Merge pull request #415 from UW-GAC/feature/sensitive-data

Add sensitive data tracking to dbGaP and CDSA workspaces

primed/cdsa/forms.py

@@ -98,6 +98,13 @@ class Meta:
 class CDSAWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
     """Form for `CDSAWorkspace` objects."""
 
+    is_sensitive = forms.TypedChoiceField(
+        coerce=lambda x: x == "True",
+        choices=((True, "Primary"), (False, "Component")),
+        widget=forms.RadioSelect,
+        label="Sensitive data?",
+    )
+
     class Meta:
         model = models.CDSAWorkspace
         fields = (
@@ -107,6 +114,7 @@ class Meta:
             "data_use_modifiers",
             "disease_term",
             "data_use_limitations",
+            "is_sensitive",
             "acknowledgments",
             "available_data",
             "disease_term",

primed/cdsa/migrations/0012_cdsaworkspace_is_sensitive_and_more.py

@@ -0,0 +1,33 @@
+# Generated by Django 4.2.8 on 2024-01-30 00:48
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("cdsa", "0011_signedagreement_add_replaced_status"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="cdsaworkspace",
+            name="is_sensitive",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether this workspace contains sensitive data.",
+                verbose_name="Sensitive?",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name="historicalcdsaworkspace",
+            name="is_sensitive",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether this workspace contains sensitive data.",
+                verbose_name="Sensitive?",
+            ),
+            preserve_default=False,
+        ),
+    ]

primed/cdsa/models.py

@@ -329,6 +329,10 @@ class CDSAWorkspace(
         help_text="Data available in this accession.",
         blank=True,
     )
+    is_sensitive = models.BooleanField(
+        verbose_name="Sensitive?",
+        help_text="Indicator of whether this workspace contains sensitive data.",
+    )
 
     class Meta:
         verbose_name = " CDSA workspace"

primed/cdsa/tables.py

@@ -310,6 +310,7 @@ class CDSAWorkspaceStaffTable(tables.Table):
         verbose_name="DUO modifiers",
         linkify_item=True,
     )
+    cdsaworkspace__is_sensitive = BooleanIconColumn(orderable=False)
     is_shared = WorkspaceSharedWithConsortiumColumn()
 
     class Meta:
@@ -320,6 +321,7 @@ class Meta:
             "cdsaworkspace__study",
             "cdsaworkspace__data_use_permission__abbreviation",
             "cdsaworkspace__data_use_modifiers",
+            "cdsaworkspace__is_sensitive",
         )
         order_by = ("name",)
 
@@ -337,6 +339,7 @@ class CDSAWorkspaceUserTable(tables.Table):
         transform=lambda x: x.abbreviation,
         verbose_name="DUO modifiers",
     )
+    cdsaworkspace__is_sensitive = BooleanIconColumn(orderable=False)
     is_shared = WorkspaceSharedWithConsortiumColumn()
 
     class Meta:
@@ -347,5 +350,6 @@ class Meta:
             "cdsaworkspace__study",
             "cdsaworkspace__data_use_permission__abbreviation",
             "cdsaworkspace__data_use_modifiers",
+            "cdsaworkspace__is_sensitive",
         )
         order_by = ("name",)

primed/cdsa/tests/factories.py

@@ -112,6 +112,7 @@ class CDSAWorkspaceFactory(DjangoModelFactory):
     requested_by = SubFactory(UserFactory)
     data_use_permission = SubFactory(DataUsePermissionFactory)
     workspace = SubFactory(WorkspaceFactory, workspace_type="cdsa")
+    is_sensitive = Faker("boolean")
 
     @post_generation
     def authorization_domains(self, create, extracted, **kwargs):

primed/cdsa/tests/test_forms.py

@@ -513,6 +513,7 @@ def test_valid(self):
             "data_use_permission": self.duo_permission,
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertTrue(form.is_valid())
@@ -527,6 +528,7 @@ def test_valid_with_one_data_use_modifier(self):
             "data_use_modifier": DataUseModifier.objects.all(),
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertTrue(form.is_valid())
@@ -541,6 +543,7 @@ def test_valid_with_two_data_use_modifiers(self):
             "data_use_modifier": DataUseModifier.objects.all(),
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertTrue(form.is_valid())
@@ -554,6 +557,7 @@ def test_invalid_missing_workspace(self):
             "data_use_permission": self.duo_permission,
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertFalse(form.is_valid())
@@ -571,6 +575,7 @@ def test_invalid_missing_study(self):
             "data_use_permission": self.duo_permission,
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertFalse(form.is_valid())
@@ -588,6 +593,7 @@ def test_invalid_missing_requested_by(self):
             "data_use_permission": self.duo_permission,
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertFalse(form.is_valid())
@@ -605,6 +611,7 @@ def test_invalid_missing_data_use_permission(self):
             # "data_use_permission": self.duo_permission,
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertFalse(form.is_valid())
@@ -622,6 +629,7 @@ def test_invalid_missing_data_use_limitations(self):
             "data_use_permission": self.duo_permission,
             # "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertFalse(form.is_valid())
@@ -639,6 +647,7 @@ def test_invalid_missing_acknowledgments(self):
             "data_use_permission": self.duo_permission,
             "data_use_limitations": "test limitations",
             # "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertFalse(form.is_valid())
@@ -647,6 +656,24 @@ def test_invalid_missing_acknowledgments(self):
         self.assertEqual(len(form.errors["acknowledgments"]), 1)
         self.assertIn("required", form.errors["acknowledgments"][0])
 
+    def test_invalid_missing_is_sensitive(self):
+        """Form is valid? when missing is_sensitive."""
+        form_data = {
+            "workspace": self.workspace,
+            "study": self.study,
+            "requested_by": self.requester,
+            "data_use_permission": self.duo_permission,
+            "data_use_limitations": "test limitations",
+            "acknowledgments": "test acknowledgmnts",
+            # "is_sensitive": False,
+        }
+        form = self.form_class(data=form_data)
+        self.assertFalse(form.is_valid())
+        self.assertEqual(len(form.errors), 1)
+        self.assertIn("is_sensitive", form.errors)
+        self.assertEqual(len(form.errors["is_sensitive"]), 1)
+        self.assertIn("required", form.errors["is_sensitive"][0])
+
     def test_invalid_duplicate_workspace(self):
         """Form is invalid with a duplicated workspace."""
         cdsa_workspace = factories.CDSAWorkspaceFactory.create()
@@ -657,6 +684,7 @@ def test_invalid_duplicate_workspace(self):
             "data_use_permission": self.duo_permission,
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertFalse(form.is_valid())
@@ -676,6 +704,7 @@ def test_valid_one_available_data(self):
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "available_data": [available_data],
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertTrue(form.is_valid())
@@ -691,6 +720,7 @@ def test_valid_two_available_data(self):
             "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "available_data": available_data,
+            "is_sensitive": False,
         }
         form = self.form_class(data=form_data)
         self.assertTrue(form.is_valid())

primed/cdsa/tests/test_models.py

@@ -620,6 +620,7 @@ def test_model_saving(self):
             acknowledgments="test acknowledgments",
             requested_by=requester,
             workspace=workspace,
+            is_sensitive=False,
         )
         instance.save()
         self.assertIsInstance(instance, models.CDSAWorkspace)
@@ -629,24 +630,6 @@ def test_str_method(self):
         instance = factories.CDSAWorkspaceFactory.create()
         self.assertIsInstance(instance.__str__(), str)
 
-    def test_can_add_data_use_permission(self):
-        """Saving a model with data_use_permission set is valid."""
-        workspace = WorkspaceFactory.create()
-        study = StudyFactory.create()
-        requester = UserFactory.create()
-        data_use_permission = DataUsePermissionFactory.create()
-        instance = models.CDSAWorkspace(
-            workspace=workspace,
-            study=study,
-            data_use_limitations="test limitations",
-            acknowledgments="test acknowledgments",
-            requested_by=requester,
-            data_use_permission=data_use_permission,
-        )
-        instance.save()
-        self.assertIsInstance(instance, models.CDSAWorkspace)
-        self.assertEqual(instance.data_use_permission, data_use_permission)
-
     def test_can_add_data_use_modifiers(self):
         """Saving a model with data_use_permission and data_use_modifiers set is valid."""
         data_use_permission = DataUsePermissionFactory.create()

primed/cdsa/tests/test_views.py

@@ -6188,6 +6188,7 @@ def test_creates_upload_workspace_without_duos(self):
                 "workspacedata-0-data_use_limitations": "test limitations",
                 "workspacedata-0-acknowledgments": "test acknowledgments",
                 "workspacedata-0-requested_by": self.requester.pk,
+                "workspacedata-0-is_sensitive": False,
             },
         )
         self.assertEqual(response.status_code, 302)
@@ -6244,6 +6245,7 @@ def test_creates_upload_workspace_with_duo_modifiers(self):
                     data_use_modifier_2.pk,
                 ],
                 "workspacedata-0-requested_by": self.requester.pk,
+                "workspacedata-0-is_sensitive": False,
             },
         )
         self.assertEqual(response.status_code, 302)
@@ -6289,6 +6291,7 @@ def test_creates_upload_workspace_with_disease_term(self):
                 "workspacedata-0-data_use_permission": data_use_permission.pk,
                 "workspacedata-0-disease_term": "foo",
                 "workspacedata-0-requested_by": self.requester.pk,
+                "workspacedata-0-is_sensitive": False,
             },
         )
         self.assertEqual(response.status_code, 302)

primed/dbgap/forms.py

@@ -30,6 +30,13 @@ class Meta:
 class dbGaPWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
     """Form for a dbGaPWorkspace object."""
 
+    is_sensitive = forms.TypedChoiceField(
+        coerce=lambda x: x == "True",
+        choices=((True, "Primary"), (False, "Component")),
+        widget=forms.RadioSelect,
+        label="Sensitive data?",
+    )
+
     class Meta:
         model = models.dbGaPWorkspace
         fields = (
@@ -39,6 +46,7 @@ class Meta:
             "dbgap_consent_abbreviation",
             "dbgap_consent_code",
             "data_use_limitations",
+            "is_sensitive",
             "acknowledgments",
             "data_use_permission",
             "disease_term",

primed/dbgap/migrations/0009_dbgapworkspace_is_sensitive_and_more.py

@@ -0,0 +1,33 @@
+# Generated by Django 4.2.8 on 2024-01-30 00:48
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("dbgap", "0008_dbgapapplication_anvil_access_group_verbose"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="dbgapworkspace",
+            name="is_sensitive",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether this workspace contains sensitive data.",
+                verbose_name="Sensitive?",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name="historicaldbgapworkspace",
+            name="is_sensitive",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether this workspace contains sensitive data.",
+                verbose_name="Sensitive?",
+            ),
+            preserve_default=False,
+        ),
+    ]

primed/dbgap/models.py

@@ -111,6 +111,10 @@ class dbGaPWorkspace(
         help_text="Data available in this accession.",
         blank=True,
     )
+    is_sensitive = models.BooleanField(
+        verbose_name="Sensitive?",
+        help_text="Indicator of whether this workspace contains sensitive data.",
+    )
 
     class Meta:
         # Add a white space to prevent autocapitalization fo the "d" in "dbGaP".

primed/dbgap/tables.py

@@ -5,7 +5,10 @@
 from django.template import Context, Template
 from django.utils.html import format_html
 
-from primed.primed_anvil.tables import WorkspaceSharedWithConsortiumColumn
+from primed.primed_anvil.tables import (
+    BooleanIconColumn,
+    WorkspaceSharedWithConsortiumColumn,
+)
 
 from . import models
 
@@ -93,6 +96,7 @@ class dbGaPWorkspaceStaffTable(tables.Table):
         verbose_name="Approved DARs",
         orderable=False,
     )
+    dbgapworkspace__is_sensitive = BooleanIconColumn(orderable=False)
     is_shared = WorkspaceSharedWithConsortiumColumn()
 
     class Meta:
@@ -103,6 +107,7 @@ class Meta:
             "dbgap_accession",
             "dbgapworkspace__dbgap_consent_abbreviation",
             "number_approved_dars",
+            "dbgapworkspace__is_sensitive",
             "is_shared",
         )
         order_by = ("name",)
@@ -133,6 +138,7 @@ class dbGaPWorkspaceUserTable(tables.Table):
     dbgapworkspace__dbgap_consent_abbreviation = tables.columns.Column(
         verbose_name="Consent"
     )
+    dbgapworkspace__is_sensitive = BooleanIconColumn(orderable=False)
     is_shared = WorkspaceSharedWithConsortiumColumn()
 
     class Meta:
@@ -142,6 +148,7 @@ class Meta:
             "billing_project",
             "dbgap_accession",
             "dbgapworkspace__dbgap_consent_abbreviation",
+            "dbgapworkspace__is_sensitive",
             "is_shared",
         )
         order_by = ("name",)