Changeset 4891

Timestamp:

Apr 7, 2009, 9:48:59 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1291: Batch importing same labeled extract in more than one array on a multi-array slide only keeps the last entry in file

There is now an option to detect this and report an error.

Location:

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport

Files:

• AbstractItemImporter.java (modified) (3 diffs)
• HybridizationImporter.java (modified) (9 diffs)

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java

@@ -354 +354 @@
         
         // Everything is ok, save values
-        /*
-        if (forJob) 
-        {
-          storeValue(wrapper, request, fileParameter);
-          storeValue(wrapper, request, ri.getParameter("mode"));
-        }
-        storeValue(wrapper, request, dataHeaderRegexpParameter);
-        storeValue(wrapper, request, dataSplitterRegexpParameter);
-        storeValue(wrapper, request, trimQuotesParameter);
-        storeValue(wrapper, request, ignoreRegexpParameter);
-        storeValue(wrapper, request, dataFooterRegexpParameter);
-        storeValue(wrapper, request, minDataColumnsParameter);
-        storeValue(wrapper, request, maxDataColumnsParameter);
-        storeValue(wrapper, request, ri.getParameter(Parameters.CHARSET_PARAMETER));
-        storeValue(wrapper, request, ri.getParameter(Parameters.DECIMAL_SEPARATOR_PARAMETER));
-        storeValue(wrapper, request, ri.getParameter(Parameters.DATE_FORMAT_PARAMETER));
-        
-        // Identification method
-        storeValue(wrapper, request, ri.getParameter("idMethod"));
-        if (forJob)
-        {
-          storeValue(wrapper, request, ri.getParameter("includeMine"));
-          storeValue(wrapper, request, ri.getParameter("includeSharedTo"));
-          storeValue(wrapper, request, ri.getParameter("includeInProject"));
-          storeValue(wrapper, request, ri.getParameter("includeOthers"));
-        }
-        
-        // Column mappings
-        storeValue(wrapper, request, complexMappings);
-        */
         for (PluginParameter pp : ri.getParameters())
         {
-//          if (pp.getName().contains("ColumnMapping"))
           if (pp.getParameterType() != null)
           {
@@ -392 +361 @@
           }
         }
-//        storeValue(wrapper, request, ri.getParameter("dataDirectory"));
         if (forJob)
         {
@@ -413 +381 @@
       
         // Error handling
-        storeValue(job, request, ri.getParameter(Parameters.LOGFILE_PARAMETER));
         response.setDryRun(Boolean.TRUE.equals(request.getParameterValue(Parameters.DRY_RUN_PARAMETER)));
-        storeValue(job, request, defaultErrorParameter);
-        storeValue(job, request, itemNotFoundErrorParameter);
-        storeValue(job, request, itemExistsErrorParameter);
-        storeValue(job, request, multipleItemsFoundErrorParameter);
-        storeValue(job, request, referenceNotFoundErrorParameter);
-        storeValue(job, request, multipleReferencesFoundErrorParameter);
-        storeValue(job, request, ri.getParameter(Parameters.INVALID_USE_OF_NULL_ERROR));
-        storeValue(job, request, stringTooLongErrorParameter);
-        storeValue(job, request, numberFormatErrorParameter);
-        storeValue(job, request, numberOutOfRangeErrorParameter);
-        storeValue(job, request, noWritePermissionToItemErrorParameter);
-        storeValue(job, request, noUsePermissionToReferenceErrorParameter);
-        
+        for (PluginParameter pp : ri.getParameters())
+        {
+          if (pp.getParameterType() != null)
+          {
+            storeValue(job, request, ri.getParameter(pp.getName()));
+          }
+        }
+
         // Save context info
         response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);    

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/HybridizationImporter.java

@@ -22 +22 @@
 package net.sf.basedb.plugins.batchimport;
 
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
@@ -31 +32 @@
 import net.sf.basedb.core.Hardware;
 import net.sf.basedb.core.Hybridization;
+import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemQuery;
@@ -39 +41 @@
 import net.sf.basedb.core.Protocol;
 import net.sf.basedb.core.ProtocolType;
+import net.sf.basedb.core.StringParameterType;
 import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.Version;
@@ -116 +119 @@
     );
   
+  private static final PluginParameter<String> multipleArrayIndexErrorParameter = 
+    new PluginParameter<String>(
+      "multipleArrayIndexError",
+      "Labeled extract on multiple arrays",
+      "What to do if trying to assign a labeled extract to more than one array " +
+      "on a multi-array hybridization\n\n"+
+      "ignore = Update the array index overriding previous settings\n" +
+      "fail = Stop with an error message",
+      new StringParameterType(255, "fail", false, 1, 0, 0, 
+        Arrays.asList( new String[] { "ignore", "fail"} ))
+    );
+
+  
   public HybridizationImporter()
   {}
@@ -156 +172 @@
   private Mapper arrayIndexMapper;
   private Mapper arraySlideMapper;
+  private boolean failIfMultipleArrayIndex;
   
   /**
@@ -194 +211 @@
   }
   
+  @Override
+  protected void addMoreErrorParameters(List<PluginParameter<?>> parameters)
+  {
+    parameters.add(multipleArrayIndexErrorParameter);
+  }
+  
   /**
     Calls {@link Hybridization#getQuery()}.
@@ -218 +241 @@
     arrayIndexMapper = getMapper(ffp, (String)job.getValue("arrayIndexColumnMapping"), null, null);
     arraySlideMapper = getMapper(ffp, (String)job.getValue("arraySlideColumnMapping"), null, null);
+    this.failIfMultipleArrayIndex = "fail".equals(getErrorOption("multipleArrayIndexError"));
   }
   
@@ -294 +318 @@
       {
         BioMaterialEvent creationEvent = hyb.getCreationEvent();
+        int currentIndex = creationEvent.getSourceGroup(parent);
         Float usedQuantity = usedQuantityMapper == null ?
             null : usedQuantityMapper.getFloat(data);
@@ -300 +325 @@
         {
           Integer arrayIndex = arrayIndexMapper.getInt(data);
-          if (arrayIndex != null) creationEvent.setSourceGroup(parent, arrayIndex);
+          if (arrayIndex != null) 
+          {
+            if (currentIndex != 0 && arrayIndex != currentIndex && failIfMultipleArrayIndex)
+            {
+              throw new InvalidDataException("Labeled extract '" + parent.getName() + 
+                  "' is already associated with array index " + currentIndex + 
+                  " on hybridization '" + hyb.getName() + "'. It is not possible to " +
+                  "also associate it with array index " + arrayIndex);
+            }
+            creationEvent.setSourceGroup(parent, arrayIndex);
+          }
         }
       }