.IDirectory;
/**
* Identifier of the experiment which corresponds to the data. This is an immutable but extendable value object class.
- * An instance of this class allows unique identification in the database.
- *
+ * An instance of this class allows unique identification in the database.
+ *
* @author Franz-Josef Elmer
*/
-public class ExperimentIdentifier
+public class ExperimentIdentifier implements IStorable
{
static final String FOLDER = "experiment_identifier";
+
static final String GROUP_CODE = "group_code";
+
static final String PROJECT_CODE = "project_code";
+
static final String EXPERIMENT_CODE = "experiment_code";
-
+
/**
* Loads the experiment identifier from the specified directory.
*
@@ -44,14 +47,16 @@ public class ExperimentIdentifier
String experimentCode = Utilities.getTrimmedString(idFolder, EXPERIMENT_CODE);
return new ExperimentIdentifier(groupCode, projectCode, experimentCode);
}
-
+
private final String groupCode;
+
private final String projectCode;
+
private final String experimentCode;
/**
* Creates an instance for the specified codes of group, project, and experiment.
- *
+ *
* @param groupCode A non-empty string of the group code.
* @param projectCode A non-empty string of the project code.
* @param experimentCode A non-empty string of the experiment code.
@@ -81,7 +86,7 @@ public class ExperimentIdentifier
{
return projectCode;
}
-
+
/**
* Returns the experiment code;
*/
@@ -89,11 +94,15 @@ public class ExperimentIdentifier
{
return experimentCode;
}
-
+
+ //
+ // IStorable
+ //
+
/**
* Saves this instance to the specified directory.
*/
- void saveTo(IDirectory directory)
+ public final void saveTo(final IDirectory directory)
{
IDirectory folder = directory.makeDirectory(FOLDER);
folder.addKeyValuePair(GROUP_CODE, groupCode);
@@ -128,6 +137,5 @@ public class ExperimentIdentifier
{
return "[group:" + groupCode + ",project:" + projectCode + ",experiment:" + experimentCode + "]";
}
-
-
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistrator.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistrator.java
index 65d97e992be8fe9a15aacd627ac70f19a39af603..4d21cd66e391ca3db98b0d33fdaf50bafc84be47 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistrator.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistrator.java
@@ -20,18 +20,21 @@ import ch.systemsx.cisd.bds.storage.IDirectory;
/**
* Registrator of the experiment which corresponds to the data. This is an immutable value object class.
- *
+ *
* @author Franz-Josef Elmer
*/
-public final class ExperimentRegistrator
+public final class ExperimentRegistrator implements IStorable
{
static final String FOLDER = "experiment_registrator";
+
static final String FIRST_NAME = "first_name";
+
static final String SECOND_NAME = "last_name";
+
static final String EMAIL = "email";
-
+
/**
- * Loads the experiment registaror from the specified directory.
+ * Loads the experiment registrator from the specified directory.
*
* @throws DataStructureException if file missing.
*/
@@ -43,14 +46,16 @@ public final class ExperimentRegistrator
String email = Utilities.getTrimmedString(folder, EMAIL);
return new ExperimentRegistrator(firstName, secondName, email);
}
-
+
private final String firstName;
+
private final String secondName;
+
private final String email;
/**
* Creates an instance for the specified name and e-mail of the registrator.
- *
+ *
* @param firstName A non-empty string of the first name.
* @param secondName A non-empty string of the second name.
* @param email A non-empty string of the email.
@@ -80,7 +85,7 @@ public final class ExperimentRegistrator
{
return secondName;
}
-
+
/**
* Returns the email.
*/
@@ -88,11 +93,15 @@ public final class ExperimentRegistrator
{
return email;
}
-
+
+ //
+ // IStorable
+ //
+
/**
* Saves this instance to the specified directory.
*/
- void saveTo(IDirectory directory)
+ public final void saveTo(final IDirectory directory)
{
IDirectory folder = directory.makeDirectory(FOLDER);
folder.addKeyValuePair(FIRST_NAME, firstName);
@@ -127,6 +136,5 @@ public final class ExperimentRegistrator
{
return firstName + " " + secondName + ", e-mail:" + email;
}
-
-
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistratorDate.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistratorDate.java
index e2a842040e287f9c6b935fc519533d4b7616b66b..b7563dec65d968a151edf7a02078ff4070454c2a 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistratorDate.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistratorDate.java
@@ -23,15 +23,16 @@ import java.util.Date;
import ch.systemsx.cisd.bds.storage.IDirectory;
/**
- * Immutable class which holds the date of registration of an experiment.
- *
+ * Immutable class which holds the date of registration of an experiment.
+ *
* @author Franz-Josef Elmer
*/
-public final class ExperimentRegistratorDate
+public final class ExperimentRegistratorDate implements IStorable
{
static final String FILE_NAME = "experiment_registration_date";
+
private static final SimpleDateFormat DATE_FORMAT = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss Z");
-
+
static ExperimentRegistratorDate loadFrom(IDirectory directory)
{
String dateAsString = Utilities.getTrimmedString(directory, FILE_NAME);
@@ -43,9 +44,9 @@ public final class ExperimentRegistratorDate
throw new DataStructureException("Couldn't be parsed as a date: " + dateAsString);
}
}
-
+
private final Date date;
-
+
/**
* Creates an instance for the specified date.
*/
@@ -61,11 +62,15 @@ public final class ExperimentRegistratorDate
{
return date;
}
-
+
+ //
+ // IStorable
+ //
+
/**
* Saves this instance to the specified directory.
*/
- void saveTo(IDirectory directory)
+ public final void saveTo(IDirectory directory)
{
directory.addKeyValuePair(FILE_NAME, DATE_FORMAT.format(date));
}
@@ -95,5 +100,5 @@ public final class ExperimentRegistratorDate
{
return DATE_FORMAT.format(date);
}
-
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Format.java b/bds/source/java/ch/systemsx/cisd/bds/Format.java
index 2c6b91ab4a9114902162cc549a1e95e439bd09ea..ed66c35b628860f156e32e9d2b0c60facfdf7cd3 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Format.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Format.java
@@ -22,13 +22,15 @@ import ch.systemsx.cisd.bds.storage.INode;
/**
* Inmutable value object of a versioned format.
- *
+ *
* @author Franz-Josef Elmer
*/
-public class Format
+public class Format implements IStorable
{
static final String FORMAT_CODE_FILE = "format_code";
+
static final String FORMAT_DIR = "format";
+
static final String FORMAT_VARIANT_FILE = "format_variant";
/**
@@ -64,9 +66,11 @@ public class Format
}
return new Format(formatCode, formatVersion, variant);
}
-
+
private final String code;
+
private final Version version;
+
private final String variant;
/**
@@ -80,7 +84,7 @@ public class Format
this.version = version;
variant = variantOrNull;
}
-
+
/**
* Returns the format code.
*/
@@ -107,7 +111,11 @@ public class Format
return variant;
}
- void saveTo(IDirectory directory)
+ //
+ // IStorable
+ //
+
+ public final void saveTo(final IDirectory directory)
{
IDirectory dir = directory.makeDirectory(FORMAT_DIR);
dir.addKeyValuePair(FORMAT_CODE_FILE, code);
@@ -130,7 +138,7 @@ public class Format
return false;
}
Format format = (Format) obj;
- return format.code.equals(code) && format.version.equals(version)
+ return format.code.equals(code) && format.version.equals(version)
&& (format.variant == null ? null == variant : format.variant.equals(variant));
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatParameter.java b/bds/source/java/ch/systemsx/cisd/bds/FormatParameter.java
index 77a834c23a08faf20ef7c619537a4baf1b63a3be..1f6f40d729a10a346e369d81723163e4f4ec1926 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatParameter.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatParameter.java
@@ -17,18 +17,19 @@
package ch.systemsx.cisd.bds;
/**
- * A format parameter with a name and a string value.
- *
+ * A format parameter with a name and a string value.
+ *
* @author Franz-Josef Elmer
*/
public final class FormatParameter
{
private final String name;
+
private final String value;
/**
* Creates an instance for the specified name and value.
- *
+ *
* @param name A non-empty string as the name of the parameter.
* @param value A non-<code>null</code> string as the value.
*/
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java b/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
index 94f6e217afe81c131ecf0e1fba1fdc19b99e450c..317734aa8de707673cc41548a9b19609754f21c1 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
@@ -26,10 +26,10 @@ import ch.systemsx.cisd.bds.storage.INode;
/**
* Implementation of {@link IFormatParameters} which allows to add {@link FormatParameter} instances.
- *
+ *
* @author Franz-Josef Elmer
*/
-class FormatParameters implements IFormatParameters
+class FormatParameters implements IFormatParameters, IStorable
{
private final Map<String, FormatParameter> parameters = new LinkedHashMap<String, FormatParameter>();
@@ -45,15 +45,19 @@ class FormatParameters implements IFormatParameters
}
}
}
-
- void saveTo(IDirectory directory)
+
+ //
+ // IStorable
+ //
+
+ public final void saveTo(final IDirectory directory)
{
for (FormatParameter parameter : parameters.values())
{
directory.addKeyValuePair(parameter.getName(), parameter.getValue());
}
}
-
+
/**
* Adds the specified parameter.
*
@@ -68,7 +72,7 @@ class FormatParameters implements IFormatParameters
}
parameters.put(name, parameter);
}
-
+
public String getValue(String parameterName)
{
FormatParameter formatParameter = parameters.get(parameterName);
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormattedDataContext.java b/bds/source/java/ch/systemsx/cisd/bds/FormattedDataContext.java
index 876bb3e091a51675f4601d17f96bc2da3aeb576d..c1c60e5360ac35a82c6fd7b1303fe08d7932ba0a 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormattedDataContext.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormattedDataContext.java
@@ -19,15 +19,17 @@ package ch.systemsx.cisd.bds;
import ch.systemsx.cisd.bds.storage.IDirectory;
/**
- * Context of {@link IFormattedData}. Argument of all constructores of concrete implementations of
- * {@link IFormattedData}.
- *
+ * Context of {@link IFormattedData}. Argument of all constructors of concrete implementations of
+ * {@link IFormattedData}.
+ *
* @author Franz-Josef Elmer
*/
class FormattedDataContext
{
private final IDirectory dataDirectory;
+
private final Format format;
+
private final IFormatParameters formatParameters;
FormattedDataContext(IDirectory dataDirectory, Format format, IFormatParameters formatParameters)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Geometry.java b/bds/source/java/ch/systemsx/cisd/bds/Geometry.java
new file mode 100644
index 0000000000000000000000000000000000000000..abafed7aa277a901640006320d85029be66645b8
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/Geometry.java
@@ -0,0 +1,133 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
+/**
+ * A <code>Geometry</code> is composed of 2 dimensions:
+ * <ul>
+ * <li>rows</li>
+ * <li>columns</li>
+ * </ul>
+ * <p>
+ * This class is not <code>abstract</code> but {@link #getGeometryDirectoryName()} must be overridden by subclasses in
+ * order to work properly.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public class Geometry implements IStorable
+{
+ static final String NOT_POSITIVE = "Given number '%d' must be > 0.";
+
+ final static String ROWS = "rows";
+
+ final static String COLUMNS = "columns";
+
+ private final int rows;
+
+ private final int columns;
+
+ protected Geometry(final int rows, final int columns)
+ {
+ assert columns > 0 : String.format(NOT_POSITIVE, columns);
+ this.columns = columns;
+ assert rows > 0 : String.format(NOT_POSITIVE, rows);
+ this.rows = rows;
+ }
+
+ /** Return the number of columns this <code>Geometry</code> is composed of. */
+ public final int getColumns()
+ {
+ return columns;
+ }
+
+ /** Return the number of rows this <code>Geometry</code> is composed of. */
+ public final int getRows()
+ {
+ return rows;
+ }
+
+ private final String toString(int number)
+ {
+ return Integer.toString(number);
+ }
+
+ /**
+ * Loads the geometry from the specified directory.
+ */
+ final static Geometry loadFrom(final IDirectory directory, final String geometryDirectoryName)
+ {
+ final IDirectory geometryFolder = Utilities.getSubDirectory(directory, geometryDirectoryName);
+ return new Geometry(Utilities.getNumber(geometryFolder, ROWS), Utilities.getNumber(geometryFolder, COLUMNS));
+ }
+
+ //
+ // IStorable
+ //
+
+ public final void saveTo(final IDirectory directory)
+ {
+ final IDirectory geometryDirectory = directory.makeDirectory(getGeometryDirectoryName());
+ geometryDirectory.addKeyValuePair(ROWS, toString(getRows()));
+ geometryDirectory.addKeyValuePair(COLUMNS, toString(getColumns()));
+ }
+
+ /**
+ * Returns the directory name where this <code>Geometry</code> is saved.
+ * <p>
+ * Currently this method is not supported and must be implemented.
+ * </p>
+ */
+ protected String getGeometryDirectoryName()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Geometry == false)
+ {
+ return false;
+ }
+ final Geometry geometry = (Geometry) obj;
+ return geometry.rows == rows && geometry.columns == columns;
+ }
+
+ @Override
+ public final int hashCode()
+ {
+
+ return 17 * 37 + getRows() + getColumns();
+ }
+
+ @Override
+ public final String toString()
+ {
+ return getRows() + "x" + getColumns();
+ }
+}
\ No newline at end of file
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IStorable.java b/bds/source/java/ch/systemsx/cisd/bds/IStorable.java
new file mode 100644
index 0000000000000000000000000000000000000000..954c5d2aa85ff4d354318b0bd8ab5a3b6e899b5f
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/IStorable.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
+/**
+ * Each implementation knows how to save itself in given <code>IDirectory</code>.
+ * <p>
+ * Note that each implementation should have a <code>static</code> method <code>loadFrom(IDirectory)</code> that
+ * knows how to construct itself from given <code>IDirectory</code>.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public interface IStorable
+{
+
+ /** Saves this implementation to given <var>directory</var>. */
+ public void saveTo(final IDirectory directory);
+}
\ No newline at end of file
diff --git a/bds/source/java/ch/systemsx/cisd/bds/MeasurementEntity.java b/bds/source/java/ch/systemsx/cisd/bds/MeasurementEntity.java
index 46ae7f3c066bbb75bcddb44df72b6a320c3400ae..a9861f378eba6d8e135624c768ff6208f15b3423 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/MeasurementEntity.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/MeasurementEntity.java
@@ -20,15 +20,17 @@ import ch.systemsx.cisd.bds.storage.IDirectory;
/**
* Enity of measurement or calculation covered by the data. This is an immutable value object class.
- *
+ *
* @author Franz-Josef Elmer
*/
-public final class MeasurementEntity
+public final class MeasurementEntity implements IStorable
{
static final String FOLDER = "measurement_entity";
+
static final String ENTITY_TYPE_DESCRIPTION = "entity_type_description";
+
static final String ENTITY_CODE = "entity_code";
-
+
/**
* Loads the enity from the specified directory.
*
@@ -41,8 +43,9 @@ public final class MeasurementEntity
String entityCode = Utilities.getTrimmedString(folder, ENTITY_CODE);
return new MeasurementEntity(entityCode, entityTypeDescription);
}
-
+
private final String entityTypeDescription;
+
private final String entityCode;
/**
@@ -74,11 +77,15 @@ public final class MeasurementEntity
{
return entityCode;
}
-
+
+ //
+ // IStorable
+ //
+
/**
* Saves this instance to the specified directory.
*/
- void saveTo(IDirectory directory)
+ public final void saveTo(IDirectory directory)
{
IDirectory folder = directory.makeDirectory(FOLDER);
folder.addKeyValuePair(ENTITY_TYPE_DESCRIPTION, entityTypeDescription);
@@ -111,6 +118,5 @@ public final class MeasurementEntity
{
return "[" + entityCode + ": " + entityTypeDescription + "]";
}
-
-
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/PlateGeometry.java b/bds/source/java/ch/systemsx/cisd/bds/PlateGeometry.java
new file mode 100644
index 0000000000000000000000000000000000000000..bbb35951e681c6b84c61638e49647a89b87f24ca
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/PlateGeometry.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
+/**
+ * An <code>AbstractGeometry</code> implementation suitable for <i>Plate</i>.
+ *
+ * @author Christian Ribeaud
+ */
+public final class PlateGeometry extends Geometry
+{
+
+ static final String PLATE_GEOMETRY = "plate_geometry";
+
+ public PlateGeometry(final int rows, final int columns)
+ {
+ super(rows, columns);
+ }
+
+ /**
+ * Loads the geometry from the specified directory.
+ */
+ static Geometry loadFrom(final IDirectory directory)
+ {
+ return loadFrom(directory, PLATE_GEOMETRY);
+ }
+
+ //
+ // Geometry
+ //
+
+ @Override
+ protected final String getGeometryDirectoryName()
+ {
+ return PLATE_GEOMETRY;
+ }
+
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java b/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
index 86a0964bb387f8d558e3fbf336f3790166fd33f4..94d4c25419e817f350ebaa014eaef932d7633f38 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
@@ -18,18 +18,17 @@ package ch.systemsx.cisd.bds;
import ch.systemsx.cisd.bds.storage.IDirectory;
-
/**
* Enumeration of processing types.
- *
+ *
* @author Franz-Josef Elmer
*/
-public enum ProcessingType
+public enum ProcessingType implements IStorable
{
OTHER, RAW_DATA, COMPUTED_DATA;
-
+
static final String PROCESSING_TYPE = "processing_type";
-
+
/**
* Resolves the specified string representation of a processing type.
*
@@ -47,13 +46,17 @@ public enum ProcessingType
}
return OTHER;
}
-
+
static ProcessingType loadFrom(IDirectory directory)
{
return resolve(Utilities.getTrimmedString(directory, PROCESSING_TYPE));
}
-
- void saveTo(IDirectory directory)
+
+ //
+ // IStorable
+ //
+
+ public final void saveTo(IDirectory directory)
{
directory.addKeyValuePair(PROCESSING_TYPE, toString());
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index bab9c8ae8ed5c340b5e4190c2301102ea5066644..a4943f6174fed67928c4147c8e83d9a04f63317f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.bds;
-
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.INode;
@@ -83,12 +82,14 @@ public class Utilities
* @param name Name of the file.
* @throws DataStructureException if the requested file does not exist.
*/
- public static String getString(IDirectory directory, String name)
+ public static String getString(final IDirectory directory, final String name)
{
+ assert directory != null : String.format("Given directory can not be null.");
+ assert name != null : String.format("Given name can not be null.");
INode node = directory.tryToGetNode(name);
if (node == null)
{
- throw new DataStructureException("File '" + name + "' missing in " + directory);
+ throw new DataStructureException("File '" + name + "' missing in '" + directory + "'.");
}
if (node instanceof IFile == false)
{
@@ -102,4 +103,17 @@ public class Utilities
{
}
+ /** For given <code>IDirectory</code> returns the number value corresponding to given <var>name</var>. */
+ public final static int getNumber(final IDirectory directory, final String name)
+ {
+ // No assertion here as 'getString(IDirectory, String)' already does it.
+ String value = getTrimmedString(directory, name);
+ try
+ {
+ return Integer.parseInt(value);
+ } catch (NumberFormatException ex)
+ {
+ throw new DataStructureException("Value of " + name + " version file is not a number: " + value);
+ }
+ }
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Version.java b/bds/source/java/ch/systemsx/cisd/bds/Version.java
index 58918ab300e16d844fc0cf7e3efd61a94d1d48c6..11721a4366375401ed19ad398a4c3016baa16d32 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Version.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Version.java
@@ -19,43 +19,34 @@ package ch.systemsx.cisd.bds;
import ch.systemsx.cisd.bds.storage.IDirectory;
/**
- * Immutable value object for the version of something.
- *
+ * Immutable value object for the version of something.
+ *
* @author Franz-Josef Elmer
*/
public final class Version
{
static final String VERSION = "version";
+
static final String MAJOR = "major";
+
static final String MINOR = "minor";
-
+
/**
* Loads the version from the specified directory.
*/
static Version loadFrom(IDirectory directory)
{
IDirectory versionFolder = Utilities.getSubDirectory(directory, VERSION);
- return new Version(getNumber(versionFolder, MAJOR), getNumber(versionFolder, MINOR));
- }
-
- private static int getNumber(IDirectory versionFolder, String name)
- {
- String value = Utilities.getTrimmedString(versionFolder, name);
- try
- {
- return Integer.parseInt(value);
- } catch (NumberFormatException ex)
- {
- throw new DataStructureException("Value of " + name + " version file is not a number: " + value);
- }
+ return new Version(Utilities.getNumber(versionFolder, MAJOR), Utilities.getNumber(versionFolder, MINOR));
}
-
+
private final int major;
+
private final int minor;
/**
* Creates a new instance for the specified major and minor number.
- *
+ *
* @param major A positive number.
* @param minor A non-negative number.
*/
@@ -82,16 +73,16 @@ public final class Version
{
return minor;
}
-
+
/**
- * Returns <code>true</code> if this version is backwards compatible to the specified version. That is,
- * if <code>version.getMajor() == this.getMajor()</code> and <code>version.getMinor() <= this.getMinor()</code>.
+ * Returns <code>true</code> if this version is backwards compatible to the specified version. That is, if
+ * <code>version.getMajor() == this.getMajor()</code> and <code>version.getMinor() <= this.getMinor()</code>.
*/
public boolean isBackwardsCompatibleWith(Version version)
{
return version.major == major && version.minor <= minor;
}
-
+
/**
* Returns the previous minor version.
*
@@ -105,7 +96,7 @@ public final class Version
}
return new Version(major, minor - 1);
}
-
+
void saveTo(IDirectory directory)
{
IDirectory versionFolder = directory.makeDirectory(VERSION);
@@ -139,7 +130,5 @@ public final class Version
{
return "V" + major + "." + minor;
}
-
-
-
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/WellGeometry.java b/bds/source/java/ch/systemsx/cisd/bds/WellGeometry.java
new file mode 100644
index 0000000000000000000000000000000000000000..893e9b6ef06113c77b3761912d3dd8823388de39
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/WellGeometry.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
+/**
+ * An <code>AbstractGeometry</code> implementation suitable for <i>Well</i>.
+ *
+ * @author Christian Ribeaud
+ */
+public final class WellGeometry extends Geometry
+{
+
+ static final String WELL_GEOMETRY = "well_geometry";
+
+ public WellGeometry(final int rows, final int columns)
+ {
+ super(rows, columns);
+ }
+
+ /**
+ * Loads the geometry from the specified directory.
+ */
+ static Geometry loadFrom(final IDirectory directory)
+ {
+ return loadFrom(directory, WELL_GEOMETRY);
+ }
+
+ //
+ // Geometry
+ //
+
+ @Override
+ protected final String getGeometryDirectoryName()
+ {
+ return WELL_GEOMETRY;
+ }
+
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
index 108c981c2bce993cc9565669f0207d3839ff6e9c..963379eea42293a396259a6f343754b45004c649 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
@@ -30,6 +30,8 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
+ * An <code>IDirectory</code> implementation.
+ *
* @author Franz-Josef Elmer
*/
class Directory extends AbstractNode implements IDirectory
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
index 0ae75b1d5f9947a31d329faacfed2da6484cebff..f851a4c3d93f0367cce2f0ffc9d2397dcd3424f7 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
@@ -22,11 +22,21 @@ import ch.systemsx.cisd.bds.storage.INode;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
/**
+ * A <code>INode</code> factory class.
+ * <p>
+ * You should prefer to use this class instead of directly instantiate the corresponding <code>INode</code>
+ * implementations.
+ * </p>
+ *
* @author Franz-Josef Elmer
*/
-class NodeFactory
+public final class NodeFactory
{
- static INode createNode(java.io.File file) throws EnvironmentFailureException
+
+ /**
+ * A <code>INode</code> factory method for given <var>file</var>.
+ */
+ public static INode createNode(final java.io.File file) throws EnvironmentFailureException
{
assert file != null : "Unspecified node";
String absolutePath = file.getAbsolutePath();
@@ -50,5 +60,6 @@ class NodeFactory
private NodeFactory()
{
+ // Can not be instantiated.
}
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..d16f1db54a468e7383c2c2d940cb0fb522fc660f
--- /dev/null
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java
@@ -0,0 +1,83 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+import java.io.File;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.IFile;
+import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
+import ch.systemsx.cisd.common.logging.LogInitializer;
+import ch.systemsx.cisd.common.utilities.FileUtilities;
+
+import static org.testng.AssertJUnit.*;
+
+/**
+ * Test cases for corresponding {@link Utilities} class.
+ *
+ * @author Christian Ribeaud
+ */
+public class UtilitiesTest
+{
+ private static final File UNIT_TEST_ROOT_DIRECTORY = new File("targets" + File.separator + "unit-test-wd");
+
+ private static final File WORKING_DIRECTORY =
+ new File(UNIT_TEST_ROOT_DIRECTORY, UtilitiesTest.class.getSimpleName());
+
+ @BeforeMethod
+ public final void setUp()
+ {
+ LogInitializer.init();
+ FileUtilities.deleteRecursively(WORKING_DIRECTORY);
+ WORKING_DIRECTORY.mkdirs();
+ assert WORKING_DIRECTORY.isDirectory() && WORKING_DIRECTORY.listFiles().length == 0;
+ WORKING_DIRECTORY.deleteOnExit();
+ }
+
+ @Test
+ public final void testGetNumber()
+ {
+ final IDirectory directory = (IDirectory) NodeFactory.createNode(WORKING_DIRECTORY);
+ final String key = "age";
+ final String value = "35";
+ final IFile file = directory.addKeyValuePair(key, value);
+ final File[] listFiles = WORKING_DIRECTORY.listFiles();
+ assertEquals(1, listFiles.length);
+ assertEquals(key, listFiles[0].getName());
+ assertEquals(value, file.getStringContent().trim());
+ try
+ {
+ Utilities.getNumber(null, null);
+ fail("Directory and name can not be null.");
+ } catch (AssertionError ex)
+ {
+ // Nothing to do here
+ }
+ try
+ {
+ Utilities.getNumber(directory, "doesNotExist");
+ fail("File 'doesNotExist' missing");
+ } catch (DataStructureException ex)
+ {
+ // Nothing to do here
+ }
+ assertEquals(35, Utilities.getNumber(directory, key));
+ }
+}
\ No newline at end of file