Changeset 1745

Timestamp:

Nov 27, 2012, 1:06:55 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #425: Generate a lab protocol for RNA -> cDNA processing

Two variants of the protocol can be created. One with a list layout and aone with a plate layout.

Location:

extensions/net.sf.basedb.reggie/branches/ticket-422

Files:

• .classpath (modified) (1 diff)
• resources/images/listview.png (added)
• resources/images/plateview.png (added)
• resources/index.jsp (modified) (1 diff)
• resources/libprep/mrna_protocol.jsp (added)
• resources/libprep/mrna_protocol2.jsp (added)
• src/net/sf/basedb/reggie/dao/MRna.java (added)
• src/net/sf/basedb/reggie/dao/Rna.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (6 diffs)

extensions/net.sf.basedb.reggie/branches/ticket-422/.classpath

@@ -9 +9 @@
   <classpathentry kind="lib" path="lib/compile/base-webclient-3.1.0.jar"/>
   <classpathentry kind="lib" path="lib/compile/base-webservices-client-3.1.0.jar"/>
-  <classpathentry kind="output" path="build"/>
+  <classpathentry kind="output" path=".build"/>
 </classpath>

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/index.jsp

@@ -289 +289 @@
             <ul>
             <li><a href="libprep/select_rna.jsp?ID=<%=ID%>">Create new mRNA plate</a>
-            <li><a href="?ID=<%=ID%>">Lab tracking protocol for mRNA and cDNA preparation</a>
+            <li><a href="libprep/mrna_protocol.jsp?ID=<%=ID%>">Lab tracking protocol for mRNA and cDNA preparation</a>
             <li><a href="?ID=<%=ID%>">Export files for mRNA quality control</a>
             <li><a href="?ID=<%=ID%>">Import mRNA quality control results</a>

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/dao/Rna.java

@@ -69 +69 @@
   }
   
+  public static Rna get(Extract extract)
+  {
+    return new Rna(extract);
+  }
   
   public static List<Rna> toRna(Collection<Extract> extracts)

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/MRnaServlet.java

@@ -2 +2 @@
 
 import java.io.IOException;
-import java.io.Writer;
-import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
@@ -17 +15 @@
 import org.json.simple.parser.JSONParser;
 
-import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Application;
 import net.sf.basedb.core.BioMaterialEventSource;
@@ -28 +25 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Extract;
-import net.sf.basedb.core.File;
 import net.sf.basedb.core.Include;
-import net.sf.basedb.core.ItemNotFoundException;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemSubtype;
-import net.sf.basedb.core.Path;
 import net.sf.basedb.core.PlateGeometry;
-import net.sf.basedb.core.PluginConfiguration;
-import net.sf.basedb.core.PluginDefinition;
-import net.sf.basedb.core.Protocol;
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.Type;
-import net.sf.basedb.core.plugin.ParameterValues;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
@@ -48 +38 @@
 import net.sf.basedb.reggie.dao.Annotationtype;
 import net.sf.basedb.reggie.dao.BioplateType;
-import net.sf.basedb.reggie.dao.ReactionPlate;
+import net.sf.basedb.reggie.dao.MRna;
 import net.sf.basedb.reggie.dao.Rna;
 import net.sf.basedb.reggie.dao.Subtype;
-import net.sf.basedb.reggie.plugins.CaliperPlateImporter;
-import net.sf.basedb.reggie.plugins.CaliperRunParametersExporter;
-import net.sf.basedb.reggie.plugins.CaliperSampleNameExporter;
-import net.sf.basedb.util.Coordinate;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ThrowableUtil;
@@ -81 +67 @@
     JSONObject json = new JSONObject();
     json.put("status", "ok");
-  
+    
     final SessionControl sc = Application.getSessionControl(ID, req.getRemoteAddr());
     DbControl dc = null;
@@ -95 +81 @@
         json.put("name", bioPlateType.generateNextName(dc, 1));
       }
+      else if ("GetUnprocessedMRnaPlates".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        
+        ItemQuery<BioPlate> query = BioPlate.getQuery();
+        query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        query.restrict(Restrictions.eq(Hql.property("eventDate"), null));
+        BioplateType.MRNA.addFilter(dc, query, true);
+        query.order(Orders.desc(Hql.property("id")));
+        
+        List<BioPlate> result = query.list(dc);
+        JSONArray jsonLists = new JSONArray();
+        for (BioPlate plate: result)
+        {
+          JSONObject jsonList = new JSONObject();
+          
+          jsonList.put("id", plate.getId());
+          jsonList.put("name", plate.getName());
+          
+          jsonLists.add(jsonList);
+        }
+        json.put("bioplates", jsonLists);
+      }
+      else if ("GetMRnaInfoForPlate".equals(cmd))
+      {
+        int mRnaPlateId = Values.getInt(req.getParameter("bioplate"));
+        dc = sc.newDbControl();
+
+        BioPlate mRnaPlate = BioPlate.getById(dc, mRnaPlateId);
+
+        ItemQuery<Extract> query = Extract.getQuery();
+        query.join(Hql.innerJoin(null, "bioWell", "bw", true));
+        query.join(Hql.innerJoin("bw", "bioPlate", "bp"));
+        query.restrict(Restrictions.eq(Hql.alias("bp"), Hql.entity(mRnaPlate)));
+        query.order(Orders.asc(Hql.property("bw", "column")));
+        query.order(Orders.asc(Hql.property("bw", "row")));
+
+        List<MRna> mrna = MRna.toList(query.list(dc));
+        JSONArray jsonMRna = new JSONArray();
+        
+        for (MRna r : mrna)
+        {
+          r.loadBioPlateLocation();
+          
+          Rna rna = r.getRna();
+          rna.loadBioPlateLocation();
+          rna.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);
+          
+          Float used = r.getItem().getCreationEvent().getUsedQuantity(rna.getItem());
+          Float remain = rna.getItem().getRemainingQuantity();
+          rna.setAnnotation("usedQuantity", used);
+          if (used != null && remain != null)
+          {
+            rna.setAnnotation("remainingQuantity", remain+used);
+          }
+          
+          r.setAnnotation("rna", rna.asJSONObject());
+          jsonMRna.add(r.asJSONObject());
+          
+        }
+                
+        json.put("mrna", jsonMRna);
+      }
+
       
     }