Changeset 1310

Timestamp:

Mar 4, 2011, 3:45:04 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #292: Check/create annotation types, etc. required by reggie

Smarter check for required permissions when a project is active. Only some of the annotation types (with personal information) need to be shared to the 'PatientCurator?' group. The other annotation types can be shared to the active project.

Important note! This code is affected by ​http://base.thep.lu.se/ticket/1583 if an item is already shared to a different project or group than the active project or 'PatientCurator?' group. This will result in a (almost) blank page that can't be used for validation or create missing items.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• README (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (9 diffs)

extensions/net.sf.basedb.reggie/trunk/README

@@ -20 +20 @@
     installation. Otherwise, just wait a bit and the automatic installation will
     find and install the new extension.
- 5. Log in as a user with Administrator priviliges. Go to the Extensions->Reggie
-    menu. Select the 'Verify/install required annotation types and other items'
-    wizard and create the required items. If the 'Reggie' menu is not visible
-    try BASE->Reload permissions menu.
- 6. Done. 
+ 5. Log in as a user with Administrator priviliges. 
+ 6. Create a project and set it as the active project. This step is
+    optional but is recommended. Running Reggie without an active project
+    will generate warning messages later on.
+ 7. Go to the Extensions->Reggie menu. Select the 'Verify/install required
+    annotation types and other items' wizard. If the 'Reggie' menu is not 
+    visible try BASE->Reload permissions menu.
+ 8. It should display a list with several error message about missing items.
+    Click on the "Create missing items" button to create them. If no project
+    was created in step 6, all annotatation types will be shared with the
+    'PatientCurator' group, otherwise only some will be shared to the
+    group and some will be shared to the active project.
+ 9. Done. 
 
  

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

@@ -25 +25 @@
 import net.sf.basedb.core.Permission;
 import net.sf.basedb.core.Project;
+import net.sf.basedb.core.ProjectKey;
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.SharedItem;
@@ -83 +84 @@
         }
         
-        // Annotation type checks
+        PermissionOptions sharedToActiveProject = null;
+        int projectId = dc.getSessionControl().getActiveProjectId();
+        if (projectId != 0)
+        {
+          sharedToActiveProject = new PermissionOptions();
+          sharedToActiveProject.set(Project.getById(dc, projectId), Permission.USE);
+        }
+        
+        // Annotation type checks 
+        // -- the first batch need to be shared to the PatientCurator group
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_PERSONAL_NUMBER, Item.BIOSOURCE, Type.STRING, 1,
             null, sharedToPatientCurator, createIfMissing));
@@ -90 +100 @@
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_ALL_FIRST_NAMES, Item.BIOSOURCE, Type.STRING, 1,
             null, sharedToPatientCurator, createIfMissing));
+        
+        // -- the second batch need only be shared to the active project or to the PatientCurator group
+        PermissionOptions effectiveOptions = sharedToActiveProject == null ?
+            sharedToPatientCurator : sharedToActiveProject;
+
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_DATE_OF_BIRTH, Item.BIOSOURCE, Type.DATE, 1,
-            null, sharedToPatientCurator, createIfMissing));
+            null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_GENDER, Item.BIOSOURCE, Type.STRING, 1,
-            new EnumerationOptions("F", "M"), sharedToPatientCurator, createIfMissing));
+            new EnumerationOptions("F", "M"), effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_LATERALITY, Item.SAMPLE, Type.STRING, 1,
-            new EnumerationOptions("LEFT", "RIGHT"), sharedToPatientCurator, createIfMissing));
+            new EnumerationOptions("LEFT", "RIGHT"), effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, Item.SAMPLE, Type.STRING, 0,
-            null, sharedToPatientCurator, createIfMissing));
+            null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_PAD, Item.SAMPLE, Type.STRING, 1, 
-            null, sharedToPatientCurator, createIfMissing));
+            null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_PAD_CASE, Item.SAMPLE, Type.STRING, 0, 
-            null, sharedToPatientCurator, createIfMissing));
+            null, effectiveOptions, createIfMissing));
         
         json.put("checks", jsonChecks);
@@ -381 +396 @@
   {
     private Map<Group, Permission> groupPermissions;
+    private Map<Project, Permission> projectPermissions;
     private String message;
     
@@ -386 +402 @@
     {
       groupPermissions = new HashMap<Group, Permission>();
+      projectPermissions = new HashMap<Project, Permission>();
     }
 
@@ -394 +411 @@
     {
       groupPermissions.put(g, p);
+    }
+
+    /**
+      Set a permission for the given project.
+    */
+    void set(Project pr, Permission p)
+    {
+      projectPermissions.put(pr, p);
     }
 
@@ -403 +428 @@
     boolean checkPermissions(SharedItem item)
     {
+      ProjectKey pKey = item.getProjectKey();
+      for (Map.Entry<Project, Permission> entry : projectPermissions.entrySet())
+      {
+        Project pr = entry.getKey();
+        Permission p = entry.getValue();
+        if (pKey == null || !pKey.getPermissions(pr).contains(p)) 
+        {
+          message = "Not shared to project: " + pr.getName() + " (" + p + ")";
+          return false;
+        }
+      }
       ItemKey key = item.getItemKey();
       for (Map.Entry<Group, Permission> entry : groupPermissions.entrySet())
@@ -414 +450 @@
           return false;
         }
-        
       }
       return true;
@@ -439 +474 @@
         mp.addPermissions(g, Collections.singleton(p));
       }
+      for (Map.Entry<Project, Permission> entry : projectPermissions.entrySet())
+      {
+        Project pr = entry.getKey();
+        Permission p = entry.getValue();
+        mp.addPermissions(pr, Collections.singleton(p));
+      }
       mp.updateKeys(item.getDbControl());
     }