From ac8f7ee9a12e272afe0ca1293d0204f132efed68 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 1 Aug 2022 12:55:41 -0400
Subject: [PATCH 01/17] Add annotation access controls at the folder level

---
 .../rest/annotation.py                        |  92 +++++++++++
 .../web_client/views/hierarchyWidget.js       | 150 ++++++++++++++++++
 2 files changed, 242 insertions(+)
 create mode 100644 girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index e4ca0e453..74dede488 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -21,6 +21,7 @@
 import cherrypy
 import orjson
 
+from bson.objectid import ObjectId
 from girder import logger
 from girder.api import access
 from girder.api.describe import Description, autoDescribeRoute, describeRoute
@@ -58,6 +59,8 @@ def __init__(self):
         self.route('GET', ('item', ':id'), self.getItemAnnotations)
         self.route('POST', ('item', ':id'), self.createItemAnnotations)
         self.route('DELETE', ('item', ':id'), self.deleteItemAnnotations)
+        self.route('GET', ('folder', ':id'), self.returnFolderAnnotations)
+        self.route('GET', ('folder', ':id', 'present'), self.existFolderAnnotations)
         self.route('GET', ('old',), self.getOldAnnotations)
         self.route('DELETE', ('old',), self.deleteOldAnnotations)
         self.route('GET', ('counts',), self.getItemListAnnotationCounts)
@@ -558,6 +561,95 @@ def deleteItemAnnotations(self, item):
                 count += 1
         return count
 
+    def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sort=False, sortDir=False):
+        recursivePipeline = [
+            {'$graphLookup': {
+                'from': 'folder',
+                'startWith': '$_id',
+                'connectFromField': '_id',
+                'connectToField': 'parentId',
+                'as': '__children'
+            }},
+            {'$unwind': {'path': '$__children'}},
+            {'$replaceRoot': {'newRoot': '$__children'}}] if recurse else []
+        accessPipeline = [
+            {'$match': {
+                '$or': [
+                    {'access.users':
+                        {'$elemMatch': {
+                            'id': user['_id'],
+                            'level': {'$gte': 2}
+                        }}},
+                    {'access.groups':
+                        {'$elemMatch': {
+                            'id': {'$in': user['groups']},
+                            'level': {'$gte': 2}
+                        }}}
+                ]
+            }}
+        ] if not user['admin'] else []
+        pipeline = [
+            {'$match': {'_id': 'none'}},
+            {'$unionWith': {
+                'coll': 'folder',
+                'pipeline': [{'$match': {'_id': ObjectId(id)}}] +
+                recursivePipeline +
+                [{'$unionWith': {
+                    'coll': 'folder',
+                    'pipeline': [{'$match': {'_id': ObjectId(id)}}]
+                }}, {'$lookup': {
+                    'from': 'item',
+                    'localField': '_id',
+                    'foreignField': 'folderId',
+                    'as': '__items'
+                }}, {'$lookup': {
+                    'from': 'annotation',
+                    'localField': '__items._id',
+                    'foreignField': 'itemId',
+                    'as': '__annotations'
+                }}, {'$unwind': '$__annotations'},
+                    {'$replaceRoot': {'newRoot': '$__annotations'}},
+                    {'$match': {'_active': {'$ne': False}}}
+                ] + accessPipeline
+            }},
+        ]
+        pipeline = pipeline + [{'$sort': {sort: sortDir}}] if sort else pipeline
+        pipeline = pipeline + [{'$skip': offset}] if offset else pipeline
+        pipeline = pipeline + [{'$limit': limit}] if limit else pipeline
+
+        return Annotation().collection.aggregate(pipeline)
+
+
+    @autoDescribeRoute(
+        Description('Check if there are any annotations from the items in a folder')
+        .param('id', 'The ID of the folder', required=True, paramType='path')
+        .param('recurse', 'Whether or not to recursively check '
+            'subfolders for annotations', required=False, default=True, dataType='boolean')
+        .errorResponse()
+    )
+    @access.public
+    def existFolderAnnotations(self, id, recurse):
+        annotations = self.getFolderAnnotations(id, recurse, self.getCurrentUser(), 1)
+        try:
+            next(annotations)
+            yield True
+        except StopIteration:
+            yield False
+
+
+    @autoDescribeRoute(
+        Description('Get the annotations from the items in a folder')
+        .param('id', 'The ID of the folder', required=True, paramType='path')
+        .param('recurse', 'Whether or not to retrieve all '
+            'annotations from subfolders', required=False, default=False, dataType='boolean')
+        .pagingParams(defaultSort='created', defaultSortDir=-1)
+        .errorResponse()
+    )
+    @access.public
+    def returnFolderAnnotations(self, id, recurse, limit, offset, sort):
+        return self.getFolderAnnotations(id, recurse, self.getCurrentUser(), limit, offset,
+                                    sort[0][0], sort[0][1])
+
     @autoDescribeRoute(
         Description('Report on old annotations.')
         .param('age', 'The minimum age in days.', required=False,
diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
new file mode 100644
index 000000000..d5d922227
--- /dev/null
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
@@ -0,0 +1,150 @@
+import $ from 'jquery';
+
+import { wrap } from '@girder/core/utilities/PluginUtils';
+import { restRequest } from '@girder/core/rest';
+import AccessWidget from '@girder/core/views/widgets/AccessWidget';
+import HierarchyWidget from '@girder/core/views/widgets/HierarchyWidget';
+import UserCollection from '@girder/core/collections/UserCollection';
+
+import AnnotationCollection from '../collections/AnnotationCollection';
+
+wrap(HierarchyWidget, 'initialize', function (initialize, settings) {
+    initialize.call(this, settings);
+
+    if (this.parentModel.get('_modelType') === 'folder') {
+        fetchCollections(this, this.parentModel.id);
+    }
+    this.folderListView.on('g:folderClicked', () => {
+        fetchCollections(this, this.parentModel.id);
+        addAccessControl(this);
+    });
+});
+
+wrap(HierarchyWidget, 'render', function (render) {
+    render.call(this);
+
+    if (this.parentModel.get('_modelType') === 'folder' && this.recurseCollection) {
+        addAccessControl(this);
+    }
+});
+
+function fetchCollections(root, folderId) {
+    restRequest({
+        type: 'GET',
+        url: 'annotation/folder/' + folderId + '/present',
+        data: {
+            id: folderId,
+            recurse: true
+        }
+    }).done((resp) => {
+        if (resp[0]) {
+            root.users = new UserCollection();
+
+            root.recurseCollection = new AnnotationCollection([], {comparator: null});
+            root.recurseCollection.altUrl = 'annotation/folder/' + folderId;
+            root.recurseCollection.fetch({
+                id: folderId,
+                sort: 'created',
+                sortDir: -1,
+                recurse: true
+            }).done(() => {
+                root.recurseCollection.each((model) => {
+                    root.users.add({'_id': model.get('creatorId')});
+                });
+                $.when.apply($, root.users.map((model) => {
+                    return model.fetch();
+                })).always(() => {
+                    root.render();
+                });
+            });
+
+            root.collection = new AnnotationCollection([], {comparator: null});
+            root.collection.altUrl = 'annotation/folder/' + folderId;
+            root.collection.fetch({
+                id: folderId,
+                sort: 'created',
+                sortDir: -1,
+                recurse: false
+            }).done(() => {
+                root.collection.each((model) => {
+                    root.users.add({'_id': model.get('creatorId')});
+                });
+                $.when.apply($, root.users.map((model) => {
+                    return model.fetch();
+                })).always(() => {
+                    root.render();
+                });
+            });
+        }
+    });
+}
+
+function addAccessControl(root) {
+    if (root.$('.g-edit-annotation-access').length === 0) {
+        if (root.$('.g-folder-actions-menu > .divider').length > 0) {
+            root.$('.g-folder-actions-menu > .divider').before(
+                '<li role="presentation">' +
+                    '<a class="g-edit-annotation-access" role="menuitem">' +
+                        '<i class="icon-lock"></i>' +
+                        'Annotation access control' +
+                    '</a>' +
+                '</li>'
+            );
+        } else {
+            root.$('.g-folder-actions-menu > .dropdown-header').after(
+                '<li role="presentation">' +
+                    '<a class="g-edit-annotation-access" role="menuitem">' +
+                        '<i class="icon-lock"></i>' +
+                        'Annotation access control' +
+                    '</a>' +
+                '</li>' +
+                '<li class="divider" role="presentation">'
+            );
+        }
+        root.events['click .g-edit-annotation-access'] = editAnnotAccess;
+        root.delegateEvents();
+    }
+}
+
+function editAnnotAccess() {
+    const model = this.recurseCollection.at(0).clone();
+    model.get('annotation').name = 'Your Annotations';
+    model.save = () => {};
+    model.updateAccess = (settings) => {
+        const access = {
+            access: model.get('access'),
+            public: model.get('public'),
+            publicFlags: model.get('publicFlags')
+        };
+        if (settings.recurse) {
+            this.recurseCollection.each((loopModel) => {
+                loopModel.set(access);
+                loopModel.updateAccess();
+            });
+        } else {
+            this.collection.each((loopModel) => {
+                loopModel.set(access);
+                loopModel.updateAccess();
+            });
+        }
+
+        this.collection.fetch(null, true);
+        this.recurseCollection.fetch(null, true);
+        model.trigger('g:accessListSaved');
+    };
+    model.fetchAccess(true)
+        .done(() => {
+            new AccessWidget({
+                el: $('#g-dialog-container'),
+                modelType: 'annotation',
+                model,
+                hideRecurseOption: false,
+                parentView: this
+            }).on('g:accessListSaved', () => {
+                this.collection.fetch(null, true);
+                this.recurseCollection.fetch(null, true);
+            });
+        });
+}
+
+export default HierarchyWidget;
\ No newline at end of file

From e3d7e98bcbe4f2323bb297fdfbe74e9b65b6dc8f Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 1 Aug 2022 13:02:41 -0400
Subject: [PATCH 02/17] Add missing newline

---
 .../web_client/views/hierarchyWidget.js                         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
index d5d922227..a1251e0aa 100644
--- a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
@@ -147,4 +147,4 @@ function editAnnotAccess() {
         });
 }
 
-export default HierarchyWidget;
\ No newline at end of file
+export default HierarchyWidget;

From f6dcd6ce2f2cd6bf4ec3b73e6c2965f8846024d2 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 1 Aug 2022 13:16:36 -0400
Subject: [PATCH 03/17] Fix linting issues

---
 .../rest/annotation.py                              | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index 74dede488..a7485cbfd 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -20,8 +20,8 @@
 
 import cherrypy
 import orjson
-
 from bson.objectid import ObjectId
+
 from girder import logger
 from girder.api import access
 from girder.api.describe import Description, autoDescribeRoute, describeRoute
@@ -561,7 +561,8 @@ def deleteItemAnnotations(self, item):
                 count += 1
         return count
 
-    def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sort=False, sortDir=False):
+    def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sort=False,
+                             sortDir=False):
         recursivePipeline = [
             {'$graphLookup': {
                 'from': 'folder',
@@ -619,12 +620,11 @@ def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sor
 
         return Annotation().collection.aggregate(pipeline)
 
-
     @autoDescribeRoute(
         Description('Check if there are any annotations from the items in a folder')
         .param('id', 'The ID of the folder', required=True, paramType='path')
         .param('recurse', 'Whether or not to recursively check '
-            'subfolders for annotations', required=False, default=True, dataType='boolean')
+               'subfolders for annotations', required=False, default=True, dataType='boolean')
         .errorResponse()
     )
     @access.public
@@ -636,19 +636,18 @@ def existFolderAnnotations(self, id, recurse):
         except StopIteration:
             yield False
 
-
     @autoDescribeRoute(
         Description('Get the annotations from the items in a folder')
         .param('id', 'The ID of the folder', required=True, paramType='path')
         .param('recurse', 'Whether or not to retrieve all '
-            'annotations from subfolders', required=False, default=False, dataType='boolean')
+               'annotations from subfolders', required=False, default=False, dataType='boolean')
         .pagingParams(defaultSort='created', defaultSortDir=-1)
         .errorResponse()
     )
     @access.public
     def returnFolderAnnotations(self, id, recurse, limit, offset, sort):
         return self.getFolderAnnotations(id, recurse, self.getCurrentUser(), limit, offset,
-                                    sort[0][0], sort[0][1])
+                                         sort[0][0], sort[0][1])
 
     @autoDescribeRoute(
         Description('Report on old annotations.')

From 06302c7b0b353d82baab0882501703d6ab527a4f Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Wed, 10 Aug 2022 13:03:21 -0400
Subject: [PATCH 04/17] Replace `yield` with `return`

---
 .../girder_large_image_annotation/rest/annotation.py          | 4 ++--
 .../web_client/views/hierarchyWidget.js                       | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index a7485cbfd..a16e2ea97 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -632,9 +632,9 @@ def existFolderAnnotations(self, id, recurse):
         annotations = self.getFolderAnnotations(id, recurse, self.getCurrentUser(), 1)
         try:
             next(annotations)
-            yield True
+            return True
         except StopIteration:
-            yield False
+            return False
 
     @autoDescribeRoute(
         Description('Get the annotations from the items in a folder')
diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
index a1251e0aa..d254b3ea2 100644
--- a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
@@ -37,7 +37,7 @@ function fetchCollections(root, folderId) {
             recurse: true
         }
     }).done((resp) => {
-        if (resp[0]) {
+        if (resp) {
             root.users = new UserCollection();
 
             root.recurseCollection = new AnnotationCollection([], {comparator: null});

From d350560a06ec47e6fb41ec41a32c955bd52257e6 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Wed, 10 Aug 2022 13:08:05 -0400
Subject: [PATCH 05/17] Add hierarchy widget to index to import it

---
 .../girder_large_image_annotation/web_client/views/index.js     | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/index.js b/girder_annotation/girder_large_image_annotation/web_client/views/index.js
index 1ce32c57f..2b3497580 100644
--- a/girder_annotation/girder_large_image_annotation/web_client/views/index.js
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/index.js
@@ -1,6 +1,7 @@
 import * as viewers from '@girder/large_image/views/imageViewerWidget';
 
 import ConfigView from './configView';
+import HierarchyWidget from './hierarchyWidget';
 import ImageViewerSelectWidget from './imageViewerSelectWidget';
 import ItemListWidget from './itemList';
 import ImageViewerWidgetAnnotationExtension from './imageViewerWidget/base';
@@ -15,6 +16,7 @@ for (var key in viewers) {
 
 export {
     ConfigView,
+    HierarchyWidget,
     ImageViewerSelectWidget,
     ItemListWidget,
     viewers as ViewerWidget

From 0e1adec4d5c6f864878ba4320499a33d8c1e5e9c Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Wed, 10 Aug 2022 14:07:46 -0400
Subject: [PATCH 06/17] Add count method for girder count header

---
 .../rest/annotation.py                        | 26 ++++++++++++++-----
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index a16e2ea97..1bea4beae 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -562,7 +562,7 @@ def deleteItemAnnotations(self, item):
         return count
 
     def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sort=False,
-                             sortDir=False):
+                             sortDir=False, count=False):
         recursivePipeline = [
             {'$graphLookup': {
                 'from': 'folder',
@@ -614,9 +614,12 @@ def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sor
                 ] + accessPipeline
             }},
         ]
-        pipeline = pipeline + [{'$sort': {sort: sortDir}}] if sort else pipeline
-        pipeline = pipeline + [{'$skip': offset}] if offset else pipeline
-        pipeline = pipeline + [{'$limit': limit}] if limit else pipeline
+        if count:
+            pipeline += [{'$count': 'count'}]
+        else:
+            pipeline = pipeline + [{'$sort': {sort: sortDir}}] if sort else pipeline
+            pipeline = pipeline + [{'$skip': offset}] if offset else pipeline
+            pipeline = pipeline + [{'$limit': limit}] if limit else pipeline
 
         return Annotation().collection.aggregate(pipeline)
 
@@ -646,8 +649,19 @@ def existFolderAnnotations(self, id, recurse):
     )
     @access.public
     def returnFolderAnnotations(self, id, recurse, limit, offset, sort):
-        return self.getFolderAnnotations(id, recurse, self.getCurrentUser(), limit, offset,
-                                         sort[0][0], sort[0][1])
+        annotations = self.getFolderAnnotations(id, recurse, self.getCurrentUser(), limit, offset,
+                                                sort[0][0], sort[0][1])
+
+        def count():
+            try:
+                return next(self.getFolderAnnotations(id, recurse, self.getCurrentUser(),
+                                                      count=True))['count']
+            except StopIteration:
+                # If there are no values to iterate over, the count is 0 and should be returned
+                return 0
+
+        annotations.count = count
+        return annotations
 
     @autoDescribeRoute(
         Description('Report on old annotations.')

From dd6f410a1bee883f229d3343533b6349a4378c25 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Fri, 12 Aug 2022 17:57:07 -0400
Subject: [PATCH 07/17] Make endpoint to set access list for folder annots

---
 .../rest/annotation.py                        |  29 ++++
 .../web_client/views/hierarchyWidget.js       | 127 ++++++------------
 2 files changed, 70 insertions(+), 86 deletions(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index 1bea4beae..8d6180710 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -61,6 +61,7 @@ def __init__(self):
         self.route('DELETE', ('item', ':id'), self.deleteItemAnnotations)
         self.route('GET', ('folder', ':id'), self.returnFolderAnnotations)
         self.route('GET', ('folder', ':id', 'present'), self.existFolderAnnotations)
+        self.route('PUT', ('folder', ':id', 'access'), self.setFolderAnnotationAccess)
         self.route('GET', ('old',), self.getOldAnnotations)
         self.route('DELETE', ('old',), self.deleteOldAnnotations)
         self.route('GET', ('counts',), self.getItemListAnnotationCounts)
@@ -663,6 +664,34 @@ def count():
         annotations.count = count
         return annotations
 
+    @autoDescribeRoute(
+        Description('Set the access for all the annotations from the items in a folder')
+        .param('id', 'The ID of the folder', required=True, paramType='path')
+        .param('access', 'The JSON-encoded access control list.')
+        .param('public', 'Whether the annotation should be publicly visible.',
+               dataType='boolean', required=False)
+        .param('recurse', 'Whether or not to retrieve all '
+               'annotations from subfolders', required=False, default=False, dataType='boolean')
+        .errorResponse('ID was invalid.')
+    )
+    @access.user
+    def setFolderAnnotationAccess(self, id, params):
+        user = self.getCurrentUser()
+        access = json.loads(params['access'])
+        public = self.boolParam('public', params, False)
+        for annotation in self.getFolderAnnotations(id, params['recurse'], user):
+            annot = Annotation().load(annotation['_id'], user=user, getElements=False)
+            annot = Annotation().setPublic(annot, public)
+            annot = Annotation().setAccessList(
+                annot, access, save=False, user=user)
+            Annotation().update({'_id': annot['_id']}, {'$set': {
+                key: annot[key] for key in ('access', 'public', 'publicFlags')
+                if key in annot
+            }})
+            yield annot
+
+
+
     @autoDescribeRoute(
         Description('Report on old annotations.')
         .param('age', 'The minimum age in days.', required=False,
diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
index d254b3ea2..7be5cac56 100644
--- a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
@@ -4,77 +4,35 @@ import { wrap } from '@girder/core/utilities/PluginUtils';
 import { restRequest } from '@girder/core/rest';
 import AccessWidget from '@girder/core/views/widgets/AccessWidget';
 import HierarchyWidget from '@girder/core/views/widgets/HierarchyWidget';
-import UserCollection from '@girder/core/collections/UserCollection';
 
-import AnnotationCollection from '../collections/AnnotationCollection';
+import AnnotationModel from '../models/AnnotationModel';
 
 wrap(HierarchyWidget, 'initialize', function (initialize, settings) {
     initialize.call(this, settings);
 
-    if (this.parentModel.get('_modelType') === 'folder') {
-        fetchCollections(this, this.parentModel.id);
-    }
     this.folderListView.on('g:folderClicked', () => {
-        fetchCollections(this, this.parentModel.id);
-        addAccessControl(this);
+        ownAnnotation(this, this.parentModel.id);
     });
 });
 
 wrap(HierarchyWidget, 'render', function (render) {
     render.call(this);
 
-    if (this.parentModel.get('_modelType') === 'folder' && this.recurseCollection) {
-        addAccessControl(this);
+    if (this.parentModel.get('_modelType') === 'folder') {
+        ownAnnotation(this, this.parentModel.id);
     }
 });
 
-function fetchCollections(root, folderId) {
+function ownAnnotation(root, folderId) {
     restRequest({
         type: 'GET',
         url: 'annotation/folder/' + folderId + '/present',
         data: {
-            id: folderId,
             recurse: true
         }
-    }).done((resp) => {
-        if (resp) {
-            root.users = new UserCollection();
-
-            root.recurseCollection = new AnnotationCollection([], {comparator: null});
-            root.recurseCollection.altUrl = 'annotation/folder/' + folderId;
-            root.recurseCollection.fetch({
-                id: folderId,
-                sort: 'created',
-                sortDir: -1,
-                recurse: true
-            }).done(() => {
-                root.recurseCollection.each((model) => {
-                    root.users.add({'_id': model.get('creatorId')});
-                });
-                $.when.apply($, root.users.map((model) => {
-                    return model.fetch();
-                })).always(() => {
-                    root.render();
-                });
-            });
-
-            root.collection = new AnnotationCollection([], {comparator: null});
-            root.collection.altUrl = 'annotation/folder/' + folderId;
-            root.collection.fetch({
-                id: folderId,
-                sort: 'created',
-                sortDir: -1,
-                recurse: false
-            }).done(() => {
-                root.collection.each((model) => {
-                    root.users.add({'_id': model.get('creatorId')});
-                });
-                $.when.apply($, root.users.map((model) => {
-                    return model.fetch();
-                })).always(() => {
-                    root.render();
-                });
-            });
+    }).done((ownsAnnot) => {
+        if (ownsAnnot) {
+            addAccessControl(root);
         }
     });
 }
@@ -107,44 +65,41 @@ function addAccessControl(root) {
 }
 
 function editAnnotAccess() {
-    const model = this.recurseCollection.at(0).clone();
-    model.get('annotation').name = 'Your Annotations';
-    model.save = () => {};
-    model.updateAccess = (settings) => {
-        const access = {
-            access: model.get('access'),
-            public: model.get('public'),
-            publicFlags: model.get('publicFlags')
-        };
-        if (settings.recurse) {
-            this.recurseCollection.each((loopModel) => {
-                loopModel.set(access);
-                loopModel.updateAccess();
-            });
-        } else {
-            this.collection.each((loopModel) => {
-                loopModel.set(access);
-                loopModel.updateAccess();
-            });
+    restRequest({
+        type: 'GET',
+        url: 'annotation/folder/' + this.parentModel.get('_id'),
+        data: {
+            recurse: true,
+            limit: 1
         }
-
-        this.collection.fetch(null, true);
-        this.recurseCollection.fetch(null, true);
-        model.trigger('g:accessListSaved');
-    };
-    model.fetchAccess(true)
-        .done(() => {
-            new AccessWidget({
-                el: $('#g-dialog-container'),
-                modelType: 'annotation',
-                model,
-                hideRecurseOption: false,
-                parentView: this
-            }).on('g:accessListSaved', () => {
-                this.collection.fetch(null, true);
-                this.recurseCollection.fetch(null, true);
+    }).done((resp) => {
+        const model = new AnnotationModel(resp[0]);
+        model.get('annotation').name = 'Your Annotations';
+        model.save = () => {};
+        model.updateAccess = (settings) => {
+            const access = {
+                access: model.get('access'),
+                public: model.get('public'),
+                publicFlags: model.get('publicFlags')
+            };
+            const defaultUpdateModel = new AnnotationModel();
+            defaultUpdateModel.id = this.parentModel.get('_id');
+            defaultUpdateModel.altUrl = 'annotation/folder';
+            defaultUpdateModel.set(access);
+            defaultUpdateModel.updateAccess(settings);
+            model.trigger('g:accessListSaved');
+        };
+        model.fetchAccess(true)
+            .done(() => {
+                new AccessWidget({
+                    el: $('#g-dialog-container'),
+                    modelType: 'annotation',
+                    model,
+                    hideRecurseOption: false,
+                    parentView: this
+                });
             });
-        });
+    });
 }
 
 export default HierarchyWidget;

From b23186743fb9dd1e0eab16dbadd17e9f8e297894 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 08:30:34 -0400
Subject: [PATCH 08/17] Fix lint error

---
 .../web_client/views/hierarchyWidget.js                         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
index 7be5cac56..ad9a906d0 100644
--- a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
@@ -91,7 +91,7 @@ function editAnnotAccess() {
         };
         model.fetchAccess(true)
             .done(() => {
-                new AccessWidget({
+                AccessWidget({
                     el: $('#g-dialog-container'),
                     modelType: 'annotation',
                     model,

From 329af9fd6ecd43aaf3fba6839e9d42dd864b266c Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 09:09:15 -0400
Subject: [PATCH 09/17] Improve endpoint user expectations

---
 .../rest/annotation.py                         | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index 8d6180710..c517d7cf4 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -625,7 +625,7 @@ def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sor
         return Annotation().collection.aggregate(pipeline)
 
     @autoDescribeRoute(
-        Description('Check if there are any annotations from the items in a folder')
+        Description('Check if the user owns any annotations for the items in a folder')
         .param('id', 'The ID of the folder', required=True, paramType='path')
         .param('recurse', 'Whether or not to recursively check '
                'subfolders for annotations', required=False, default=True, dataType='boolean')
@@ -633,7 +633,10 @@ def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sor
     )
     @access.public
     def existFolderAnnotations(self, id, recurse):
-        annotations = self.getFolderAnnotations(id, recurse, self.getCurrentUser(), 1)
+        user = self.getCurrentUser()
+        if not user:
+            return []
+        annotations = self.getFolderAnnotations(id, recurse, user, 1)
         try:
             next(annotations)
             return True
@@ -641,7 +644,7 @@ def existFolderAnnotations(self, id, recurse):
             return False
 
     @autoDescribeRoute(
-        Description('Get the annotations from the items in a folder')
+        Description('Get the user-owned annotations from the items in a folder')
         .param('id', 'The ID of the folder', required=True, paramType='path')
         .param('recurse', 'Whether or not to retrieve all '
                'annotations from subfolders', required=False, default=False, dataType='boolean')
@@ -650,7 +653,10 @@ def existFolderAnnotations(self, id, recurse):
     )
     @access.public
     def returnFolderAnnotations(self, id, recurse, limit, offset, sort):
-        annotations = self.getFolderAnnotations(id, recurse, self.getCurrentUser(), limit, offset,
+        user = self.getCurrentUser()
+        if not user:
+            return []
+        annotations = self.getFolderAnnotations(id, recurse, user, limit, offset,
                                                 sort[0][0], sort[0][1])
 
         def count():
@@ -665,7 +671,7 @@ def count():
         return annotations
 
     @autoDescribeRoute(
-        Description('Set the access for all the annotations from the items in a folder')
+        Description('Set the access for all the user-owned annotations from the items in a folder')
         .param('id', 'The ID of the folder', required=True, paramType='path')
         .param('access', 'The JSON-encoded access control list.')
         .param('public', 'Whether the annotation should be publicly visible.',
@@ -677,6 +683,8 @@ def count():
     @access.user
     def setFolderAnnotationAccess(self, id, params):
         user = self.getCurrentUser()
+        if not user:
+            return []
         access = json.loads(params['access'])
         public = self.boolParam('public', params, False)
         for annotation in self.getFolderAnnotations(id, params['recurse'], user):

From ed036e94698fdfb345c5b1cf0a22714aa5872cea Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 09:09:43 -0400
Subject: [PATCH 10/17] Fix lint

---
 .../girder_large_image_annotation/rest/annotation.py             | 1 -
 1 file changed, 1 deletion(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index c517d7cf4..e3e6e993a 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -699,7 +699,6 @@ def setFolderAnnotationAccess(self, id, params):
             yield annot
 
 
-
     @autoDescribeRoute(
         Description('Report on old annotations.')
         .param('age', 'The minimum age in days.', required=False,

From cbed60e3e393585e95c13c7408f352f955620d43 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 09:16:37 -0400
Subject: [PATCH 11/17] Remove extra line

---
 .../girder_large_image_annotation/rest/annotation.py             | 1 -
 1 file changed, 1 deletion(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index e3e6e993a..4005b3a7b 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -698,7 +698,6 @@ def setFolderAnnotationAccess(self, id, params):
             }})
             yield annot
 
-
     @autoDescribeRoute(
         Description('Report on old annotations.')
         .param('age', 'The minimum age in days.', required=False,

From b832046561c11500fadb771332b99b7183017105 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 10:05:00 -0400
Subject: [PATCH 12/17] Fix issue from lint fix

---
 .../web_client/views/hierarchyWidget.js                         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
index ad9a906d0..93589a4d4 100644
--- a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
@@ -91,7 +91,7 @@ function editAnnotAccess() {
         };
         model.fetchAccess(true)
             .done(() => {
-                AccessWidget({
+                new AccessWidget({// eslint-disable-line no-new
                     el: $('#g-dialog-container'),
                     modelType: 'annotation',
                     model,

From 6ee1943b93ebfc13d337db1161312be28db0b9c9 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 15:23:57 -0400
Subject: [PATCH 13/17] Fix duplicate annotation returns from pipeline

---
 .../girder_large_image_annotation/rest/annotation.py  | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index 4005b3a7b..84de00149 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -573,7 +573,11 @@ def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sor
                 'as': '__children'
             }},
             {'$unwind': {'path': '$__children'}},
-            {'$replaceRoot': {'newRoot': '$__children'}}] if recurse else []
+            {'$replaceRoot': {'newRoot': '$__children'}},
+            {'$unionWith': {
+                'coll': 'folder',
+                'pipeline': [{'$match': {'_id': ObjectId(id)}}]
+            }}] if recurse else []
         accessPipeline = [
             {'$match': {
                 '$or': [
@@ -596,10 +600,7 @@ def getFolderAnnotations(self, id, recurse, user, limit=False, offset=False, sor
                 'coll': 'folder',
                 'pipeline': [{'$match': {'_id': ObjectId(id)}}] +
                 recursivePipeline +
-                [{'$unionWith': {
-                    'coll': 'folder',
-                    'pipeline': [{'$match': {'_id': ObjectId(id)}}]
-                }}, {'$lookup': {
+                [{'$lookup': {
                     'from': 'item',
                     'localField': '_id',
                     'foreignField': 'folderId',

From 666ee38323f8f183e15a21c2412883bfdeb31646 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 15:38:56 -0400
Subject: [PATCH 14/17] Add time limit and count to update access endpoint

---
 .../girder_large_image_annotation/rest/annotation.py        | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index 84de00149..372cea27b 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -683,11 +683,13 @@ def count():
     )
     @access.user
     def setFolderAnnotationAccess(self, id, params):
+        setResponseTimeLimit(86400)
         user = self.getCurrentUser()
         if not user:
             return []
         access = json.loads(params['access'])
         public = self.boolParam('public', params, False)
+        count = 0
         for annotation in self.getFolderAnnotations(id, params['recurse'], user):
             annot = Annotation().load(annotation['_id'], user=user, getElements=False)
             annot = Annotation().setPublic(annot, public)
@@ -697,7 +699,9 @@ def setFolderAnnotationAccess(self, id, params):
                 key: annot[key] for key in ('access', 'public', 'publicFlags')
                 if key in annot
             }})
-            yield annot
+            count += 1
+
+        return {'updated': count}
 
     @autoDescribeRoute(
         Description('Report on old annotations.')

From 7b3786f24fe03b378c406b82c82ca3c66764b050 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 15:40:41 -0400
Subject: [PATCH 15/17] Remove default value from `setAccessList` call

---
 .../girder_large_image_annotation/rest/annotation.py            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/girder_annotation/girder_large_image_annotation/rest/annotation.py b/girder_annotation/girder_large_image_annotation/rest/annotation.py
index 372cea27b..1e61eeaa4 100644
--- a/girder_annotation/girder_large_image_annotation/rest/annotation.py
+++ b/girder_annotation/girder_large_image_annotation/rest/annotation.py
@@ -694,7 +694,7 @@ def setFolderAnnotationAccess(self, id, params):
             annot = Annotation().load(annotation['_id'], user=user, getElements=False)
             annot = Annotation().setPublic(annot, public)
             annot = Annotation().setAccessList(
-                annot, access, save=False, user=user)
+                annot, access, user=user)
             Annotation().update({'_id': annot['_id']}, {'$set': {
                 key: annot[key] for key in ('access', 'public', 'publicFlags')
                 if key in annot

From 62a6b5041663b20462f482a849c6f59b5d0664ef Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 18:27:07 -0400
Subject: [PATCH 16/17] Remove unnecessary `HierarchyWidget` wrapper

---
 .../web_client/views/hierarchyWidget.js                   | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
index 93589a4d4..8070e3a0a 100644
--- a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
@@ -7,14 +7,6 @@ import HierarchyWidget from '@girder/core/views/widgets/HierarchyWidget';
 
 import AnnotationModel from '../models/AnnotationModel';
 
-wrap(HierarchyWidget, 'initialize', function (initialize, settings) {
-    initialize.call(this, settings);
-
-    this.folderListView.on('g:folderClicked', () => {
-        ownAnnotation(this, this.parentModel.id);
-    });
-});
-
 wrap(HierarchyWidget, 'render', function (render) {
     render.call(this);
 

From 5337f0a24959467f815d44f8db4b4ece5f8a4c01 Mon Sep 17 00:00:00 2001
From: eagw <emi.gradywillis@kitware.com>
Date: Mon, 15 Aug 2022 18:28:54 -0400
Subject: [PATCH 17/17] Fix HTML inconsistency

---
 .../web_client/views/hierarchyWidget.js                      | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
index 8070e3a0a..e28f8cb56 100644
--- a/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
+++ b/girder_annotation/girder_large_image_annotation/web_client/views/hierarchyWidget.js
@@ -41,14 +41,13 @@ function addAccessControl(root) {
                 '</li>'
             );
         } else {
-            root.$('.g-folder-actions-menu > .dropdown-header').after(
+            root.$('ul.g-folder-actions-menu').append(
                 '<li role="presentation">' +
                     '<a class="g-edit-annotation-access" role="menuitem">' +
                         '<i class="icon-lock"></i>' +
                         'Annotation access control' +
                     '</a>' +
-                '</li>' +
-                '<li class="divider" role="presentation">'
+                '</li>'
             );
         }
         root.events['click .g-edit-annotation-access'] = editAnnotAccess;