Changeset 4844

Timestamp:

Mar 25, 2009, 1:23:49 PM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1269: Biomaterial batch importers should use alphanumeric coordinate system for wells

Location:

trunk

Files:

• doc/src/docbook/appendix/incompatible.xml (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/batchimport/ExtractImporter.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/SampleImporter.java (modified) (4 diffs)

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

@@ -43 +43 @@
     </para>
   </note>
+  
+  <sect1 id="appendix.incompatible.2.11">
+    <title>BASE 2.11 release</title>
+    
+    <bridgehead>
+      Biomaterial batch importers uses a different coordinate system 
+      to target biowells
+    </bridgehead>
+    <para>
+      The batch importers previously used the same coordinate system 
+      for locating biowells on a plate that BASE uses internally. A 
+      0-based numerical coordinate pair. This has now been changed to use 
+      the more logical alphanumeric 1-based coordinate system typically found on plates. 
+      As an example files should now specify A1, B2, C3 instead of [0,0],
+      [1,1] or [2,2]. Files that use the "old" coordinate system must
+      be updated to the new coordinate system, or the imported data will
+      end up in incorrect wells or in no well at all. The change affects three 
+      batch importers:
+    </para>
+    <itemizedlist>
+      <listitem>
+      <para><classname docapi="net.sf.basedb.plugins.batchimport">SampleImporter</classname></para>
+      </listitem>
+      <listitem>
+      <para><classname docapi="net.sf.basedb.plugins.batchimport">ExtractImporter</classname></para>
+      </listitem>
+      <listitem>
+      <para><classname docapi="net.sf.basedb.plugins.batchimport">LabeledExtractImporter</classname></para>
+      </listitem>
+    </itemizedlist>
+    
+    <note>
+      It is still possible to use purely numerical coordinates, but they must
+      be 1-based and not 0-based as before!
+    </note>
+    
+    <warning>
+      The new coordinate system only affects the batch importers. The BASE
+      web client will still display the internal 0-based coordinate values.
+      BASE users should be aware of this, particularly if they use the table
+      exporter to generate template files intended for import at a later
+      time. In this case the coordinates in the template file needs to be 
+      edited before importing.
+    </warning>
+  </sect1>
   
   <sect1 id="appendix.incompatible.2.10">

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ExtractImporter.java

@@ -42 +42 @@
 import net.sf.basedb.core.plugin.AboutImpl;
 import net.sf.basedb.core.plugin.GuiContext;
+import net.sf.basedb.util.Coordinate;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.parser.FlatFileParser;
@@ -223 +224 @@
       if (plate != null)
       {
-        Integer row = bioWellRowMapper.getInt(data);
-        Integer column = bioWellColMapper.getInt(data);       
+        String row = bioWellRowMapper.getValue(data);
+        String column = bioWellColMapper.getValue(data);        
         if (column != null && row != null)
         {
-          well = plate.getBioWell(row, column);;
+          // Convert alphanumeric (1-based) to 0-based numerical coordinate
+          int r = Coordinate.alphaToNumeric(row) - 1;
+          int c = Coordinate.alphaToNumeric(column) - 1;
+          well = plate.getBioWell(r, c);
         }
       }

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java

@@ -43 +43 @@
 import net.sf.basedb.core.plugin.AboutImpl;
 import net.sf.basedb.core.plugin.GuiContext;
+import net.sf.basedb.util.Coordinate;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.parser.FlatFileParser;
@@ -261 +262 @@
       if (plate != null)
       {
-        Integer row = bioWellRowMapper.getInt(data);
-        Integer column = bioWellColMapper.getInt(data);       
+        String row = bioWellRowMapper.getValue(data);
+        String column = bioWellColMapper.getValue(data);        
         if (column != null && row != null)
         {
-          well = plate.getBioWell(row, column);;
+          // Convert alphanumeric (1-based) to 0-based numerical coordinate
+          int r = Coordinate.alphaToNumeric(row) - 1;
+          int c = Coordinate.alphaToNumeric(column) - 1;
+          well = plate.getBioWell(r, c);
         }
       }

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/SampleImporter.java

@@ -42 +42 @@
 import net.sf.basedb.core.plugin.AboutImpl;
 import net.sf.basedb.core.plugin.GuiContext;
+import net.sf.basedb.util.Coordinate;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.parser.FlatFileParser;
@@ -145 +146 @@
         "bioWellRowColumnMapping",
         "Biowell row",
-        "Mapping that picks the row of the biowell in the data columns. "+
+        "Mapping that picks the row of the biowell in the data columns. " +
+        "The row coordinate is usually given as alphabetical letters, " +
+        "A, B, C, etc, but it can also be given as a numerical value " +
+        "where A=1, B=2 and so on. Note that BASE internally uses a " +
+        "0-based coordinate system. The coordinate values given in the " +
+        "file are converted to this system before data is saved. "+
         "Example: \\Biowell row\\",
         optionalColumnMapping
@@ -157 +163 @@
         "bioWellColColumnMapping",
         "Biowell column",
-        "Mapping that picks the column of the biowell in the data columns. "+
+        "Mapping that picks the column of the biowell in the data columns. " +
+        "The column coordinate is usually given as a number, but alphabetical " +
+        "letters are also supported, A=1, B=2 and so on. Note that BASE internally uses a " +
+        "0-based coordinate system. The coordinate values given in the " +
+        "file are converted to this system before data is saved. "+
         "Example: \\Biowell column\\",
         optionalColumnMapping
@@ -319 +329 @@
       if (plate != null)
       {
-        Integer row = bioWellRowMapper.getInt(data);
-        Integer column = bioWellColMapper.getInt(data);       
+        String row = bioWellRowMapper.getValue(data);
+        String column = bioWellColMapper.getValue(data);        
         if (column != null && row != null)
         {
-          well = plate.getBioWell(row, column);;
+          // Convert alphanumeric (1-based) to 0-based numerical coordinate
+          int r = Coordinate.alphaToNumeric(row) - 1;
+          int c = Coordinate.alphaToNumeric(column) - 1;
+          well = plate.getBioWell(r, c);
         }
       }