Merge branch 'dependabot/pip/django-allauth-0.61.1' of github.com:UW-…

…GAC/primed-django into dependabot/pip/django-allauth-0.61.1

.env.dist

@@ -23,3 +23,8 @@ DJANGO_EMAIL_PORT=
 DJANGO_EMAIL_HOST_USER=
 DJANGO_EMAIL_HOST_PASSWORD=
 DJANGO_EMAIL_USE_TLS=
+
+# drupal api
+DRUPAL_API_CLIENT_ID=
+DRUPAL_API_CLIENT_SECRET=
+DRUPAL_API_REL_PATH=

.github/workflows/ci.yml

@@ -50,7 +50,7 @@ jobs:
         # ahead of planned upgrades we can add versions as
         # needed
         python-version: [3.8]
-        mariadb-version: ["10.4"]
+        mariadb-version: ["10.4", "10.5"]
 
     services:
       mysql:

add_cdsa_example_data.py

@@ -8,14 +8,23 @@
     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 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)
 
@@ -28,11 +37,8 @@
 )
 
 # Create a couple signed CDSAs.
-dup = DataUsePermissionFactory.create(abbreviation="GRU")
-dum = DataUseModifierFactory.create(abbreviation="NPU")
-
-# create the CDSA auth group
-cdsa_group = ManagedGroupFactory.create(name=settings.ANVIL_CDSA_GROUP_NAME)
+dup = DataUsePermission.objects.get(abbreviation="GRU")
+dum = DataUseModifier.objects.get(abbreviation="NPU")
 
 # Create some study sites.
 StudySiteFactory.create(short_name="CC", full_name="Coordinating Center")
@@ -47,7 +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"),
 )
@@ -60,7 +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"),
 )
@@ -73,7 +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"),
 )
@@ -86,7 +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"),
 )
@@ -113,6 +119,8 @@
     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.",
+    requires_study_review=True,
 )
 GroupGroupMembershipFactory.create(
     parent_group=cdsa_group, child_group=cdsa_1006.signed_agreement.anvil_access_group
@@ -123,7 +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,
 )
@@ -136,7 +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,
 )
@@ -219,5 +227,17 @@
     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)
+
+
+# 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,
+)

add_data_prep_example_data.py

@@ -0,0 +1,44 @@
+# Temporary script to create some test data.
+# Run with: python manage.py shell < add_data_prep_example_data.py
+
+
+from primed.cdsa.tests.factories import CDSAWorkspaceFactory
+from primed.dbgap.tests.factories import dbGaPWorkspaceFactory
+from primed.miscellaneous_workspaces.tests import factories
+from primed.primed_anvil.tests.factories import StudyFactory
+
+# Create a dbGaP workspace.
+fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study")
+workspace_dbgap = dbGaPWorkspaceFactory.create(
+    dbgap_study_accession__dbgap_phs=7,
+    dbgap_study_accession__studies=[fhs],
+    dbgap_version=33,
+    dbgap_participant_set=12,
+    dbgap_consent_code=1,
+    dbgap_consent_abbreviation="HMB",
+    workspace__name="DBGAP_FHS_v33_p12_HMB",
+)
+
+# Create a data prep workspace.
+workspace_dbgap_prep = factories.DataPrepWorkspaceFactory.create(
+    target_workspace=workspace_dbgap.workspace,
+    workspace__name="DBGAP_FHS_v33_p12_HMB_PREP",
+)
+
+
+# Create a CDSA workspace.
+workspace_cdsa = CDSAWorkspaceFactory.create(
+    study__short_name="MESA",
+    workspace__name="CDSA_MESA_HMB",
+)
+
+# Create a data prep workspace.
+factories.DataPrepWorkspaceFactory.create(
+    target_workspace=workspace_cdsa.workspace,
+    workspace__name="CDSA_MESA_HMB_PREP_1",
+    is_active=False,
+)
+workspace_cdsa_prep = factories.DataPrepWorkspaceFactory.create(
+    target_workspace=workspace_cdsa.workspace,
+    workspace__name="CDSA_MESA_HMB_PREP_2",
+)

config/settings/base.py

@@ -85,6 +85,7 @@
     "simple_history",
     "dbbackup",
     "django_htmx",
+    "constance",
 ]
 
 LOCAL_APPS = [
@@ -205,6 +206,7 @@
                 "django.template.context_processors.static",
                 "django.template.context_processors.tz",
                 "django.contrib.messages.context_processors.messages",
+                "constance.context_processors.config",
                 "primed.utils.context_processors.settings_context",
             ],
         },
@@ -368,6 +370,17 @@
 # https://django-tables2.readthedocs.io/en/latest/pages/custom-rendering.html?highlight=django_tables2_template#available-templates
 DJANGO_TABLES2_TEMPLATE = "django_tables2/bootstrap5.html"
 
+# django-constance
+# ------------------------------------------------------------------------------
+CONSTANCE_CONFIG = {
+    "ANNOUNCEMENT_TEXT": ("", "Site-wide announcement message", str),
+}
+
+CONSTANCE_BACKEND = "constance.backends.database.DatabaseBackend"
+CONSTANCE_IGNORE_ADMIN_VERSION_CHECK = True
+# CONSTANCE_DATABASE_CACHE_BACKEND = "default"
+CONSTANCE_DATABASE_CACHE_AUTOFILL_TIMEOUT = None
+
 # django-anvil-consortium-manager
 # ------------------------------------------------------------------------------
 ANVIL_API_SERVICE_ACCOUNT_FILE = env("ANVIL_API_SERVICE_ACCOUNT_FILE")
@@ -390,3 +403,13 @@
 # Specify the subject for AnVIL account verification emails.
 ANVIL_ACCOUNT_LINK_EMAIL_SUBJECT = "Verify your AnVIL account email"
 ANVIL_ACCOUNT_VERIFY_NOTIFICATION_EMAIL = "[email protected]"
+
+DRUPAL_API_CLIENT_ID = env("DRUPAL_API_CLIENT_ID", default="")
+DRUPAL_API_CLIENT_SECRET = env("DRUPAL_API_CLIENT_SECRET", default="")
+DRUPAL_API_REL_PATH = env("DRUPAL_API_REL_PATH", default="mockapi")
+DRUPAL_DATA_AUDIT_DEACTIVATE_USERS = env(
+    "DRUPAL_DATA_AUDIT_DEACTIVATE_USERS", default=False
+)
+DRUPAL_DATA_AUDIT_REMOVE_USER_SITES = env(
+    "DRUPAL_DATA_AUDIT_REMOVE_USER_SITES", default=False
+)

primed/cdsa/adapters.py

@@ -1,5 +1,8 @@
 from anvil_consortium_manager.adapters.workspace import BaseWorkspaceAdapter
 from anvil_consortium_manager.forms import WorkspaceForm
+from anvil_consortium_manager.models import Workspace
+
+from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceUserTable
 
 from . import forms, models, tables
 
@@ -18,3 +21,22 @@ 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):
+        extra_context = {}
+        associated_data_prep = Workspace.objects.filter(
+            dataprepworkspace__target_workspace=workspace
+        )
+        extra_context["associated_data_prep_workspaces"] = DataPrepWorkspaceUserTable(
+            associated_data_prep
+        )
+        extra_context["data_prep_active"] = associated_data_prep.filter(
+            dataprepworkspace__is_active=True
+        ).exists()
+        # Get the primary CDSA for this study, assuming it exists.
+        try:
+            extra_context["primary_cdsa"] = workspace.cdsaworkspace.get_primary_cdsa()
+        except models.DataAffiliateAgreement.DoesNotExist:
+            extra_context["primary_cdsa"] = None
+
+        return extra_context

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()