Merge pull request #271 from UW-GAC/main

Deploy to stage

config/settings/base.py

@@ -371,6 +371,8 @@
     "gregor_django.gregor_anvil.adapters.UploadWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.CombinedConsortiumDataWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.ReleaseWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.DCCProcessingWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.DCCProcessedDataWorkspaceAdapter",
 ]
 ANVIL_ACCOUNT_ADAPTER = "gregor_django.gregor_anvil.adapters.AccountAdapter"
 

gregor_django/gregor_anvil/adapters.py

@@ -104,3 +104,29 @@ class ReleaseWorkspaceAdapter(BaseWorkspaceAdapter):
     workspace_data_model = models.ReleaseWorkspace
     workspace_data_form_class = forms.ReleaseWorkspaceForm
     workspace_detail_template_name = "gregor_anvil/releaseworkspace_detail.html"
+
+
+class DCCProcessingWorkspaceAdapter(BaseWorkspaceAdapter):
+    """Adapter for DCCProcessingWorkspace."""
+
+    type = "dcc_processing"
+    name = "DCC processing workspace"
+    description = "Workspaces used for DCC processing of data."
+    list_table_class = tables.DCCProcessingWorkspaceTable
+    workspace_data_model = models.DCCProcessingWorkspace
+    workspace_data_form_class = forms.DCCProcessingWorkspaceForm
+    workspace_detail_template_name = "gregor_anvil/dccprocessingworkspace_detail.html"
+
+
+class DCCProcessedDataWorkspaceAdapter(BaseWorkspaceAdapter):
+    """Adapter for DCCProcessedDataWorkspace."""
+
+    type = "dcc_processed_data"
+    name = "DCC processed data workspace"
+    description = "Workspaces containing data processed by the DCC and hosted by AnVIL."
+    list_table_class = tables.DCCProcessedDataWorkspaceTable
+    workspace_data_model = models.DCCProcessedDataWorkspace
+    workspace_data_form_class = forms.DCCProcessedDataWorkspaceForm
+    workspace_detail_template_name = (
+        "gregor_anvil/dccprocesseddataworkspace_detail.html"
+    )

gregor_django/gregor_anvil/admin.py

@@ -59,6 +59,22 @@ class PartnerGroupAdmin(SimpleHistoryAdmin):
     )
 
 
+@admin.register(models.UploadCycle)
+class UploadCycleAdmin(SimpleHistoryAdmin):
+    """Admin class for the UploadCycle model."""
+
+    list_display = (
+        "cycle",
+        "start_date",
+        "end_date",
+    )
+    sortable_by = (
+        "cycle",
+        "start_date",
+        "end_date",
+    )
+
+
 @admin.register(models.UploadWorkspace)
 class UploadWorkspaceAdmin(SimpleHistoryAdmin):
     """Admin class for the UploadWorkspace model."""
@@ -73,6 +89,7 @@ class UploadWorkspaceAdmin(SimpleHistoryAdmin):
     list_filter = (
         "research_center",
         "consent_group",
+        "upload_cycle",
     )
     sortable_by = (
         "id",
@@ -81,17 +98,68 @@ class UploadWorkspaceAdmin(SimpleHistoryAdmin):
     )
 
 
-@admin.register(models.UploadCycle)
-class UploadCycleAdmin(SimpleHistoryAdmin):
-    """Admin class for the UploadCycle model."""
+@admin.register(models.ExampleWorkspace)
+class ExampleWorkspaceAdmin(SimpleHistoryAdmin):
+    """Admin class for the ExampleWorkspace model."""
 
     list_display = (
-        "cycle",
-        "start_date",
-        "end_date",
+        "id",
+        "workspace",
     )
     sortable_by = (
-        "cycle",
-        "start_date",
-        "end_date",
+        "id",
+        "workspace",
+    )
+
+
+@admin.register(models.TemplateWorkspace)
+class TemplateWorkspaceAdmin(SimpleHistoryAdmin):
+    """Admin class for the TemplateWorkspace model."""
+
+    list_display = (
+        "id",
+        "workspace",
+    )
+    sortable_by = (
+        "id",
+        "workspace",
+    )
+
+
+@admin.register(models.CombinedConsortiumDataWorkspace)
+class CombinedConsortiumDataWorkspaceAdmin(SimpleHistoryAdmin):
+    """Admin class for the CombinedConsortiumDataWorkspace model."""
+
+    list_display = (
+        "id",
+        "workspace",
+        "upload_cycle",
+    )
+    list_filter = ("upload_cycle",)
+    sortable_by = (
+        "id",
+        "workspace",
+        "upload_cycle",
+    )
+
+
+@admin.register(models.ReleaseWorkspace)
+class ReleaseWorkspaceAdmin(SimpleHistoryAdmin):
+    """Admin class for the ReleaseWorkspace model."""
+
+    list_display = (
+        "id",
+        "workspace",
+        "upload_cycle",
+        "consent_group",
+    )
+    list_filter = (
+        "upload_cycle",
+        "consent_group",
+    )
+    sortable_by = (
+        "id",
+        "workspace",
+        "upload_cycle",
+        "consent_group",
     )

gregor_django/gregor_anvil/forms.py

@@ -193,3 +193,33 @@ def clean(self):
             # that all upload_workspaces have the same upload_cycle.
             if upload_cycle != upload_workspaces[0].upload_cycle:
                 raise ValidationError(self.ERROR_UPLOAD_CYCLE)
+
+        return cleaned_data
+
+
+class DCCProcessingWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
+    """Form for a DCCProcessingWorkspace object."""
+
+    ERROR_UPLOAD_CYCLE = (
+        "upload_cycle must match upload_cycle of all upload_workspaces."
+    )
+
+    class Meta:
+        model = models.DCCProcessingWorkspace
+        fields = (
+            "upload_cycle",
+            "purpose",
+            "workspace",
+        )
+
+
+class DCCProcessedDataWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
+    """Form for a DCCProcessedDataWorkspace object."""
+
+    class Meta:
+        model = models.DCCProcessedDataWorkspace
+        fields = (
+            "upload_cycle",
+            "consent_group",
+            "workspace",
+        )

gregor_django/gregor_anvil/migrations/0014_alter_uploadcycle_options.py

@@ -0,0 +1,17 @@
+# Generated by Django 3.2.19 on 2023-06-20 23:37
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('gregor_anvil', '0013_remove_version_fields'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='uploadcycle',
+            options={'ordering': ['cycle']},
+        ),
+    ]

gregor_django/gregor_anvil/migrations/0015_dccworkspaces.py

@@ -0,0 +1,95 @@
+# Generated by Django 3.2.19 on 2023-07-10 22:20
+
+from django.conf import settings
+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', '0012_managedgroup_email_unique'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('gregor_anvil', '0014_alter_uploadcycle_options'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='HistoricalDCCProcessingWorkspace',
+            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')),
+                ('purpose', models.TextField(help_text='The type of processing that is done in this workspace.')),
+                ('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)),
+                ('history_user', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='+', to=settings.AUTH_USER_MODEL)),
+                ('upload_cycle', models.ForeignKey(blank=True, db_constraint=False, help_text='Upload cycle associated with this workspace.', null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='gregor_anvil.uploadcycle')),
+                ('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 dcc processing workspace',
+                'verbose_name_plural': 'historical dcc processing workspaces',
+                'ordering': ('-history_date', '-history_id'),
+                'get_latest_by': ('history_date', 'history_id'),
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+        migrations.CreateModel(
+            name='HistoricalDCCProcessedDataWorkspace',
+            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')),
+                ('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, help_text='Consent group associated with this data.', 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)),
+                ('upload_cycle', models.ForeignKey(blank=True, db_constraint=False, help_text='Upload cycle associated with this workspace.', null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='gregor_anvil.uploadcycle')),
+                ('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 dcc processed data workspace',
+                'verbose_name_plural': 'historical dcc processed data workspaces',
+                'ordering': ('-history_date', '-history_id'),
+                'get_latest_by': ('history_date', 'history_id'),
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+        migrations.CreateModel(
+            name='DCCProcessingWorkspace',
+            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')),
+                ('purpose', models.TextField(help_text='The type of processing that is done in this workspace.')),
+                ('upload_cycle', models.ForeignKey(help_text='Upload cycle associated with this workspace.', on_delete=django.db.models.deletion.PROTECT, to='gregor_anvil.uploadcycle')),
+                ('workspace', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, to='anvil_consortium_manager.workspace')),
+            ],
+            options={
+                'get_latest_by': 'modified',
+                'abstract': False,
+            },
+        ),
+        migrations.CreateModel(
+            name='DCCProcessedDataWorkspace',
+            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')),
+                ('consent_group', models.ForeignKey(help_text='Consent group associated with this data.', on_delete=django.db.models.deletion.PROTECT, to='gregor_anvil.consentgroup')),
+                ('upload_cycle', models.ForeignKey(help_text='Upload cycle associated with this workspace.', on_delete=django.db.models.deletion.PROTECT, to='gregor_anvil.uploadcycle')),
+                ('workspace', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, to='anvil_consortium_manager.workspace')),
+            ],
+        ),
+        migrations.AddConstraint(
+            model_name='dccprocesseddataworkspace',
+            constraint=models.UniqueConstraint(fields=('upload_cycle', 'consent_group'), name='unique_dcc_processed_data_workspace'),
+        ),
+    ]

gregor_django/gregor_anvil/models.py

@@ -95,6 +95,11 @@ class UploadCycle(TimeStampedModel, models.Model):
     # Django simple history.
     history = HistoricalRecords()
 
+    class Meta:
+        ordering = [
+            "cycle",
+        ]
+
     def __str__(self):
         return "U{cycle:02d}".format(cycle=self.cycle)
 
@@ -199,3 +204,39 @@ def get_dbgap_accession(self):
         return "phs{phs:06d}.v{v}.p{p}".format(
             phs=self.phs, v=self.dbgap_version, p=self.dbgap_participant_set
         )
+
+
+class DCCProcessingWorkspace(TimeStampedModel, BaseWorkspaceData):
+
+    upload_cycle = models.ForeignKey(
+        UploadCycle,
+        on_delete=models.PROTECT,
+        help_text="Upload cycle associated with this workspace.",
+    )
+    purpose = models.TextField(
+        help_text="The type of processing that is done in this workspace."
+    )
+
+
+class DCCProcessedDataWorkspace(TimeStampedModel, BaseWorkspaceData):
+    """A workspace to store DCC processed data, split by consent (e.g., re-aligned CRAMs and gVCFs)."""
+
+    upload_cycle = models.ForeignKey(
+        UploadCycle,
+        on_delete=models.PROTECT,
+        help_text="Upload cycle associated with this workspace.",
+    )
+    consent_group = models.ForeignKey(
+        ConsentGroup,
+        help_text="Consent group associated with this data.",
+        on_delete=models.PROTECT,
+    )
+
+    class Meta:
+        constraints = [
+            # Model uniqueness.
+            models.UniqueConstraint(
+                name="unique_dcc_processed_data_workspace",
+                fields=["upload_cycle", "consent_group"],
+            ),
+        ]

gregor_django/gregor_anvil/tables.py

@@ -226,3 +226,33 @@ class Meta:
 
     def render_number_workspaces(self, record):
         return record.releaseworkspace.upload_workspaces.count()
+
+
+class DCCProcessingWorkspaceTable(tables.Table):
+    """A table for Workspaces that includes fields from DCCProcessingWorkspace."""
+
+    name = tables.columns.Column(linkify=True)
+
+    class Meta:
+        model = Workspace
+        fields = (
+            "name",
+            "dccprocessingworkspace__upload_cycle",
+            "dccprocessingworkspace__purpose",
+        )
+
+
+class DCCProcessedDataWorkspaceTable(WorkspaceSharedWithConsortiumTable, tables.Table):
+    """A table for Workspaces that includes fields from DCCProcessedDataWorkspace."""
+
+    name = tables.columns.Column(linkify=True)
+    dccprocesseddataworkspace__consent_group = tables.columns.Column(linkify=True)
+
+    class Meta:
+        model = Workspace
+        fields = (
+            "name",
+            "dccprocesseddataworkspace__upload_cycle",
+            "dccprocesseddataworkspace__consent_group",
+            "is_shared",
+        )