From ddd2f4f005374de3f04209c0fd18ae092faff786 Mon Sep 17 00:00:00 2001
From: Jake Wagoner <jakewagoneredu@gmail.com>
Date: Tue, 16 Apr 2024 10:37:42 -0600
Subject: [PATCH 1/8] Update get_contents

---
 shapeworks_cloud/core/models.py | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/shapeworks_cloud/core/models.py b/shapeworks_cloud/core/models.py
index de6d0532..214c0d24 100644
--- a/shapeworks_cloud/core/models.py
+++ b/shapeworks_cloud/core/models.py
@@ -25,6 +25,9 @@ def get_contents(self):
         def truncate_filename(filename):
             return filename.split('/')[-1]
 
+        def truncate_anatomy(anatomy_type):
+            return anatomy_type.replace('anatomy_', '')
+
         group_list = [
             Segmentation.objects.filter(subject__dataset=self),
             Mesh.objects.filter(subject__dataset=self),
@@ -34,12 +37,20 @@ def truncate_filename(filename):
 
         for shape_group in group_list:
             for shape in shape_group:
-                ret.append(
-                    {
+                anatomy = truncate_anatomy(
+                    (shape.anatomy_type if hasattr(shape, 'anatomy_type') else shape.modality)
+                )
+                if (shape.subject.name in [s['name'] for s in ret]):
+                    subject = next((s for s in ret if s['name'] == shape.subject.name), None)
+                    subject['shape_' + anatomy] = truncate_filename(shape.file.name)
+                else:
+                    subject = {
                         'name': shape.subject.name,  # type: ignore
-                        'shape_1': truncate_filename(shape.file.name),  # type: ignore
+                        'shape_' + anatomy: truncate_filename(shape.file.name),  # type: ignore
                     }
-                )
+                    ret.append(subject)
+
+        print(ret)
         return ret
 
 

From 1f5d3cdf9aa711ab21ee21b3ce509abb6767ecd4 Mon Sep 17 00:00:00 2001
From: Jake Wagoner <jakewagoneredu@gmail.com>
Date: Tue, 16 Apr 2024 11:42:17 -0600
Subject: [PATCH 2/8] Update groom fix

---
 shapeworks_cloud/core/models.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/shapeworks_cloud/core/models.py b/shapeworks_cloud/core/models.py
index 214c0d24..fa6da621 100644
--- a/shapeworks_cloud/core/models.py
+++ b/shapeworks_cloud/core/models.py
@@ -37,12 +37,15 @@ def truncate_anatomy(anatomy_type):
 
         for shape_group in group_list:
             for shape in shape_group:
-                anatomy = truncate_anatomy(
-                    (shape.anatomy_type if hasattr(shape, 'anatomy_type') else shape.modality)
-                )
+                if hasattr(shape, 'anatomy_type'):
+                    anatomy = truncate_anatomy(shape.anatomy_type)
+                    label = 'shape_'
+                else:
+                    anatomy = shape.modality
+                    label = 'image_'
                 if (shape.subject.name in [s['name'] for s in ret]):
                     subject = next((s for s in ret if s['name'] == shape.subject.name), None)
-                    subject['shape_' + anatomy] = truncate_filename(shape.file.name)
+                    subject[label + anatomy] = truncate_filename(shape.file.name)
                 else:
                     subject = {
                         'name': shape.subject.name,  # type: ignore
@@ -50,7 +53,6 @@ def truncate_anatomy(anatomy_type):
                     }
                     ret.append(subject)
 
-        print(ret)
         return ret
 
 

From 114f7ecf7ac141949b0d9d4dd6e386a9e0b101f9 Mon Sep 17 00:00:00 2001
From: Jake Wagoner <jakewagoneredu@gmail.com>
Date: Tue, 16 Apr 2024 11:51:27 -0600
Subject: [PATCH 3/8] Client side read-only

---
 web/shapeworks/src/components/Analysis/PCA.vue       | 5 +++--
 web/shapeworks/src/components/DeepSSM/DeepSSMTab.vue | 3 ++-
 web/shapeworks/src/views/Main.vue                    | 9 ++++++++-
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/web/shapeworks/src/components/Analysis/PCA.vue b/web/shapeworks/src/components/Analysis/PCA.vue
index 0fa62aec..e7901be7 100644
--- a/web/shapeworks/src/components/Analysis/PCA.vue
+++ b/web/shapeworks/src/components/Analysis/PCA.vue
@@ -192,7 +192,8 @@ import { groupBy } from '../../helper';
         pcaInfo,
         animate,
         menu,
-        showConfirmation
+        showConfirmation,
+        selectedProject,
       };
     },
   };
@@ -230,7 +231,7 @@ import { groupBy } from '../../helper';
           bottom
           right
         >
-          <template v-slot:activator="{ on, attrs }">
+          <template v-slot:activator="{ on, attrs }" v-if="selectedProject && !selectedProject.readonly">
             <v-btn
               dark
               icon
diff --git a/web/shapeworks/src/components/DeepSSM/DeepSSMTab.vue b/web/shapeworks/src/components/DeepSSM/DeepSSMTab.vue
index e9c65c8f..b231196a 100644
--- a/web/shapeworks/src/components/DeepSSM/DeepSSMTab.vue
+++ b/web/shapeworks/src/components/DeepSSM/DeepSSMTab.vue
@@ -180,6 +180,7 @@ export default {
         });
 
         return {
+            selectedProject,
             openExpansionPanel,
             controlsTabs,
             prepData,
@@ -257,7 +258,7 @@ export default {
     <div class="pa-3" v-else>
         <div class="loading-dialog"><v-dialog v-model="deepSSMLoadingData" width="10%">Fetching results...  <v-progress-circular indeterminate align-center></v-progress-circular></v-dialog></div>
         <v-expansion-panels v-model="openExpansionPanel">
-            <v-expansion-panel>
+            <v-expansion-panel v-if="selectedProject && !selectedProject.readonly">
                 <v-expansion-panel-header>Controls</v-expansion-panel-header>
                 <v-expansion-panel-content>
                     <v-tabs v-model="controlsTabs">
diff --git a/web/shapeworks/src/views/Main.vue b/web/shapeworks/src/views/Main.vue
index 9ed8ce06..24db4fec 100644
--- a/web/shapeworks/src/views/Main.vue
+++ b/web/shapeworks/src/views/Main.vue
@@ -603,7 +603,14 @@ export default {
                         </v-tab-item>
                         <v-tab href="#info">Info</v-tab>
                         <v-tab-item value="info">
-                            <info-tab />
+                            <span
+                                v-if="selectedProject && selectedProject.readonly"
+                                class="red--text pa-3"
+                            >
+                                This project is read only.
+                                No operations may be performed.
+                            </span>
+                            <info-tab v-else />
                         </v-tab-item>
                         <v-tab href="#groom">Groom</v-tab>
                         <v-tab-item value="groom">

From af93ca68fb5fc8e6f92a2209a888c41e6de3fb6e Mon Sep 17 00:00:00 2001
From: Jake Wagoner <jakewagoneredu@gmail.com>
Date: Tue, 16 Apr 2024 11:53:02 -0600
Subject: [PATCH 4/8] Lint fix

---
 shapeworks_cloud/core/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/shapeworks_cloud/core/models.py b/shapeworks_cloud/core/models.py
index fa6da621..13c5848f 100644
--- a/shapeworks_cloud/core/models.py
+++ b/shapeworks_cloud/core/models.py
@@ -43,7 +43,7 @@ def truncate_anatomy(anatomy_type):
                 else:
                     anatomy = shape.modality
                     label = 'image_'
-                if (shape.subject.name in [s['name'] for s in ret]):
+                if shape.subject.name in [s['name'] for s in ret]:
                     subject = next((s for s in ret if s['name'] == shape.subject.name), None)
                     subject[label + anatomy] = truncate_filename(shape.file.name)
                 else:

From 3501e3aa4b0c9a411d60a464e62c3e54fa42ed3f Mon Sep 17 00:00:00 2001
From: Jake Wagoner <jakewagoneredu@gmail.com>
Date: Tue, 16 Apr 2024 11:59:15 -0600
Subject: [PATCH 5/8] Update hanging "shape_" assumption for new projects

---
 shapeworks_cloud/core/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/shapeworks_cloud/core/models.py b/shapeworks_cloud/core/models.py
index 13c5848f..bcf2fc20 100644
--- a/shapeworks_cloud/core/models.py
+++ b/shapeworks_cloud/core/models.py
@@ -49,7 +49,7 @@ def truncate_anatomy(anatomy_type):
                 else:
                     subject = {
                         'name': shape.subject.name,  # type: ignore
-                        'shape_' + anatomy: truncate_filename(shape.file.name),  # type: ignore
+                        label + anatomy: truncate_filename(shape.file.name),  # type: ignore
                     }
                     ret.append(subject)
 

From 6dd52af6bbb83dc30f0bb0a1e26e29d7147a6d68 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 16 Apr 2024 18:06:28 +0000
Subject: [PATCH 6/8] Add server-side action prevention for read-only projects

---
 shapeworks_cloud/core/rest.py | 42 +++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/shapeworks_cloud/core/rest.py b/shapeworks_cloud/core/rest.py
index d226be62..657cffea 100644
--- a/shapeworks_cloud/core/rest.py
+++ b/shapeworks_cloud/core/rest.py
@@ -227,6 +227,13 @@ def get_serializer_class(self):
         else:
             return serializers.ProjectSerializer
 
+    def edit_allowed(self, request, **kwargs):
+        project = self.get_object()
+        user = self.request.user
+        if project.readonly and not user.is_staff:
+            return False
+        return True
+
     def create(self, request, **kwargs):
         data = request.data
         if 'creator' not in data:
@@ -283,6 +290,11 @@ def clone(self, request, **kwargs):
         methods=['POST'],
     )
     def set_thumbnail(self, request, **kwargs):
+        if not self.edit_allowed(request, **kwargs):
+            return Response(
+                'Project is read only.',
+                status=status.HTTP_403_FORBIDDEN,
+            )
         project = self.get_object()
         form_data = request.data
         encoded_thumbnail = form_data.get('encoding')
@@ -312,6 +324,11 @@ def download(self, request, **kwargs):
         methods=['POST'],
     )
     def set_landmarks(self, request, **kwargs):
+        if not self.edit_allowed(request, **kwargs):
+            return Response(
+                'Project is read only.',
+                status=status.HTTP_403_FORBIDDEN,
+            )
         project = self.get_object()
         form_data = request.data
         landmarks_info = form_data.get('info')
@@ -372,6 +389,11 @@ def set_landmarks(self, request, **kwargs):
         methods=['POST'],
     )
     def set_constraints(self, request, **kwargs):
+        if not self.edit_allowed(request, **kwargs):
+            return Response(
+                'Project is read only.',
+                status=status.HTTP_403_FORBIDDEN,
+            )
         project = self.get_object()
         form_data = request.data
         constraints_locations = form_data.get('locations')
@@ -411,6 +433,11 @@ def set_constraints(self, request, **kwargs):
         methods=['POST'],
     )
     def groom(self, request, **kwargs):
+        if not self.edit_allowed(request, **kwargs):
+            return Response(
+                'Project is read only.',
+                status=status.HTTP_403_FORBIDDEN,
+            )
         project = self.get_object()
         form_data = request.data
         form_data = {k: str(v) for k, v in form_data.items()}
@@ -437,6 +464,11 @@ def groom(self, request, **kwargs):
         methods=['POST'],
     )
     def optimize(self, request, **kwargs):
+        if not self.edit_allowed(request, **kwargs):
+            return Response(
+                'Project is read only.',
+                status=status.HTTP_403_FORBIDDEN,
+            )
         project = self.get_object()
         form_data = request.data
         form_data = {k: str(v) for k, v in form_data.items()}
@@ -475,6 +507,11 @@ def optimize(self, request, **kwargs):
         methods=['POST'],
     )
     def analyze(self, request, **kwargs):
+        if not self.edit_allowed(request, **kwargs):
+            return Response(
+                'Project is read only.',
+                status=status.HTTP_403_FORBIDDEN,
+            )
         project = self.get_object()
 
         params = request.data
@@ -518,6 +555,11 @@ def analyze(self, request, **kwargs):
         methods=['POST'],
     )
     def deepssm_run(self, request, **kwargs):
+        if not self.edit_allowed(request, **kwargs):
+            return Response(
+                'Project is read only.',
+                status=status.HTTP_403_FORBIDDEN,
+            )
         project = self.get_object()
         form_data = request.data
         form_data = {k: str(v) for k, v in form_data.items()}

From be9e8ca840645bdd84e031f3f2b2be34439dd76f Mon Sep 17 00:00:00 2001
From: Jake Wagoner <jakewagoneredu@gmail.com>
Date: Tue, 16 Apr 2024 12:56:58 -0600
Subject: [PATCH 7/8] Linting and type ignore comments

---
 shapeworks_cloud/core/models.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/shapeworks_cloud/core/models.py b/shapeworks_cloud/core/models.py
index bcf2fc20..2fbcedb3 100644
--- a/shapeworks_cloud/core/models.py
+++ b/shapeworks_cloud/core/models.py
@@ -41,10 +41,12 @@ def truncate_anatomy(anatomy_type):
                     anatomy = truncate_anatomy(shape.anatomy_type)
                     label = 'shape_'
                 else:
-                    anatomy = shape.modality
+                    anatomy = shape.modality  # type: ignore
                     label = 'image_'
-                if shape.subject.name in [s['name'] for s in ret]:
-                    subject = next((s for s in ret if s['name'] == shape.subject.name), None)
+                if shape.subject.name in [s['name'] for s in ret]:  # type: ignore
+                    subject = next(
+                        (s for s in ret if s['name'] == shape.subject.name), None
+                    )  # type: ignore
                     subject[label + anatomy] = truncate_filename(shape.file.name)
                 else:
                     subject = {

From 587e81f6ef4770b094a2863a1fadc2f1ca4b661d Mon Sep 17 00:00:00 2001
From: Jake Wagoner <jakewagoneredu@gmail.com>
Date: Tue, 16 Apr 2024 13:10:00 -0600
Subject: [PATCH 8/8] Type fix #2

---
 shapeworks_cloud/core/models.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/shapeworks_cloud/core/models.py b/shapeworks_cloud/core/models.py
index 2fbcedb3..90b40e87 100644
--- a/shapeworks_cloud/core/models.py
+++ b/shapeworks_cloud/core/models.py
@@ -20,7 +20,7 @@ class Dataset(TimeStampedModel, models.Model):
     publications = models.TextField(blank=True, default='')
 
     def get_contents(self):
-        ret = []
+        ret = []  # type: ignore
 
         def truncate_filename(filename):
             return filename.split('/')[-1]
@@ -45,9 +45,9 @@ def truncate_anatomy(anatomy_type):
                     label = 'image_'
                 if shape.subject.name in [s['name'] for s in ret]:  # type: ignore
                     subject = next(
-                        (s for s in ret if s['name'] == shape.subject.name), None
-                    )  # type: ignore
-                    subject[label + anatomy] = truncate_filename(shape.file.name)
+                        (s for s in ret if s['name'] == shape.subject.name), None  # type: ignore
+                    )
+                    subject[label + anatomy] = truncate_filename(shape.file.name)  # type: ignore
                 else:
                     subject = {
                         'name': shape.subject.name,  # type: ignore