SE-187 LMC: change BDS to allow symbolic links to original data

SVN: 14484

bds/source/java/ch/systemsx/cisd/bds/Format.java

@@ -165,8 +165,7 @@ public class Format implements IStorable
     }
 
     /**
-     * Returns the <code>IFormatParameterFactory</code> implementation for this
-     * <code>Format</code>.
+     * Returns the <code>IFormatParameterFactory</code> implementation for this <code>Format</code>.
      */
     public IFormatParameterFactory getFormatParameterFactory()
     {
@@ -180,7 +179,18 @@ public class Format implements IStorable
      * returns an empty list.
      * </p>
      */
-    public List<String> getParameterNames()
+    public List<String> getMandatoryParameterNames()
+    {
+        return Collections.emptyList();
+    }
+
+    /**
+     * Returns an unmodifiable list of optional parameters that are specific to this format.
+     * <p>
+     * Default implementation returns an empty list.
+     * </p>
+     */
+    public List<String> getOptionalParameterNames()
     {
         return Collections.emptyList();
     }

bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java

@@ -66,7 +66,7 @@ public interface IFormatParameterFactory
      * Creates a <code>FormatParameter</code> from given <var>value</var>.
      * 
      * @param name name of the format parameter. Usually it is one of the values returned by
-     *            {@link Format#getParameterNames()}.
+     *            {@link Format#getMandatoryParameterNames()}.
      * @param value generic value that should help to construct the <code>FormatParameter</code>.
      * @return <code>null</code> if no appropriate <code>FormatParameter</code> could be created
      *         from given <code>value</code>.

bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java

@@ -77,12 +77,19 @@ public final class FormatParameterFactory implements IFormatParameterFactory
                     .parseInt(value));
         } else if (nodeName.equals(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA))
         {
-            return new FormatParameter(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA, Utilities.Boolean
-                    .fromString(value));
+            return createBooleanParameter(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA, value);
+        } else if (nodeName.equals(HCSImageFormatV1_0.IS_INCOMING_SYMBOLIC_LINK))
+        {
+            return createBooleanParameter(HCSImageFormatV1_0.IS_INCOMING_SYMBOLIC_LINK, value);
         }
         return formatParameter;
     }
 
+    private static FormatParameter createBooleanParameter(String name, String value)
+    {
+        return new FormatParameter(name, Utilities.Boolean.fromString(value));
+    }
+
     public final FormatParameter createFormatParameter(final String name, final String value)
     {
         if (name.equals(PlateGeometry.PLATE_GEOMETRY))
@@ -103,6 +110,9 @@ public final class FormatParameterFactory implements IFormatParameterFactory
         {
             return new FormatParameter(name, Integer.parseInt(value));
         } else if (name.equals(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA))
+        {
+            return new FormatParameter(name, Utilities.Boolean.fromString(value));
+        } else if (name.equals(HCSImageFormatV1_0.IS_INCOMING_SYMBOLIC_LINK))
         {
             return new FormatParameter(name, Utilities.Boolean.fromString(value));
         }

bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java

@@ -45,6 +45,13 @@ public final class HCSImageFormatV1_0 extends Format
      */
     public final static String NUMBER_OF_CHANNELS = "number_of_channels";
 
+    /**
+     * Boolean flag specifying whether the items in the incoming folder are just a symbolic links to
+     * the original data. In this case we do not move any data. Instead we create symbolic link to
+     * original data which points to the same place as the link in incoming directory.
+     */
+    public final static String IS_INCOMING_SYMBOLIC_LINK = "incoming_items_are_symbolic_link";
+
     /**
      * The format parameters that must be defined so that this implementation is able to work
      * properly.
@@ -52,9 +59,12 @@ public final class HCSImageFormatV1_0 extends Format
      * These parameters are located in <code>metadata/parameters</code>.
      * </p>
      */
-    private final static String[] FORMAT_PARAMETERS = new String[]
+    private final static String[] MANDATORY_FORMAT_PARAMETERS = new String[]
         { WellGeometry.WELL_GEOMETRY, NUMBER_OF_CHANNELS, CONTAINS_ORIGINAL_DATA };
 
+    private final static String[] OPTIONAL_FORMAT_PARAMETERS = new String[]
+        { IS_INCOMING_SYMBOLIC_LINK };
+
     /**
      * The one and only one instance.
      */
@@ -70,9 +80,15 @@ public final class HCSImageFormatV1_0 extends Format
     //
 
     @Override
-    public final List<String> getParameterNames()
+    public final List<String> getMandatoryParameterNames()
+    {
+        return Arrays.asList(MANDATORY_FORMAT_PARAMETERS);
+    }
+
+    @Override
+    public List<String> getOptionalParameterNames()
     {
-        return Arrays.asList(FORMAT_PARAMETERS);
+        return Arrays.asList(OPTIONAL_FORMAT_PARAMETERS);
     }
 
     @Override

bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java

@@ -56,6 +56,9 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
 
     private final boolean containsOriginalData;
 
+    /** see {@link HCSImageFormatV1_0#IS_INCOMING_SYMBOLIC_LINK} */
+    private final boolean isIncomingSymbolicLink;
+
     private final Geometry wellGeometry;
 
     private final Geometry plateGeometry;
@@ -72,7 +75,8 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
     public HCSImageFormattedData(final FormattedDataContext context)
     {
         super(context);
-        this.containsOriginalData = figureContainsOriginalData(getFormatParameters());
+        IFormatParameters formatParameters = getFormatParameters();
+        this.containsOriginalData = figureContainsOriginalData(formatParameters);
         if (containsOriginalData)
         {
             this.originalDataDirectoryOrNull =
@@ -81,15 +85,16 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
         {
             this.originalDataDirectoryOrNull = null;
         }
+        this.isIncomingSymbolicLink = figureIsIncomingSymbolicLink(formatParameters);
 
         IDirectory standardDataDirectory =
                 Utilities.getSubDirectory(dataDirectory, DataStructureV1_0.DIR_STANDARD);
         this.standardDataDirectoryCache =
                 new DirectoryContentCache(standardDataDirectory, createChannelDirNameProvider());
 
-        this.wellGeometry = figureWellGeometry(getFormatParameters());
-        this.plateGeometry = figurePlateGeometry(getFormatParameters());
-        this.channelCount = figureChannelCount(getFormatParameters());
+        this.wellGeometry = figureWellGeometry(formatParameters);
+        this.plateGeometry = figurePlateGeometry(formatParameters);
+        this.channelCount = figureChannelCount(formatParameters);
     }
 
     private static int figureChannelCount(IFormatParameters params)
@@ -113,11 +118,29 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
                 .toBoolean();
     }
 
+    private static boolean figureIsIncomingSymbolicLink(IFormatParameters params)
+    {
+        String paramName = HCSImageFormatV1_0.IS_INCOMING_SYMBOLIC_LINK;
+        if (params.containsParameter(paramName))
+        {
+            return ((Utilities.Boolean) params.getValue(paramName)).toBoolean();
+        } else
+        {
+            return false; // default value
+        }
+    }
+
     public final boolean containsOriginalData()
     {
         return containsOriginalData;
     }
 
+    /** see {@link HCSImageFormatV1_0#IS_INCOMING_SYMBOLIC_LINK} */
+    public final boolean isIncomingSymbolicLink()
+    {
+        return isIncomingSymbolicLink;
+    }
+
     public final Geometry getWellGeometry()
     {
         return wellGeometry;
@@ -489,7 +512,7 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
         super.assertValidFormatAndFormatParameters();
         final IFormatParameters formatParameters = getFormatParameters();
         final Set<String> notPresent = new HashSet<String>();
-        for (final String formatParameterName : format.getParameterNames())
+        for (final String formatParameterName : format.getMandatoryParameterNames())
         {
             if (formatParameters.containsParameter(formatParameterName) == false)
             {

bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java

@@ -35,12 +35,15 @@ public interface IHCSImageFormattedData extends IFormattedData
      * Returns <code>true</code> if the data structure contains the original data.
      */
     public boolean containsOriginalData();
-    
+
+    /** see {@link HCSImageFormatV1_0#IS_INCOMING_SYMBOLIC_LINK} */
+    public boolean isIncomingSymbolicLink();
+
     /**
      * Returns the number of channels.
      */
     public int getChannelCount();
-    
+
     /**
      * Returns the geometric arrangement of the tiles of a well.
      */
@@ -51,11 +54,9 @@ public interface IHCSImageFormattedData extends IFormattedData
      */
     public Geometry getPlateGeometry();
 
-    
     /**
      * For given <var>channel</var>, given <var>wellLocation</var> and given <var>tileLocation</var>
-     * returns the corresponding <code>INode</code> (found in <code>data/standard</code>
-     * directory).
+     * returns the corresponding <code>INode</code> (found in <code>data/standard</code> directory).
      * 
      * @return this could be, for instance, a {@link ILink} pointing to the
      *         <code>data/original</code> directory or a {@link IFile} that can be extracted
@@ -71,15 +72,14 @@ public interface IHCSImageFormattedData extends IFormattedData
      *            incoming data set directory.
      * @param imageRelativePath relative path (to <var>imageRootDirectory</var>) name of the image
      *            file that is going to be added in the <code>standard</code> directory.
-     * @return the new <code>INode</code> just added (encapsulated in returned
-     *         <code>NodePath</code>) with its path in the <code>standard</code> directory.
-     *         Never returns <code>null</code>.
+     * @return the new <code>INode</code> just added (encapsulated in returned <code>NodePath</code>
+     *         ) with its path in the <code>standard</code> directory. Never returns
+     *         <code>null</code>.
      * @throws DataStructureException if a node already exists at given coordinates.
      */
     public NodePath addStandardNode(final File imageRootDirectory, final String imageRelativePath,
             final int channel, final Location wellLocation, final Location tileLocation)
             throws DataStructureException;
-    
 
     //
     // Helper classes

bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java

@@ -16,7 +16,6 @@
 
 package ch.systemsx.cisd.bds.storage;
 
-import java.io.File;
 import java.util.List;
 
 /**
@@ -73,10 +72,7 @@ public interface IDirectory extends INode, Iterable<INode>
      *         {@link IDirectory} if <code>file</code> is a folder, or {@link IFile} if
      *         <code>file</code> is a plain file.
      */
-    // TODO 2007-12-03, Tomasz Pylak review: this generic interface should not use java.io.File. Is
-    // the 'move' parameter possible to implement in HDF5? Maybe those operations should be done
-    // before, depending on the implementation which is used?
-    public INode addFile(final File file, final String nameOrNull, final boolean move);
+    public INode addFile(final java.io.File file, final String nameOrNull, final boolean move);
 
     /**
      * Removes given <var>node</var> from this directory.

bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java

@@ -94,7 +94,7 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
         context.checking(new Expectations()
             {
                 {
-                    for (final String formatParameterName : format.getParameterNames())
+                    for (final String formatParameterName : format.getMandatoryParameterNames())
                     {
                         one(formatParameters).containsParameter(formatParameterName);
                         will(returnValue(true));