Merge pull request #509 from UW-GAC/feature/cdsa-requires-study-review

Add a requires_study_review field for DataAffiliateAgreements

add_cdsa_example_data.py

@@ -20,6 +20,11 @@
 # Load duos
 call_command("load_duo")
 
+# create the CDSA auth group
+cdsa_group = ManagedGroupFactory.create(name=settings.ANVIL_CDSA_GROUP_NAME)
+# Add PRIMED ADMINS group
+cc_admins_group = ManagedGroupFactory.create(name=settings.ANVIL_CC_ADMINS_GROUP_NAME)
+
 # Create major versions
 major_version = factories.AgreementMajorVersionFactory.create(version=1)
 
@@ -35,9 +40,6 @@
 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)
-
 # Create some study sites.
 StudySiteFactory.create(short_name="CC", full_name="Coordinating Center")
 StudySiteFactory.create(short_name="CARDINAL", full_name="CARDINAL")
@@ -51,7 +53,7 @@
     signed_agreement__representative=UserFactory.create(name="Ken Rice"),
     signed_agreement__signing_institution="UW",
     signed_agreement__representative_role="Contact PI",
-    signed_agreement__is_primary=True,
+    is_primary=True,
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CC"),
 )
@@ -64,7 +66,7 @@
     signed_agreement__representative=UserFactory.create(name="Sally Adebamowo"),
     signed_agreement__signing_institution="UM",
     signed_agreement__representative_role="Contact PI",
-    signed_agreement__is_primary=True,
+    is_primary=True,
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
@@ -77,7 +79,7 @@
     signed_agreement__representative=UserFactory.create(name="Bamidele Tayo"),
     signed_agreement__signing_institution="Loyola",
     signed_agreement__representative_role="Co-PI",
-    signed_agreement__is_primary=False,
+    is_primary=False,
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
@@ -90,7 +92,7 @@
     signed_agreement__representative=UserFactory.create(name="Brackie Mitchell"),
     signed_agreement__signing_institution="UM",
     signed_agreement__representative_role="Co-I",
-    signed_agreement__is_primary=False,
+    is_primary=False,
     signed_agreement__version=v11,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
@@ -118,6 +120,7 @@
     study=Study.objects.get(short_name="MESA"),
     signed_agreement__version=v10,
     additional_limitations="This data can only be used for testing the app.",
+    requires_study_review=True,
 )
 GroupGroupMembershipFactory.create(
     parent_group=cdsa_group, child_group=cdsa_1006.signed_agreement.anvil_access_group
@@ -128,7 +131,7 @@
     signed_agreement__representative=UserFactory.create(name="Wendy"),
     signed_agreement__signing_institution="JHU",
     signed_agreement__representative_role="Field Center PI",
-    signed_agreement__is_primary=False,
+    is_primary=False,
     study=Study.objects.get(short_name="MESA"),
     signed_agreement__version=v10,
 )
@@ -141,7 +144,7 @@
     signed_agreement__representative=UserFactory.create(name="Jerry"),
     signed_agreement__signing_institution="Lundquist",
     signed_agreement__representative_role="Analysis Center PI",
-    signed_agreement__is_primary=False,
+    is_primary=False,
     study=Study.objects.get(short_name="MESA"),
     signed_agreement__version=v10,
 )
@@ -227,3 +230,14 @@
     additional_limitations="Additional limitations for workspace.",
 )
 cdsa_workspace_2.data_use_modifiers.add(dum)
+
+
+# Add a workspace with no primary cdsa.
+cdsa_workspace_3 = factories.CDSAWorkspaceFactory.create(
+    workspace__billing_project__name="demo-primed-cdsa",
+    workspace__name="DEMO_PRIMED_CDSA_ARIC_1",
+    study=Study.objects.create(
+        short_name="ARIC", full_name="Atherosclerosis Risk in Communities"
+    ),
+    data_use_permission=dup,
+)

primed/cdsa/admin.py

@@ -46,13 +46,13 @@ class SignedAgreement(SimpleHistoryAdmin):
         "cc_id",
         "representative",
         "type",
-        "is_primary",
+        # "is_primary",
         "date_signed",
         "version",
     )
     list_filter = (
         "type",
-        "is_primary",
+        # "is_primary",
         "version",
         "status",
     )
@@ -79,7 +79,7 @@ class MemberAgreementAdmin(SimpleHistoryAdmin):
     )
     list_filter = (
         "study_site",
-        "signed_agreement__is_primary",
+        # "signed_agreement__is_primary",
         "signed_agreement__status",
     )
 
@@ -94,7 +94,7 @@ class DataAffiliateAgreementAdmin(SimpleHistoryAdmin):
     )
     list_filter = (
         "study",
-        "signed_agreement__is_primary",
+        # "signed_agreement__is_primary",
         "signed_agreement__status",
     )
 
@@ -108,7 +108,7 @@ class NonDataAffiliateAgreementAdmin(SimpleHistoryAdmin):
         "affiliation",
     )
     list_filter = (
-        "signed_agreement__is_primary",
+        # "signed_agreement__is_primary",
         "signed_agreement__status",
     )
 

primed/cdsa/audit/signed_agreement_audit.py

@@ -119,9 +119,6 @@ class SignedAgreementAccessAudit(PRIMEDAudit):
     PRIMARY_NOT_ACTIVE = "Primary agreement for this CDSA is not active."
 
     # Other errors
-    ERROR_NON_DATA_AFFILIATE_COMPONENT = (
-        "Non-data affiliate agreements must be primary."
-    )
     ERROR_OTHER_CASE = "Signed Agreement did not match any expected situations."
 
     results_table_class = SignedAgreementAccessAuditTable
@@ -218,23 +215,15 @@ def _audit_component_agreement(self, signed_agreement):
         if hasattr(signed_agreement, "memberagreement"):
             # Member
             primary_qs = models.SignedAgreement.objects.filter(
-                is_primary=True,
+                memberagreement__is_primary=True,
                 memberagreement__study_site=signed_agreement.memberagreement.study_site,
             )
         elif hasattr(signed_agreement, "dataaffiliateagreement"):
             # Data affiliate
             primary_qs = models.SignedAgreement.objects.filter(
-                is_primary=True,
+                dataaffiliateagreement__is_primary=True,
                 dataaffiliateagreement__study=signed_agreement.dataaffiliateagreement.study,
             )
-        elif hasattr(signed_agreement, "nondataaffiliateagreement"):
-            self.errors.append(
-                OtherError(
-                    signed_agreement=signed_agreement,
-                    note=self.ERROR_NON_DATA_AFFILIATE_COMPONENT,
-                )
-            )
-            return
         primary_exists = primary_qs.exists()
         primary_active = primary_qs.filter(
             status=models.SignedAgreement.StatusChoices.ACTIVE,
@@ -320,7 +309,8 @@ def _audit_component_agreement(self, signed_agreement):
         )  # pragma: no cover
 
     def _audit_signed_agreement(self, signed_agreement):
-        if signed_agreement.is_primary:
+        agreement_type = signed_agreement.get_agreement_type()
+        if not hasattr(agreement_type, "is_primary") or agreement_type.is_primary:
             self._audit_primary_agreement(signed_agreement)
         else:
             self._audit_component_agreement(signed_agreement)

primed/cdsa/audit/workspace_audit.py

@@ -153,7 +153,7 @@ def _audit_workspace(self, workspace):
             child_group=self.anvil_cdsa_group,
         ).exists()
         primary_qs = models.DataAffiliateAgreement.objects.filter(
-            study=workspace.study, signed_agreement__is_primary=True
+            study=workspace.study, is_primary=True
         )
         primary_exists = primary_qs.exists()
 

primed/cdsa/forms.py

@@ -22,12 +22,6 @@ class Meta:
 class SignedAgreementForm(Bootstrap5MediaFormMixin, forms.ModelForm):
     """Form for a SignedAgreement object."""
 
-    is_primary = forms.TypedChoiceField(
-        coerce=lambda x: x == "True",
-        choices=((True, "Primary"), (False, "Component")),
-        widget=forms.RadioSelect,
-        label="Agreement type",
-    )
     version = forms.ModelChoiceField(
         queryset=models.AgreementVersion.objects.filter(major_version__is_valid=True)
     )
@@ -41,7 +35,6 @@ class Meta:
             "signing_institution",
             "version",
             "date_signed",
-            "is_primary",
         )
         widgets = {
             "representative": autocomplete.ModelSelect2(
@@ -63,21 +56,38 @@ class Meta:
 
 
 class MemberAgreementForm(forms.ModelForm):
+    is_primary = forms.TypedChoiceField(
+        coerce=lambda x: x == "True",
+        choices=((True, "Primary"), (False, "Component")),
+        widget=forms.RadioSelect,
+        label="Agreement type",
+    )
+
     class Meta:
         model = models.MemberAgreement
         fields = (
             "signed_agreement",
             "study_site",
+            "is_primary",
         )
 
 
 class DataAffiliateAgreementForm(Bootstrap5MediaFormMixin, forms.ModelForm):
+    is_primary = forms.TypedChoiceField(
+        coerce=lambda x: x == "True",
+        choices=((True, "Primary"), (False, "Component")),
+        widget=forms.RadioSelect,
+        label="Agreement type",
+    )
+
     class Meta:
         model = models.DataAffiliateAgreement
         fields = (
             "signed_agreement",
             "study",
+            "is_primary",
             "additional_limitations",
+            "requires_study_review",
         )
         widgets = {
             "study": autocomplete.ModelSelect2(

primed/cdsa/helpers.py

@@ -13,7 +13,7 @@ def get_study_records_table():
     """Return the queryset for study records."""
     qs = models.DataAffiliateAgreement.objects.filter(
         signed_agreement__status=models.SignedAgreement.StatusChoices.ACTIVE,
-        signed_agreement__is_primary=True,
+        is_primary=True,
     )
     return tables.StudyRecordsTable(qs)
 

primed/cdsa/migrations/0018_dataaffiliateagreement_requires_study_review_and_more.py

@@ -0,0 +1,29 @@
+# Generated by Django 4.2.10 on 2024-03-15 20:48
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("cdsa", "0017_alter_cdsaworkspace_additional_limitations_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="dataaffiliateagreement",
+            name="requires_study_review",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether indicates investigators need to have an approved PRIMED paper proposal where this dataset was selected and approved in order to work with data brought under this CDSA.",
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicaldataaffiliateagreement",
+            name="requires_study_review",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether indicates investigators need to have an approved PRIMED paper proposal where this dataset was selected and approved in order to work with data brought under this CDSA.",
+            ),
+        ),
+    ]

primed/cdsa/migrations/0019_alter_signedagreement_is_primary.py

@@ -0,0 +1,29 @@
+# Generated by Django 4.2.10 on 2024-03-18 17:24
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("cdsa", "0018_dataaffiliateagreement_requires_study_review_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalsignedagreement",
+            name="is_primary",
+            field=models.BooleanField(
+                help_text="Indicator of whether this is a primary Agreement (and not a component Agreement).",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="signedagreement",
+            name="is_primary",
+            field=models.BooleanField(
+                help_text="Indicator of whether this is a primary Agreement (and not a component Agreement).",
+                null=True,
+            ),
+        ),
+    ]

primed/cdsa/migrations/0020_dataaffiliateagreement_is_primary_and_more.py

@@ -0,0 +1,49 @@
+# Generated by Django 4.2.10 on 2024-03-15 22:43
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("cdsa", "0019_alter_signedagreement_is_primary"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="dataaffiliateagreement",
+            name="is_primary",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether this is a primary Agreement (and not a component Agreement).",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name="historicaldataaffiliateagreement",
+            name="is_primary",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether this is a primary Agreement (and not a component Agreement).",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name="historicalmemberagreement",
+            name="is_primary",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether this is a primary Agreement (and not a component Agreement).",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name="memberagreement",
+            name="is_primary",
+            field=models.BooleanField(
+                default=False,
+                help_text="Indicator of whether this is a primary Agreement (and not a component Agreement).",
+            ),
+            preserve_default=False,
+        ),
+    ]