Merge pull request #631 from UW-GAC/deploy/stage

Deploy to prod

.github/workflows/ci.yml

@@ -28,11 +28,11 @@ jobs:
         backend: ["sqlite", "mariadb"]
         mariadb-version: ["10.4"]
         include:
-          - python-version: 3.12  # Possible future version.
+          - python-version: "3.10"  # Future ubuntu 22.04 upgrade.
             backend: "mariadb"
-            mariadb-version: "10.5"
+            mariadb-version: "10.6"
             pip-recompile: true
-          - python-version: 3.12  # Possible future version.
+          - python-version: 3.12  # Future ubuntu 24.04.01 upgrade.
             backend: "mariadb"
             mariadb-version: "10.11"
             pip-recompile: true

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.9
+    rev: v0.5.1
     hooks:
       # Run the linter.
       - id: ruff

gregor_django/gregor_anvil/migrations/0024_member_upload_groups.py

@@ -0,0 +1,55 @@
+# Generated by Django 4.2.13 on 2024-07-09 21:53
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('anvil_consortium_manager', '0019_accountuserarchive'),
+        ('gregor_anvil', '0023_resourceworkspace_add_brief_description'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='historicalpartnergroup',
+            name='member_group',
+            field=models.ForeignKey(blank=True, db_constraint=False, help_text='The AnVIL group containing members from this Partner Group.', null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='anvil_consortium_manager.managedgroup'),
+        ),
+        migrations.AddField(
+            model_name='historicalpartnergroup',
+            name='uploader_group',
+            field=models.ForeignKey(blank=True, db_constraint=False, help_text='The group that has write/upload access to workspaces associated with this Partner Group.', null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='anvil_consortium_manager.managedgroup'),
+        ),
+        migrations.AddField(
+            model_name='historicalresearchcenter',
+            name='member_group',
+            field=models.ForeignKey(blank=True, db_constraint=False, help_text='The AnVIL group containing members from this Research Center.', null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='anvil_consortium_manager.managedgroup'),
+        ),
+        migrations.AddField(
+            model_name='historicalresearchcenter',
+            name='uploader_group',
+            field=models.ForeignKey(blank=True, db_constraint=False, help_text='The group that has write/upload access to workspaces associated with this Research Center.', null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='anvil_consortium_manager.managedgroup'),
+        ),
+        migrations.AddField(
+            model_name='partnergroup',
+            name='member_group',
+            field=models.OneToOneField(blank=True, help_text='The AnVIL group containing members from this Partner Group.', null=True, on_delete=django.db.models.deletion.PROTECT, related_name='partner_group_of_members', to='anvil_consortium_manager.managedgroup'),
+        ),
+        migrations.AddField(
+            model_name='partnergroup',
+            name='uploader_group',
+            field=models.OneToOneField(blank=True, help_text='The group that has write/upload access to workspaces associated with this Partner Group.', null=True, on_delete=django.db.models.deletion.PROTECT, related_name='partner_group_of_uploaders', to='anvil_consortium_manager.managedgroup'),
+        ),
+        migrations.AddField(
+            model_name='researchcenter',
+            name='member_group',
+            field=models.OneToOneField(blank=True, help_text='The AnVIL group containing members from this Research Center.', null=True, on_delete=django.db.models.deletion.PROTECT, related_name='research_center_of_members', to='anvil_consortium_manager.managedgroup'),
+        ),
+        migrations.AddField(
+            model_name='researchcenter',
+            name='uploader_group',
+            field=models.OneToOneField(blank=True, help_text='The group that has write/upload access to workspaces associated with this Research Center.', null=True, on_delete=django.db.models.deletion.PROTECT, related_name='research_center_of_uploaders', to='anvil_consortium_manager.managedgroup'),
+        ),
+    ]

gregor_django/gregor_anvil/models.py

@@ -1,4 +1,4 @@
-from anvil_consortium_manager.models import BaseWorkspaceData
+from anvil_consortium_manager.models import BaseWorkspaceData, ManagedGroup
 from django.core.exceptions import ValidationError
 from django.core.validators import MinValueValidator
 from django.db import models
@@ -42,6 +42,24 @@ class ResearchCenter(TimeStampedModel, models.Model):
     full_name = models.CharField(max_length=255, unique=True)
     """The full name of the Research Center."""
 
+    member_group = models.OneToOneField(
+        ManagedGroup,
+        on_delete=models.PROTECT,
+        help_text="The AnVIL group containing members from this Research Center.",
+        related_name="research_center_of_members",
+        blank=True,
+        null=True,
+    )
+
+    uploader_group = models.OneToOneField(
+        ManagedGroup,
+        on_delete=models.PROTECT,
+        help_text="The group that has write/upload access to workspaces associated with this Research Center.",
+        related_name="research_center_of_uploaders",
+        blank=True,
+        null=True,
+    )
+
     history = HistoricalRecords()
 
     def __str__(self):
@@ -56,6 +74,12 @@ def get_absolute_url(self):
         """Return the absolute url for this object."""
         return reverse("gregor_anvil:research_centers:detail", args=[self.pk])
 
+    def clean(self):
+        """Custom cleaning methods."""
+        # Members group and uploaders group must be different.
+        if self.member_group and self.uploader_group and self.member_group == self.uploader_group:
+            raise ValidationError("member_group and uploader_group must be different!")
+
 
 class PartnerGroup(TimeStampedModel, models.Model):
     """A model to track Partner Groups"""
@@ -66,6 +90,24 @@ class PartnerGroup(TimeStampedModel, models.Model):
     full_name = models.CharField(max_length=255, unique=True)
     """The full name of the Partner Group"""
 
+    member_group = models.OneToOneField(
+        ManagedGroup,
+        on_delete=models.PROTECT,
+        help_text="The AnVIL group containing members from this Partner Group.",
+        related_name="partner_group_of_members",
+        null=True,
+        blank=True,
+    )
+
+    uploader_group = models.OneToOneField(
+        ManagedGroup,
+        on_delete=models.PROTECT,
+        help_text="The group that has write/upload access to workspaces associated with this Partner Group.",
+        related_name="partner_group_of_uploaders",
+        null=True,
+        blank=True,
+    )
+
     history = HistoricalRecords()
 
     def __str__(self):
@@ -80,6 +122,12 @@ def get_absolute_url(self):
         """Return the absolute url for this object."""
         return reverse("gregor_anvil:partner_groups:detail", args=[self.pk])
 
+    def clean(self):
+        """Custom cleaning methods."""
+        # Members group and uploaders group must be different.
+        if self.member_group and self.uploader_group and self.member_group == self.uploader_group:
+            raise ValidationError("member_group and uploader_group must be different!")
+
 
 class UploadCycle(TimeStampedModel, models.Model):
     """A model tracking the upload cycles that exist in the app."""

gregor_django/gregor_anvil/tests/test_migrations.py

@@ -35,9 +35,10 @@ def prepare(self):
             FACTORY_CLASS=WorkspaceFactory,
             billing_project=factory.create(BillingProject, FACTORY_CLASS=BillingProjectFactory),
         )
+        research_center_1 = ResearchCenter.objects.create(short_name="rc1", full_name="Research Center 1")
         self.u_1 = UploadWorkspace.objects.create(
             version=1,
-            research_center=factory.create(ResearchCenter, FACTORY_CLASS=factories.ResearchCenterFactory),
+            research_center=research_center_1,
             consent_group=consent_group,
             workspace=workspace,
         )
@@ -47,9 +48,10 @@ def prepare(self):
             FACTORY_CLASS=WorkspaceFactory,
             billing_project=factory.create(BillingProject, FACTORY_CLASS=BillingProjectFactory),
         )
+        research_center_2 = ResearchCenter.objects.create(short_name="rc2", full_name="Research Center 2")
         self.u_2 = UploadWorkspace.objects.create(
             version=1,
-            research_center=factory.create(ResearchCenter, FACTORY_CLASS=factories.ResearchCenterFactory),
+            research_center=research_center_2,
             consent_group=consent_group,
             workspace=workspace,
         )
@@ -59,9 +61,10 @@ def prepare(self):
             FACTORY_CLASS=WorkspaceFactory,
             billing_project=factory.create(BillingProject, FACTORY_CLASS=BillingProjectFactory),
         )
+        research_center_3 = ResearchCenter.objects.create(short_name="rc3", full_name="Research Center 3")
         self.u_3 = UploadWorkspace.objects.create(
             version=2,
-            research_center=factory.create(ResearchCenter, FACTORY_CLASS=factories.ResearchCenterFactory),
+            research_center=research_center_3,
             consent_group=consent_group,
             workspace=workspace,
         )

gregor_django/gregor_anvil/tests/test_models.py

@@ -1,6 +1,6 @@
 from datetime import date, timedelta
 
-from anvil_consortium_manager.tests.factories import WorkspaceFactory
+from anvil_consortium_manager.tests.factories import ManagedGroupFactory, WorkspaceFactory
 from django.core.exceptions import NON_FIELD_ERRORS, ValidationError
 from django.db.utils import IntegrityError
 from django.test import TestCase
@@ -78,7 +78,25 @@ class ResearchCenterTest(TestCase):
 
     def test_model_saving(self):
         """Creation using the model constructor and .save() works."""
-        instance = models.ResearchCenter(full_name="Test name", short_name="TEST")
+        instance = models.ResearchCenter(
+            full_name="Test name",
+            short_name="TEST",
+        )
+        instance.full_clean()
+        instance.save()
+        self.assertIsInstance(instance, models.ResearchCenter)
+
+    def test_model_saving_with_groups(self):
+        """Creation using the model constructor and .save() works."""
+        member_group = ManagedGroupFactory.create()
+        uploader_group = ManagedGroupFactory.create()
+        instance = models.ResearchCenter(
+            full_name="Test name",
+            short_name="TEST",
+            member_group=member_group,
+            uploader_group=uploader_group,
+        )
+        instance.full_clean()
         instance.save()
         self.assertIsInstance(instance, models.ResearchCenter)
 
@@ -103,6 +121,54 @@ def test_unique_short_name(self):
         with self.assertRaises(IntegrityError):
             instance2.save()
 
+    def test_member_group_uploader_group_must_be_different(self):
+        """The same group cannot be used as the members group and uploaders group."""
+        group = ManagedGroupFactory.create()
+        instance = models.ResearchCenter(
+            full_name="Test name",
+            short_name="TEST",
+            member_group=group,
+            uploader_group=group,
+        )
+        with self.assertRaises(ValidationError) as e:
+            instance.full_clean()
+        self.assertEqual(len(e.exception.error_dict), 1)
+        self.assertIn(NON_FIELD_ERRORS, e.exception.error_dict)
+        self.assertEqual(len(e.exception.error_dict[NON_FIELD_ERRORS]), 1)
+        self.assertIn("must be different", str(e.exception.error_dict[NON_FIELD_ERRORS][0]))
+
+    def test_error_two_rcs_same_member_group(self):
+        """Cannot have the same member group for two RCs."""
+        member_group = ManagedGroupFactory.create()
+        factories.ResearchCenterFactory.create(member_group=member_group)
+        instance = factories.ResearchCenterFactory.build(
+            full_name="Test name",
+            short_name="TEST",
+            member_group=member_group,
+        )
+        with self.assertRaises(ValidationError) as e:
+            instance.full_clean()
+        self.assertEqual(len(e.exception.error_dict), 1)
+        self.assertIn("member_group", e.exception.error_dict)
+        self.assertEqual(len(e.exception.error_dict["member_group"]), 1)
+        self.assertIn("already exists", str(e.exception.error_dict["member_group"][0]))
+
+    def test_error_two_rcs_same_uploader_group(self):
+        """Cannot have the same uploader group for two RCs."""
+        uploader_group = ManagedGroupFactory.create()
+        factories.ResearchCenterFactory.create(uploader_group=uploader_group)
+        instance = factories.ResearchCenterFactory.build(
+            full_name="Test name",
+            short_name="TEST",
+            uploader_group=uploader_group,
+        )
+        with self.assertRaises(ValidationError) as e:
+            instance.full_clean()
+        self.assertEqual(len(e.exception.error_dict), 1)
+        self.assertIn("uploader_group", e.exception.error_dict)
+        self.assertEqual(len(e.exception.error_dict["uploader_group"]), 1)
+        self.assertIn("already exists", str(e.exception.error_dict["uploader_group"][0]))
+
 
 class UploadCycleTest(TestCase):
     """Tests for the UploadCycle model."""
@@ -422,6 +488,103 @@ def test_duplicated_workspace(self):
             instance_2.save()
 
 
+class PartnerGroupTest(TestCase):
+    """Tests for the ResearchCenter model."""
+
+    def test_model_saving(self):
+        """Creation using the model constructor and .save() works."""
+        instance = models.PartnerGroup(
+            full_name="Test name",
+            short_name="TEST",
+        )
+        instance.full_clean()
+        instance.save()
+        self.assertIsInstance(instance, models.PartnerGroup)
+
+    def test_model_saving_with_groups(self):
+        """Creation using the model constructor and .save() works."""
+        member_group = ManagedGroupFactory.create()
+        uploader_group = ManagedGroupFactory.create()
+        instance = models.PartnerGroup(
+            full_name="Test name",
+            short_name="TEST",
+            member_group=member_group,
+            uploader_group=uploader_group,
+        )
+        instance.full_clean()
+        instance.save()
+        self.assertIsInstance(instance, models.PartnerGroup)
+
+    def test_str_method(self):
+        """The custom __str__ method returns the correct string."""
+        instance = factories.PartnerGroupFactory.create(short_name="Test")
+        instance.save()
+        self.assertIsInstance(instance.__str__(), str)
+        self.assertEqual(instance.__str__(), "Test")
+
+    def test_get_absolute_url(self):
+        """The get_absolute_url() method works."""
+        instance = factories.PartnerGroupFactory()
+        self.assertIsInstance(instance.get_absolute_url(), str)
+
+    def test_unique_short_name(self):
+        """Saving a model with a duplicate short name fails."""
+        factories.PartnerGroupFactory.create(short_name="FOO")
+        instance2 = models.PartnerGroup(short_name="FOO", full_name="full name")
+        with self.assertRaises(ValidationError):
+            instance2.full_clean()
+        with self.assertRaises(IntegrityError):
+            instance2.save()
+
+    def test_member_group_uploader_group_must_be_different(self):
+        """The same group cannot be used as the members group and uploaders group."""
+        group = ManagedGroupFactory.create()
+        instance = models.PartnerGroup(
+            full_name="Test name",
+            short_name="TEST",
+            member_group=group,
+            uploader_group=group,
+        )
+        with self.assertRaises(ValidationError) as e:
+            instance.full_clean()
+        self.assertEqual(len(e.exception.error_dict), 1)
+        self.assertIn(NON_FIELD_ERRORS, e.exception.error_dict)
+        self.assertEqual(len(e.exception.error_dict[NON_FIELD_ERRORS]), 1)
+        self.assertIn("must be different", str(e.exception.error_dict[NON_FIELD_ERRORS][0]))
+
+    def test_error_two_groups_same_member_group(self):
+        """Cannot have the same member group for two RCs."""
+        member_group = ManagedGroupFactory.create()
+        factories.PartnerGroupFactory.create(member_group=member_group)
+        instance = factories.PartnerGroupFactory.build(
+            full_name="Test name",
+            short_name="TEST",
+            member_group=member_group,
+        )
+        with self.assertRaises(ValidationError) as e:
+            instance.full_clean()
+        self.assertEqual(len(e.exception.error_dict), 1)
+        self.assertIn("member_group", e.exception.error_dict)
+        self.assertEqual(len(e.exception.error_dict["member_group"]), 1)
+        self.assertIn("already exists", str(e.exception.error_dict["member_group"][0]))
+
+    def test_error_two_groups_same_uploader_group(self):
+        """Cannot have the same uploader group for two RCs."""
+        uploader_group = ManagedGroupFactory.create()
+        factories.PartnerGroupFactory.create(uploader_group=uploader_group)
+        instance = factories.PartnerGroupFactory.build(
+            full_name="Test name",
+            short_name="TEST",
+            uploader_group=uploader_group,
+        )
+        with self.assertRaises(ValidationError) as e:
+            instance.full_clean()
+        self.assertEqual(len(e.exception.error_dict), 1)
+        self.assertIn("uploader_group", e.exception.error_dict)
+        self.assertEqual(len(e.exception.error_dict["uploader_group"]), 1)
+        self.assertIn("already exists", str(e.exception.error_dict["uploader_group"][0]))
+
+
 class PartnerUploadWorkspaceTest(TestCase):
     """Tests for the PartnerUploadWorkspace model."""