fix:

- ETL server in HCS_FORMAT mode.
add:
- TODOs and FIXMEs,

SVN: 2944

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

@@ -131,9 +131,11 @@ public class Format implements IStorable
     /**
      * Returns an unmodifiable list of mandatory parameters that are specific to this format.
      * <p>
-     * They can be found in <code>metadata/parameters</code> directory. Default implementation retuns an empty list.
+     * They can be found in <code>metadata/parameters</code> directory. Default implementation returns an empty list.
      * </p>
      */
+    // TODO 2007-12-05, Christian Ribeaud: Right place for this here? This gets lost as soon as Format gets instantiated
+    // in the runtime.
     public List<String> getParameterNames()
     {
         return Collections.emptyList();

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

@@ -47,7 +47,7 @@ public interface IFormatParameterFactory
 
             public final FormatParameter createFormatParameter(final String name, final String value)
             {
-                return null;
+                return new FormatParameter(name, value);
             }
         };
 

bds/source/java/ch/systemsx/cisd/bds/UnknownFormat1_0.java

@@ -23,7 +23,7 @@ package ch.systemsx.cisd.bds;
  */
 public final class UnknownFormat1_0 extends Format
 {
-    private static final String FORMAT_CODE = "UNKNOWN";
+    public static final String FORMAT_CODE = "UNKNOWN";
     /**
      * The one and only one instance.
      */

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

@@ -67,7 +67,7 @@ public final class ChannelList implements IStorable, Iterable<Channel>
             final List<Channel> channels = new ArrayList<Channel>(size);
             for (int i = 0; i < size; i++)
             {
-                channels.add(new Channel(i, 0));
+                channels.add(new Channel(i + 1, 0));
             }
             return new ChannelList(channels);
         } catch (NumberFormatException ex)

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

@@ -95,6 +95,9 @@ public final class FormatParameterFactory implements IFormatParameterFactory
         } else if (name.equals(ChannelList.NUMBER_OF_CHANNELS))
         {
             return new FormatParameter(name, ChannelList.createChannelListFromString(value));
+        } else if (name.equals(HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA))
+        {
+            return new FormatParameter(name, Boolean.valueOf(value));
         }
         return IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY.createFormatParameter(name, value);
     }

bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormat1_0.java

@@ -31,7 +31,7 @@ import ch.systemsx.cisd.bds.Version;
 public final class HCSImageFormat1_0 extends Format
 {
 
-    private static final String FORMAT_CODE = "HCS_IMAGE";
+    public static final String FORMAT_CODE = "HCS_IMAGE";
 
     /** Key for setting the measurement device that was used to take the data of this data set. */
     public final static String DEVICE_ID = "device_id";

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

@@ -153,8 +153,16 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
     public final NodePath addStandardNode(final String originalFilePath, int channel, final Location plateLocation,
             final Location wellLocation)
     {
-        // This will check all parameters but originalFileName.
-        INode node = tryGetStandardNodeAt(channel, plateLocation, wellLocation);
+        // This will check all parameters but originalFilePath.
+        INode node = null;
+        // TODO 2007-12-05, Christian Ribeaud: Improve this.
+        try
+        {
+            node = tryGetStandardNodeAt(channel, plateLocation, wellLocation);
+        } catch (DataStructureException ex)
+        {
+            // Nothing to do here.
+        }
         if (node != null)
         {
             throw new DataStructureException(String.format(
@@ -190,8 +198,8 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
                                     originalFilePath, channel, plateLocation, wellLocation));
         }
         final char sep = Constants.PATH_SEPARATOR;
-        final String standardNodePath = channelDir.getName() + sep + plateRowDir.getName() + sep + plateColumnDir + sep
-                + wellFileName;
+        final String standardNodePath =
+                channelDir.getName() + sep + plateRowDir.getName() + sep + plateColumnDir + sep + wellFileName;
         return new NodePath(node, standardNodePath);
     }