Changeset 1372

Timestamp:

May 23, 2011, 4:40:03 PM (11 years ago)

Author:

Martin Svensson

Message:

References #317. The installation wizzard install new annotations. The new specimentube form is almost complete, some background-functionality is still missing.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• META-INF/servlets.xml (modified) (1 diff)
• resources/index.jsp (modified) (4 diffs)
• resources/specimentube.jsp (added)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/SpecimenTube.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/SpecimenTubeServlet.java (added)

extensions/net.sf.basedb.reggie/trunk/META-INF/servlets.xml

@@ -17 +17 @@
     <servlet-class>net.sf.basedb.reggie.servlet.ConsentFormServlet</servlet-class>
   </servlet>
+  <servlet>
+    <servlet-name>SpecimenTubeRegistration</servlet-name>
+    <servlet-class>net.sf.basedb.reggie.servlet.SpecimenTubeServlet</servlet-class>
+  </servlet>
 
 </servlets>

extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

@@ -7 +7 @@
   import="net.sf.basedb.core.Group"
   import="net.sf.basedb.core.DbControl"
+  import="net.sf.basedb.core.Item"
+  import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.SessionControl"
   import="net.sf.basedb.core.SystemItems"
@@ -31 +33 @@
   boolean isAdmin = false;
   boolean isPatientCurator = false;
+  boolean hasCreateSamplePermission = false;
   try
   {
@@ -50 +53 @@
   catch (RuntimeException ex)
   {}
+  try
+  {
+    if (sc.hasPermission(Permission.CREATE, Item.SAMPLE))
+    {
+      hasCreateSamplePermission = true;
+    }
+  }
+  catch(RuntimeException ex)
+  {}
 %>
 <base:page type="default" >
@@ -150 +162 @@
         <%
       }
+      if (hasCreateSamplePermission)
+      {
+        %>
+        <dt>
+          <table border="0" cellspacing="0" cellpadding="0">
+          <tr>
+            <td><base:icon image="file.gif" style="padding-right: 4px;"/></td>
+            <td><a href="specimentube.jsp?ID=<%=ID%>">Specimen tube registration wizard</a></td>
+          </tr>
+          </table>
+        </dt>
+        <dd>
+          <ul>
+          <li>Register new specimen tubes.
+          <li>Update existing specimen tubes.
+          </ul>
+        </dd>
+        <%
+      }
       %>
       </dl>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/Reggie.java

@@ -118 +118 @@
   public static final String ANNOTATION_CONSENT_DATE = "ConsentDate";
 
+  /**
+    The name of the "ArrivalDate" annotation type, used
+    for samples (Specimen tube). It is a timestamp annotation.
+  */
+  public static final String ANNOTATION_ARRIVAL_DATE = "ArrivalDate";
+  
+  /**
+    The name of the "NofDeliveredTubes" annotation type, used
+    for samples (Specimen tube). It is an Integer annotation type.
+  */
+  public static final String ANNOTATION_NOF_DELIVERED_TUBES = "NofDeliveredTubes";
   
   /**

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/SpecimenTube.java

@@ -6 +6 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Include;
+import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Sample;
@@ -68 +69 @@
   }
   
+  
+  public static SpecimenTube findByTubeName(DbControl dc, String tubeName)
+  {
+    SpecimenTube tube = null;
+    
+    ItemQuery<Sample> tubeQuery = Sample.getQuery();
+    tubeQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string(tubeName)));
+    tubeQuery.order(Orders.desc(Hql.property("name")));       
+    tubeQuery.include(Include.ALL);
+    
+    List<Sample> tubes = tubeQuery.list(dc);
+    if (tubes.size() > 1)
+    {
+      throw new InvalidDataException(
+          "More than one specimen tube with the name " + tubeName + " was found. " +
+          "This wizard can't be used until that is corrected.");
+    }
+    if (tubes.size() == 1)
+    {
+      tube = new SpecimenTube(tubes.get(0));
+    }
+    return tube;
+  }
+  
   private SpecimenTube(Sample sample)
   {

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

@@ -125 +125 @@
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_CONSENT_DATE, Item.SAMPLE, Type.DATE, 1, 
             null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_ARRIVAL_DATE, Item.SAMPLE, Type.DATE, 1, 
+            null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_NOF_DELIVERED_TUBES, Item.SAMPLE, Type.STRING, 1, 
+            null, effectiveOptions, createIfMissing));
         
         json.put("checks", jsonChecks);