Changeset 1427 for extensions

Timestamp:

Oct 28, 2011, 2:59:21 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #335: Use item subtypes - step 1

The installation wizard now check and create the following subtypes:

• Patient
• Case
• Specimen
• Histology
• Lysate

Location:

extensions/net.sf.basedb.reggie/branches/2.0-dev

Files:

• resources/install.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/Reggie.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/dao/Subtype.java (added)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (6 diffs)

extensions/net.sf.basedb.reggie/branches/2.0-dev/resources/install.jsp

@@ -85 +85 @@
     }
     lastItemType = check.itemType;
+    var name = check.name;
+    if (check.mainType) name += ' <span class="itemsubtype">[' + check.mainType + ']</span>'; 
     if (check.id)
     {
       html += '<td><div class="link" onclick="itemOnClick(event, \''+check.itemType+'\','+check.id+')"';
-      html += ' title="View this item (use CTRL, ALT or SHIFT to edit)">'+check.name+'</div></td>';
+      html += ' title="View this item (use CTRL, ALT or SHIFT to edit)">'+name+'</div></td>';
     }
     else
     {
-      html += '<td><i>' + check.name + '</i></td>';
+      html += '<td><i>' + name + '</i></td>';
     }
     html += '<td><img src="../../images/'+icon+'"></td><td>';

extensions/net.sf.basedb.reggie/branches/2.0-dev/src/net/sf/basedb/reggie/Reggie.java

@@ -15 +15 @@
 import net.sf.basedb.core.ItemNotFoundException;
 import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.ItemSubtype;
 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.Restrictions;
+import net.sf.basedb.reggie.dao.Subtype;
 
 /**
@@ -177 +179 @@
    */
   public static final String ANNOTATION_PARTITION_DATE = "PartitionDate";
+  
+  
+  /**
+    List all subtypes for the given item type that has the given name.
+    @since 2.0
+  */
+  public static List<ItemSubtype> listSubtypes(DbControl dc, Subtype subtype)
+  {
+    ItemQuery<ItemSubtype> query = ItemSubtype.getQuery(subtype.getMainType());
+    query.restrict(
+      Restrictions.eq(
+        Hql.property("name"), 
+        Expressions.parameter("name", subtype.getName(), Type.STRING)
+      ));
+    query.include(Include.ALL);
+    return query.list(dc);
+  }
+  
+  /**
+    Find a single item subtype with the given name. If exactly one is found it 
+    is returned, otherwise null is returned or an exception is thrown
+    depending on the exceptionIfNotFound parameter.
+  */
+  public static ItemSubtype findSubtype(DbControl dc, Subtype subtype, boolean exceptionIfNotFound)
+  {
+    List<ItemSubtype> result = listSubtypes(dc, subtype);
+    ItemSubtype s = null;
+    if (result.size() == 0)
+    {
+      if (exceptionIfNotFound) throw new ItemNotFoundException("ItemSubtype["+subtype.getName()+"]");
+    }
+    else if (result.size() > 1)
+    {
+      if (exceptionIfNotFound) throw new InvalidDataException("Found > 1 ItemSubtype["+subtype.getName()+"]");
+    }
+    else
+    {
+      s = result.get(0);
+    }
+    return s;
+  }
   
   /**

extensions/net.sf.basedb.reggie/branches/2.0-dev/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -2 +2 @@
 
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -23 +22 @@
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemKey;
+import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.MultiPermissions;
 import net.sf.basedb.core.Permission;
@@ -31 +31 @@
 import net.sf.basedb.core.Type;
 import net.sf.basedb.reggie.Reggie;
+import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.EqualsHelper;
 import net.sf.basedb.util.error.ThrowableUtil;
@@ -92 +93 @@
           sharedToActiveProject.set(Project.getById(dc, projectId), Permission.USE);
         }
+        
+        Map<String, Item> subtypeItems = new HashMap<String, Item>();
+        
+        // Subtype checks
+        jsonChecks.add(checkSubtype(dc, Subtype.PATIENT, createIfMissing));
+        jsonChecks.add(checkSubtype(dc, Subtype.CASE, createIfMissing, Subtype.PATIENT));
+        jsonChecks.add(checkSubtype(dc, Subtype.SPECIMEN,createIfMissing, Subtype.CASE));
+        jsonChecks.add(checkSubtype(dc, Subtype.HISTOLOGY, createIfMissing, Subtype.SPECIMEN));
+        jsonChecks.add(checkSubtype(dc, Subtype.LYSATE, createIfMissing, Subtype.SPECIMEN));
         
         // Annotation type checks 
@@ -146 +156 @@
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_PARTITION_DATE, new Item[]{Item.SAMPLE, Item.EXTRACT}, Type.DATE, 1,
             null, effectiveOptions, createIfMissing));
+        
         
         json.put("checks", jsonChecks);
@@ -430 +441 @@
   }
 
-  
+  /**
+    Create a subtype with the given options. The subtype is created in
+    a separate transaction.
+    @since 2.0
+  */
+  public ItemSubtype createSubtype(SessionControl sc, Subtype def, Subtype... relatedTo)
+  {
+    ItemSubtype subtype = null;
+    DbControl dc = sc.newDbControl();
+    try
+    {
+      subtype = ItemSubtype.getNew(dc, def.getMainType());
+      subtype.setName(def.getName());
+      
+      if (relatedTo != null)
+      {
+        for (Subtype related : relatedTo)
+        {
+          subtype.setRelatedSubtype(related.load(dc));
+        }
+      }
+      
+      dc.saveItem(subtype);
+      dc.commit();
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+    return subtype;
+  }
+  
+  /**
+    Check for an existing item subtype with the given options.
+    A JSONObject is returned with the result. The following 
+    keys are used:
+    <ul>
+    <li>itemType: ITEMSUBTYPE
+    <li>name: The name of the subtype
+    <li>id: The id of the subtype if it exists
+    <li>mainType: The main item type that the subtype applies to
+    <li>status: ok, error, or missing
+    <li>message: A descriptive message in case of an error
+    </ul>
+    @since 2.0
+  */
+  @SuppressWarnings("unchecked")
+  public JSONObject checkSubtype(DbControl dc, Subtype subtype, 
+    boolean createIfMissing, Subtype... relatedTo)
+  {
+  
+    JSONObject json = new JSONObject();
+    JSONArray jsonMessages = new JSONArray();
+    json.put("itemType", Item.ITEMSUBTYPE.name());
+    json.put("name", subtype.getName());
+    json.put("mainType", subtype.getMainType().name());
+      
+    List<ItemSubtype> result = Reggie.listSubtypes(dc, subtype);
+    if (result.size() == 0)
+    {
+      if (createIfMissing)
+      {
+        ItemSubtype s = createSubtype(dc.getSessionControl(), subtype, relatedTo);
+        json.put("id", s.getId());
+        json.put("status", "ok");
+        jsonMessages.add("Created");
+      }
+      else
+      {
+        json.put("status", "missing");
+        jsonMessages.add("Not found");
+      }
+    }
+    else if (result.size() > 1)
+    {
+      json.put("status", "error");
+      jsonMessages.add("Found > 1 subtype");
+    }
+    else
+    {
+      ItemSubtype s = result.get(0);
+      json.put("id", s.getId());
+      json.put("status", "ok"); // For now -- more checks below
+      
+      if (relatedTo != null)
+      {
+        for (Subtype related : relatedTo)
+        {
+          ItemSubtype r = s.getRelatedSubtype(related.getMainType());
+          if (r == null)
+          {
+            json.put("status", "error");
+            jsonMessages.add("Should be related to '" + related.getName() + "'");
+          }
+          else if (!r.getName().equals(related.getName()))
+          {
+            json.put("status", "error");
+            jsonMessages.add("Should be related to: '" + 
+                related.getName() + "' not '" + r.getName() + "'");
+          }
+        }
+      }
+      
+    }
+    if (jsonMessages.size() == 0) jsonMessages.add("Ok");
+    json.put("messages", jsonMessages);
+    return json;
+
+  }
+  
+
   /**
     Store options for enumerated annotation types.