Changeset 6461

Timestamp:

Nov 1, 2021, 2:16:43 PM (15 months ago)

Author:

Nicklas Nordborg

Message:

References #1346: Implement support for OncoArray? SNP data

Added BeadChip and Scan item subtype and several new annotation types related to those items (BeadChipID, BeadChipType, BeadChipPosition and ScanDate).

DNA/Genotyping is a new value for the Pipeline annotation.

Location:

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

Files:

• dao/Annotationtype.java (modified) (1 diff)
• dao/Pipeline.java (modified) (1 diff)
• dao/Subtype.java (modified) (1 diff)
• servlet/InstallServlet.java (modified) (5 diffs)

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

@@ -1301 +1301 @@
 
   /**
+    The "BeadChipID" annotation, used for physical bioassays (BeadChip).
+    @since 4.34
+  */
+  public static final Annotationtype BEADCHIP_ID = 
+    new Annotationtype("BeadChipID", Type.STRING, false, Item.PHYSICALBIOASSAY);
+  
+  /**
+    The "BeadChipType" annotation, used for physical bioassays (BeadChip).
+    @since 4.34
+  */
+  public static final Annotationtype BEADCHIP_TYPE = 
+    new Annotationtype("BeadChipType", Type.STRING, false, Item.PHYSICALBIOASSAY);
+
+  /**
+    The "BeadChipPosition" annotation, used for extracts (BloodDNA).
+    @since 4.34
+  */
+  public static final Annotationtype BEADCHIP_POSITION = 
+    new Annotationtype("BeadChipPosition", Type.STRING, false, Item.EXTRACT);
+
+  /**
+    The "ScanDate" annotation, used for derived bioassays (Scan). It is
+    a timestamp annotation.
+    @since 4.34
+  */
+  public static final Annotationtype SCAN_DATE = 
+    new Annotationtype("ScanDate", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY);
+  
+  /**
     The "ClusterStart" annotation, used for physical bioassays (FlowCell).
     The date the flow cell was clustered.

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

@@ -64 +64 @@
   public static final Pipeline RNASEQ_HISAT_VARIANTCALL = new Pipeline("RNASEQ_HISAT_VARIANTCALL", "RNAseq/Hisat/VariantCall");
   
+  /**
+    Pipeline for genotyping from blood DNA.
+    @since 4.34
+  */
+  public static final Pipeline DNA_GENOTYPING = new Pipeline("DNA_GENOTYPING", "DNA/Genotyping");
   
   /**

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

@@ -251 +251 @@
   public static final Subtype FLOW_CELL = new Subtype("FlowCell", "FlowCell", null, null, Item.PHYSICALBIOASSAY, false);
   
+  /**
+    The definition of the "BeadChip" physical bioassay subtype.
+    @since 4.34
+  */
+  public static final Subtype BEAD_CHIP = new Subtype("BeadChip", "BeadChip", null, null, Item.PHYSICALBIOASSAY, false);
+  
+  /**
+    The definition of the "Scan" derived bioassay subtype.
+    @since 4.34
+  */
+  public static final Subtype SCAN = new Subtype("Scan", "Scan", null, null, Item.DERIVEDBIOASSAY, false);
   
   /**

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

@@ -310 +310 @@
         jsonChecks.add(checkSubtype(dc, Subtype.CLUSTER_GENERATOR, null, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.FLOW_CELL, null, createIfMissing, Subtype.POOLED_LIBRARY_ALIQUOT, Subtype.CLUSTER_GENERATOR, Subtype.CLUSTER_PROTOCOL)); 
+        jsonChecks.add(checkSubtype(dc, Subtype.BEAD_CHIP, null, createIfMissing, Subtype.BLOOD_DNA)); 
+        jsonChecks.add(checkSubtype(dc, Subtype.SCAN, null, createIfMissing, Subtype.BEAD_CHIP)); 
         jsonChecks.add(checkSubtype(dc, Subtype.BIOANALYZER_PDF, null, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.CALIPER_PDF, null, createIfMissing));
@@ -516 +518 @@
             new ValueOptions(Pipeline.RNA_SEQ.getName(), Pipeline.MIPS.getName(), 
               Pipeline.RNASEQ_LEGACY.getName(), Pipeline.RNASEQ_HISAT_STRINGTIE.getName(),
-              Pipeline.RNASEQ_HISAT_VARIANTCALL.getName()), 
+              Pipeline.RNASEQ_HISAT_VARIANTCALL.getName(), Pipeline.DNA_GENOTYPING.getName()), 
             createIfMissing, effectivePermissionsUse));
         
@@ -611 +613 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.FAILED_LANES, 0, null, createIfMissing, effectivePermissionsUse));
 
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_ID, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_TYPE, 1, 
+            new ValueOptions("OncoArray500K"),
+            createIfMissing, effectivePermissionsUse));
+        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.SEQUENCING_START, 1, null, createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_TURN_AROUND, 1, null, createIfMissing, effectivePermissionsUse));
@@ -846 +855 @@
 
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BLOOD_DNA, createIfMissing, 
-            Annotationtype.ND_CONC, Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT));
+            Annotationtype.ND_CONC, Annotationtype.BEADCHIP_POSITION,
+            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT));
 
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SPECIMEN, createIfMissing, 
@@ -1036 +1046 @@
             Annotationtype.PIPELINE,
             Annotationtype.PLATE_PROCESS_RESULT, Annotationtype.SEQUENCING_RESULT));
+        
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BEAD_CHIP, createIfMissing, 
+            Annotationtype.BEADCHIP_ID, Annotationtype.BEADCHIP_TYPE,
+            Annotationtype.PLATE_PROCESS_RESULT, Annotationtype.PIPELINE
+          ));
+        
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SCAN, createIfMissing, 
+            Annotationtype.DATA_FILES_FOLDER, Annotationtype.SCAN_DATE,
+            Annotationtype.ANALYSIS_RESULT,
+            Annotationtype.PIPELINE
+          ));
         
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCING_RUN, createIfMissing,