Changeset 6476

Timestamp:

Nov 5, 2021, 11:24:48 AM (15 months ago)

Author:

Nicklas Nordborg

Message:

References #1346: Implement support for OncoArray? SNP data

Added more annotation types for GenotypeCall items for storing data extracted from the GTC files.

Location:

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

Files:

• dao/Annotationtype.java (modified) (1 diff)
• servlet/InstallServlet.java (modified) (2 diffs)

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

@@ -1712 +1712 @@
     new Annotationtype("QC_GenoTypeComment", Type.STRING, false, Item.DERIVEDBIOASSAY);
   
+  
+  /**
+    The "CallDate" annotation type, used for derived bioassays (GenotypeCall).
+    @since 4.34
+  */
+  public static final Annotationtype CALL_DATE = 
+    new Annotationtype("CallDate", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY);
+
+  /**
+    The "NumCalls" annotation type, used for derived bioassays (GenotypeCall).
+    @since 4.34
+  */
+  public static final Annotationtype NUM_CALLS = 
+    new Annotationtype("NumCalls", Type.INT, false, Item.DERIVEDBIOASSAY);
+  
+  /**
+    The "NumNoCalls" annotation type, used for derived bioassays (GenotypeCall).
+    @since 4.34
+  */
+  public static final Annotationtype NUM_NO_CALLS = 
+    new Annotationtype("NumNoCalls", Type.INT, false, Item.DERIVEDBIOASSAY);
+
+  /**
+    The "CallRate" annotation type, used for derived bioassays (GenotypeCall).
+    @since 4.34
+  */
+  public static final Annotationtype CALL_RATE = 
+    new Annotationtype("CallRate", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
+
+  /**
+    The "GC10" annotation type, used for derived bioassays (GenotypeCall).
+    @since 4.34
+  */
+  public static final Annotationtype GC10 = 
+    new Annotationtype("GC10", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
+  
+  /**
+    The "GC50" annotation type, used for derived bioassays (GenotypeCall).
+    @since 4.34
+  */
+  public static final Annotationtype GC50 = 
+    new Annotationtype("GC50", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
+
+  /**
+    The "LogRDev" annotation type, used for derived bioassays (GenotypeCall).
+    @since 4.34
+  */
+  public static final Annotationtype LOG_R_DEV = 
+    new Annotationtype("LogRDev", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
+    
   /**
     The "mBAF_SNPCount" annotation, used for derived bioassays (AlignedSequences).

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

@@ -626 +626 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_POSITION, 1, null, createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCAN_DATE, 1, null, createIfMissing, effectivePermissionsUse));
+
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.CALL_DATE, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_CALLS, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_NO_CALLS, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.CALL_RATE, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.GC10, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.GC50, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.LOG_R_DEV, 1, null, createIfMissing, effectivePermissionsUse));
         
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_START, 1, null, createIfMissing, effectivePermissionsUse));
@@ -1066 +1074 @@
 
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.GENOTYPE_CALL, createIfMissing, 
-            Annotationtype.DATA_FILES_FOLDER, 
-            Annotationtype.ANALYSIS_RESULT,
-            Annotationtype.PIPELINE
+            Annotationtype.CALL_DATE, Annotationtype.NUM_CALLS, Annotationtype.NUM_NO_CALLS,
+            Annotationtype.CALL_RATE, Annotationtype.GC10, Annotationtype.GC50,
+            Annotationtype.LOG_R_DEV, Annotationtype.DATA_FILES_FOLDER, 
+            Annotationtype.ANALYSIS_RESULT, Annotationtype.PIPELINE
           ));