Changeset 6475

Timestamp:

Nov 5, 2021, 9:20:14 AM (15 months ago)

Author:

Nicklas Nordborg

Message:

References #1346: Implement support for OncoArray? SNP data

Added GenotypeCall derived bioassay type and related file and software type.

Location:

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

Files:

• dao/Datafiletype.java (modified) (1 diff)
• dao/Mimetype.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/Datafiletype.java

@@ -89 +89 @@
 
   /**
+    Genotype call file.
+    @since 4.34
+  */
+  public static final Datafiletype GTC = 
+    new Datafiletype("GTC", "net.sf.basedb.reggie.gtc", 
+      Item.DERIVEDBIOASSAY, "gtc", Subtype.GENOTYPE_CALL_FILE,
+      true, true,
+      "Genotype call file");
+
+  /**
     Get the file type by name of the static constant defined in this class.
     

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

@@ -38 +38 @@
     new Mimetype("text/plain", "vcf", "Variant call format", Subtype.VARIANT_CALL_FORMAT);
   
-    
+  /**
+    The definition of the "GTC" type.
+    @since 4.34
+  */
+  public static final Mimetype GTC = 
+    new Mimetype("application/octet-stream", "gtc", "Genotype call", Subtype.GENOTYPE_CALL_FILE);
+  
   /**
     Get the MIME type by name of the static constant defined in this class.

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

@@ -262 +262 @@
   */
   public static final Subtype SCAN = new Subtype("Scan", "Scan", null, null, Item.DERIVEDBIOASSAY, false);
-  
+
+  /**
+    The definition of the "GenotypeCall" derived bioassay subtype.
+    @since 4.34
+  */
+  public static final Subtype GENOTYPE_CALL = new Subtype("GenotypeCall", "GenotypeCall", null, null, Item.DERIVEDBIOASSAY, false);
+
+  /**
+    The definition of the "Genotyping" software subtype.
+    @since 4.34
+  */
+  public static final Subtype GENOTYPING_SOFTWARE = new Subtype("Genotyping", null, null, null, Item.SOFTWARE, false);
+
+  /**
+    File subtype for genotype call files.
+    @since 4.34
+  */
+  public static final Subtype GENOTYPE_CALL_FILE = new Subtype("Genotype call", null, null, null, Item.FILE, false);
+
   /**
     The definition of the "SequencingRun" derived bioassay subtype.

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

@@ -259 +259 @@
         JSONObject jsonSubtype_SEQUENCE_DATA = checkSubtype(dc, Subtype.SEQUENCE_DATA, null, createIfMissing);
         JSONObject jsonSubtype_ALIGNED_SEQUENCE_DATA = checkSubtype(dc, Subtype.ALIGNED_SEQUENCE_DATA, null, createIfMissing);
+        JSONObject jsonSubtype_GENOTYPE_CALL_FILE = checkSubtype(dc, Subtype.GENOTYPE_CALL_FILE, null, createIfMissing);
 
         // Data file types
@@ -265 +266 @@
         jsonChecks.add(checkDataFileType(dc, Datafiletype.FPKM, createIfMissing));
         jsonChecks.add(checkDataFileType(dc, Datafiletype.VCF, createIfMissing));
+        jsonChecks.add(checkDataFileType(dc, Datafiletype.GTC, createIfMissing));
         
         // Platforms
@@ -311 +313 @@
         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.SCAN, null, createIfMissing, Subtype.BEAD_CHIP));
+        jsonChecks.add(checkSubtype(dc, Subtype.GENOTYPING_SOFTWARE, null, createIfMissing));
+        jsonChecks.add(jsonSubtype_GENOTYPE_CALL_FILE);
+        jsonChecks.add(checkSubtype(dc, Subtype.GENOTYPE_CALL, Datafiletype.GTC, createIfMissing, Subtype.SCAN, Subtype.GENOTYPING_SOFTWARE)); 
         jsonChecks.add(checkSubtype(dc, Subtype.BIOANALYZER_PDF, null, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.CALIPER_PDF, null, createIfMissing));
@@ -1059 +1064 @@
             Annotationtype.PIPELINE
           ));
+
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.GENOTYPE_CALL, createIfMissing, 
+            Annotationtype.DATA_FILES_FOLDER, 
+            Annotationtype.ANALYSIS_RESULT,
+            Annotationtype.PIPELINE
+          ));
         
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCING_RUN, createIfMissing, 
@@ -1280 +1291 @@
         jsonChecks.add(checkMimeType(dc, Mimetype.GDX, createIfMissing));
         jsonChecks.add(checkMimeType(dc, Mimetype.VCF, createIfMissing));
+        jsonChecks.add(checkMimeType(dc, Mimetype.GTC, createIfMissing));
         
         // Special items