Changeset 4986

Timestamp:

Sep 28, 2018, 11:51:47 AM (5 years ago)

Author:

olle

Message:

Refs #1029. Support added for blood annotations "Tube label" and "Whole blood", where values are stored for the Blood item in new String and Boolean annotations, respectively:

1. JSP file case_summary_alt_rec.jsp in resources/reports/ updated in blood section with new data rows for values of "Tube label" and "Whole blood", where the "Tube label" data is set to belong to class "confidential", requiring a Patient Curator or Administrator for inspection.
2. Javascript file case_summary_alt_rec.js in resources/reports/ updated in function caseInfoLoaded(response) to enter the values for "Tube label" and "Whole blood" obtained for the case from servlet CaseSummaryServlet and make it available for display in the case summary JSP page in the blood section.
3. Java class/file Annotationtype.java in src/net/sf/basedb/meludi/dao/ updated:
   a. New public static final Annotationtype.TUBE_LABEL entry added. It is a String annotation for sample (Blood) items, with value logging disabled.
   b. New public static final Annotationtype.WHOLE_BLOOD entry added. It is a Boolean annotation for sample (Blood) items.
4. Java class/file InstallServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) updated for commands "Validate" and "Install" to add check for new annotation types Annotationtype.TUBE_LABEL and Annotationtype.WHOLE_BLOOD, where Annotationtype.TUBE_LABEL is restricted to Patient Curator use. Also, the annotation types are added to annotation type category "Blood".
5. Java servlet class/file CaseSummaryServlet.java in src/net/sf/basedb/meludi/servlet/ updated in private method void loadBloodInfo(DbControl dc, Blood blood) to load values for Annotationtype.TUBE_LABEL and Annotationtype.WHOLE_BLOOD and couple the values to JSON keys "tubeLabel" and "wholeBlood", respectively.

Location:

extensions/net.sf.basedb.meludi/trunk

Files:

• resources/reports/case_summary_alt_rec.js (modified) (2 diffs)
• resources/reports/case_summary_alt_rec.jsp (modified) (2 diffs)
• src/net/sf/basedb/meludi/dao/Annotationtype.java (modified) (1 diff)
• src/net/sf/basedb/meludi/servlet/CaseSummaryServlet.java (modified) (1 diff)
• src/net/sf/basedb/meludi/servlet/InstallServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.meludi/trunk/resources/reports/case_summary_alt_rec.js

@@ -136 +136 @@
           var b = blood[i];
           cs.addColumn('blood.name', cs.asLink('SAMPLE', b));
+          cs.addColumn('blood.tubeLabel', Strings.encodeTags(b.tubeLabel));
           cs.addColumn('blood.registrationDate', cs.asDate(b.registrationDate));
           cs.addColumn('blood.consent', cs.asConsent(b.consent, cs.asDate(b.consentDate)));
@@ -143 +144 @@
           cs.addColumn('blood.storageBox', cs.asBioPlateLocation(b.bioWell));
           cs.addColumn('blood.serum', Strings.encodeTags(b.serum));
+          cs.addColumn('blood.wholeBlood', b.wholeBlood);
           cs.addColumn('blood.comment', Strings.encodeTags(b.comment));
         }

extensions/net.sf.basedb.meludi/trunk/resources/reports/case_summary_alt_rec.jsp

@@ -264 +264 @@
           </thead>
           <tbody id="blood-details" class="info-details">
+            <tr id="blood.tubeLabel" class="confidential">
+              <th>Tube label</th>
+            </tr>
             <tr id="blood.registrationDate">
               <th>Registration date</th>
@@ -284 +287 @@
             <tr id="blood.serum">
               <th>Serum</th>
+            </tr>
+            <tr id="blood.wholeBlood">
+              <th>Whole blood</th>
             </tr>
             <tr id="blood.comment" class="comment dynamic-column">

extensions/net.sf.basedb.meludi/trunk/src/net/sf/basedb/meludi/dao/Annotationtype.java

@@ -114 +114 @@
     new Annotationtype("BloodSample", Type.STRING, false, Item.SAMPLE);
 */
+
+  /**
+    The "TubeLabel" annotation type, used
+    for samples (Blood). It is a string annotation type.
+  */
+  public static final Annotationtype TUBE_LABEL = 
+    new Annotationtype("TubeLabel", Type.STRING, true, Item.SAMPLE);
+
+  /**
+    The "WholeBlood" annotation type, used
+    for samples (Blood). It is a boolean annotation.
+  */
+  public static final Annotationtype WHOLE_BLOOD = 
+    new Annotationtype("WholeBlood", Type.BOOLEAN, false, Item.SAMPLE);
 
   /**

extensions/net.sf.basedb.meludi/trunk/src/net/sf/basedb/meludi/servlet/CaseSummaryServlet.java

@@ -957 +957 @@
     blood.loadAnnotations(dc, "bloodSample", Annotationtype.BLOOD_SAMPLE, null);
 */
+    blood.loadAnnotations(dc, "tubeLabel", Annotationtype.TUBE_LABEL, null);
+    blood.loadAnnotations(dc, "wholeBlood", Annotationtype.WHOLE_BLOOD, null);
     blood.setAnnotation("comment", s.getDescription());
   }

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

@@ -233 +233 @@
         
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.BLOOD_SAMPLING_DATETIME, 1, null, effectivePermissionsUse, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.TUBE_LABEL, 1,  null, patientCuratorUse, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.WHOLE_BLOOD, 1, null, effectivePermissionsUse, createIfMissing));
 
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.SAMPLING_DATE, 1, null, effectivePermissionsUse, createIfMissing));
@@ -443 +445 @@
             Annotationtype.CONSENT, Annotationtype.CONSENT_DATE,
             Annotationtype.CASE_ID,
+            Annotationtype.TUBE_LABEL,
             Annotationtype.BLOOD_SAMPLING_DATETIME,
+            Annotationtype.WHOLE_BLOOD,
             Annotationtype.OTHER_PATH_NOTE));