Changeset 1341 for extensions

Timestamp:

Apr 11, 2011, 2:57:42 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #307: Consent form registration

Added "Consent" annotation to the installation servlet. The "Personal information wizard" and the "Referral form wizard" are now aware of this annotation and should refuse to work with cases that are annotated with anything else than "Yes".

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/index.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/Case.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/ReferralFormServlet.java (modified) (5 diffs)

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

@@ -132 +132 @@
         <%
       }
+      if (isPatientCurator || isAdmin)
+      {
+        %>
+        <dt>
+          <table border="0" cellspacing="0" cellpadding="0">
+          <tr>
+            <td><base:icon image="file.gif" style="padding-right: 4px;"/></td>
+            <td><a href="consentform.jsp?ID=<%=ID%>">Consent form registration wizard</a></td>
+          </tr>
+          </table>
+        </dt>
+        <dd>
+          <ul>
+          <li>Register consent forms.
+          </ul>
+        </dd>
+        <%
+      }
       %>
       </dl>

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

@@ -104 +104 @@
   public static final String ANNOTATION_RNALATER_DATETIME = "RNALaterDateTime";
 
+  
+  /**
+    The name of the "Consent" annotation type, used
+    for samples (Case). It is an enumerated string annotation 
+    type with three options: Yes, No and Not asked
+  */
+  public static final String ANNOTATION_CONSENT = "Consent";
+  
   /**
     The name of the "PatientCurator" group. Members of this group

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

@@ -12 +12 @@
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.Type;
@@ -195 +196 @@
   }
   
+  /**
+    Verify that the patient has given their permission to participate in the
+    study. Due to the order that things get registered, a non-existing "Consent"
+    annotation is accepted. If the annotation exists the answer must be "Yes",
+    or an exception is thrown.
+  */
+  public void verifyConsent(DbControl dc, AnnotationType consentType)
+  {
+    if (consentType == null)
+    {
+      consentType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_CONSENT, true);
+    }
+    String consent = (String)Reggie.getAnnotationValue(getItem(), consentType);
+    if (consent != null && !consent.equals("Yes"))
+    {
+      throw new PermissionDeniedException("The case (" + getOriginalName() + 
+        ") has not agreed to participate in the study.");
+    }
+
+  }
   
 }

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

@@ -100 +100 @@
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_ALL_FIRST_NAMES, Item.BIOSOURCE, Type.STRING, 1,
             null, sharedToPatientCurator, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_CONSENT, Item.SAMPLE, Type.STRING, 1, 
+            new EnumerationOptions("Yes", "No", "Not asked"), sharedToPatientCurator, createIfMissing));
         
         // -- the second batch need only be shared to the active project or to the PatientCurator group

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

@@ -87 +87 @@
         if (theCase != null)
         {
+          theCase.verifyConsent(dc, null);
+          
           // Load the patient associated with the case
           Patient patient = Patient.findByCase(dc, theCase);

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

@@ -12 +12 @@
 import org.json.simple.JSONObject;
 
+import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.AnyToAny;
 import net.sf.basedb.core.Application;
@@ -28 +29 @@
 import net.sf.basedb.core.query.Restriction;
 import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.dao.Case;
 import net.sf.basedb.util.Values;
@@ -71 +73 @@
         int directoryId = Values.getInt(req.getParameter("directoryId"));
         String pattern = Values.getString(req.getParameter("pattern"));
+        
+        AnnotationType consentType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_CONSENT, true);
         
         Directory dir = Directory.getById(dc, directoryId);
@@ -132 +136 @@
                 jsonFile.put("message", "No case found");
               }
+              else
+              {
+                // Found a case -- verify that consent is given
+                theCase.verifyConsent(dc, consentType);
+              }
             }
           }
@@ -137 +146 @@
           {
             jsonFile.put("message", ex.getMessage());
+            theCase = null;
           }