Changeset 7861

Timestamp:

Oct 21, 2020, 7:39:15 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #2224: Files should be annotatable

Adding file loading from protocol nodes and validation to the "Item overview".

Location:

trunk/src/core/net/sf/basedb/util/overview

Files:

• OverviewUtil.java (modified) (2 diffs)
• Validator.java (modified) (2 diffs)
• loader/BasicItemNodeLoaderFactory.java (modified) (1 diff)
• loader/FileLoader.java (added)
• loader/ProtocolLoader.java (modified) (1 diff)
• validator/BasicItemNodeValidatorFactory.java (modified) (1 diff)
• validator/FileValidator.java (added)

trunk/src/core/net/sf/basedb/util/overview/OverviewUtil.java

@@ -100 +100 @@
             Validator.MISSING_DERIVEDBIOASSAY, Validator.MISSING_ARRAYDESIGN, Validator.MISSING_PROTOCOL, 
             Validator.MISSING_HARDWARE, Validator.MISSING_SOFTWARE, Validator.MISSING_TAG,
-            Validator.MISSING_KIT,
+            Validator.MISSING_KIT, Validator.MISSING_FILE,
             Validator.MISSING_ARRAYSLIDE, Validator.MISSING_ARRAYBATCH, Validator.MISSING_ANYTOANY
           })
@@ -112 +112 @@
             Validator.INCORRECT_DERIVEDBIOASSAY_TYPE, Validator.INCORRECT_PROTOCOLTYPE,
             Validator.INCORRECT_HARDWARETYPE, Validator.INCORRECT_SOFTWARETYPE,
-            Validator.INCORRECT_TAGTYPE, Validator.INCORRECT_KITTYPE
+            Validator.INCORRECT_TAGTYPE, Validator.INCORRECT_KITTYPE, Validator.INCORRECT_FILETYPE
           })
         );

trunk/src/core/net/sf/basedb/util/overview/Validator.java

@@ -103 +103 @@
   
   /**
+    Validator rule that checks for denied access to (data) files. 
+    Default severity level is WARNING.
+    @since 3.17
+  */
+  public static final Validator MISSING_FILE = new Validator(
+      "missing.file", "Missing file", 
+      "Checks if a file has been specified for items that should have a file",
+      "Missing file", Severity.WARNING
+    );
+
+  
+  /**
     Validator rule that checks for denied access to data file types. 
     Default severity level is WARNING.
@@ -584 +596 @@
     );
 
+  /**
+    Validator rule that checks if the file attached to an item
+    has a correct file type. Default severity level is WARNING.
+    @since 3.17
+  */
+  public static final Validator INCORRECT_FILETYPE = new Validator(
+      "subtype.file", "Incorrect file subtype",
+      "Checks if the file attached to an item has a correct file type.",
+      "Incorrect file subtype", Severity.WARNING
+    );
+  
   /**
     Validator that checks if the parent biosource of a sample

trunk/src/core/net/sf/basedb/util/overview/loader/BasicItemNodeLoaderFactory.java

@@ -247 +247 @@
     registerCheckedNodeLoader(Item.FILESETMEMBER, DataFileLoader.class);
     registerCheckedNodeLoader(Item.ANYTOANY, AnyToAnyLoader.class);
+    registerCheckedNodeLoader(Item.FILE, FileLoader.class);
     
   }

trunk/src/core/net/sf/basedb/util/overview/loader/ProtocolLoader.java

@@ -110 +110 @@
   protected void loadPropertyChildNodes(DbControl dc, OverviewContext context, Node protocolNode)
   {
+    getNodeLoader(context, Item.FILE).createPropertyNode(dc, context, protocolNode);
     getNodeLoader(context, Item.ANNOTATION).createPropertyNode(dc, context, protocolNode);
     getNodeLoader(context, "PROTOCOL.PARAMETER").createPropertyNode(dc, context, protocolNode);

trunk/src/core/net/sf/basedb/util/overview/validator/BasicItemNodeValidatorFactory.java

@@ -219 +219 @@
     registerCheckedNodeValidator(Item.FILESETMEMBER, DataFileValidator.class);
     registerCheckedNodeValidator(Item.ANYTOANY, AnyToAnyValidator.class);
+    registerCheckedNodeValidator(Item.FILE, FileValidator.class);
   }