From d8fd8fe4ed66522aa78e3c7f4705e326a4cb4278 Mon Sep 17 00:00:00 2001
From: Stephen Kraffmiller <skraffmiller@hmdc.harvard.edu>
Date: Mon, 26 Jul 2021 09:10:57 -0400
Subject: [PATCH 1/3] #118 fix show deleted

---
 .../dataverse/ManageFilePermissionsPage.java  | 26 +++++++++++++++----
 .../webapp/permissions-manage-files.xhtml     |  4 +--
 2 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java b/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
index 6d0e2f77c50..ef64b114034 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
@@ -115,6 +115,17 @@ public TreeMap<AuthenticatedUser, List<DataFile>> getFileAccessRequestMap() {
     }
     
     
+    private boolean backingShowDeleted = true;
+
+    public String showDeletedCheckboxChange() {
+
+        if (backingShowDeleted != showDeleted) {
+            initMaps();
+            backingShowDeleted = showDeleted;
+        }
+        return "";
+    }
+    
     public String init() {
         if (dataset.getId() != null) {
             dataset = datasetService.find(dataset.getId());
@@ -136,17 +147,22 @@ private void initMaps() {
         // initialize files and usergroup list
         roleAssigneeMap.clear();
         fileMap.clear();
-        fileAccessRequestMap.clear();        
+        fileAccessRequestMap.clear();   
                
         for (DataFile file : dataset.getFiles()) {
             
-            boolean fileIsDeleted = !((dataset.getLatestVersion().isDraft() && file.getFileMetadata().getDatasetVersion().isDraft())
-                    || (dataset.getLatestVersion().isReleased() && file.getFileMetadata().getDatasetVersion().equals(dataset.getLatestVersion())));
             // only include if the file is restricted (or its draft version is restricted)
             //Added a null check in case there are files that have no metadata records SEK 
             //for 6587 make sure that a file is in the current version befor adding to the fileMap SEK 2/11/2020
-                if (file.getFileMetadata() != null && (file.isRestricted() || file.getFileMetadata().isRestricted())
-                    && (!fileIsDeleted || isShowDeleted())) {
+                if (file.getFileMetadata() != null && (file.isRestricted() || file.getFileMetadata().isRestricted())) {
+                    //only test if file is deleted if it's restricted
+                    boolean fileIsDeleted = !((dataset.getLatestVersion().isDraft() && file.getFileMetadata().getDatasetVersion().isDraft())
+                            || (dataset.getLatestVersion().isReleased() && file.getFileMetadata().getDatasetVersion().equals(dataset.getLatestVersion())));
+
+                    if (!isShowDeleted() && fileIsDeleted) {
+                        //if don't show deleted and is deleted get out.
+                        break;
+                    }
                 // we get the direct role assignments assigned to the file
                 List<RoleAssignment> ras = roleService.directRoleAssignments(file);
                 List<RoleAssignmentRow> raList = new ArrayList<>(ras.size());
diff --git a/src/main/webapp/permissions-manage-files.xhtml b/src/main/webapp/permissions-manage-files.xhtml
index 054f97aec80..49e2ff86768 100644
--- a/src/main/webapp/permissions-manage-files.xhtml
+++ b/src/main/webapp/permissions-manage-files.xhtml
@@ -50,7 +50,7 @@
                                             </p:commandLink>
                                         </div>
                                         <div class="panel-group">
-                                            <p:selectBooleanCheckbox value="#{manageFilePermissionsPage.showDeleted}" itemLabel="#{bundle['dataverse.permissionsFiles.files.includeDeleted']}" onchange="#{manageFilePermissionsPage.init()}">
+                                            <p:selectBooleanCheckbox value="#{manageFilePermissionsPage.showDeleted}" itemLabel="#{bundle['dataverse.permissionsFiles.files.includeDeleted']}"  onchange="#{manageFilePermissionsPage.showDeletedCheckboxChange()}">
                                                 <p:ajax update="filesFragment, usersGroups"/>
                                             </p:selectBooleanCheckbox>
                                         </div>
@@ -156,7 +156,7 @@
                                     </p:fragment>
                                     <p:fragment id="filesFragment">
                                         <div class="panel-group">
-                                            <p:selectBooleanCheckbox value="#{manageFilePermissionsPage.showDeleted}" itemLabel="#{bundle['dataverse.permissionsFiles.files.includeDeleted']}" onchange="#{manageFilePermissionsPage.init()}">
+                                            <p:selectBooleanCheckbox value="#{manageFilePermissionsPage.showDeleted}" itemLabel="#{bundle['dataverse.permissionsFiles.files.includeDeleted']}" onchange="#{manageFilePermissionsPage.showDeletedCheckboxChange()}">
                                                 <p:ajax update="filesFragment, usersGroups"/>
                                             </p:selectBooleanCheckbox>
                                         </div>

From b6a056697026b4e007f7628d59f74a85c714cd8c Mon Sep 17 00:00:00 2001
From: Stephen Kraffmiller <skraffmiller@hmdc.harvard.edu>
Date: Mon, 26 Jul 2021 10:19:16 -0400
Subject: [PATCH 2/3] #118 fix file mapping wrt deleted files

---
 .../edu/harvard/iq/dataverse/ManageFilePermissionsPage.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java b/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
index ef64b114034..36a0b7cc692 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
@@ -160,8 +160,8 @@ private void initMaps() {
                             || (dataset.getLatestVersion().isReleased() && file.getFileMetadata().getDatasetVersion().equals(dataset.getLatestVersion())));
 
                     if (!isShowDeleted() && fileIsDeleted) {
-                        //if don't show deleted and is deleted get out.
-                        break;
+                        //if don't show deleted and is deleted go to next file...
+                        continue;
                     }
                 // we get the direct role assignments assigned to the file
                 List<RoleAssignment> ras = roleService.directRoleAssignments(file);

From 15865803309e5c0c5f4de3be61a43e5a5661e5e5 Mon Sep 17 00:00:00 2001
From: Stephen Kraffmiller <skraffmiller@hmdc.harvard.edu>
Date: Mon, 26 Jul 2021 14:04:05 -0400
Subject: [PATCH 3/3] #118 simplify checkbox change method

---
 .../edu/harvard/iq/dataverse/ManageFilePermissionsPage.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java b/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
index 36a0b7cc692..c728062a5a8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
@@ -117,13 +117,13 @@ public TreeMap<AuthenticatedUser, List<DataFile>> getFileAccessRequestMap() {
     
     private boolean backingShowDeleted = true;
 
-    public String showDeletedCheckboxChange() {
+    public void showDeletedCheckboxChange() {
 
         if (backingShowDeleted != showDeleted) {
             initMaps();
             backingShowDeleted = showDeleted;
         }
-        return "";
+
     }
     
     public String init() {