Changeset 4306

Timestamp:

May 21, 2008, 3:39:59 PM (15 years ago)

Author:

Nicklas Nordborg

Message:

References #1015: Add reporter list from tables that list reporters/reporter info

It is now working from dynamic queries as well.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/Reporter.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ReporterData.java (modified) (1 diff)
• www/views/experiments/explorer/search/index.jsp (modified) (3 diffs)
• www/views/experiments/explorer/search/list.jsp (modified) (3 diffs)
• www/views/experiments/spotdata/index.jsp (modified) (2 diffs)
• www/views/experiments/spotdata/list_spotdata.jsp (modified) (2 diffs)
• www/views/reporterlists/edit_reporterlist.jsp (modified) (2 diffs)
• www/views/reporterlists/index.jsp (modified) (4 diffs)

trunk/src/core/net/sf/basedb/core/Reporter.java

@@ -121 +121 @@
     return rd;
   }
+  
+  /**
+    Get a proxy reporter object. This method is usefult when linking
+    reporters to other items, and you are sure that a reporter with the given ID
+    exists. Since this method doesn't hit the database, there are some things to 
+    be aware of:
+    <ul>
+    <li>There is no check to see if a reporter with the given ID exists or
+      not
+    <li>The returned object doesn't contain any reporter information
+      except the ID.
+    </ul>
+    
+    @param reporterId The ID of the reporter
+    @return A reporter object
+    @since 2.8
+  */
+  public static ReporterData getProxy(int reporterId)
+  {
+    return new ReporterData(reporterId);
+  }
 
   /**

trunk/src/core/net/sf/basedb/core/data/ReporterData.java

@@ -60 +60 @@
 
   /**
+    Create a reporter object with a given ID.
+    @param id The reporter ID
+    @since 2.8
+  */
+  public ReporterData(int id)
+  {
+    setId(id);
+  }
+  
+  /**
     The maximum length of the external ID that can be stored in the database.
     @see #setExternalId(String)

trunk/www/views/experiments/explorer/search/index.jsp

@@ -33 +33 @@
   import="net.sf.basedb.core.ItemContext"
   import="net.sf.basedb.core.BioAssaySet"
+  import="net.sf.basedb.core.DynamicSpotQuery"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.ExperimentExplorer"
@@ -38 +39 @@
   import="net.sf.basedb.util.Values"
   import="net.sf.basedb.clients.web.util.HTML"
+  import="java.util.Collections"
 %>
 <%
@@ -68 +70 @@
     redirect = listPage;
   }
+  else if ("CreateReporterList".equals(cmd))
+  {
+    ItemContext cc = explorer.getAndSetReporterContext(sc, pageContext);
+    DynamicSpotQuery query = explorer.getReporterQuery(dc, Collections.singletonList("@id"));
+    cc.setQuery(query);
+    redirect = "../../../reporterlists/index.jsp?ID="+ID+
+        "&cmd=NewItem&addReporters=1&formId=&fromContext=" + cc.getItemType().name() + 
+        "&subContext="+cc.getSubContext() + "&name=" + HTML.urlEncode(bioAssaySet.getName());
+  }
+
   else
   {

trunk/www/views/experiments/explorer/search/list.jsp

@@ -31 +31 @@
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.BioAssaySet"
   import="net.sf.basedb.core.Experiment"
@@ -157 +158 @@
       }
     }
+    function newReporterList()
+    {
+      Table.submitToPopup(formId, 'CreateReporterList', 540, 400);
+    }
   </script>
   </base:head>
@@ -231 +236 @@
           title="Columns&hellip;" 
           tooltip="Show, hide and re-order columns" 
+        />
+        <tbl:button
+          image="add.png"
+          onclick="newReporterList()"
+          title="New reporter list&hellip;"
+          tooltip="Create a new reporter list from matching reporters"
+          visible="<%=sc.hasPermission(Permission.CREATE, Item.REPORTERLIST)%>"
         />
       </tbl:toolbar>

trunk/www/views/experiments/spotdata/index.jsp

@@ -41 +41 @@
   import="java.util.Map"
   import="java.util.HashMap"
+  import="java.util.Collections"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -127 +128 @@
     redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+spot+data";
   }
+  else if ("CreateReporterList".equals(cmd))
+  {
+    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, pageContext, defaultContext);
+    dc = sc.newDbControl();
+    if (bas != null) dc.reattachItem(bas);
+    if (ba != null) dc.reattachItem(ba);
+    final DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
+    cc.configureQuery(dc, query, Collections.singletonList("@id"));
+    cc.setQuery(query);
+    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
+      "&cmd=NewItem&addReporters=1&formId=&fromContext=SPOTDATA&subContext=" + subContext +
+      "&name=" + HTML.urlEncode(ba != null ? ba.getName() : bas.getName());
+  }
+  
   else
   {

trunk/www/views/experiments/spotdata/list_spotdata.jsp

@@ -169 +169 @@
       }
     }
+    function newReporterList()
+    {
+      Table.submitToPopup(formId, 'CreateReporterList', 540, 400);
+    }
     </script>
   </base:head>
@@ -306 +310 @@
           title="Columns&hellip;" 
           tooltip="Show, hide and re-order columns" 
+        />
+        <tbl:button
+          image="add.png"
+          onclick="newReporterList()"
+          title="New reporter list&hellip;"
+          tooltip="Create a new reporter list from matching spots"
+          visible="<%=sc.hasPermission(Permission.CREATE, Item.REPORTERLIST)%>"
         />
         <tbl:button 

trunk/www/views/reporterlists/edit_reporterlist.jsp

@@ -56 +56 @@
   boolean mergeReporterLists = false;
   int numSelectedLists = cc.getSelected().size();
-  String formId = Values.getString(request.getParameter("formId"), "reporters");
+  String formId = request.getParameter("formId");
   String fromContext = Values.getString(request.getParameter("fromContext"), "REPORTER");
   String subContext = request.getParameter("subContext");
@@ -154 +154 @@
     }
     // Get the ID:s of all selected reorters
-    var selectedItems;
+    var selectedItems = new Array();
     function getSelectedItems()
     {
-      if (!selectedItems)
-      {
-        selectedItems = window.opener.Table.getSelected('<%=formId%>');
-      }
+      <%
+      if (formId != null)
+      {
+        %>
+        if (!selectedItems)
+        {
+          selectedItems = window.opener.Table.getSelected('<%=formId%>');
+        }
+        <%
+      }
+      %>
       return selectedItems;
     }

trunk/www/views/reporterlists/index.jsp

@@ -32 +32 @@
   import="net.sf.basedb.core.ReporterList"
   import="net.sf.basedb.core.FileType"
+  import="net.sf.basedb.core.Reporter"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.Type"
@@ -37 +38 @@
   import="net.sf.basedb.core.DataQuery"
   import="net.sf.basedb.core.ItemQuery"
+  import="net.sf.basedb.core.DynamicQuery"
   import="net.sf.basedb.core.DataResultIterator"
+  import="net.sf.basedb.core.DynamicResultIterator"
   import="net.sf.basedb.core.MultiPermissions"
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.ItemAlreadyExistsException"
   import="net.sf.basedb.core.data.ReporterData"
+  import="net.sf.basedb.core.query.Query"
   import="net.sf.basedb.core.query.Restrictions"
   import="net.sf.basedb.core.query.Expressions"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.query.SqlResult"
   import="net.sf.basedb.util.RemovableUtil"
   import="net.sf.basedb.util.ShareableUtil"
@@ -147 +152 @@
         Item fromContext = Item.valueOf(request.getParameter("fromContext"));
         String subContext = Values.getString(request.getParameter("subContext"), "");
-        DataQuery<ReporterData> query = 
-          (DataQuery<ReporterData>)sc.getCurrentContext(fromContext, subContext).getQuery();
+        Query query = sc.getCurrentContext(fromContext, subContext).getQuery();
         if ("all".equals(which))
         {
@@ -169 +173 @@
         // else -- no modifications to the query mean that we only get the current page
         
-        DataResultIterator<ReporterData> result = query.iterate(dc);
-        while (result.hasNext())
-        {
-          ReporterData reporter = result.next();
-          if (reporter != null) rl.addReporter(reporter, null);
+        if (query instanceof DataQuery)
+        {
+          DataResultIterator<ReporterData> result = ((DataQuery<ReporterData>)query).iterate(dc);
+          while (result.hasNext())
+          {
+            ReporterData reporter = result.next();
+            if (reporter != null) rl.addReporter(reporter, null);
+          }
+        }
+        else if (query instanceof DynamicQuery)
+        {
+          DynamicResultIterator result = ((DynamicQuery)query).iterate(dc);
+          while (result.hasNext())
+          {
+            SqlResult i = result.next();
+            int reporterId = i.getInt(1);
+            if (reporterId != 0)
+            {
+              rl.addReporter(Reporter.getProxy(reporterId), null);
+            }
+          }
         }
       }