Changeset 4972

Timestamp:

Sep 20, 2018, 1:42:21 PM (5 years ago)

Author:

Nicklas Nordborg

Message:

References #1054: Even more functionality in the Flagged alignment wizard

Added two new annotation types: DoNotUse and DoNotUseComment.

They should be set on any item (from Specimen all the way down to RawBioassay?) to indicate that it should not be used in the future for some reason (as indicated by the comment). The DoNotUse is a string enumeration with possible values: Specimen, Lysate, RNA, Library. The value should reflect the top-most item where there is a problem. For example, if an RNA is contaminated, then DoNotUse=RNA for the RNA and all items downstreams.

Location:

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

Files:

• dao/Annotationtype.java (modified) (1 diff)
• servlet/InstallServlet.java (modified) (9 diffs)

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

@@ -1426 +1426 @@
   
   /**
+    The "DoNotUse" annotation type which is a flag to indicate that
+    a biomaterial (sample or extract) is not correct and it should
+    not be used. The typical problems are mixups in the QiaCube or
+    contamination in the lib-prep. The flag is also put on all child items.
+    The value is an enumeration that indicates the topmost item type.
+    @since 4.20
+  */
+  public static final Annotationtype DO_NOT_USE = 
+    new Annotationtype("DoNotUse", Type.STRING, false, Item.SAMPLE, Item.EXTRACT, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
+  
+  /**
+    A comment that goes with the "DoNotUse" annotations.
+    @since 4.20
+  */
+  public static final Annotationtype DO_NOT_USE_COMMENT = 
+    new Annotationtype("DoNotUseComment", Type.STRING, false, Item.SAMPLE, Item.EXTRACT, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
+  
+  /**
     The "SerialNumber" annotation, used for hardware items.
     It is a string annotation containing a typically unique 

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

@@ -587 +587 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_GENOTYPE_COMMENT, 1, null, createIfMissing, effectivePermissionsUse));
         
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.DO_NOT_USE, 1, 
+            new ValueOptions("Specimen", "Lysate", "RNA", "Library"), 
+            createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.DO_NOT_USE_COMMENT, 1, null, createIfMissing, effectivePermissionsUse));
+        
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.BARCODE_SEQUENCE, 1, null, createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.SERIAL_NUMBER, 1, null, createIfMissing, effectivePermissionsUse));
@@ -690 +695 @@
             Annotationtype.SAMPLING_DATETIME, Annotationtype.SPECIMEN_TYPE,
             Annotationtype.LINKED_SPECIMEN, Annotationtype.YELLOW_LABEL, 
-            Annotationtype.COMPLETED_DATE,
+            Annotationtype.COMPLETED_DATE, 
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
             Annotationtype.AUTO_PROCESSING));
         
@@ -713 +719 @@
             Annotationtype.RLT_PLUS, Annotationtype.BETA_MERCA,
             Annotationtype.REAGENT_DX, Annotationtype.QIA_SHREDDER,
-            Annotationtype.RESERVED_BY, Annotationtype.AUTO_PROCESSING
+            Annotationtype.RESERVED_BY, 
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
+            Annotationtype.AUTO_PROCESSING
             ));
         
@@ -725 +733 @@
             Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER,
             Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL,
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
             Annotationtype.AUTO_PROCESSING, Annotationtype.FLAG));
         
@@ -746 +755 @@
             Annotationtype.BUFFER_AW1, Annotationtype.BUFFER_AW2,
             Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER,
-            Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL
+            Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL,
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT
             ));
         
@@ -756 +766 @@
             Annotationtype.BUFFER_AW1, Annotationtype.BUFFER_AW2,
             Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER,
-            Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL
+            Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL,
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT
             ));
 
@@ -788 +799 @@
             Annotationtype.DILUTION_DATE, Annotationtype.DILUTION_OPERATOR,
             Annotationtype.NEOPREP_DATE, Annotationtype.NEOPREP_DATE,
-            Annotationtype.POOL_SCHEMA, Annotationtype.BARCODE_VARIANT, Annotationtype.PLATE_PROCESS_RESULT));
+            Annotationtype.POOL_SCHEMA, Annotationtype.BARCODE_VARIANT, 
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
+            Annotationtype.PLATE_PROCESS_RESULT));
 
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.POOLED_LIBRARY, createIfMissing,
@@ -822 +835 @@
             Annotationtype.FRAGMENT_SIZE_AVG, Annotationtype.FRAGMENT_SIZE_STDEV,
             Annotationtype.DATA_FILES_FOLDER,
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
             Annotationtype.AUTO_PROCESSING
           ));
@@ -836 +850 @@
             Annotationtype.QC_GENOTYPE_COUNT, Annotationtype.QC_GENOTYPE_HET_PCT,
             Annotationtype.QC_GENOTYPE_STATUS, Annotationtype.QC_GENOTYPE_VERIFIED,
-            Annotationtype.QC_GENOTYPE_COMMENT, Annotationtype.AUTO_PROCESSING
+            Annotationtype.QC_GENOTYPE_COMMENT, 
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
+            Annotationtype.AUTO_PROCESSING
           ));