Merge pull request #506 from UW-GAC/feature/cdsa-data-affiliate-addit…

…ional-limitations

Track additional limitations associated with Data Affiliate CDSAs

add_cdsa_example_data.py

@@ -8,14 +8,18 @@
     ManagedGroupFactory,
 )
 from django.conf import settings
+from django.core.management import call_command
 
 from primed.cdsa.tests import factories
-from primed.duo.tests.factories import DataUseModifierFactory, DataUsePermissionFactory
+from primed.duo.models import DataUseModifier, DataUsePermission
 from primed.primed_anvil.models import Study, StudySite
 from primed.primed_anvil.tests.factories import StudyFactory, StudySiteFactory
 from primed.users.models import User
 from primed.users.tests.factories import UserFactory
 
+# Load duos
+call_command("load_duo")
+
 # Create major versions
 major_version = factories.AgreementMajorVersionFactory.create(version=1)
 
@@ -28,8 +32,8 @@
 )
 
 # Create a couple signed CDSAs.
-dup = DataUsePermissionFactory.create(abbreviation="GRU")
-dum = DataUseModifierFactory.create(abbreviation="NPU")
+dup = DataUsePermission.objects.get(abbreviation="GRU")
+dum = DataUseModifier.objects.get(abbreviation="NPU")
 
 # create the CDSA auth group
 cdsa_group = ManagedGroupFactory.create(name=settings.ANVIL_CDSA_GROUP_NAME)
@@ -113,6 +117,7 @@
     signed_agreement__signing_institution="UW",
     study=Study.objects.get(short_name="MESA"),
     signed_agreement__version=v10,
+    additional_limitations="This data can only be used for testing the app.",
 )
 GroupGroupMembershipFactory.create(
     parent_group=cdsa_group, child_group=cdsa_1006.signed_agreement.anvil_access_group
@@ -219,5 +224,6 @@
     workspace__name="DEMO_PRIMED_CDSA_MESA_2",
     study=Study.objects.get(short_name="MESA"),
     data_use_permission=dup,
+    additional_limitations="Additional limitations for workspace.",
 )
 cdsa_workspace_2.data_use_modifiers.add(dum)

primed/cdsa/adapters.py

@@ -18,3 +18,14 @@ class CDSAWorkspaceAdapter(BaseWorkspaceAdapter):
     workspace_data_model = models.CDSAWorkspace
     workspace_data_form_class = forms.CDSAWorkspaceForm
     workspace_detail_template_name = "cdsa/cdsaworkspace_detail.html"
+
+    def get_extra_detail_context_data(self, workspace, request):
+        # Get the primary CDSA for this study, assuming it exists.
+        extra_context = {}
+        # Data use limitations from CDSA
+        try:
+            extra_context["primary_cdsa"] = workspace.cdsaworkspace.get_primary_cdsa()
+        except models.DataAffiliateAgreement.DoesNotExist:
+            extra_context["primary_cdsa"] = None
+
+        return extra_context

primed/cdsa/forms.py

@@ -77,6 +77,7 @@ class Meta:
         fields = (
             "signed_agreement",
             "study",
+            "additional_limitations",
         )
         widgets = {
             "study": autocomplete.ModelSelect2(
@@ -114,7 +115,7 @@ class Meta:
             "data_use_permission",
             "data_use_modifiers",
             "disease_term",
-            "data_use_limitations",
+            "additional_limitations",
             "gsr_restricted",
             "acknowledgments",
             "available_data",

primed/cdsa/migrations/0015_dataaffiliateagreement_additional_limitations_and_more.py

@@ -0,0 +1,29 @@
+# Generated by Django 4.2.10 on 2024-03-12 21:38
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("cdsa", "0014_gsr_restricted_help_and_verbose"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="dataaffiliateagreement",
+            name="additional_limitations",
+            field=models.TextField(
+                blank=True,
+                help_text="Additional limitations on data use as specified in the signed CDSA.",
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicaldataaffiliateagreement",
+            name="additional_limitations",
+            field=models.TextField(
+                blank=True,
+                help_text="Additional limitations on data use as specified in the signed CDSA.",
+            ),
+        ),
+    ]

primed/cdsa/migrations/0016_rename_data_use_limitations_cdsaworkspace_additional_limitations_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.2.10 on 2024-03-14 18:35
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("cdsa", "0015_dataaffiliateagreement_additional_limitations_and_more"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="cdsaworkspace",
+            old_name="data_use_limitations",
+            new_name="additional_limitations",
+        ),
+        migrations.RenameField(
+            model_name="historicalcdsaworkspace",
+            old_name="data_use_limitations",
+            new_name="additional_limitations",
+        ),
+    ]

primed/cdsa/migrations/0017_alter_cdsaworkspace_additional_limitations_and_more.py

@@ -0,0 +1,32 @@
+# Generated by Django 4.2.10 on 2024-03-14 18:36
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "cdsa",
+            "0016_rename_data_use_limitations_cdsaworkspace_additional_limitations_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="cdsaworkspace",
+            name="additional_limitations",
+            field=models.TextField(
+                blank=True,
+                help_text="Additional data use limitations that cannot be captured by DUO.",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalcdsaworkspace",
+            name="additional_limitations",
+            field=models.TextField(
+                blank=True,
+                help_text="Additional data use limitations that cannot be captured by DUO.",
+            ),
+        ),
+    ]

primed/cdsa/models.py

@@ -277,13 +277,28 @@ class DataAffiliateAgreement(TimeStampedModel, AgreementTypeModel, models.Model)
         help_text="Study that this agreement is associated with.",
     )
     anvil_upload_group = models.ForeignKey(ManagedGroup, on_delete=models.PROTECT)
+    additional_limitations = models.TextField(
+        blank=True,
+        help_text="Additional limitations on data use as specified in the signed CDSA.",
+    )
 
     def get_absolute_url(self):
         return reverse(
             "cdsa:signed_agreements:data_affiliates:detail",
             kwargs={"cc_id": self.signed_agreement.cc_id},
         )
 
+    def clean(self):
+        super().clean()
+        if (
+            self.additional_limitations
+            and hasattr(self, "signed_agreement")
+            and not self.signed_agreement.is_primary
+        ):
+            raise ValidationError(
+                "Additional limitations are only allowed for primary agreements."
+            )
+
     def get_agreement_group(self):
         return self.study
 
@@ -318,8 +333,9 @@ class CDSAWorkspace(
         on_delete=models.PROTECT,
         help_text="The study associated with data in this workspace.",
     )
-    data_use_limitations = models.TextField(
-        help_text="""The full data use limitations for this workspace."""
+    additional_limitations = models.TextField(
+        help_text="""Additional data use limitations that cannot be captured by DUO.""",
+        blank=True,
     )
     acknowledgments = models.TextField(
         help_text="Acknowledgments associated with data in this workspace."
@@ -337,3 +353,12 @@ class CDSAWorkspace(
     class Meta:
         verbose_name = " CDSA workspace"
         verbose_name_plural = " CDSA workspaces"
+
+    def get_primary_cdsa(self):
+        """Return the primary, valid CDSA associated with this workspace."""
+        cdsa = DataAffiliateAgreement.objects.get(
+            study=self.study,
+            signed_agreement__is_primary=True,
+            signed_agreement__status=SignedAgreement.StatusChoices.ACTIVE,
+        )
+        return cdsa

primed/cdsa/tests/factories.py

@@ -107,7 +107,6 @@ class Meta:
 class CDSAWorkspaceFactory(DjangoModelFactory):
 
     study = SubFactory(StudyFactory)
-    data_use_limitations = Faker("paragraph")
     acknowledgments = Faker("paragraph")
     requested_by = SubFactory(UserFactory)
     data_use_permission = SubFactory(DataUsePermissionFactory)

primed/cdsa/tests/test_forms.py

@@ -1,6 +1,7 @@
 """Tests for the `cdsa` app."""
 
 from anvil_consortium_manager.tests.factories import WorkspaceFactory
+from django.core.exceptions import NON_FIELD_ERRORS
 from django.test import TestCase
 
 from primed.duo.models import DataUseModifier
@@ -416,6 +417,35 @@ def test_invalid_signed_agreement_wrong_type(self):
         self.assertEqual(len(form.errors["signed_agreement"]), 1)
         self.assertIn("expected type", form.errors["signed_agreement"][0])
 
+    def test_valid_primary_with_additional_limitations(self):
+        """Form is valid with necessary input."""
+        signed_agreement = factories.SignedAgreementFactory.create(
+            type=models.SignedAgreement.DATA_AFFILIATE, is_primary=True
+        )
+        form_data = {
+            "signed_agreement": signed_agreement,
+            "study": self.study,
+            "additional_limitations": "test limitations",
+        }
+        form = self.form_class(data=form_data)
+        self.assertTrue(form.is_valid())
+
+    def test_invalid_component_with_additional_limitations(self):
+        """Form is valid with necessary input."""
+        signed_agreement = factories.SignedAgreementFactory.create(
+            type=models.SignedAgreement.DATA_AFFILIATE, is_primary=False
+        )
+        form_data = {
+            "signed_agreement": signed_agreement,
+            "study": self.study,
+            "additional_limitations": "test limitations",
+        }
+        form = self.form_class(data=form_data)
+        self.assertFalse(form.is_valid())
+        self.assertIn(NON_FIELD_ERRORS, form.errors)
+        self.assertEqual(len(form.errors[NON_FIELD_ERRORS]), 1)
+        self.assertIn("only allowed for primary", form.errors[NON_FIELD_ERRORS][0])
+
 
 class NonDataAffiliateAgreementFormTest(TestCase):
     """Tests for the NonDataAffiliateAgreementForm class."""
@@ -511,7 +541,6 @@ def test_valid(self):
             "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -526,7 +555,6 @@ def test_valid_with_one_data_use_modifier(self):
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
             "data_use_modifier": DataUseModifier.objects.all(),
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -541,7 +569,6 @@ def test_valid_with_two_data_use_modifiers(self):
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
             "data_use_modifier": DataUseModifier.objects.all(),
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -555,7 +582,6 @@ def test_invalid_missing_workspace(self):
             "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -573,7 +599,6 @@ def test_invalid_missing_study(self):
             # "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -591,7 +616,6 @@ def test_invalid_missing_requested_by(self):
             "study": self.study,
             # "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -609,7 +633,6 @@ def test_invalid_missing_data_use_permission(self):
             "study": self.study,
             "requested_by": self.requester,
             # "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -620,23 +643,20 @@ def test_invalid_missing_data_use_permission(self):
         self.assertEqual(len(form.errors["data_use_permission"]), 1)
         self.assertIn("required", form.errors["data_use_permission"][0])
 
-    def test_invalid_missing_data_use_limitations(self):
+    def test_valid_additional_limitations(self):
         """Form is invalid when missing data_use_limitations."""
         form_data = {
             "workspace": self.workspace,
             "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            # "data_use_limitations": "test limitations",
+            "additional_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
         form = self.form_class(data=form_data)
-        self.assertFalse(form.is_valid())
-        self.assertEqual(len(form.errors), 1)
-        self.assertIn("data_use_limitations", form.errors)
-        self.assertEqual(len(form.errors["data_use_limitations"]), 1)
-        self.assertIn("required", form.errors["data_use_limitations"][0])
+        self.assertTrue(form.is_valid())
+        self.assertEqual(form.instance.additional_limitations, "test limitations")
 
     def test_invalid_missing_acknowledgments(self):
         """Form is invalid when missing acknowledgments."""
@@ -645,7 +665,6 @@ def test_invalid_missing_acknowledgments(self):
             "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             # "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -663,7 +682,6 @@ def test_invalid_missing_gsr_restricted(self):
             "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             # "gsr_restricted": False,
         }
@@ -682,7 +700,6 @@ def test_invalid_duplicate_workspace(self):
             "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "gsr_restricted": False,
         }
@@ -701,7 +718,6 @@ def test_valid_one_available_data(self):
             "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "available_data": [available_data],
             "gsr_restricted": False,
@@ -717,7 +733,6 @@ def test_valid_two_available_data(self):
             "study": self.study,
             "requested_by": self.requester,
             "data_use_permission": self.duo_permission,
-            "data_use_limitations": "test limitations",
             "acknowledgments": "test acknowledgmnts",
             "available_data": available_data,
             "gsr_restricted": False,