Merge pull request #407 from UW-GAC/feature/partner-upload-workspaces

Add partner upload workspaces

config/settings/base.py

@@ -372,6 +372,7 @@
     "gregor_django.gregor_anvil.adapters.ExampleWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.TemplateWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.UploadWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.PartnerUploadWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.CombinedConsortiumDataWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.ReleaseWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.DCCProcessingWorkspaceAdapter",

gregor_django/gregor_anvil/adapters.py

@@ -57,6 +57,19 @@ def get_autocomplete_queryset(self, queryset, q, forwarded={}):
         return queryset
 
 
+class PartnerUploadWorkspaceAdapter(BaseWorkspaceAdapter):
+    """Adapter for PartnerUploadWorkspaces."""
+
+    type = "partner_upload"
+    name = "Partner upload workspace"
+    description = "Workspaces that contain data uploaded by a Partner Group "
+    list_table_class = tables.PartnerUploadWorkspaceTable
+    workspace_data_model = models.PartnerUploadWorkspace
+    workspace_data_form_class = forms.PartnerUploadWorkspaceForm
+    workspace_form_class = WorkspaceForm
+    workspace_detail_template_name = "gregor_anvil/partneruploadworkspace_detail.html"
+
+
 class ExampleWorkspaceAdapter(BaseWorkspaceAdapter):
     """Adapter for ExampleWorkspaces."""
 

gregor_django/gregor_anvil/admin.py

@@ -98,6 +98,30 @@ class UploadWorkspaceAdmin(SimpleHistoryAdmin):
     )
 
 
+@admin.register(models.PartnerUploadWorkspace)
+class PartnerUploadWorkspaceAdmin(SimpleHistoryAdmin):
+    """Admin class for the PartnerUploadWorkspace model."""
+
+    list_display = (
+        "id",
+        "workspace",
+        "partner_group",
+        "consent_group",
+        "version",
+    )
+    list_filter = (
+        "partner_group",
+        "consent_group",
+        "version",
+    )
+    sortable_by = (
+        "id",
+        "workspace",
+        "partner_group",
+        "version",
+    )
+
+
 @admin.register(models.ExampleWorkspace)
 class ExampleWorkspaceAdmin(SimpleHistoryAdmin):
     """Admin class for the ExampleWorkspace model."""

gregor_django/gregor_anvil/forms.py

@@ -41,6 +41,26 @@ class Meta:
         )
 
 
+class PartnerUploadWorkspaceForm(forms.ModelForm):
+    """Form for a PartnerUploadWorkspace object."""
+
+    class Meta:
+        model = models.PartnerUploadWorkspace
+        fields = (
+            "partner_group",
+            "consent_group",
+            "version",
+            "date_completed",
+            "workspace",
+        )
+        help_texts = {
+            "date_completed": "Do not select a date until validation has been completed in this workspace.",
+        }
+        widgets = {
+            "date_completed": CustomDateInput(),
+        }
+
+
 class ExampleWorkspaceForm(forms.ModelForm):
     """Form for a ExampleWorkspace object."""
 

gregor_django/gregor_anvil/migrations/0018_partneruploadworkspace_and_more.py

@@ -0,0 +1,186 @@
+# Generated by Django 4.2.8 on 2023-12-15 23:55
+
+from django.conf import settings
+import django.core.validators
+from django.db import migrations, models
+import django.db.models.deletion
+import django_extensions.db.fields
+import simple_history.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("anvil_consortium_manager", "0015_add_new_permissions"),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ("gregor_anvil", "0017_remove_releaseworkspace_upload_workspaces"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="PartnerUploadWorkspace",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                (
+                    "created",
+                    django_extensions.db.fields.CreationDateTimeField(
+                        auto_now_add=True, verbose_name="created"
+                    ),
+                ),
+                (
+                    "modified",
+                    django_extensions.db.fields.ModificationDateTimeField(
+                        auto_now=True, verbose_name="modified"
+                    ),
+                ),
+                (
+                    "version",
+                    models.IntegerField(
+                        help_text="The version of this workspace for this PartnerGroup and ConsentGroup.",
+                        validators=[django.core.validators.MinValueValidator(1)],
+                    ),
+                ),
+                (
+                    "date_completed",
+                    models.DateField(
+                        blank=True,
+                        help_text="The date when uploads to this workspace and data validation were completed.",
+                        null=True,
+                    ),
+                ),
+                (
+                    "consent_group",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.PROTECT,
+                        to="gregor_anvil.consentgroup",
+                    ),
+                ),
+                (
+                    "partner_group",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.PROTECT,
+                        to="gregor_anvil.partnergroup",
+                    ),
+                ),
+                (
+                    "workspace",
+                    models.OneToOneField(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to="anvil_consortium_manager.workspace",
+                    ),
+                ),
+            ],
+        ),
+        migrations.CreateModel(
+            name="HistoricalPartnerUploadWorkspace",
+            fields=[
+                (
+                    "id",
+                    models.BigIntegerField(
+                        auto_created=True, blank=True, db_index=True, verbose_name="ID"
+                    ),
+                ),
+                (
+                    "created",
+                    django_extensions.db.fields.CreationDateTimeField(
+                        auto_now_add=True, verbose_name="created"
+                    ),
+                ),
+                (
+                    "modified",
+                    django_extensions.db.fields.ModificationDateTimeField(
+                        auto_now=True, verbose_name="modified"
+                    ),
+                ),
+                (
+                    "version",
+                    models.IntegerField(
+                        help_text="The version of this workspace for this PartnerGroup and ConsentGroup.",
+                        validators=[django.core.validators.MinValueValidator(1)],
+                    ),
+                ),
+                (
+                    "date_completed",
+                    models.DateField(
+                        blank=True,
+                        help_text="The date when uploads to this workspace and data validation were completed.",
+                        null=True,
+                    ),
+                ),
+                ("history_id", models.AutoField(primary_key=True, serialize=False)),
+                ("history_date", models.DateTimeField(db_index=True)),
+                ("history_change_reason", models.CharField(max_length=100, null=True)),
+                (
+                    "history_type",
+                    models.CharField(
+                        choices=[("+", "Created"), ("~", "Changed"), ("-", "Deleted")],
+                        max_length=1,
+                    ),
+                ),
+                (
+                    "consent_group",
+                    models.ForeignKey(
+                        blank=True,
+                        db_constraint=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.DO_NOTHING,
+                        related_name="+",
+                        to="gregor_anvil.consentgroup",
+                    ),
+                ),
+                (
+                    "history_user",
+                    models.ForeignKey(
+                        null=True,
+                        on_delete=django.db.models.deletion.SET_NULL,
+                        related_name="+",
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+                (
+                    "partner_group",
+                    models.ForeignKey(
+                        blank=True,
+                        db_constraint=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.DO_NOTHING,
+                        related_name="+",
+                        to="gregor_anvil.partnergroup",
+                    ),
+                ),
+                (
+                    "workspace",
+                    models.ForeignKey(
+                        blank=True,
+                        db_constraint=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.DO_NOTHING,
+                        related_name="+",
+                        to="anvil_consortium_manager.workspace",
+                    ),
+                ),
+            ],
+            options={
+                "verbose_name": "historical partner upload workspace",
+                "verbose_name_plural": "historical partner upload workspaces",
+                "ordering": ("-history_date", "-history_id"),
+                "get_latest_by": ("history_date", "history_id"),
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+        migrations.AddConstraint(
+            model_name="partneruploadworkspace",
+            constraint=models.UniqueConstraint(
+                fields=("partner_group", "consent_group", "version"),
+                name="unique_partner_upload_workspace_data",
+            ),
+        ),
+    ]

gregor_django/gregor_anvil/models.py

@@ -113,6 +113,26 @@ def get_absolute_url(self):
         """Return the absolute url for this object."""
         return reverse("gregor_anvil:upload_cycles:detail", args=[self.cycle])
 
+    def get_partner_upload_workspaces(self):
+        """Return a queryset of PartnerUploadWorkspace objects that are included in this upload cycle.
+
+        For a given PartnerGroup and ConsentGroup, the workspace with the highest version that also has a date_completed
+        that is before the end_date of this upload cycle is included.
+        """
+        qs = PartnerUploadWorkspace.objects.filter(
+            date_completed__lte=self.end_date
+        ).order_by("-version")
+        # This is not ideal, but we can't use .distinct on fields.
+        pks_to_keep = []
+        for partner_group in PartnerGroup.objects.all():
+            for consent_group in ConsentGroup.objects.all():
+                instance = qs.filter(
+                    partner_group=partner_group, consent_group=consent_group
+                ).first()
+                if instance:
+                    pks_to_keep.append(instance.pk)
+        return qs.filter(pk__in=pks_to_keep)
+
 
 class UploadWorkspace(TimeStampedModel, BaseWorkspaceData):
     """A model to track additional data about an upload workspace."""
@@ -137,6 +157,35 @@ class Meta:
         ]
 
 
+class PartnerUploadWorkspace(TimeStampedModel, BaseWorkspaceData):
+    """A model to track additional data about a partner workspace."""
+
+    partner_group = models.ForeignKey(PartnerGroup, on_delete=models.PROTECT)
+    """The PartnerGroup providing data for this Workspace."""
+
+    consent_group = models.ForeignKey(ConsentGroup, on_delete=models.PROTECT)
+    """The ConsentGroup associated with this workspace."""
+
+    version = models.IntegerField(
+        validators=[MinValueValidator(1)],
+        help_text="The version of this workspace for this PartnerGroup and ConsentGroup.",
+    )
+    date_completed = models.DateField(
+        help_text="The date when uploads to this workspace and data validation were completed.",
+        null=True,
+        blank=True,
+    )
+
+    class Meta:
+        constraints = [
+            # Model uniqueness.
+            models.UniqueConstraint(
+                name="unique_partner_upload_workspace_data",
+                fields=["partner_group", "consent_group", "version"],
+            ),
+        ]
+
+
 class ExampleWorkspace(TimeStampedModel, BaseWorkspaceData):
     """A model to track example workspaces."""
 

gregor_django/gregor_anvil/tables.py

@@ -150,6 +150,24 @@ class Meta:
         )
 
 
+class PartnerUploadWorkspaceTable(WorkspaceConsortiumAccessTable, tables.Table):
+    """A table for Workspaces that includes fields from PartnerUploadWorkspace."""
+
+    name = tables.columns.Column(linkify=True)
+    partneruploadworkspace__partner_group = tables.columns.Column(linkify=True)
+
+    class Meta:
+        model = Workspace
+        fields = (
+            "name",
+            "partneruploadworkspace__partner_group",
+            "partneruploadworkspace__consent_group",
+            "partneruploadworkspace__version",
+            "partneruploadworkspace__date_completed",
+            "consortium_access",
+        )
+
+
 class TemplateWorkspaceTable(WorkspaceConsortiumAccessTable, tables.Table):
     """A table for Workspaces that includes fields from TemplateWorkspace."""
 

gregor_django/gregor_anvil/tests/factories.py

@@ -66,7 +66,18 @@ class UploadWorkspaceFactory(DjangoModelFactory):
 
     class Meta:
         model = models.UploadWorkspace
-        django_get_or_create = ["research_center", "consent_group"]
+
+
+class PartnerUploadWorkspaceFactory(DjangoModelFactory):
+    """A factory for the UploadWorkspace model."""
+
+    partner_group = SubFactory(PartnerGroupFactory)
+    consent_group = SubFactory(ConsentGroupFactory)
+    version = Faker("random_int", min=1)
+    workspace = SubFactory(WorkspaceFactory, workspace_type="partner_upload")
+
+    class Meta:
+        model = models.PartnerUploadWorkspace
 
 
 class ExampleWorkspaceFactory(DjangoModelFactory):