Merge pull request #649 from UW-GAC/main

Deploy to stage

.github/workflows/pip-compile.yml

@@ -6,6 +6,8 @@ on:
 
 jobs:
   update-requirements-files:
+    permissions:
+      pull-requests: write
     runs-on: ubuntu-latest
 
     steps:

add_cdsa_example_data.py

@@ -70,6 +70,7 @@
     signed_agreement__version=v10,
     study_site=cc,
 )
+cdsa_1001.signed_agreement.representative.study_sites.add(cc)
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1001.signed_agreement.anvil_access_group)
 
 cdsa_1002 = factories.MemberAgreementFactory.create(
@@ -81,6 +82,7 @@
     signed_agreement__version=v10,
     study_site=cardinal,
 )
+cdsa_1002.signed_agreement.representative.study_sites.add(cardinal)
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1002.signed_agreement.anvil_access_group)
 
 cdsa_1003 = factories.MemberAgreementFactory.create(

primed/primed_anvil/migrations/0007_studysite_member_group.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.2.13 on 2024-07-10 20:21
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('anvil_consortium_manager', '0019_accountuserarchive'),
+        ('primed_anvil', '0006_studysite_drupal_node_id'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='studysite',
+            name='member_group',
+            field=models.ForeignKey(blank=True, help_text='The AnVIL Managed Group associated with this site.', null=True, on_delete=django.db.models.deletion.PROTECT, to='anvil_consortium_manager.managedgroup'),
+        ),
+    ]

primed/primed_anvil/migrations/0008_alter_studysite_member_group.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.2.13 on 2024-07-10 20:24
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('anvil_consortium_manager', '0019_accountuserarchive'),
+        ('primed_anvil', '0007_studysite_member_group'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='studysite',
+            name='member_group',
+            field=models.OneToOneField(blank=True, help_text='The AnVIL Managed Group associated with this site.', null=True, on_delete=django.db.models.deletion.PROTECT, to='anvil_consortium_manager.managedgroup'),
+        ),
+    ]

primed/primed_anvil/models.py

@@ -1,3 +1,4 @@
+from anvil_consortium_manager.models import ManagedGroup
 from django.conf import settings
 from django.db import models
 from django.urls import reverse
@@ -37,6 +38,15 @@ class StudySite(TimeStampedModel, models.Model):
     full_name = models.CharField(max_length=255)
     """The full name of the Study Sites."""
 
+    member_group = models.OneToOneField(
+        ManagedGroup,
+        on_delete=models.PROTECT,
+        help_text="The AnVIL Managed Group associated with this site.",
+        null=True,
+        blank=True,
+        unique=True,
+    )
+
     drupal_node_id = models.IntegerField(blank=True, null=True)
     """Reference node ID for entity in drupal"""
 

primed/primed_anvil/tables.py

@@ -156,8 +156,11 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, extra_columns=extra_columns, **kwargs)
 
 
-class UserAccountSingleGroupMembershipTable(tables.Table):
-    """A table with users and info about whether they are members of a group."""
+class UserAccountTable(tables.Table):
+    """A table for `User`s with `Account` information."""
+
+    name = tables.Column(linkify=True)
+    account = tables.Column(linkify=True, verbose_name="AnVIL account")
 
     class Meta:
         model = User
@@ -167,8 +170,13 @@ class Meta:
         )
         order_by = ("name",)
 
-    name = tables.Column(linkify=lambda record: record.get_absolute_url())
-    account = tables.Column(verbose_name="AnVIL account")
+
+class UserAccountSingleGroupMembershipTable(UserAccountTable):
+    """A table with users and info about whether they are members of a group."""
+
+    class Meta(UserAccountTable.Meta):
+        pass
+
     is_group_member = tables.BooleanColumn(verbose_name="Has access?", default=False)
 
     def __init__(self, *args, managed_group=None, **kwargs):

primed/primed_anvil/tests/test_models.py

@@ -1,5 +1,6 @@
 """Tests of models in the `primed_anvil` app."""
 
+from anvil_consortium_manager.tests.factories import ManagedGroupFactory
 from django.core.exceptions import ValidationError
 from django.db.utils import IntegrityError
 from django.test import TestCase
@@ -48,6 +49,7 @@ class StudySiteTest(TestCase):
     def test_model_saving(self):
         """Creation using the model constructor and .save() works."""
         instance = models.StudySite(full_name="Test name", short_name="TEST")
+        instance.full_clean()
         instance.save()
         self.assertIsInstance(instance, models.StudySite)
 
@@ -72,6 +74,24 @@ def test_unique_short_name(self):
         with self.assertRaises(IntegrityError):
             instance2.save()
 
+    def test_can_set_members_group(self):
+        member_group = ManagedGroupFactory.create()
+        instance = models.StudySite(full_name="Test name", short_name="TEST", member_group=member_group)
+        instance.full_clean()
+        instance.save()
+        self.assertIsInstance(instance, models.StudySite)
+
+    def test_same_member_group_different_sites(self):
+        member_group = ManagedGroupFactory.create()
+        factories.StudySiteFactory.create(member_group=member_group)
+        instance = factories.StudySiteFactory.build(member_group=member_group)
+        with self.assertRaises(ValidationError) as e:
+            instance.full_clean()
+        self.assertEqual(len(e.exception.message_dict), 1)
+        self.assertIn("member_group", e.exception.message_dict)
+        self.assertEqual(len(e.exception.message_dict["member_group"]), 1)
+        self.assertIn("Study site with this Member group already exists.", e.exception.message_dict["member_group"][0])
+
 
 class AvailableDataTest(TestCase):
     """Tests for the AvailableData model."""

primed/primed_anvil/tests/test_tables.py

@@ -255,6 +255,35 @@ def test_render_not_workspace(self):
             column.render(None, "foo", None)
 
 
+class UserAccountTableTest(TestCase):
+    """Tests for the UserAccountTable class."""
+
+    def setUp(self):
+        self.managed_group = ManagedGroupFactory.create()
+
+    def test_row_count_with_no_objects(self):
+        table = tables.UserAccountTable(User.objects.all())
+        self.assertEqual(len(table.rows), 0)
+
+    def test_row_count_with_one_object(self):
+        UserFactory.create()
+        table = tables.UserAccountTable(User.objects.all())
+        self.assertEqual(len(table.rows), 1)
+
+    def test_row_count_with_two_objects(self):
+        UserFactory.create_batch(2)
+        table = tables.UserAccountTable(User.objects.all())
+        self.assertEqual(len(table.rows), 2)
+
+    def test_ordering(self):
+        """Users are ordered alphabetically by name"""
+        user_foo = UserFactory.create(name="Foo")
+        user_bar = UserFactory.create(name="Bar")
+        table = tables.UserAccountTable(User.objects.all())
+        self.assertEqual(table.data[0], user_bar)
+        self.assertEqual(table.data[1], user_foo)
+
+
 class UserAccountSingleGroupMembershipTableTest(TestCase):
     """Tests for the UserAccountSingleGroupMembershipTable class."""
 

primed/primed_anvil/tests/test_views.py

@@ -3,6 +3,7 @@
 from anvil_consortium_manager import models as acm_models
 from anvil_consortium_manager.tests.factories import (
     AccountFactory,
+    GroupAccountMembershipFactory,
     ManagedGroupFactory,
     WorkspaceGroupSharingFactory,
 )
@@ -17,13 +18,13 @@
 from django.test import RequestFactory, TestCase
 from django.urls import reverse
 
-from primed.cdsa.tables import CDSAWorkspaceStaffTable, CDSAWorkspaceUserTable
+from primed.cdsa.tables import CDSAWorkspaceStaffTable, CDSAWorkspaceUserTable, MemberAgreementTable
 from primed.cdsa.tests.factories import (
     CDSAWorkspaceFactory,
     DataAffiliateAgreementFactory,
     MemberAgreementFactory,
 )
-from primed.dbgap.tables import dbGaPWorkspaceStaffTable, dbGaPWorkspaceUserTable
+from primed.dbgap.tables import dbGaPApplicationTable, dbGaPWorkspaceStaffTable, dbGaPWorkspaceUserTable
 from primed.dbgap.tests.factories import (
     dbGaPApplicationFactory,
     dbGaPStudyAccessionFactory,
@@ -843,6 +844,22 @@ def test_view_status_code_with_invalid_pk(self):
         with self.assertRaises(Http404):
             self.get_view()(request, pk=obj.pk + 1)
 
+    def test_table_classes(self):
+        """Table classes are correct."""
+        obj = self.model_factory.create()
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(obj.pk))
+        self.assertIn("tables", response.context_data)
+        self.assertEqual(len(response.context_data["tables"]), 4)
+        self.assertIsInstance(response.context_data["tables"][0], tables.UserAccountTable)
+        self.assertEqual(len(response.context_data["tables"][0].data), 0)
+        self.assertIsInstance(response.context_data["tables"][1], dbGaPApplicationTable)
+        self.assertEqual(len(response.context_data["tables"][1].data), 0)
+        self.assertIsInstance(response.context_data["tables"][2], MemberAgreementTable)
+        self.assertEqual(len(response.context_data["tables"][2].data), 0)
+        self.assertIsInstance(response.context_data["tables"][3], tables.AccountTable)
+        self.assertEqual(len(response.context_data["tables"][3].data), 0)
+
     def test_site_user_table(self):
         """Contains a table of site users with the correct users."""
         obj = self.model_factory.create()
@@ -883,6 +900,45 @@ def test_cdsa_table(self):
         self.assertIn(site_cdsa, table.data)
         self.assertNotIn(other_cdsa, table.data)
 
+    def test_site_user_table_when_member_group_is_set(self):
+        """The site user table is the correct class when the member group is set."""
+        member_group = ManagedGroupFactory.create()
+        obj = self.model_factory.create(member_group=member_group)
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(obj.pk))
+        table = response.context_data["tables"][0]
+        self.assertIsInstance(table, tables.UserAccountSingleGroupMembershipTable)
+        self.assertEqual(table.managed_group, member_group)
+
+    def test_member_group_table(self):
+        member_group = ManagedGroupFactory.create()
+        obj = self.model_factory.create(member_group=member_group)
+        account = AccountFactory.create(verified=True)
+        GroupAccountMembershipFactory.create(account=account, group=member_group)
+        other_account = AccountFactory.create(verified=True)
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(obj.pk))
+        table = response.context_data["tables"][3]
+        self.assertEqual(len(table.rows), 1)
+        self.assertIn(account, table.data)
+        self.assertNotIn(other_account, table.data)
+
+    def test_member_table_group_not_set(self):
+        obj = self.model_factory.create()
+        AccountFactory.create(verified=True)
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(obj.pk))
+        table = response.context_data["tables"][3]
+        self.assertEqual(len(table.rows), 0)
+
+    def test_link_to_member_group(self):
+        """Response includes a link to the member group if it exists."""
+        member_group = ManagedGroupFactory.create()
+        obj = self.model_factory.create(member_group=member_group)
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(obj.pk))
+        self.assertContains(response, member_group.get_absolute_url())
+
 
 class StudySiteListTest(TestCase):
     """Tests for the StudySiteList view."""

primed/primed_anvil/views.py

@@ -5,7 +5,7 @@
     AnVILConsortiumManagerStaffViewRequired,
     AnVILConsortiumManagerViewRequired,
 )
-from anvil_consortium_manager.models import AnVILProjectManagerAccess, Workspace
+from anvil_consortium_manager.models import Account, AnVILProjectManagerAccess, Workspace
 from dal import autocomplete
 from django.contrib.auth import get_user_model
 from django.contrib.auth.mixins import LoginRequiredMixin
@@ -33,7 +33,6 @@
     OpenAccessWorkspaceStaffTable,
     OpenAccessWorkspaceUserTable,
 )
-from primed.users.tables import UserTable
 
 from . import filters, helpers, models, tables
 
@@ -124,19 +123,25 @@ class StudySiteDetail(AnVILConsortiumManagerStaffViewRequired, MultiTableMixin,
     """View to show details about a `StudySite`."""
 
     model = models.StudySite
-    tables = [
-        UserTable,
-        dbGaPApplicationTable,
-        MemberAgreementTable,
-    ]
 
-    # def get_table(self):
-    #     return UserTable(User.objects.filter(study_sites=self.object))
-    def get_tables_data(self):
+    def get_tables(self):
         user_qs = User.objects.filter(study_sites=self.object)
+        if self.object.member_group:
+            user_table = tables.UserAccountSingleGroupMembershipTable(user_qs, managed_group=self.object.member_group)
+        else:
+            user_table = tables.UserAccountTable(user_qs, exclude="study_sites")
         dbgap_qs = dbGaPApplication.objects.filter(principal_investigator__study_sites=self.object)
         cdsa_qs = MemberAgreement.objects.filter(study_site=self.object)
-        return [user_qs, dbgap_qs, cdsa_qs]
+        if self.object.member_group:
+            account_qs = Account.objects.filter(groupaccountmembership__group=self.object.member_group)
+        else:
+            account_qs = Account.objects.none()
+        return [
+            user_table,
+            dbGaPApplicationTable(dbgap_qs),
+            MemberAgreementTable(cdsa_qs),
+            tables.AccountTable(account_qs, exclude=("number_groups")),
+        ]
 
 
 class StudySiteList(AnVILConsortiumManagerStaffViewRequired, SingleTableView):