Changeset 5774

Timestamp:

Dec 4, 2019, 12:59:44 PM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1209: Add support for storing TMA specimen

Added new subtype for TMASpecimen and annotation types TMABlock and TMABlockPos.

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• dao/Annotationtype.java (modified) (1 diff)
• dao/Subtype.java (modified) (1 diff)
• servlet/InstallServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

@@ -414 +414 @@
     new Annotationtype("LinkedSpecimen", Type.STRING, false, Item.SAMPLE);
 
+  /**
+    Name of TMA block were a TMASpecimen is located.
+    @since 4.25
+   */
+  public static final Annotationtype TMA_BLOCK = 
+    new Annotationtype("TMABlock", Type.STRING, false, Item.SAMPLE);
+  
+  /**
+    Position on TMA block were a TMASpecimen is located.
+    @since 4.25
+   */
+  public static final Annotationtype TMA_BLOCK_POS = 
+    new Annotationtype("TMABlockPos", Type.STRING, false, Item.SAMPLE);
   
   /**

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

@@ -92 +92 @@
   public static final Subtype NO_SPECIMEN = new Subtype("NoSpecimen", null, null, "S", Item.SAMPLE, false);
 
-  
+  /**
+    The definition of the "TMASpecimen" subtype.
+    @since 4.25
+  */
+  public static final Subtype TMA_SPECIMEN = new Subtype("TMASpecimen", null, "tma", "T", Item.SAMPLE, false);
+
   /**
     The definition of the "Histology" subtype.

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -272 +272 @@
         jsonChecks.add(checkSubtype(dc, Subtype.SPECIMEN,null, createIfMissing, Subtype.CASE));
         jsonChecks.add(checkSubtype(dc, Subtype.NO_SPECIMEN,null, createIfMissing, Subtype.CASE));
+        jsonChecks.add(checkSubtype(dc, Subtype.TMA_SPECIMEN,null, createIfMissing, Subtype.CASE));
         jsonChecks.add(checkSubtype(dc, Subtype.HISTOLOGY_PROTOCOL, null, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.HISTOLOGY, null, createIfMissing, Subtype.SPECIMEN, Subtype.HISTOLOGY_PROTOCOL));
@@ -439 +440 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.PARTITION_DATE, 1, null, createIfMissing, effectivePermissionsUse));
 
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.TMA_BLOCK, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.TMA_BLOCK_POS, 1, null, createIfMissing, effectivePermissionsUse));
+
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.RLT_PLUS, 1, null, createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.BETA_MERCA, 1, null, createIfMissing, effectivePermissionsUse));
@@ -769 +773 @@
             Annotationtype.LINKED_SPECIMEN, Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT
             ));
+
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.TMA_SPECIMEN, createIfMissing, 
+            Annotationtype.TMA_BLOCK, Annotationtype.TMA_BLOCK_POS,
+            Annotationtype.PAD
+            ));
         
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.HISTOLOGY, createIfMissing,