Changeset 4977

Timestamp:

Sep 24, 2018, 9:37:40 AM (5 years ago)

Author:

Nicklas Nordborg

Message:

References #1054: Even more functionality in the Flagged alignment wizard

Messages are registration now reports number of specimen, lysates, rna and libraries instead of total number. Also fixed so that messages are correct for "one" and "multiple" items.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/GenotypeServlet.java (modified) (7 diffs)

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

@@ -429 +429 @@
         if (numChecked > 0)
         {
-          jsonMessages.add(0, numChecked + " alignments have been checked and will be used for future genotype QC comparisons.");
+          jsonMessages.add(0, countMessage(numChecked, "alignment has", "alignments have") + " been checked and will be used for future genotype QC comparisons.");
         }
         dc.commit();
@@ -478 +478 @@
           }
         }
-        if (numReProcess > 0) jsonMessages.add(numReProcess + " items has been scheduled for re-processing");
-        if (numFlagged > 0) jsonMessages.add(numFlagged + " alignments have been flagged");
-        if (numComments > 0) jsonMessages.add(numComments + " comments have been updated");
+        if (numReProcess > 0) jsonMessages.add(countMessage(numReProcess, "item has", "items have") + " been scheduled for re-processing");
+        if (numFlagged > 0) jsonMessages.add(countMessage(numFlagged, "alignment has", "alignments have") + " been flagged");
+        if (numComments > 0) jsonMessages.add(countMessage(numComments, "comment has", "comments have") + " been updated");
         dc.commit();
         
@@ -500 +500 @@
         ItemSubtype mergedType = Subtype.MERGED_SEQUENCES.get(dc);
         ItemSubtype alignedType = Subtype.ALIGNED_SEQUENCES.get(dc);
+        ItemSubtype specimenType = Subtype.SPECIMEN.get(dc);
+        ItemSubtype lysateType = Subtype.LYSATE.get(dc);
+        ItemSubtype rnaType = Subtype.RNA.get(dc);
+        ItemSubtype libraryType = Subtype.LIBRARY.get(dc);
         ItemList flaggedAlignments = BiomaterialList.FLAGGED_ALIGNMENT.get(dc);
         
@@ -506 +510 @@
         checker.preloadSpecimenData(dc);
 
+        // Items marked with DoNotUse - total and per item type
         int numRootDoNotUse = 0;
+        int numSpecimen = 0;
+        int numLysate = 0;
+        int numRna = 0;
+        int numLibrary = 0;
+        
         int numTotalDoNotUse = 0;
         int numUnflagged = 0;
@@ -562 +572 @@
               jsonDebug.add("[Debug]Do not use: " + basicItem + " ["+doNotUse+"]");
               numTotalDoNotUse++;
-              if (basicItem == rootItem) numRootDoNotUse++;
+              if (basicItem == rootItem) 
+              {
+                numRootDoNotUse++;
+                if (specimenType.equals(subtype)) numSpecimen++;
+                else if (lysateType.equals(subtype)) numLysate++;
+                else if (rnaType.equals(subtype)) numRna++;
+                else if (libraryType.equals(subtype)) numLibrary++;
+              }
             }
             
@@ -639 +656 @@
         if (numRootDoNotUse > 0)
         {
-          jsonMessages.add(numRootDoNotUse + " main items and " + (numTotalDoNotUse-numRootDoNotUse) + " related items marked as DoNotUse.");
+          StringBuilder msg = new StringBuilder();
+          if (numSpecimen > 0)
+          {
+            msg.append(countMessage(numSpecimen, "specimen", "specimens"));
+          }
+          if (numLysate > 0)
+          {
+            if (msg.length() > 0) msg.append(", ");
+            msg.append(countMessage(numLysate, "lysate", "lysates"));
+          }
+          if (numRna > 0)
+          {
+            if (msg.length() > 0) msg.append(", ");
+            msg.append(countMessage(numRna, "RNA", "RNA"));
+          }
+          if (numLibrary > 0)
+          {
+            if (msg.length() > 0) msg.append(", ");
+            msg.append(countMessage(numLibrary, "library", "libraries"));
+          }
+          jsonMessages.add(msg + " and " + countMessage(numTotalDoNotUse-numRootDoNotUse, "related item", "related items") + " marked as DoNotUse.");
         }
         
         if (numDisabled > 0)
         {
-          jsonMessages.add(numDisabled + " alignments have been disabled for future genotype checks.");
+          jsonMessages.add(countMessage(numDisabled, "alignment has", "alignments have") + " been disabled for future genotype checks.");
         }
 
         if (numOkToUse > 0)
         {
-          jsonMessages.add(numOkToUse + " alignments are ok to use.");
+          jsonMessages.add(countMessage(numOkToUse, "alignment is", "alignments are") + " ok to use.");
         }
         
         if (numAutoUnflagged > 0)
         {
-          jsonMessages.add(numAutoUnflagged + " related alignments have been automatically unflagged.");
+          jsonMessages.add(countMessage(numAutoUnflagged, "related alignment has", "related alignments have") + " been automatically unflagged.");
         }
         
@@ -958 +995 @@
   }
 
+  private String countMessage(int count, String one, String more)
+  {
+    return count + " " + (count > 1 ? more : one);
+  }
+  
 }