Changeset 5798

Timestamp:

Dec 18, 2019, 11:34:55 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1209: Add support for storing TMA specimen

Added SampleOwner annotation and added this to the TMASpecimenImporter as a job parameter. All TMA samples in a given import will get the same value.

Location:

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

Files:

• dao/Annotationtype.java (modified) (1 diff)
• plugins/TMASpecimenImporter.java (modified) (6 diffs)
• servlet/InstallServlet.java (modified) (2 diffs)

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

@@ -429 +429 @@
   public static final Annotationtype TMA_BLOCK_POS = 
     new Annotationtype("TMABlockPos", Type.STRING, false, Item.SAMPLE);
+  
+  /**
+    Annotation to be used on samples/extracts that are
+    "owned" by an external partner. First use case is
+    TMA specimen, but could be used for other external
+    items as well.
+    @since 4.25
+  */
+  public static final Annotationtype SAMPLE_OWNER =
+    new Annotationtype("SampleOwner", Type.STRING, false, Item.SAMPLE, Item.EXTRACT);
   
   /**

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

@@ -237 +237 @@
         storeValue(wrapper, request, ri.getParameter(Parameters.LOGFILE_PARAMETER));
         storeValue(wrapper, request, excelSheetParameter);
+        storeValue(wrapper, request, ri.getParameter("sampleOwner"));
         storeValue(wrapper, request, ri.getParameter("idMethod"));
 
@@ -283 +284 @@
   private Mapper commentMapper;
   private String lastTMA_XId;
+  private String sampleOwner;
   
   private boolean dryRun; 
@@ -294 +296 @@
     this.dryRun = job.getJob().isDryRun();
     this.idMethod = getIdMethod(job.getValue("idMethod"));
+    this.sampleOwner = job.getValue("sampleOwner");
     this.caseQuery = Sample.getQuery();
     Subtype.CASE.addFilter(dc, caseQuery);
@@ -355 +358 @@
     Annotationtype.TMA_BLOCK_POS.setAnnotationValue(dc, tmaSpecimen, tmaBlockPosMapper.getString(data));
     Annotationtype.PAD.setAnnotationValue(dc, tmaSpecimen, padMapper.getString(data));
+    Annotationtype.SAMPLE_OWNER.setAnnotationValue(dc, tmaSpecimen, sampleOwner);
     
     numCreated++;
@@ -410 +414 @@
         parameters.add(Parameters.logFileParameter(null, null, null));
         parameters.add(Parameters.dryRunParameter(null, null, null));
+        
+        parameters.add(new PluginParameter<>("sampleOwner", "Sample owner", 
+          "Name of PI or other external entity that is the owner of TMA samples.", 
+          new StringParameterType(255, null, true)));
         
         Enumeration<String, String> idMethods = new Enumeration<String, String>();
@@ -420 +428 @@
           "The method to use for finding existing cases. The plug-in can use either the " +
           "SCAN-B ID or the Release ID.",
-          new StringParameterType(null, null, true, 1, 0, 0, idMethods)
+          new StringParameterType(255, null, true, 1, 0, 0, idMethods)
         );
         parameters.add(idMethodParameter);

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

@@ -442 +442 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.TMA_BLOCK, 1, null, createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.TMA_BLOCK_POS, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SAMPLE_OWNER, 1, null, createIfMissing, effectivePermissionsUse));
 
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.RLT_PLUS, 1, null, createIfMissing, effectivePermissionsUse));
@@ -784 +785 @@
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.TMA_SPECIMEN, createIfMissing, 
             Annotationtype.TMA_BLOCK, Annotationtype.TMA_BLOCK_POS,
-            Annotationtype.PAD
+            Annotationtype.PAD, Annotationtype.SAMPLE_OWNER
             ));