Changeset 5755

Timestamp:

Nov 25, 2019, 9:40:49 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1202: Add check for duplicate barcode template in the MIPs library registration

Other MIPs plates that has not yet been pooled are now loaded in the MIPs library registration so that a warning message can be displayed if the same barcode template is selected more than once. It is still possible to register but it requires the extra "checkbox verification" step.

Location:

extensions/net.sf.basedb.reggie/branches/4.24-stable

Files:

• resources/mipsprep/lib_registration.js (modified) (3 diffs)
• src/net/sf/basedb/reggie/query/AnyToAnyRestriction.java (modified) (5 diffs)
• src/net/sf/basedb/reggie/servlet/MipsServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/branches/4.24-stable/resources/mipsprep/lib_registration.js

@@ -137 +137 @@
       var tmp = templates[i];
       var option = new Option(tmp.name, tmp.id);
+      option.template = tmp;
       frm.barcodeTemplate[frm.barcodeTemplate.length] = option;
     }
@@ -147 +148 @@
     
     Wizard.setInputStatus('barcodeTemplate');
+    Wizard.hideGoNextConfirmation();
     barcodeTemplateIsValid = false;
     
@@ -164 +166 @@
     
     barcodeTemplateIsValid = true;
-    Wizard.setInputStatus('barcodeTemplate', 'valid');
+
+    var template = frm.barcodeTemplate[frm.barcodeTemplate.selectedIndex].template;
+    if (template.otherPlates && template.otherPlates.length > 0)
+    {
+      var msg = 'This template is also used by ' + Strings.encodeTags(template.otherPlates[0].name);
+      if (template.otherPlates.length > 1)
+      {
+        msg += ' and '+(template.otherPlates.length-1)+' more plate(s)';
+      }
+      Wizard.setInputStatus('barcodeTemplate', 'warning', msg);
+      Wizard.showGoNextConfirmation(true, 'Verify registration of plate with duplicate barcode template');
+    }
+    else
+    {
+      Wizard.setInputStatus('barcodeTemplate', 'valid');
+    }
   }
   

extensions/net.sf.basedb.reggie/branches/4.24-stable/src/net/sf/basedb/reggie/query/AnyToAnyRestriction.java

@@ -2 +2 @@
 
 import java.util.Collection;
+import java.util.Collections;
 
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.Type;
+import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Query;
 import net.sf.basedb.core.query.QueryElement;
 import net.sf.basedb.core.query.Restriction;
+import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.util.EqualsHelper;
 
@@ -29 +33 @@
   public static AnyToAnyRestriction exists(String linkName, Item linkedTo)
   {
-    return new AnyToAnyRestriction(linkName, linkedTo, true);
+    Restriction link = linkedTo == null ? null :
+      Restrictions.eq(Hql.property("at", "toType"), Expressions.integer(linkedTo.getValue()));
+    return new AnyToAnyRestriction(linkName, link, true);
   }
+
+  /**
+    Create a restriction that restrict a query to return
+    items that has a linked item with the given link name.
+    An optional restriction can be used to limit the query
+    to on the linked item (use "at" as prefix in the HQL).
+    @since 4.24.1
+  */
+  public static AnyToAnyRestriction exists(String linkName, Restriction restriction)
+  {
+    return new AnyToAnyRestriction(linkName, restriction, true);
+  }
+
   
   /**
@@ -39 +58 @@
   public static AnyToAnyRestriction missing(String linkName, Item linkedTo)
   {
-    return new AnyToAnyRestriction(linkName, linkedTo, false);
+    Restriction link = linkedTo == null ? null :
+        Restrictions.eq(Hql.property("at", "toType"), Expressions.integer(linkedTo.getValue()));
+    return new AnyToAnyRestriction(linkName, link, false);
   }
   
   private final String parameterName;
-  private final String subQuery;
+  private final Restriction linkRestriction;
   private final String linkName;
   private final boolean hasLink;
   
-  private AnyToAnyRestriction(String linkName, Item linkedTo, boolean hasLink) 
+  private AnyToAnyRestriction(String linkName, Restriction linkRestriction, boolean hasLink) 
   {
     this.linkName = linkName;
     this.hasLink = hasLink;
     this.parameterName = "LN" + System.identityHashCode(this);
-    StringBuilder sb = new StringBuilder();
-    sb.append("(SELECT at.fromId FROM AnyToAnyData at WHERE at.name = :");
-    sb.append(parameterName);
-    if (linkedTo != null)
-    {
-      sb.append(" AND at.toType=").append(linkedTo.getValue());
-    }
-    sb.append(")");
-    this.subQuery = sb.toString();
+    this.linkRestriction = linkRestriction;
   }
   
@@ -67 +80 @@
   {
     query.setParameter(parameterName, linkName, Type.STRING);
-    return query.getRootAlias() + (hasLink ? ".id = ANY" : ".id <> ALL") + subQuery;
+    return query.getRootAlias() + (hasLink ? ".id = ANY" : ".id <> ALL") + getSubQuery(query, dc);
   }
 
@@ -73 +86 @@
   public Collection<? extends QueryElement> getChildren()
   {
-    return null;
+    return linkRestriction != null ? Collections.singleton(linkRestriction) : null;
   }
 
+  private String getSubQuery(Query query, DbControl dc)
+  {
+    StringBuilder sb = new StringBuilder();
+    sb.append("(SELECT at.fromId FROM AnyToAnyData at WHERE at.name = :");
+    sb.append(parameterName);
+    if (linkRestriction != null)
+    {
+      if (query == null)
+      {
+        sb.append(" AND ").append(linkRestriction.toString());
+      }
+      else
+      {
+        sb.append(" AND ").append(linkRestriction.toQl(query, dc));
+      }
+    }
+    sb.append(")");
+    return sb.toString();
+  }
   
   @Override
   public String toString()
   {
-    return (hasLink ? "id = ANY" : "id <> ALL") + subQuery;
+    return (hasLink ? "id = ANY" : "id <> ALL") + getSubQuery(null, null);
   }
   

extensions/net.sf.basedb.reggie/branches/4.24-stable/src/net/sf/basedb/reggie/servlet/MipsServlet.java

@@ -65 +65 @@
 import net.sf.basedb.reggie.plugins.AliquotImporter;
 import net.sf.basedb.reggie.plugins.AliquotImporter.AliquotPlate;
+import net.sf.basedb.reggie.query.AnyToAnyRestriction;
 import net.sf.basedb.util.EqualsHelper;
 import net.sf.basedb.util.FileUtil;
@@ -348 +349 @@
         query.order(Orders.asc(Hql.property("name")));
         
+        // Find other MIPs plates with a given template that has not yet been pooled
+        // We use this information to display a warning if registering more than one plate with
+        // the same barcode template since that is typically a mistake
+        ItemQuery<BioPlate> unpooledQuery = BioPlate.getQuery();
+        unpooledQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        // Only MIPs plates that are not destroyed
+        BioplateType.MIPS.addFilter(dc, unpooledQuery, true);
+        // Must have a PLATE_PROCESS_RESULT=Success annotation
+        unpooledQuery.join(Annotations.innerJoin(null, Annotationtype.PLATE_PROCESS_RESULT.load(dc), "ppr"));
+        unpooledQuery.restrict(Restrictions.eq(Hql.alias("ppr"), Expressions.string(ReactionPlate.PROCESS_SUCCESSFUL)));
+        // Must NOT have a PoolDate annotation
+        unpooledQuery.join(Annotations.leftJoin(null, Annotationtype.POOL_DATE.load(dc), "pd"));
+        unpooledQuery.restrict(Restrictions.eq(Hql.alias("pd"), null));
+        // Filter on BarcodeTemplate link
+        unpooledQuery.restrict(AnyToAnyRestriction.exists("BarcodeTemplate", 
+          Restrictions.eq(Hql.property("at", "toId"), Hql.entityParameter("template", Item.BIOPLATE))));
+        unpooledQuery.order(Orders.asc(Hql.property("name")));
+        
         List<BioPlate> result = query.list(dc);
         JSONArray jsonPlates = new JSONArray();
@@ -359 +378 @@
           jsonPlate.put("comments", plate.getDescription());
           jsonPlates.add(jsonPlate);
+          
+          JSONArray jsonUnpooled = new JSONArray();
+          unpooledQuery.setEntityParameter("template", plate);
+          for (BioPlate unpooled : unpooledQuery.list(dc))
+          {
+            JSONObject jsonUP = new JSONObject();
+            jsonUP.put("id", unpooled.getId());
+            jsonUP.put("name", unpooled.getName());
+            jsonUnpooled.add(jsonUP);
+          }
+          jsonPlate.put("otherPlates", jsonUnpooled);
+          
         }
         json.put("templates", jsonPlates);