Merge pull request #219 from UW-GAC/deploy/stage

Deploy to production

config/settings/base.py

@@ -200,7 +200,6 @@
                 "django.template.context_processors.tz",
                 "django.contrib.messages.context_processors.messages",
                 "gregor_django.utils.context_processors.settings_context",
-                "anvil_consortium_manager.context_processors.workspace_adapter",
             ],
         },
     }
@@ -357,6 +356,7 @@
     "gregor_django.gregor_anvil.adapters.TemplateWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.UploadWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.CombinedConsortiumDataWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.ReleaseWorkspaceAdapter",
 ]
 ANVIL_ACCOUNT_ADAPTER = "gregor_django.gregor_anvil.adapters.AccountAdapter"
 

gregor_django/gregor_anvil/adapters.py

@@ -30,6 +30,7 @@ class UploadWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "upload"
     name = "Upload workspace"
+    description = "Workspaces that contain data uploaded by RCs in a given upload cycle"
     list_table_class = tables.UploadWorkspaceTable
     workspace_data_model = models.UploadWorkspace
     workspace_data_form_class = forms.UploadWorkspaceForm
@@ -41,6 +42,9 @@ class ExampleWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "example"
     name = "Example workspace"
+    description = (
+        "Workspaces that contain examples of using AnVIL, working with data, etc."
+    )
     list_table_class = WorkspaceTable
     workspace_data_model = models.ExampleWorkspace
     workspace_data_form_class = forms.ExampleWorkspaceForm
@@ -52,6 +56,7 @@ class TemplateWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "template"
     name = "Template workspace"
+    description = "Template workspaces that can be cloned to create other workspaces"
     list_table_class = tables.TemplateWorkspaceTable
     workspace_data_model = models.TemplateWorkspace
     workspace_data_form_class = forms.TemplateWorkspaceForm
@@ -63,9 +68,22 @@ class CombinedConsortiumDataWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "combined_consortium"
     name = "Combined consortium data workspace"
+    description = "Workspaces for internal consortium use that contain data tables combined across upload workspaces"
     list_table_class = WorkspaceTable
     workspace_data_model = models.CombinedConsortiumDataWorkspace
     workspace_data_form_class = forms.CombinedConsortiumDataWorkspaceForm
     workspace_detail_template_name = (
         "gregor_anvil/combinedconsortiumdataworkspace_detail.html"
     )
+
+
+class ReleaseWorkspaceAdapter(BaseWorkspaceAdapter):
+    """Adapter for ReleaseWorkspace."""
+
+    type = "release"
+    name = "Release workspace"
+    description = "Workspaces for release to the general scientific community via dbGaP"
+    list_table_class = tables.ReleaseWorkspaceTable
+    workspace_data_model = models.ReleaseWorkspace
+    workspace_data_form_class = forms.ReleaseWorkspaceForm
+    workspace_detail_template_name = "gregor_anvil/releaseworkspace_detail.html"

gregor_django/gregor_anvil/forms.py

@@ -66,3 +66,75 @@ def clean_upload_workspaces(self):
                 ValidationError(self.ERROR_UPLOAD_VERSION_DOES_NOT_MATCH),
             )
         return data
+
+
+class CustomDateInput(forms.widgets.DateInput):
+    input_type = "date"
+
+
+class ReleaseWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
+    """Form for a ReleaseWorkspace object."""
+
+    ERROR_CONSENT_DOES_NOT_MATCH = (
+        "Consent group must match consent group of upload workspaces."
+    )
+    ERROR_UPLOAD_WORKSPACE_CONSENT = (
+        "Consent group for upload workspaces must be the same."
+    )
+
+    class Meta:
+        model = models.ReleaseWorkspace
+        fields = (
+            "consent_group",
+            "upload_workspaces",
+            "full_data_use_limitations",
+            "dbgap_version",
+            "dbgap_participant_set",
+            "date_released",
+            "workspace",
+        )
+        help_texts = {
+            "upload_workspaces": """Upload workspaces contributing to this Release Workspace.
+                                    All upload workspaces must have the same consent group.""",
+            "date_released": """Do not select a date for this field unless the workspace has been
+                               released to the scientific community.""",
+        }
+        widgets = {
+            # We considered checkboxes for workspaces with default all checked.
+            # Unfortunately we need to select only those with a given consent, not all workspaces.
+            # So go back to the ModelSelect2Multiple widget.
+            "upload_workspaces": autocomplete.ModelSelect2Multiple(
+                url="gregor_anvil:upload_workspaces:autocomplete",
+                attrs={"data-theme": "bootstrap-5"},
+                forward=["consent_group"],
+            ),
+            # "date_released": forms.SelectDateInput(),
+            # "date_released": forms.DateInput(),
+            # "date_released": AdminDateWidget(),
+            "date_released": CustomDateInput(),
+        }
+
+    def clean_upload_workspaces(self):
+        """Validate that all UploadWorkspaces have the same consent group."""
+        data = self.cleaned_data["upload_workspaces"]
+        versions = set([x.consent_group for x in data])
+        if len(versions) > 1:
+            self.add_error(
+                "upload_workspaces",
+                ValidationError(self.ERROR_UPLOAD_WORKSPACE_CONSENT),
+            )
+        return data
+
+    def clean(self):
+        """Validate that consent_group matches the consent group for upload_workspaces."""
+        cleaned_data = super().clean()
+        # Make sure that the consent group specified matches the consent group for the upload_workspaces.
+        consent_group = cleaned_data.get("consent_group")
+        upload_workspaces = cleaned_data.get("upload_workspaces")
+        if consent_group and upload_workspaces:
+            # We only need to check the first workspace since the clean_upload_workspaces method checks
+            # that all upload_workspaces have the same consent.
+            if consent_group != upload_workspaces[0].consent_group:
+                raise ValidationError(self.ERROR_CONSENT_DOES_NOT_MATCH)
+
+        return cleaned_data

gregor_django/gregor_anvil/migrations/0007_releaseworkspace.py

@@ -0,0 +1,65 @@
+# Generated by Django 3.2.16 on 2023-03-27 18:47
+
+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', '0008_workspace_is_locked'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('gregor_anvil', '0006_combinedconsortiumdataworkspace_historicalcombinedconsortiumdataworkspace'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='ReleaseWorkspace',
+            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')),
+                ('full_data_use_limitations', models.TextField(help_text='The full data use limitations for this workspace.')),
+                ('dbgap_version', models.IntegerField(help_text='Version of the release (should be the same as dbGaP version).', validators=[django.core.validators.MinValueValidator(1)], verbose_name=' dbGaP version')),
+                ('dbgap_participant_set', models.IntegerField(help_text='dbGaP participant set of the workspace', validators=[django.core.validators.MinValueValidator(1)], verbose_name=' dbGaP participant set')),
+                ('date_released', models.DateField(blank=True, help_text='Date that this workspace was released to the scientific community.', null=True)),
+                ('consent_group', models.ForeignKey(help_text='Consent group for the data in this workspace.', on_delete=django.db.models.deletion.PROTECT, to='gregor_anvil.consentgroup')),
+                ('upload_workspaces', models.ManyToManyField(help_text='Upload workspaces contributing data to this workspace.', to='gregor_anvil.UploadWorkspace')),
+                ('workspace', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, to='anvil_consortium_manager.workspace')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='HistoricalReleaseWorkspace',
+            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')),
+                ('full_data_use_limitations', models.TextField(help_text='The full data use limitations for this workspace.')),
+                ('dbgap_version', models.IntegerField(help_text='Version of the release (should be the same as dbGaP version).', validators=[django.core.validators.MinValueValidator(1)], verbose_name=' dbGaP version')),
+                ('dbgap_participant_set', models.IntegerField(help_text='dbGaP participant set of the workspace', validators=[django.core.validators.MinValueValidator(1)], verbose_name=' dbGaP participant set')),
+                ('date_released', models.DateField(blank=True, help_text='Date that this workspace was released to the scientific community.', 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, help_text='Consent group for the data in this workspace.', 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)),
+                ('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 release workspace',
+                'verbose_name_plural': 'historical release workspaces',
+                'ordering': ('-history_date', '-history_id'),
+                'get_latest_by': ('history_date', 'history_id'),
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+        migrations.AddConstraint(
+            model_name='releaseworkspace',
+            constraint=models.UniqueConstraint(fields=('consent_group', 'dbgap_version'), name='unique_release_workspace'),
+        ),
+    ]

gregor_django/gregor_anvil/models.py

@@ -101,3 +101,52 @@ class CombinedConsortiumDataWorkspace(TimeStampedModel, BaseWorkspaceData):
     upload_workspaces = models.ManyToManyField(
         UploadWorkspace, help_text="Upload workspaces"
     )
+
+
+class ReleaseWorkspace(TimeStampedModel, BaseWorkspaceData):
+    """A model to track a workspace for release to the scientific community."""
+
+    phs = 3047
+    """dbGaP-assigned phs for the GREGoR study."""
+
+    consent_group = models.ForeignKey(
+        ConsentGroup,
+        help_text="Consent group for the data in this workspace.",
+        on_delete=models.PROTECT,
+    )
+    upload_workspaces = models.ManyToManyField(
+        UploadWorkspace,
+        help_text="Upload workspaces contributing data to this workspace.",
+    )
+    full_data_use_limitations = models.TextField(
+        help_text="The full data use limitations for this workspace."
+    )
+    dbgap_version = models.IntegerField(
+        verbose_name=" dbGaP version",
+        validators=[MinValueValidator(1)],
+        help_text="Version of the release (should be the same as dbGaP version).",
+    )
+    dbgap_participant_set = models.IntegerField(
+        verbose_name=" dbGaP participant set",
+        validators=[MinValueValidator(1)],
+        help_text="dbGaP participant set of the workspace",
+    )
+    date_released = models.DateField(
+        null=True,
+        blank=True,
+        help_text="Date that this workspace was released to the scientific community.",
+    )
+
+    class Meta:
+        constraints = [
+            # Model uniqueness.
+            models.UniqueConstraint(
+                name="unique_release_workspace",
+                fields=["consent_group", "dbgap_version"],
+            ),
+        ]
+
+    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
+        )

gregor_django/gregor_anvil/tables.py

@@ -90,3 +90,28 @@ class Meta:
     def render_workspace_type(self, value):
         adapter_names = workspace_adapter_registry.get_registered_names()
         return adapter_names[value] + "s"
+
+
+class ReleaseWorkspaceTable(tables.Table):
+    """A table for Workspaces that includes fields from ReleaseWorkspace."""
+
+    name = tables.columns.Column(linkify=True)
+    number_workspaces = tables.columns.Column(
+        accessor="pk",
+        verbose_name="Number of workspaces",
+        orderable=False,
+    )
+
+    class Meta:
+        model = Workspace
+        fields = (
+            "name",
+            "releaseworkspace__consent_group",
+            "releaseworkspace__dbgap_version",
+            "releaseworkspace__dbgap_participant_set",
+            "number_workspaces",
+            "releaseworkspace__date_released",
+        )
+
+    def render_number_workspaces(self, record):
+        return record.releaseworkspace.upload_workspaces.count()

gregor_django/gregor_anvil/tests/factories.py

@@ -76,3 +76,20 @@ class Meta:
         WorkspaceFactory,
         workspace_type="combined_consortium",
     )
+
+
+class ReleaseWorkspaceFactory(DjangoModelFactory):
+    """A factory for the ReleaseWorkspace model."""
+
+    class Meta:
+        model = models.ReleaseWorkspace
+
+    full_data_use_limitations = Faker("paragraph")
+    consent_group = SubFactory(ConsentGroupFactory)
+    dbgap_version = Faker("random_int", min=1, max=10)
+    dbgap_participant_set = Faker("random_int", min=1, max=10)
+
+    workspace = SubFactory(
+        WorkspaceFactory,
+        workspace_type="release",
+    )