Changeset 5778

Timestamp:

Dec 9, 2019, 9:37:42 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1209: Add support for storing TMA specimen

Implemented support for importing annotations TMABlock, TMABlockPos and PAD.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/TMASpecimenImporter.java (modified) (8 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/TMASpecimenImporter.java

@@ -35 +35 @@
 import net.sf.basedb.plugins.util.Parameters;
 import net.sf.basedb.reggie.Reggie;
+import net.sf.basedb.reggie.dao.Annotationtype;
 import net.sf.basedb.reggie.dao.Case;
 import net.sf.basedb.reggie.dao.ReggieItem;
@@ -70 +71 @@
       );
 
-  
+  private static final PluginParameter<String> tmaBlockColumnMapping = new PluginParameter<String>(
+      "tmaBlockColumnMapping",
+      "TMA Block",
+      "Mapping that picks the name of the TMA Block on which the specimen is located. This " +
+      "parameter is required. " +
+      "Example: \\TMABlock\\",
+      requiredColumnMapping
+      );
+  
+  private static final PluginParameter<String> tmaBlockPosColumnMapping = new PluginParameter<String>(
+      "tmaBlockPosColumnMapping",
+      "TMA Block Position",
+      "Mapping that picks the position on the TMA block were the specimen is located. This " +
+      "parameter is required. " +
+      "Example: \\TMABlockPos\\",
+      requiredColumnMapping
+      );
+  
+  private static final PluginParameter<String> padColumnMapping = new PluginParameter<String>(
+      "padColumnMapping",
+      "PAD",
+      "Mapping that picks the PAD id that was used to create the TMA. This " +
+      "parameter is required. " +
+      "Example: \\PAD\\",
+      requiredColumnMapping
+      );
+
   public TMASpecimenImporter()
   {}
@@ -183 +210 @@
         storeValue(wrapper, request, complexMappings);
         storeValue(wrapper, request, caseColumnMapping);
+        storeValue(wrapper, request, tmaBlockColumnMapping);
+        storeValue(wrapper, request, tmaBlockPosColumnMapping);
+        storeValue(wrapper, request, padColumnMapping);
         
         response.setDryRun(Boolean.TRUE.equals(request.getParameterValue(Parameters.DRY_RUN_PARAMETER)));
@@ -205 +235 @@
   private ItemQuery<Sample> caseQuery;
   private Mapper caseMapper;
+  private Mapper tmaBlockMapper;
+  private Mapper tmaBlockPosMapper;
+  private Mapper padMapper;
   private String lastTMA_XId;
   
@@ -230 +263 @@
   {
     caseMapper = getMapper(ffp, job.getValue("caseColumnMapping"), null, null);
+    tmaBlockMapper = getMapper(ffp, job.getValue("tmaBlockColumnMapping"), null, null);
+    tmaBlockPosMapper = getMapper(ffp, job.getValue("tmaBlockPosColumnMapping"), null, null);
+    padMapper = getMapper(ffp, job.getValue("padColumnMapping"), null, null);
     numCreated = 0;
   }
@@ -249 +285 @@
     }
 
-    Case theCase = Case.get(cases.get(0));
-    String tmaName = theCase.getNextTMASpecimenName(dc);
+    Sample theCase = cases.get(0);
+    Case c = Case.get(theCase);
+    String tmaName = c.getNextTMASpecimenName(dc);
     if (lastTMA_XId == null)
     {
@@ -266 +303 @@
     tmaSpecimen.setName(tmaName);
     tmaSpecimen.setExternalId(lastTMA_XId);
-    tmaSpecimen.getCreationEvent().setSource(theCase.getItem());
+    tmaSpecimen.getCreationEvent().setSource(theCase);
     dc.saveItem(tmaSpecimen);
+    
+    Annotationtype.TMA_BLOCK.setAnnotationValue(dc, tmaSpecimen, tmaBlockMapper.getString(data));
+    Annotationtype.TMA_BLOCK_POS.setAnnotationValue(dc, tmaSpecimen, tmaBlockPosMapper.getString(data));
+    Annotationtype.PAD.setAnnotationValue(dc, tmaSpecimen, padMapper.getString(data));
     
     numCreated++;
@@ -339 +380 @@
         parameters.add(complexMappings);
         parameters.add(caseColumnMapping);
+        parameters.add(tmaBlockColumnMapping);
+        parameters.add(tmaBlockPosColumnMapping);
+        parameters.add(padColumnMapping);
         
         configureParser = new RequestInformation