Changeset 4080

Timestamp:

Jan 15, 2008, 2:58:53 PM (15 years ago)

Author:

Nicklas Nordborg

Message:

References #894: Support for array designs with other feature identification methods than coordinates

The functionality is now implemented. Test programs run fine with the COORDINATES method. Needs testing with the other methods. RawBioAssay?.updateArrayDesign needs to be recoded.

Location:

trunk

Files:

• doc/src/docbook/appendix/incompatible.xml (modified) (1 diff)
• doc/src/docbook/developerdoc/api_overview.xml (modified) (2 diffs)
• doc/src/docbook/figures/uml/datalayer.arrays.png (modified) (previous)
• doc/src/uml/baseuml.mdzip (modified) (previous)
• src/clients/migrate/net/sf/basedb/clients/migrate/ArrayBlockTransfer.java (modified) (2 diffs)
• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/ArrayDesign.java (modified) (6 diffs)
• src/core/net/sf/basedb/core/FeatureBatcher.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/FeatureIdentificationMethod.java (added)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawDataBatcher.java (modified) (12 diffs)
• src/core/net/sf/basedb/core/Update.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/data/ArrayDesignData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/FeatureData.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/data/RawData.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java (modified) (4 diffs)
• src/plugins/core/net/sf/basedb/plugins/PrintMapFlatFileImporter.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/RawDataFlatFileImporter.java (modified) (13 diffs)
• src/plugins/core/net/sf/basedb/plugins/ReporterMapFlatFileImporter.java (modified) (20 diffs)
• src/test/TestArrayDesign.java (modified) (4 diffs)
• src/test/net/sf/basedb/test/merge/MergeTest.java (modified) (3 diffs)

trunk/doc/src/docbook/appendix/incompatible.xml

@@ -45 +45 @@
     </para>
   </note>
+  
+  <sect1 id="appendix.incompatible.2.6">
+    <title>BASE 2.6 release</title>
+    
+    <bridgehead>Feature identification methods</bridgehead>
+    <para>
+      Array design features can now be identified by three different methods:
+      COORDINATES, POSITION and EXTERNAL_ID. The coordinates method was the
+      only one supported earlier. 
+    </para>
+    
+    <itemizedlist>
+    <listitem>
+      <para>
+      Client and plug-in code that depends on features having unique COORDINATES 
+      may no longer work if used with an array design using a different identification method.
+      Code that is, directly or indirectly, using a 
+      <classname docapi="net.sf.basedb.core">FeatureBatcher</classname> or 
+      <classname docapi="net.sf.basedb.core">RawDataBatcher</classname> are 
+      probably affected by this. For example, includes raw data importers which 
+      doesn't know how to set the position or the feature ID when those identification
+      methods are used.
+      </para>
+    </listitem>
+    
+    <listitem>
+      <para>
+      The POSITION identification method will require a unqiue position number. 
+      This value used to be an auto-generated sequence starting at 1. The other
+      identification methods will still do that, but when using the POSITION identification
+      method the only requirement is that the position value is a unique positive integer. 
+      Client or plug-in code that depends on the position beeing a number between
+      1 and the number of features may fail if used with an array design using 
+      the POSITION identification method.
+      </para>
+    </listitem>   
+    </itemizedlist>
+
+  </sect1>  
   
   <sect1 id="appendix.incompatible.2.5">

trunk/doc/src/docbook/developerdoc/api_overview.xml

@@ -1958 +1958 @@
           from plates. In the first case the features on an array design
           are described by a reporter map. A reporter map is a file
-          that maps a coordinate on an array design to a reporter. 
+          that maps a coordinate (block, meta-grid, row, column), 
+          position or an external ID on an array design to a 
+          reporter. Which method to use is given by the 
+          <property>ArrayDesign.featureIdentificationMethod</property> property. 
           The coordinate system on an array design is divided into blocks.
           Each block can be identified either by a <property>blockNumber</property>
@@ -1965 +1968 @@
           contains several <classname docapi="net.sf.basedb.core.data">FeatureData</classname> items, each
           one identified by a row and column coordinate. Platforms that doesn't
-          divide the array design into block should create a single super-block
-          that holds all features.
+          divide the array design into blocks or doesn't use the coordinate system at all
+          must still create a single super-block that holds all features. 
         </para>
         

trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayBlockTransfer.java

@@ -33 +33 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.FeatureBatcher;
+import net.sf.basedb.core.FeatureIdentificationMethod;
 import net.sf.basedb.core.ItemNotFoundException;
 import net.sf.basedb.core.Plate;
@@ -113 +114 @@
           ArrayDesign arrayDesign = ArrayDesign.getById(dc, base2Id);
           PreparedStatement ps = prepareStatementFromFile("selectArrayBlocksByArrayType");
-          FeatureBatcher featureBatcher = arrayDesign.getFeatureBatcher();
+          FeatureBatcher featureBatcher = arrayDesign.getFeatureBatcher(FeatureIdentificationMethod.COORDINATES);
           log.debug("Setting batch size to: " + getBatchSize());
           featureBatcher.setBatchSize(getBatchSize());

trunk/src/core/common-queries.xml

@@ -3014 +3014 @@
     </description>
   </query>
+  
+  <query id="SET_FEATUREIDENTIFICATIONMETHOD_ON_ARRAYDESIGNS" type="HQL">
+    <sql>
+      UPDATE ArrayDesignData ad
+      SET ad.featureIdentificationMethod = :method
+      WHERE ad.featureIdentificationMethod IS NULL
+    </sql>
+    <description>
+      A HQL query that set the featureIdentificationMethod property 
+      on all array designs with a null value.
+    </description>
+  </query>
 
 </predefined-queries>

trunk/src/core/net/sf/basedb/core/ArrayDesign.java

@@ -107 +107 @@
     ad.setName("New array design");
     ad.setPlatform(platform);
+    ad.getData().setFeatureIdentificationMethod(FeatureIdentificationMethod.NONE.getValue());
     return ad;
   }
@@ -126 +127 @@
     ad.setName("New array design");
     ad.setVariant(variant);
+    ad.getData().setFeatureIdentificationMethod(FeatureIdentificationMethod.NONE.getValue());
     return ad;
   }
@@ -422 +424 @@
 
   /**
+    Get the method used to identify features on this array design.
+    @return A <code>FeatureIdentificationMethod</code>
+    @since 2.6
+  */
+  public FeatureIdentificationMethod getFeatureIdentificationMethod()
+  {
+    return FeatureIdentificationMethod.fromValue(getData().getFeatureIdentificationMethod());
+  }
+  
+  /**
     Get a query that returns the plates that are used by this arraydesign.
     @return An {@link ItemQuery} object
@@ -638 +650 @@
   
   /**
+    Get a feature batcher that uses the COORDINATES feature identification
+    method.
+    @deprecated Use {@link #getFeatureBatcher(FeatureIdentificationMethod)} instead
+  */
+  public FeatureBatcher getFeatureBatcher()
+    throws PermissionDeniedException, BaseException
+  {
+    return getFeatureBatcher(FeatureIdentificationMethod.COORDINATES);
+  }
+
+  /**
     Get a feature batcher which can be used to add regular features to the
     array design.   
@@ -644 +667 @@
     file-only platform. The must store feature information in files 
     instead. See {@link Platform} and {@link DataFileType}.
+    @param fiMethod The method to use for identifying features
     @return The feature batcher of the array design.
     @throws PermissionDeniedException If raw data has already been added
       or the logged in user doesn't have write permission
     @throws BaseException If there is another error
-  */
-  public FeatureBatcher getFeatureBatcher()
+    @since 2.6
+  */
+  public FeatureBatcher getFeatureBatcher(FeatureIdentificationMethod fiMethod)
     throws PermissionDeniedException, BaseException
   {
@@ -661 +686 @@
       throw new PermissionDeniedException("Features has already been added to "+this.getName());
     }
+    if (fiMethod == FeatureIdentificationMethod.NONE)
+    {
+      throw new InvalidDataException("Feature identification method NONE is not supported: " + this.getName());
+    }
+    getData().setFeatureIdentificationMethod(fiMethod.getValue());
     if (featureBatcher == null)
     {

trunk/src/core/net/sf/basedb/core/FeatureBatcher.java

@@ -34 +34 @@
 import java.sql.PreparedStatement;
 import java.sql.SQLException;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.TreeSet;
 
 /**
   Batcher class for Features or AffyFeatures. A single instance can be used
   for features belonging to a single {@link ArrayDesign}.
+  <p>
+  Create new {@link FeatureData} objects with either
+  {@link #newFeature(ArrayDesignBlock, ReporterData)} or
+  {@link #newFeature(ArrayDesignBlock, Well)}. Use the latter method if the array
+  desing is connected to plates.
+  <p>
+  Depending on the {@link FeatureIdentificationMethod} used by the array design,
+  you must set different properties on the <code>FeatureData</code> object.
+  
+  <ul>
+  <li>NONE: Not supported
+  <li>COORDINATES: {@link FeatureData#setRow(int)} and {@link FeatureData#setColumn(int)}
+  <li>POSITION: {@link FeatureData#setPosition(int)}
+  <li>EXTERNAL_ID: {@link FeatureData#setExternalId(String)}
+  </ul>
+  
+  For all methods, each feature that is inserted must have a unqiue value. For example,
+  there can't be two features with the same external ID if the EXTERNAL_ID method is 
+  used. Values for the methods that are not used can still be set and saved to the
+  database, but the uniqueness is not checked. The position number will be auto-generated 
+  (and overwritten) if the identification method is not POSITION.
   
   @base.modified $Date$
@@ -76 +100 @@
   private final ArrayDesignData arrayDesignData;
   
+  private final FeatureIdentificationMethod fiMethod;
+  
+  /**
+    Holds identification of already inserted features.
+  */
+  private Set<Object> featureIds;
+  
   /**
     Keeps track of the position number.
@@ -81 +112 @@
   private int currentPosition = 0;
 
+  @SuppressWarnings("unchecked")
   FeatureBatcher(DbControl dc, ArrayDesign arrayDesign) 
     throws BaseException
@@ -87 +119 @@
     this.arrayDesign = arrayDesign;
     this.arrayDesignData = arrayDesign.getData();
+    this.fiMethod = arrayDesign.getFeatureIdentificationMethod();
+    this.featureIds = fiMethod.caseInsensitive() && HibernateUtil.getDbEngine().caseInsensitiveComparison() ?
+      new TreeSet(String.CASE_INSENSITIVE_ORDER) : new HashSet();
     setDbControl(dc);
   }
@@ -105 +140 @@
     <li>The data object is not null
     <li>An array design block has been specfied
+    <li>The postion number is > 0
+    <li>The external id is not null or too long
+    <li>The feature identification is unique
     <li>The data object belongs to the correct array design
     <li>The reporter match the well's reporter if a well has been specified
-    <li>
     </ul>
   */
@@ -116 +153 @@
     if (data == null) throw new InvalidUseOfNullException("data");
 
+    // Array design block must be set
     ArrayDesignBlockData adb = (ArrayDesignBlockData)getPropertyValue(data, "arrayDesignBlock");
     if (adb == null) throw new InvalidUseOfNullException("arrayDesignBlock");
     
+    // Position must be > 0
+    if (data.getPosition() <= 0)
+    {
+      throw new NumberOutOfRangeException("position", data.getPosition(), 1, false);
+    }
+
+    // External ID must not be too long
+    data.setExternalId(StringUtil.setNullableString(data.getExternalId(), 
+      "externalId", FeatureData.MAX_EXTERNAL_ID_LENGTH));
+
+    // Feature identifier must be unique
+    Object featureId = fiMethod.getIdentifier(data);
+    if (featureIds.contains(featureId))
+    {
+      throw new InvalidDataException("Another feature with the same identifier already exists: " + 
+        fiMethod.toString() + "=" + featureId);
+    }
+    featureIds.add(featureId);
+
     // verify that the data object belongs to the correct raw bioassay
     if (!arrayDesignData.equals(adb.getArrayDesign()))
@@ -144 +201 @@
     throws BaseException
   {
-    setPropertyValue(data, "position", ++currentPosition);
+    if (fiMethod != FeatureIdentificationMethod.POSITION)
+    {
+      data.setPosition(++currentPosition);
+    }
     super.insert(data);
   }

trunk/src/core/net/sf/basedb/core/Install.java

@@ -107 +107 @@
     method.
   */
-  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(48).intValue();
+  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(49).intValue();
   
   public static synchronized void createTables(boolean update, final ProgressReporter progress)

trunk/src/core/net/sf/basedb/core/RawDataBatcher.java

@@ -146 +146 @@
   private org.hibernate.Query findReporter;
 
-  /*
+  /**
+    The method to use for identifying features.
+  */
+  private FeatureIdentificationMethod fiMethod;
+  
+  /**
     Holds info about the features of an array design. Using the
-    coordinates we can look up position number and reporter on
+    feature identifier we can look up position number and reporter on
     each location and verify this against the raw data.
-  */
-  private final Map<FeatureCoordinate, FeatureData> preloaded;
+    @see FeatureIdentificationMethod
+  */
+  private final Map<Object, FeatureData> preloaded;
   
   /**
@@ -171 +177 @@
       throw new BaseException("Raw data for raw data type '" + rawDataType + "' is not stored in the database.");
     }
-    
-    if (arrayDesign != null && arrayDesign.getHasFeatures())
+
+    this.fiMethod = arrayDesign != null && arrayDesign.getHasFeatures() ?
+        FeatureIdentificationMethod.fromValue(arrayDesign.getFeatureIdentificationMethod()) :
+        FeatureIdentificationMethod.NONE;
+
+    if (fiMethod != FeatureIdentificationMethod.NONE)
     {
       org.hibernate.Query query = HibernateUtil.getPredefinedQuery(dc.getStatelessSession(), "COUNT_FEATURES_FOR_ARRAYDESIGN");
@@ -182 +192 @@
       query.setInteger("arrayDesign", arrayDesign.getId());
       int numFeatures = HibernateUtil.loadData(Long.class, query).intValue();
-      preloaded = new HashMap<FeatureCoordinate, FeatureData>(numFeatures);
+      preloaded = new HashMap<Object, FeatureData>(numFeatures);
       query = HibernateUtil.getPredefinedQuery(dc.getStatelessSession(), "PRELOAD_FEATURES");
       /*
@@ -196 +206 @@
       while (si.hasNext())
       {
-        FeatureData f = si.next();
-        FeatureCoordinate fc = Feature.getFeatureCoordinate(f);
-        preloaded.put(fc, f);
+        FeatureData feature = si.next();
+        Object featureId = fiMethod.getIdentifier(feature);
+        preloaded.put(featureId, feature);
       }
       si.close();
@@ -223 +233 @@
     <li>The data object is not null
     <li>The data object belongs to the correct raw bioassay
+    <li>The position value is > 0
     <li>All of the extra properties using the 
       {@link ExtendedProperty#validateValue(Object)} method
@@ -231 +242 @@
   {
     if (data == null) throw new InvalidUseOfNullException("data");
+
+    // Position must be > 0
+    if (data.getPosition() <= 0)
+    {
+      throw new NumberOutOfRangeException("position", data.getPosition(), 1, false);
+    }
     
     // verify that the data object belongs to the correct raw bioassay
@@ -252 +269 @@
     throws BaseException
   {
-    doInsert(data, null, false);
+    doInsert(data, null, null, false);
   }
   
@@ -337 +354 @@
   /**
     Insert a raw data spot and verify the external id of the 
-    reporter. The external id is only verified if the raw bioassauy
+    reporter. The external id is only verified if the raw bioassay
     is connected to an array design with features. The external id
     is verified to match the external id of the reporter attached to
@@ -348 +365 @@
       be found at the feature of this spot
     @throws BaseException If the insertion failed. 
+    @deprecated
   */
   public void insert(RawData data, String externalReporterId)
     throws BaseException
   {
-    doInsert(data, externalReporterId, true);
-  }
-
+    doInsert(data, externalReporterId, null, true);
+  }
+
+  public void insert(RawData data, String externalReporterId, String externalFeatureId)
+  {
+    doInsert(data, externalReporterId, externalFeatureId, true);
+  }
+  
   /**
     Do the actual insert.
   */
-  void doInsert(RawData data, String externalReporterId, boolean validateReporterId)
+  void doInsert(RawData data, String externalReporterId, String externalFeatureId, boolean validateReporterId)
     throws BaseException
   {
@@ -364 +387 @@
     if (preloaded == null)
     {
-      setPropertyValue(data, "position", ++currentPosition);
+      if (data.getPosition() == 0) data.setPosition(++currentPosition);
       // If no reporter has been set on the RawData object we try to find the external id
       if (externalReporterId != null && data.getReporter() == null)
@@ -384 +407 @@
     else
     {
-      FeatureCoordinate fc = new FeatureCoordinate(data.getBlock(), data.getMetaGridX(),
-        data.getMetaGridY(), data.getRow(), data.getColumn());
-      FeatureData f = preloaded.get(fc);
+      Object featureId = fiMethod.getIdentifier(data, externalFeatureId);
+      FeatureData f = preloaded.get(featureId);
       if (f == null)
       {
-        throw new ItemNotFoundException("Feature[row="+data.getRow()+", column="+data.getColumn()+
-          ", block="+data.getBlock()+", metaGridX="+data.getMetaGridX()+", metaGridY="+data.getMetaGridY()+
-          "]");
+        throw new ItemNotFoundException("Feature["+ fiMethod.toString() + "=" + featureId + "]");
       }
       ReporterData r = f.getReporter();
@@ -404 +424 @@
         }
       }
-      setPropertyValue(data, "position", f.getPosition());
+      data.setPosition(f.getPosition());
       setPropertyValue(data, "feature", f);
       data.setReporter(r);

trunk/src/core/net/sf/basedb/core/Update.java

@@ -553 +553 @@
     </td>
   </tr>
+
+  <tr>
+    <td>49</td>
+    <td>
+      <ul>
+      <li>Added {@link net.sf.basedb.core.data.FeatureData#getExternalId()}
+      <li>Added {@link net.sf.basedb.core.data.ArrayDesignData#getFeatureIdentificationMethod()}
+      </ul>
+      The update sets the identification method to COORDINATES for all existing
+      array designs, and deletes the unique index on row, column, block on
+      the Features table.
+    </td>
+  </tr>
+  
   </table>
 
@@ -779 +793 @@
       }
       
-      if (schemaVersion < 46)
-      {
-        if (progress != null) progress.display((int)(45*progress_factor), "--Updating schema version: " + schemaVersion + " -> 46...");
-        schemaVersion = setSchemaVersionInTransaction(session, 46);
-      }
-
-      if (schemaVersion < 47)
-      {
-        if (progress != null) progress.display((int)(46*progress_factor), "--Updating schema version: " + schemaVersion + " -> 47...");
-        schemaVersion = setSchemaVersionInTransaction(session, 47);
-      }
-      
+      // Schemaversion 46-48 only updates the version number
       if (schemaVersion < 48)
       {
@@ -797 +800 @@
       }
 
+      if (schemaVersion < 49)
+      {
+        if (progress != null) progress.display((int)(48*progress_factor), "--Updating schema version: " + schemaVersion + " -> 49...");
+        schemaVersion = updateToSchemaVersion49(session);
+      }
+      
+      
       sc.logout();
       if (progress != null) progress.display(100, "Database updated successfully.");
@@ -1977 +1987 @@
     return schemaVersion;   
   }
+  
+  /**
+    Find the unique index on Feature (row, column and block) and remove it.
+    
+    @return The new schema version (=49)
+  */
+  private static int updateToSchemaVersion49(org.hibernate.Session session)
+    throws BaseException
+  {
+    final int schemaVersion = 49;
+    org.hibernate.Transaction tx = null;
+    try
+    {
+      Connection connection = HibernateUtil.getConnection(session);
+      DatabaseMetaData metaData = null;
+      TableInfo info = null;
+      try
+      {
+        metaData = connection.getMetaData();
+        Table table = new Table("Features");
+        info = new TableInfo(table, metaData);
+      }
+      catch (SQLException ex)
+      {
+        throw new BaseException(ex);
+      }
+  
+      tx = HibernateUtil.newTransaction(session);
+      DbEngine dbEngine = HibernateUtil.getDbEngine();
+      String indexName = info.findIndexName("uniquecoordinate", 
+        new HashSet<String>(Arrays.asList(new String[] {"arraydesignblock_id", "row", "column"})));
+      if (indexName != null)
+      {
+        String sql = dbEngine.getDropIndexSql(null, null, "Features", indexName, true);
+        try
+        {
+          Statement st = connection.createStatement();
+          log.info("Dropping index: " + sql);
+          st.executeUpdate(sql);
+          st.close();
+        }
+        catch (SQLException ex)
+        {
+          throw new BaseException(ex);
+        }
+      }
+  
+      // Update the schema version number
+      setSchemaVersion(session, schemaVersion);
+  
+      // Commit the changes
+      HibernateUtil.commit(tx);
+      log.info("updateToSchemaVersion49: OK");
+    }
+    catch (BaseException ex)
+    {
+      if (tx != null) HibernateUtil.rollback(tx); 
+      log.error("updateToSchemaVersion49: FAILED", ex);
+      throw ex;
+    }
+    return schemaVersion;
+  } 
   
   /**
@@ -2348 +2420 @@
           */
           HibernateUtil.executeUpdate(query);
-        }       
+        }
+        
+        if (schemaVersion < 49)
+        {
+          // Set featureIdentificationMethod to COORDINATE for all array designs
+          org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+            "SET_FEATUREIDENTIFICATIONMETHOD_ON_ARRAYDESIGNS");
+          /*
+            UPDATE ArrayDesignData ad
+            SET ad.featureIdentificationMethod = :method
+            WHERE ad.featureIdentificationMethod IS NULL
+          */
+          query.setInteger("method", FeatureIdentificationMethod.COORDINATES.getValue());
+          HibernateUtil.executeUpdate(query);
+        }
         
         //  Commit the changes

trunk/src/core/net/sf/basedb/core/data/ArrayDesignData.java

@@ -156 +156 @@
   }
   
+  private int featureIdentificationMethod;
+  /**
+    The method to use for identiying features.
+    1 = COORDINATES, 2 = POSITION, 3 = EXTERNAL_ID
+    @hibernate.property column="`identification_method`" type="int" not-null="true"
+    @since 2.6
+  */
+  public int getFeatureIdentificationMethod()
+  {
+    return featureIdentificationMethod;
+  }
+  public void setFeatureIdentificationMethod(int featureIdentificationMethod)
+  {
+    this.featureIdentificationMethod = featureIdentificationMethod;
+  }
+  
+  
   private Set<ArrayDesignBlockData> arrayDesignBlocks;
   /**

trunk/src/core/net/sf/basedb/core/data/FeatureData.java

@@ -67 +67 @@
     Get the column coordinate of the feature.
     @hibernate.property type="int" update="false"
-    @hibernate.column name="`column`" not-null="true" unique-key="uniquecoordinate"
+    @hibernate.column name="`column`" not-null="true"
   */
   public int getColumn()
@@ -83 +83 @@
     Get the row coordinate of the feature.
     @hibernate.property type="int" update="false"
-    @hibernate.column name="`row`" not-null="true" unique-key="uniquecoordinate"
+    @hibernate.column name="`row`" not-null="true"
   */
   public int getRow()
@@ -104 +104 @@
     return position;
   }
-  void setPosition(int position)
+  /**
+    This method was private until 2.6. The value will be overwritten with an
+    autogenerated value unless the feature identification method is POSITION.
+    The value must be a positive integer.
+    @since 2.6
+  */
+  public void setPosition(int position)
   {
     this.position = position;
   }
 
+  /**
+    The maximum length of the external ID that can be stored in the database.
+    @see #setExternalId(String)
+  */
+  public static final int MAX_EXTERNAL_ID_LENGTH = 255;
+  private String externalId;
+  /**
+    Get the external id for this <code>FeatureData</code> item. If given,
+    it must be unique per array design.
+    @return The features external ID.
+    @hibernate.property column="`external_id`" type="string" length="255" not-null="false" update="false"
+    @since 2.6
+  */
+  public String getExternalId()
+  {
+    return externalId;
+  }
+  public void setExternalId(String externalId)
+  {
+    this.externalId = externalId;
+  }
+  
   private ArrayDesignBlockData arrayDesignBlock;
   /**
@@ -115 +143 @@
 
     @hibernate.many-to-one outer-join="false" update="false"
-    @hibernate.column name="`arraydesignblock_id`" not-null="true" unique-key="uniquecoordinate" 
+    @hibernate.column name="`arraydesignblock_id`" not-null="true"
   */
   ArrayDesignBlockData getArrayDesignBlock()

trunk/src/core/net/sf/basedb/core/data/RawData.java

@@ -116 +116 @@
     return position;
   }
-  void setPosition(int position)
+  /**
+    This method was private before 2.6. If the raw bioassay is connected to
+    an array design which uses the POSITION feature identifier method
+    a value must be set. If the raw bioassay is connected to an array design
+    which uses another feature identifier method this value will be overwritten
+    with the position value from the feature. If the raw bioassay is not connected
+    to an array design a position will be automatically generated if no value
+    has been set, ie. if the value is 0.
+    The value must be a positive integer.
+    @param position The position number of the spot
+    @since 2.6
+  */
+  public void setPosition(int position)
   {
     this.position = position;

trunk/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java

@@ -43 +43 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Experiment;
+import net.sf.basedb.core.FeatureIdentificationMethod;
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.Include;
@@ -92 +93 @@
   to an experiment.
   <p>
-  Since the data files doesn't have any coordinate information, the plug-in create
-  fake coordinates like this: block=1, column=1, row=linenumber in file.
-  The linenmbers start with 1 at the first data line, ie. header lines are not counted.
+  Since the data files doesn't have any coordinate information the importer will 
+  use one of the following methods.
+  
+  <ul>
+  <li>
+    If no array design has been selected or if the array design is using the
+    {@link FeatureIdentificationMethod#COORDINATES} method for identifying features:
+    The plug-in create fake coordinates like this: block=1, column=1, row=linenumber in file.
+    The linenmbers start with 1 at the first data line, ie. header lines are not counted.
+
+  <li>
+    If the array design uses the {@link FeatureIdentificationMethod#POSITION}
+    method for identiyfing features: The plug-in sets the position=line number in file.
+    The linenmbers start with 1 at the first data line, ie. header lines are not counted.
+    
+  <li>
+    If the array design uses the {@link FeatureIdentificationMethod#EXTERNAL_ID}
+    method for identifying features. The plug-in assumes that the feature ID is the
+    same as the reporter ID.
+  </ul>
+  
+  <p>
+  NOTE! Since the methods are not conflicting with each other, there will not
+  be an actual check which method to use by this plug-in. We will simple set all
+  values as specified above and let the BASE core handle the identification.
 
   @author nicklas
@@ -417 +440 @@
   {
     String externalId = reporterMapper.getValue(data);
+    int lineNo = data.dataLineNo();
     for (BatchAndMapHolder holder : holders)
     {
       RawData raw = holder.batcher.newRawData();
+      raw.setPosition(lineNo);
       raw.setBlock(1);
       raw.setColumn(1);
-      raw.setRow(data.dataLineNo());
+      raw.setRow(lineNo);
       for (Map.Entry<RawDataProperty, Mapper> entry : holder.mappers.entrySet())
       {
@@ -429 +454 @@
         raw.setExtended(ep.getName(), ep.parseString(m.getValue(data), numberFormat, nullIfException));
       }
-      holder.batcher.insert(raw, externalId);
+      holder.batcher.insert(raw, externalId, externalId);
     }
     numInserted++;

trunk/src/plugins/core/net/sf/basedb/plugins/PrintMapFlatFileImporter.java

@@ -33 +33 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.FeatureBatcher;
+import net.sf.basedb.core.FeatureIdentificationMethod;
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileParameterType;
@@ -326 +327 @@
     }
     
-    batcher = arrayDesign.getFeatureBatcher();
+    batcher = arrayDesign.getFeatureBatcher(FeatureIdentificationMethod.COORDINATES);
     numFeatures = 0;
     numBlocks = 0;

trunk/src/plugins/core/net/sf/basedb/plugins/RawDataFlatFileImporter.java

@@ -50 +50 @@
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.StringParameterType;
+import net.sf.basedb.core.data.FeatureData;
 import net.sf.basedb.core.data.RawData;
 import net.sf.basedb.core.data.ReporterData;
@@ -115 +116 @@
   private static final StringParameterType requiredColumnMapping = new StringParameterType(255, null, true);
   
+  private static final PluginParameter<String> positionColumnMapping = new PluginParameter<String>(
+    "positionColumnMapping",
+    "Position",
+    "Mapping that picks the spot's position from the data columns. This column is only " +
+    "used when the raw data is connected to an array design which uses the POSITION method " +
+    "for identifying features. If the raw data is not connected to an array design " +
+    "position values will automatically be generated if no mapping has been specified. In all" +
+    "cases, position value must be unique." +
+    "Mapping example: \\Position\\",
+    optionalColumnMapping
+    );
+
+  
   private static final PluginParameter<String> blockColumnMapping = new PluginParameter<String>(
     "blockColumnMapping",
     "Block",
-    "Mapping that picks the spot's block from the data columns. " +
+    "Mapping that picks the spot's block number from the data columns. This column is only " +
+    "used when the raw data is connected to an array design which uses the COORDINATES method " +
+    "for identifying features. In all other cases, the value is stored as is." +
     "For example: \\Block\\",
     optionalColumnMapping
@@ -126 +142 @@
     "columnColumnMapping",
     "Column",
-    "Mapping that picks the spot's column in the block from the data columns. " +
+    "Mapping that picks the spot's column coordinate from the data columns. This column is only " +
+    "used when the raw data is connected to an array design which uses the COORDINATES method " +
+    "for identifying features. In all other cases, the value is stored as is." +
     "For example: \\Column\\",
     optionalColumnMapping
@@ -134 +152 @@
     "rowColumnMapping",
     "Row",
-    "Mapping that picks the spot's row in the block from the data columns. " +
+    "Mapping that picks the spot's row coordinate from the data columns. This column is only " +
+    "used when the raw data is connected to an array design which uses the COORDINATES method " +
+    "for identifying features. In all other cases, the value is stored as is." +
     "For example: \\Row\\",
     optionalColumnMapping
@@ -142 +162 @@
     "metaGridXColumnMapping",
     "MetaGridX",
-    "Mapping that picks the spot's meta-Grid X-axis from the data columns. " +
+    "Mapping that picks the spot's meta-Grid X-axis from the data columns. This column is only " +
+    "used when the raw data is connected to an array design which uses the COORDINATES method " +
+    "for identifying features. In all other cases, the value is stored as is." +
     "For example: \\Meta grid X\\",
     optionalColumnMapping
@@ -150 +172 @@
     "metaGridYColumnMapping",
     "MetaGridY",
-    "Mapping that picks the spot's meta-Grid Y-axis from the data columns. " +
+    "Mapping that picks the spot's meta-Grid Y-axis from the data columns. This column is only " +
+    "used when the raw data is connected to an array design which uses the COORDINATES method " +
+    "for identifying features. In all other cases, the value is stored as is." +
     "For example: \\Meta grid Y\\",
     optionalColumnMapping
@@ -178 +202 @@
     requiredColumnMapping
     );
+
+  private static final PluginParameter<String> featureIdColumnMapping = new PluginParameter<String>(
+      "featureIdColumnMapping",
+      "Feature ID",
+      "Mapping that picks the spot's feature ID from the data columns. " +
+      "This column is only used when the raw data is connected to an array design " +
+      "which uses the EXTERNAL_ID method for identifying features. The value is not saved " +
+      "to the database." +
+      "For example: \\Feature ID\\",
+      optionalColumnMapping
+    );
+  
   
   protected static final PluginParameter<String> missingReporterErrorParameter = new PluginParameter<String>(
@@ -226 +262 @@
   private FileSetMember rawDataMember;
 
+  private Mapper featureIdMapper;
   private Mapper reporterMapper;
+  private Mapper positionMapper;
   private Mapper blockMapper;
   private Mapper columnMapper;
@@ -529 +567 @@
     reporterMapper = getMapper(ffp, (String)configuration.getValue("reporterIdColumnMapping"), 
       cropStrings ? ReporterData.MAX_EXTERNAL_ID_LENGTH : null, nullMapper);
-
+    
+    featureIdMapper = getMapper(ffp, (String)configuration.getValue("featureIdColumnMapping"), 
+      cropStrings ? FeatureData.MAX_EXTERNAL_ID_LENGTH : null, nullMapper);
+
+    positionMapper = getMapper(ffp, (String)configuration.getValue("positionColumnMapping"), null, nullMapper);
     blockMapper = getMapper(ffp, (String)configuration.getValue("blockColumnMapping"), null, nullMapper);
     columnMapper = getMapper(ffp, (String)configuration.getValue("columnColumnMapping"), null, nullMapper);
@@ -584 +626 @@
 
     String externalId = reporterMapper.getValue(data);
+    String featureId = featureIdMapper.getValue(data);
+    Integer position = positionMapper.getInt(data);
+    if (position != null) raw.setPosition(position);
     raw.setBlock(blockMapper.getInt(data));
     raw.setColumn(columnMapper.getInt(data));
@@ -599 +644 @@
     }
 
-    batcher.insert(raw, externalId);
+    batcher.insert(raw, externalId, featureId);
     numInserted++;
   }
@@ -633 +678 @@
     {
       allColumnMappings = new ArrayList<PluginParameter<String>>();
+      allColumnMappings.add(positionColumnMapping);
       allColumnMappings.add(blockColumnMapping);
       allColumnMappings.add(columnColumnMapping);
@@ -641 +687 @@
       allColumnMappings.add(yColumnMapping);
       allColumnMappings.add(reporterIdColumnMapping);
+      allColumnMappings.add(featureIdColumnMapping);
       for(RawDataProperty rdp : rdt.getProperties())
       {

trunk/src/plugins/core/net/sf/basedb/plugins/ReporterMapFlatFileImporter.java

@@ -33 +33 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.FeatureBatcher;
+import net.sf.basedb.core.FeatureIdentificationMethod;
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileParameterType;
@@ -38 +39 @@
 import net.sf.basedb.core.FileStoreUtil;
 import net.sf.basedb.core.FileType;
+import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.InvalidUseOfNullException;
 import net.sf.basedb.core.ItemContext;
@@ -94 +96 @@
       "Reporter map importer",
       "This plugin is used to import features to an ArrayDesign from a simple flat file.",
-      "2.0",
+      "2.6",
       "2006, Base 2 development team",
       null,
@@ -109 +111 @@
   private static final StringParameterType optionalColumnMapping = new StringParameterType(255, null, false);
   
-
+  private static final PluginParameter<String> featureIdentificationParameter = 
+    new PluginParameter<String>(
+      "featureIdentification",
+      "Identify features by",
+      "Choose which method to use for identifying features: \n" +
+      "COORDINATES: Use block, meta-grid, row and column coordinates\n" +
+      "POSITION: Use a position number only\n" +
+      "EXTERNAL_ID: Use the feature ID value (string)\n" +
+      "In all cases, the identifier value must be unique.",
+      new StringParameterType(255, "COORDINATES", true, 1, 0, 0, 
+        Arrays.asList(new String[] {"COORDINATES", "POSITION", "EXTERNAL_ID"}))
+    );
+  
   private static final PluginParameter<String> reporterIdColumnMapping = new PluginParameter<String>(
     "reporterIdColumnMapping",
@@ -117 +131 @@
     requiredColumnMapping
     );
-
+  
+  private static final PluginParameter<String> featureIdColumnMapping = new PluginParameter<String>(
+    "featureIdColumnMapping",
+    "Feature ID",
+    "Mapping that picks the feature's ID from the data columns. This column is " +
+    "only used when the array design uses the EXTERNAL_ID method for " +
+    "identifying features. In the other cases, the value is just stored as it is." +
+    "For example: \\Feature ID\\",
+    optionalColumnMapping
+    );
+
+  private static final PluginParameter<String> positionColumnMapping = new PluginParameter<String>(
+    "positionColumnMapping",
+    "Position",
+    "Mapping that picks the feature's position from the data columns. This column is only " +
+    "used when the array design uses the POSITION method " +
+    "for identifying features. The other identification methods will always " +
+    "overwrite the position with an autogenerated value." +
+    "Mapping example: \\Position\\",
+    optionalColumnMapping
+    );
+  
+  
   private static final PluginParameter<String> blockColumnMapping = new PluginParameter<String>(
     "blockColumnMapping",
     "Block",
-    "Mapping that picks the feature's block number from the data columns. "+
-    "You must specify either this mapping or mappings for the meta coordinates. " +
+    "Mapping that picks the feature's block number from the data columns. This column is only " +
+    "used when the array design uses the COORDINATES method " +
+    "for identifying features. In the other cases, the value is just stored as it is. " +
+    "You must specify either this mapping or mappings for the meta coordinates when using " +
+    "the COORDINATES method. " +
     "Example: \\Block\\",
     optionalColumnMapping
@@ -130 +169 @@
     "metaGridXColumnMapping",
     "Meta grid X",
-    "Mapping that picks the feature's meta grid X coordinate from the data columns. "+
-    "Required if you don't specify a block mapping. Example: \\Meta grid X\\",
+    "Mapping that picks the feature's meta grid X coordinate from the data columns. This column is only " +
+    "used when the array design uses the COORDINATES method " +
+    "for identifying features. In the other cases, the value is just stored as it is. " +
+    "You must specify either this mapping or mappings for the block number when using " +
+    "the COORDINATES method. Example: \\Meta grid X\\",
     optionalColumnMapping
     );
@@ -138 +180 @@
     "metaGridYColumnMapping",
     "Meta grid Y",
-    "Mapping that picks the feature's meta grid Y coordinate from the data columns. " +
-    "Required if you don't specify a block mapping. Example: \\Meta grid Y\\",
+    "Mapping that picks the feature's meta grid Y coordinate from the data columns. This column is only " +
+    "used when the array design uses the COORDINATES method " +
+    "for identifying features. In the other cases, the value is just stored as it is. " +
+    "You must specify either this mapping or mappings for the block number when using " +
+    "the COORDINATES method. Example: \\Meta grid Y\\",
     optionalColumnMapping
     );
@@ -147 +192 @@
     "Column",
     "Mapping that picks the feature's column position in a block from the data columns. " +
-    "For example: \\Column\\",
-    requiredColumnMapping
+    "This column is only used when the array design uses the COORDINATES method " +
+    "for identifying features. In the other cases, the value is just stored as it is. " +
+    "This value is required when using the COORDINATES method. Example: \\Column\\",
+    optionalColumnMapping
     );
   
@@ -155 +202 @@
     "Row",
     "Mapping that picks the feature's row position in a block from the data columns. " +
-    "For example: \\Row\\",
-    requiredColumnMapping
+    "This column is only used when the array design uses the COORDINATES method " +
+    "for identifying features. In the other cases, the value is just stored as it is. " +
+    "This value is required when using the COORDINATES method. Example: \\Row\\",
+    optionalColumnMapping
     );
   
@@ -190 +239 @@
   private boolean errorIfNotFound;
   private Mapper reporterMapper;
+  private Mapper featureIdMapper;
+  private Mapper positionMapper;
   private Mapper blockMapper;
   private Mapper columnMapper;
@@ -328 +379 @@
         }
         
-        // Check that either block or meta coordinates have been mapped
-        String blockMapping = (String)request.getParameterValue("blockColumnMapping");
-        String metaGridXMapping = (String)request.getParameterValue("metaGridXColumnMapping");
-        String metaGridYMapping = (String)request.getParameterValue("metaGridYColumnMapping");
-        if (blockMapping == null && (metaGridXMapping == null || metaGridYMapping == null))
+        // Check that enough mappings have been set for the 
+        // specific feature identification method
+        String fiParameter = (String)request.getParameterValue("featureIdentification");
+        FeatureIdentificationMethod fiMethod = fiParameter == null ?
+          FeatureIdentificationMethod.COORDINATES :
+          FeatureIdentificationMethod.valueOf(fiParameter);
+        
+        List<Throwable> mapErrors = new ArrayList<Throwable>();
+        if (fiMethod == FeatureIdentificationMethod.COORDINATES)
         {
-          response.setError("You must at least map either block or meta coordinates to columns.", null);
+          String blockMapping = (String)request.getParameterValue("blockColumnMapping");
+          String metaGridXMapping = (String)request.getParameterValue("metaGridXColumnMapping");
+          String metaGridYMapping = (String)request.getParameterValue("metaGridYColumnMapping");
+          String columnMapping = (String)request.getParameterValue("columnColumnMapping");
+          String rowMapping = (String)request.getParameterValue("rowColumnMapping");
+          
+          if (blockMapping == null && (metaGridXMapping == null || metaGridYMapping == null))
+          {
+            mapErrors.add(new InvalidDataException("You must at least map either block or meta coordinates to columns."));
+          }
+          if (columnMapping == null)  mapErrors.add(new InvalidUseOfNullException("Column"));
+          if (rowMapping == null) mapErrors.add(new InvalidUseOfNullException("Row"));
+        }
+        else if (fiMethod == FeatureIdentificationMethod.POSITION)
+        {
+          String positionMapping = (String)request.getParameterValue("positionColumnMapping");
+          if (positionMapping == null) mapErrors.add(new InvalidUseOfNullException("Position"));
+        }
+        else if (fiMethod == FeatureIdentificationMethod.EXTERNAL_ID)
+        {
+          String positionMapping = (String)request.getParameterValue("featureIdColumnMapping");
+          if (positionMapping == null) mapErrors.add(new InvalidUseOfNullException("Feature ID"));
+        }
+        else
+        {
+          response.setError("Unknown feature identification method: " + fiMethod, null);
           return;
+        }
+        if (mapErrors.size() > 0)
+        {
+          response.setError("Missing column mapping for feature identification method: " 
+            + fiMethod, mapErrors);
         }
         
@@ -350 +435 @@
 
         // Column mappings
+        storeValue(configuration, request, featureIdentificationParameter);
         storeValue(configuration, request, complexMappings);
         boolean allowComplex = "allow".equals(request.getParameterValue(complexMappings.getName()));
@@ -379 +465 @@
         storeValue(job, request, invalidUseOfNullErrorParameter);
         storeValue(job, request, numberFormatErrorParameter);
+        storeValue(job, request, stringTooLongErrorParameter);
         
         response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);
@@ -408 +495 @@
     File reporterMapFile = (File)job.getValue("file");
     arrayDesign = ArrayDesign.getById(dc, arrayDesign.getId());
+    if (arrayDesign.getNumDbFeatures() > 0)
+    {
+      throw new PermissionDeniedException("The array design already has features. "+arrayDesign.getName()+"["+arrayDesign.getId()+"]");
+    }
+    String fiParameter = (String)configuration.getValue("featureIdentification");
+    FeatureIdentificationMethod fiMethod = fiParameter == null ?
+      FeatureIdentificationMethod.COORDINATES :
+      FeatureIdentificationMethod.valueOf(fiParameter);
     reporterMapMember = FileStoreUtil.setGenericDataFile(dc, arrayDesign, 
         FileType.REPORTER_MAP, DataFileType.GENERIC_REPORTER_MAP, reporterMapFile);
-    if (arrayDesign.getNumDbFeatures() > 0)
-    {
-      throw new PermissionDeniedException("The array design already has features. "+arrayDesign.getName()+"["+arrayDesign.getId()+"]");
-    }
-    batcher = arrayDesign.getFeatureBatcher();
+    batcher = arrayDesign.getFeatureBatcher(fiMethod);
     reporterBatcher = ReporterBatcher.getNew(dc);
     this.ffp = ffp;
@@ -439 +530 @@
   protected void beginData()
   {
+    boolean cropStrings = ("crop".equals(job.getValue("stringTooLongError")));
     Mapper nullMapper = new ConstantMapper((String)null);
-    reporterMapper = getMapper(ffp, (String)configuration.getValue("reporterIdColumnMapping"), null, nullMapper);
+    reporterMapper = getMapper(ffp, (String)configuration.getValue("reporterIdColumnMapping"), 
+      cropStrings ? ReporterData.MAX_EXTERNAL_ID_LENGTH : null, nullMapper);
+    featureIdMapper = getMapper(ffp, (String)configuration.getValue("featureIdColumnMapping"), 
+      cropStrings ? FeatureData.MAX_EXTERNAL_ID_LENGTH : null, nullMapper);
+    positionMapper = getMapper(ffp, (String)configuration.getValue("positionColumnMapping"), null, nullMapper);
     blockMapper = getMapper(ffp, (String)configuration.getValue("blockColumnMapping"), null, nullMapper);
     columnMapper = getMapper(ffp, (String)configuration.getValue("columnColumnMapping"), null, nullMapper);
@@ -453 +549 @@
   {
     String externalId = reporterMapper.getValue(data);
+    String featureId = featureIdMapper.getValue(data);
     ReporterData reporter = externalId == null ? 
       null : reporterBatcher.getByExternalId(externalId, errorIfNotFound);
@@ -474 +571 @@
     
     FeatureData feature = batcher.newFeature(adb, reporter);
+    Integer position = positionMapper.getInt(data);
     Integer row = rowMapper.getInt(data);
     Integer column = columnMapper.getInt(data);
-    if (row == null) throw new InvalidUseOfNullException("row");
-    if (column == null) throw new InvalidUseOfNullException("column");
-    feature.setRow(row);
-    feature.setColumn(column);
+    feature.setPosition(position == null ? 0 : position);
+    if (row != null)
+    {
+      feature.setRow(row);
+      if (row > adb.getBlockSizeY()) adb.setBlockSizeY(row);
+    }
+    if (column != null)
+    {
+      feature.setColumn(column);
+      if (column > adb.getBlockSizeX()) adb.setBlockSizeX(feature.getColumn());
+    }
     
     batcher.insert(feature);
     numFeatures++;
-    if (feature.getRow() > adb.getBlockSizeY())
-    {
-      adb.setBlockSizeY(feature.getRow());
-    }
-    if (feature.getColumn() > adb.getBlockSizeX())
-    {
-      adb.setBlockSizeX(feature.getColumn());
-    }
   }
 
@@ -535 +632 @@
       allColumnMappings = new ArrayList<PluginParameter<String>>();
       allColumnMappings.add(reporterIdColumnMapping);
+      allColumnMappings.add(featureIdColumnMapping);
+      allColumnMappings.add(positionColumnMapping);
       allColumnMappings.add(blockColumnMapping);
       allColumnMappings.add(metaGridXColumnMapping);
@@ -593 +692 @@
       parameters.add(invalidUseOfNullErrorParameter);
       parameters.add(numberFormatErrorParameter);
+      parameters.add(stringTooLongErrorParameter);
       
       configureJob = new RequestInformation
@@ -626 +726 @@
       // Column mappings
       parameters.add(mappingSection);
+      parameters.add(featureIdentificationParameter);
       parameters.add(complexMappings);
       parameters.addAll(getAllColumnMappings());

trunk/src/test/TestArrayDesign.java

@@ -31 +31 @@
 import net.sf.basedb.core.Feature;
 import net.sf.basedb.core.FeatureBatcher;
+import net.sf.basedb.core.FeatureIdentificationMethod;
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileSetMember;
@@ -328 +329 @@
       }
       
-      FeatureBatcher batcher = ad.getFeatureBatcher();
+      FeatureBatcher batcher = ad.getFeatureBatcher(FeatureIdentificationMethod.COORDINATES);
       int block = 1;
       int row = 1;
@@ -395 +396 @@
         wells.addAll(plate.getWells().list(dc));
       }
-      FeatureBatcher batcher = ad.getFeatureBatcher();
+      FeatureBatcher batcher = ad.getFeatureBatcher(FeatureIdentificationMethod.COORDINATES);
       int block = 1;
       int row = 1;
@@ -549 +550 @@
       dc = TestUtil.getDbControl();
       ArrayDesign ad = ArrayDesign.getById(dc, arrayDesignId);
-      FeatureBatcher featureBatcher = ad.getFeatureBatcher();
+      FeatureBatcher featureBatcher = ad.getFeatureBatcher(FeatureIdentificationMethod.COORDINATES);
       ReporterBatcher reporterBatcher = ReporterBatcher.getNew(dc);
     

trunk/src/test/net/sf/basedb/test/merge/MergeTest.java

@@ -42 +42 @@
 import net.sf.basedb.core.Experiment;
 import net.sf.basedb.core.FeatureBatcher;
+import net.sf.basedb.core.FeatureIdentificationMethod;
 import net.sf.basedb.core.Formula;
 import net.sf.basedb.core.ItemParameterType;
@@ -200 +201 @@
     TestUtil.write("--Creating features for array design: " + design.getName() + "\n");
     dc.reattachItem(design);
-    FeatureBatcher batcher = design.getFeatureBatcher();
+    FeatureBatcher batcher = design.getFeatureBatcher(FeatureIdentificationMethod.COORDINATES);
     ReporterBatcher reporterBatcher = ReporterBatcher.getNew(dc);
     for (int block = 1; block <= 10; block++)
@@ -252 +253 @@
         rawData.setExtended("ch1FgMean", ch1 + noise);
         rawData.setExtended("ch2FgMean", ch1 * ratio - noise);
-        batcher.insert(rawData, externalId);
+        batcher.insert(rawData, externalId, null);
       }
     }