Changeset 1518

Timestamp:

Jan 23, 2012, 11:39:49 AM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #350: Blood referral form registration wizard

There is now support for creating and updating 'Blood' samples. If there is already patient information for the case it is loaded automatically.

The personal information registration wizard has been updated to also check for blood registration.

Thus, it should now work to use both wizards in any order. Consent information is still not considered.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• META-INF/servlets.xml (modified) (1 diff)
• resources/bloodform.jsp (modified) (11 diffs)
• src/net/sf/basedb/reggie/dao/Blood.java (added)
• src/net/sf/basedb/reggie/dao/Patient.java (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/ReggieItem.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/dao/Subtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/BloodRegistrationServlet.java (added)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (4 diffs)

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

@@ -12 +12 @@
     <servlet-name>ReferralForm</servlet-name>
     <servlet-class>net.sf.basedb.reggie.servlet.ReferralFormServlet</servlet-class>
+  </servlet>
+  <servlet>
+    <servlet-name>BloodRegistration</servlet-name>
+    <servlet-class>net.sf.basedb.reggie.servlet.BloodRegistrationServlet</servlet-class>
   </servlet>
   <servlet>

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

@@ -30 +30 @@
 <script language="JavaScript">
 
-var debug = false;
+var debug = true;
 var currentStep = 1;
 var pnrIsValid = false;
@@ -39 +39 @@
 
 var patientInfo = null;
-var caseInfo = null;
+var bloodInfo = null;
 
 function init()
@@ -156 +156 @@
   caseIsValid = true;
   
-  getCaseInfo();
+  getBloodInfo();
 }
 
@@ -303 +303 @@
 }
 
-function getCaseInfo()
+function getBloodInfo()
 {
   // Check entered case and pnr with AJAX
@@ -309 +309 @@
   var caseName = frm.caseName.value;
   var request = Ajax.getXmlHttpRequest();
-  var url = 'PersonalRegistration.servlet?ID=<%=ID%>&cmd=GetCaseInfo';
+  var url = 'BloodRegistration.servlet?ID=<%=ID%>&cmd=GetBloodInfo';
   url += '&caseName=' + caseName;
   request.open("GET", url, false); 
@@ -324 +324 @@
   
   // Get biosource information from the AJAX response
-  caseInfo = response.caseInfo;
-  
-  if (caseInfo && caseInfo.patient)
-  {
-    frm.personalNumber.value = caseInfo.patient.personalNumber;
+  bloodInfo = response.bloodInfo;
+  
+  if (bloodInfo && bloodInfo.patient)
+  {
+    frm.personalNumber.value = bloodInfo.patient.personalNumber;
     gotoStep2();
   }
@@ -403 +403 @@
   currentStep = 3;
   
-  var updateMode = caseInfo.id && caseInfo.patient;
+  var updateMode = bloodInfo.id && bloodInfo.patient;
     
-  Main.show('caseSection');
+  Main.show('bloodSection');
+  
+  if (updateMode)
+  {
+    
+    if (bloodInfo.samplingDate != null)
+    {
+      frm.samplingDate.value = bloodInfo.samplingDate.substring(0, 8);
+      frm.samplingTime.value = bloodInfo.samplingDate.substring(9, 13);
+      samplingDateTimeOnChange();
+    }
+    if (bloodInfo.freezerDate != null)
+    {
+      frm.freezerDate.value = bloodInfo.freezerDate.substring(0, 8);
+      frm.freezerTime.value = bloodInfo.freezerDate.substring(9, 13);
+      freezerDateTimeOnChange();
+    }
+    frm.serum.checked = bloodInfo.serum == 'Yes';
+  }
   
   Main.hide('gonext');
@@ -429 +447 @@
   var frm = document.forms['reggie'];
 
-  caseInfo.samplingDate = Main.trimString(frm.samplingDate.value + ' ' + frm.samplingTime.value);
-  caseInfo.freezerDate = Main.trimString(frm.freezerDate.value + ' ' + frm.freezerTime.value);
-  caseInfo.serum = frm.serum.checked ? true : false;
+  bloodInfo.samplingDate = Main.trimString(frm.samplingDate.value + ' ' + frm.samplingTime.value);
+  bloodInfo.freezerDate = Main.trimString(frm.freezerDate.value + ' ' + frm.freezerTime.value);
+  bloodInfo.serum = frm.serum.checked ? "Yes" : "No";
 
   frm.samplingDate.disabled = true;
@@ -438 +456 @@
   frm.freezerTime.disabled = true;
 
-  var updateMode = caseInfo.id && caseInfo.patient;
+  var updateMode = bloodInfo.id && bloodInfo.patient;
   var submitInfo = new Object();
   submitInfo.patientInfo = patientInfo;
-  submitInfo.caseInfo = caseInfo;
+  submitInfo.bloodInfo = bloodInfo;
 
   if (debug) Main.debug(JSON.stringify(submitInfo));
@@ -447 +465 @@
   var request = Ajax.getXmlHttpRequest();
   var url = 'BloodRegistration.servlet?ID=<%=ID%>&cmd=';
-  url += updateMode ? 'UpdateCase' : 'CreateCase';
+  url += updateMode ? 'UpdateBlood' : 'CreateBlood';
   request.open("POST", url, false);
   request.setRequestHeader("Content-Type", "application/json");
@@ -622 +640 @@
 
 
-  <!-- 3. Case registration -->
-  <div id="caseSection" style="display: none;">
+  <!-- 3. Blood registration -->
+  <div id="bloodSection" style="display: none;">
   <p>
   <table border="0" cellspacing="0" cellpadding="0" class="stepform">
   <tr>
     <td rowspan="2" class="stepno">3</td>
-    <td class="steptitle" id="step3.title">Create new case</td>
+    <td class="steptitle" id="step3.title">Create new blood</td>
   </tr>
   <tr>

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

@@ -78 +78 @@
   }
   
+  /**
+    Find the patient the blood case is linked with. Null is returned if
+    not found.
+    @since 2.2
+  */
+  public static Patient findByBlood(DbControl dc, Blood blood)
+  {
+    Patient patient = null;
+    Sample s = blood.getSample();
+    BioSource b = s.getParentType() == Item.BIOSOURCE ? (BioSource)s.getParent() : null;
+    if (b != null)
+    {
+      patient = new Patient(b);
+    }
+    return patient;
+  }
+
   
   /**

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

@@ -53 +53 @@
     Initialize a JSON object with information. Subclasses
     should override this method if the need to put in more
-    than the 'id', 'name' or loaded annotations (see {@link #loadAnnotations(String, AnnotationType)})
+    than the 'id', 'name' or loaded annotations (see {@link #loadAnnotations(String, AnnotationType, ValueConverter)})
   */
   protected void initJSON(JSONObject json)
@@ -98 +98 @@
     Utility method that first finds the annotation type using
     {@link Reggie#findAnnotationType(DbControl, net.sf.basedb.core.Item, String, boolean)}
-    and then calls {@link #loadAnnotations(String, AnnotationType)}.
+    and then calls {@link #loadAnnotations(String, AnnotationType, ValueConverter)}.
   */
   public void loadAnnotations(DbControl dc, String jsonKey, String annotationTypeName, ValueConverter converter)

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

@@ -93 +93 @@
     Load the subtype as a BASE item.
     @param dc The DbControl to use for database access
-    @return
+    @return An ItemSubtype object
   */
   public ItemSubtype load(DbControl dc)

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

@@ -26 +26 @@
 import net.sf.basedb.reggie.converter.DateToStringConverter;
 import net.sf.basedb.reggie.converter.StringToDateConverter;
+import net.sf.basedb.reggie.dao.Blood;
 import net.sf.basedb.reggie.dao.Case;
 import net.sf.basedb.reggie.dao.Patient;
@@ -76 +77 @@
         String caseName = req.getParameter("caseName");
         Case theCase = Case.findByName(dc, caseName);
+        Patient patient = null;
         List<SpecimenTube> specimenTubes = null;
         JSONObject jsonCase = null;
@@ -102 +104 @@
 
           // Load the patient associated with the case
-          Patient patient = Patient.findByCase(dc, theCase);
-          // The patient can be null if (for example) we have only registered consent=yes so far
-          if (patient != null) 
-          {
-            patient.loadDefaultAnnotations(dc);
-            jsonCase.put("patient", patient.asJSONObject());
-          }
+          patient = Patient.findByCase(dc, theCase);
         }
         else
@@ -116 +112 @@
           jsonCase = new JSONObject();
           jsonCase.put("name", caseName);
-        }
-
+          
+          // Also check for a blood sample so that we can get patient information
+          Blood blood = Blood.findByCaseName(dc, caseName);
+          if (blood != null) patient = Patient.findByBlood(dc, blood);
+        }
+
+        // The patient can be null if (for example) we have only registered consent=yes so far
+        if (patient != null) 
+        {
+          patient.loadDefaultAnnotations(dc);
+          jsonCase.put("patient", patient.asJSONObject());
+        }
+        
         // Load specimen tube annotations
         JSONArray jsonTubes = new JSONArray();