Changeset 6465

Timestamp:

Nov 3, 2021, 1:39:48 PM (15 months ago)

Author:

Nicklas Nordborg

Message:

References #1347: Updates to registration of specimen handled by external lab

The library importer will now select the plate type depending on the format of the Plate well value. If the value is digit:digit the STRIP_1x8 is selected otherwise the PLATE_8x12.

Location:

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/plugins

Files:

• FutureSpecimenImporter.java (modified) (1 diff)
• cmd/LibraryInfo.java (modified) (8 diffs)
• cmd/PlateWellValidator.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/plugins/FutureSpecimenImporter.java

@@ -415 +415 @@
     else
     {
-      BioplateType plateType = BioplateType.EXTERNAL_LIBRARY;
+      BioplateType plateType = info.libPlateType;
+      if (plateType == null) plateType = BioplateType.EXTERNAL_LIBRARY; // Should not happen if LibraryInfo.valid==TRUE
       plate = BioPlate.getNew(dc, plateType.getPlateGeometry(dc), plateType.get(dc));
       plate.setName(plateType.getNextPlateName(dc, true));

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/plugins/cmd/LibraryInfo.java

@@ -47 +47 @@
   public Protocol protocol;
   public BioPlate libPlate;
+  public BioplateType libPlateType = BioplateType.EXTERNAL_LIBRARY;
   
   public boolean valid;
@@ -55 +56 @@
     {
       plateId = section.getRequiredEntry("Plate name", PatternValidator.CMD_ID);
-      well = section.getRequiredEntry("Plate well", PlateWellValidator.PLATE_8x12);
+      ValidPlateCoordinateWithType plateWell = section.getRequiredEntry("Plate well", PlateOrStripValidator.INSTANCE);
+      if (plateWell != null)
+      {
+        well = plateWell.plateCoordinate;
+        libPlateType = plateWell.plateType;
+      }
   
       if (plateId != null && well != null && ctx != null)
@@ -63 +69 @@
         {
           String coordinate = Coordinate.numericToAlpha(well.getRow()+1)+(well.getColumn()+1);
-          String msg = "LibPlate well ["+coordinate+"; ExternalRef="+plateId+"] duplicated in file: ";
+          String msg = "Plate well ["+coordinate+"; ExternalRef="+plateId+"] duplicated in file: ";
           section.addErrorMessage(msg+duplicate.getFile().getName());
           duplicate.addErrorMessage(msg+section.getFile().getName());
@@ -69 +75 @@
       }
       
-      if (plateId != null) libPlate = findExistingLibPlate(plateId, section);
+      if (plateId != null) libPlate = findExistingLibPlate(plateId, libPlateType, section);
       if (libPlate != null && well != null)
       {
@@ -82 +88 @@
       
       barcode = section.getRequiredEntry("Barcode", BarcodeValidator.INSTANCE);
-      // TODO -- protocol
       protocol = section.getRequiredEntry("Protocol", ProtocolValidator.LIB_PROTOCOL);
     }
@@ -88 +93 @@
   }
   
-  private BioPlate findExistingLibPlate(String plateId, JsonSection section)
+  private BioPlate findExistingLibPlate(String plateId, BioplateType plateType, JsonSection section)
   {
     BioPlate libPlate = null;
@@ -94 +99 @@
     ItemQuery<BioPlate> query = BioPlate.getQuery();
     query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
-    BioplateType.EXTERNAL_LIBRARY.addFilter(dc, query, false);
+    if (plateType != null)
+    {
+      plateType.addFilter(dc, query, false);
+    }
     query.join(Annotations.innerJoin(null, Annotationtype.EXTERNAL_REF.load(dc), "eref"));
     query.restrict(Restrictions.eq(Hql.alias("eref"), Expressions.string(plateId)));
@@ -196 +204 @@
   }
 
+  /**
+    Validator implementation that delegates to either STRIP_1x8 validator if
+    the coordinate is specified as 'digit:digit' or to PLATE_8x12 otherwise.
+    @since 4.33.4
+  */
+  static class PlateOrStripValidator
+    implements ValueValidator<String, ValidPlateCoordinateWithType>
+  {
+    static final PlateOrStripValidator INSTANCE = new PlateOrStripValidator();
+    
+    @Override
+    public Class<String> getExpectedClass() 
+    {
+      return String.class;
+    }
+
+    @Override
+    public ValidPlateCoordinateWithType isValid(DbControl dc, String value, JsonSection section, String entryKey) 
+    {
+      ValidPlateCoordinateWithType result = new ValidPlateCoordinateWithType();
+      PlateWellValidator validator;
+      if (value.matches("\\d\\:\\d"))
+      {
+        validator = PlateWellValidator.STRIP_1x8;
+        result.plateType = BioplateType.EXTERNAL_LIBRARY_STRIP;
+      }
+      else
+      {
+        validator = PlateWellValidator.PLATE_8x12;
+        result.plateType = BioplateType.EXTERNAL_LIBRARY;
+      }
+      result.plateCoordinate = validator.isValid(dc, value, section, entryKey);
+      return result;
+    }
+  }
+  
+  /**
+    Holds the validated plate type and coordinate.
+  */
+  static class ValidPlateCoordinateWithType
+  {
+    PlateCoordinate plateCoordinate;
+    BioplateType plateType;
+  }
 }

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/plugins/cmd/PlateWellValidator.java

@@ -25 +25 @@
   */
   public static final PlateWellValidator PLATE_8x12 = new PlateWellValidator(8, 12);
+  
+  /**
+    Validator for strips with 1 row and 8 columns.
+    @since 4.33.4
+  */
+  public static final PlateWellValidator STRIP_1x8 = new PlateWellValidator(1, 8);
   
   /**