Changeset 8027

Timestamp:

Jan 13, 2022, 7:45:03 AM (7 months ago)

Author:

Nicklas Nordborg

Message:

Fixes #2276: The raw bioassay batch importer should be able to set the "file spots" value

File:

• branches/3.19-stable/src/plugins/core/net/sf/basedb/plugins/batchimport/RawBioAssayImporter.java (modified) (5 diffs)

branches/3.19-stable/src/plugins/core/net/sf/basedb/plugins/batchimport/RawBioAssayImporter.java

@@ -162 +162 @@
     );
 
-  
+  protected static final PluginParameter<String> fileSpotsMapping = 
+    new PluginParameter<String>(
+        "fileSpotsMapping",
+        "File spots",
+        "Mapping that picks the number of spots of the bioassay that are stored in files. The " +
+        "values must be in the numeric format specified by the 'Number format' parameter." +
+        "Example: \\Spots\\",
+        optionalColumnMapping
+    );
+
   public RawBioAssayImporter()
   {}
@@ -198 +207 @@
   private Mapper fileTypeMapper;
   private Mapper fileMapper;
+  private Mapper fileSpotsMapper;
   private String dataDirectory;
   
@@ -264 +274 @@
     parameters.add(fileTypeColumnMapping);
     parameters.add(fileColumnMapping);
+    parameters.add(fileSpotsMapping);
     parameters.add(permissionTemplateColumnMapping);
   }
@@ -297 +308 @@
     fileTypeMapper = getMapper(ffp, (String)job.getValue("fileTypeColumnMapping"), null, null);
     fileMapper = getMapper(ffp, (String)job.getValue("fileColumnMapping"), null, null);
+    fileSpotsMapper = getMapper(ffp, (String)job.getValue("fileSpotsMapping"), null, null);
     dataDirectory = (String)job.getValue("dataDirectory");
     if (dataDirectory != null && !dataDirectory.endsWith("/"))
@@ -390 +402 @@
       rba.setParentExtract(extractFromBioAssay);
     }
-    
+    if (fileSpotsMapper != null) rba.setNumFileSpots(fileSpotsMapper.getInt(data));
     if (!rba.hasData())
     {