Merge pull request #229 from UW-GAC/deploy/stage

Deploy to prod

config/settings/base.py

@@ -321,16 +321,24 @@
         "API_URL": DRUPAL_SITE_URL,
         "OVERRIDE_NAME": "Gregor Consortium Site Login",
         "SCOPES": [
+            # This role will be used to grant ACM view permission.
             {
                 "drupal_machine_name": "dcc_staff",
                 "request_scope": True,
                 "django_group_name": "DCC Staff",
             },
+            # This role will be use dto grant ACM edit permission.
             {
                 "drupal_machine_name": "dcc_acm_admin",
                 "request_scope": True,
                 "django_group_name": "DCC ACM Admin",
             },
+            # For now we can use the "DSA completed" group to determine who can link their accounts.
+            {
+                "drupal_machine_name": "dsa_completed",
+                "request_scope": True,
+                "django_group_name": "DSA completed",
+            },
         ],
     }
 }

gregor_django/gregor_anvil/adapters.py

@@ -1,6 +1,5 @@
 from anvil_consortium_manager.adapters.account import BaseAccountAdapter
 from anvil_consortium_manager.adapters.workspace import BaseWorkspaceAdapter
-from anvil_consortium_manager.tables import WorkspaceTable
 from django.db.models import Q
 
 from . import forms, models, tables
@@ -36,6 +35,17 @@ class UploadWorkspaceAdapter(BaseWorkspaceAdapter):
     workspace_data_form_class = forms.UploadWorkspaceForm
     workspace_detail_template_name = "gregor_anvil/uploadworkspace_detail.html"
 
+    def get_autocomplete_queryset(self, queryset, q, forwarded={}):
+        """Filter to Accounts where the email or the associated user name matches the query `q`."""
+        consent_group = forwarded.get("consent_group", None)
+        if consent_group:
+            queryset = queryset.filter(consent_group=consent_group)
+
+        if q:
+            queryset = queryset.filter(workspace__name__icontains=q)
+
+        return queryset
+
 
 class ExampleWorkspaceAdapter(BaseWorkspaceAdapter):
     """Adapter for ExampleWorkspaces."""
@@ -45,7 +55,7 @@ class ExampleWorkspaceAdapter(BaseWorkspaceAdapter):
     description = (
         "Workspaces that contain examples of using AnVIL, working with data, etc."
     )
-    list_table_class = WorkspaceTable
+    list_table_class = tables.DefaultWorkspaceTable
     workspace_data_model = models.ExampleWorkspace
     workspace_data_form_class = forms.ExampleWorkspaceForm
     workspace_detail_template_name = "anvil_consortium_manager/workspace_detail.html"
@@ -69,7 +79,7 @@ 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
+    list_table_class = tables.DefaultWorkspaceTable
     workspace_data_model = models.CombinedConsortiumDataWorkspace
     workspace_data_form_class = forms.CombinedConsortiumDataWorkspaceForm
     workspace_detail_template_name = (

gregor_django/gregor_anvil/admin.py

@@ -41,6 +41,24 @@ class ResearchCenterAdmin(SimpleHistoryAdmin):
     )
 
 
+@admin.register(models.PartnerGroup)
+class PartnerGroupAdmin(SimpleHistoryAdmin):
+    """Admin class for the PartnerGroup model."""
+
+    list_display = (
+        "short_name",
+        "full_name",
+    )
+    search_fields = (
+        "short_name",
+        "full_name",
+    )
+    sortable_by = (
+        "short_name",
+        "full_name",
+    )
+
+
 @admin.register(models.UploadWorkspace)
 class UploadWorkspaceAdmin(SimpleHistoryAdmin):
     """Admin class for the UploadWorkspace model."""

gregor_django/gregor_anvil/forms.py

@@ -4,6 +4,7 @@
 from dal import autocomplete
 from django import forms
 from django.core.exceptions import ValidationError
+from django.urls import reverse
 
 from . import models
 
@@ -51,7 +52,10 @@ class Meta:
         }
         widgets = {
             "upload_workspaces": autocomplete.ModelSelect2Multiple(
-                url="gregor_anvil:upload_workspaces:autocomplete",
+                url=reverse(
+                    "anvil_consortium_manager:workspaces:autocomplete_by_type",
+                    args=["upload"],
+                ),
                 attrs={"data-theme": "bootstrap-5"},
             ),
         }

gregor_django/gregor_anvil/migrations/0008_historicalpartnergroup_partnergroup.py

@@ -0,0 +1,54 @@
+# Generated by Django 3.2.16 on 2023-04-27 17:10
+
+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 = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('gregor_anvil', '0007_releaseworkspace'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='PartnerGroup',
+            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')),
+                ('short_name', models.CharField(max_length=15, unique=True)),
+                ('full_name', models.CharField(max_length=255)),
+            ],
+            options={
+                'get_latest_by': 'modified',
+                'abstract': False,
+            },
+        ),
+        migrations.CreateModel(
+            name='HistoricalPartnerGroup',
+            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')),
+                ('short_name', models.CharField(db_index=True, max_length=15)),
+                ('full_name', models.CharField(max_length=255)),
+                ('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)),
+            ],
+            options={
+                'verbose_name': 'historical partner group',
+                'verbose_name_plural': 'historical partner groups',
+                'ordering': ('-history_date', '-history_id'),
+                'get_latest_by': ('history_date', 'history_id'),
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+    ]

gregor_django/gregor_anvil/migrations/0009_unique_full_names.py

@@ -0,0 +1,33 @@
+# Generated by Django 3.2.16 on 2023-04-27 19:41
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('gregor_anvil', '0008_historicalpartnergroup_partnergroup'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='historicalpartnergroup',
+            name='full_name',
+            field=models.CharField(db_index=True, max_length=255),
+        ),
+        migrations.AlterField(
+            model_name='historicalresearchcenter',
+            name='full_name',
+            field=models.CharField(db_index=True, max_length=255),
+        ),
+        migrations.AlterField(
+            model_name='partnergroup',
+            name='full_name',
+            field=models.CharField(max_length=255, unique=True),
+        ),
+        migrations.AlterField(
+            model_name='researchcenter',
+            name='full_name',
+            field=models.CharField(max_length=255, unique=True),
+        ),
+    ]

gregor_django/gregor_anvil/models.py

@@ -38,7 +38,7 @@ class ResearchCenter(TimeStampedModel, models.Model):
     short_name = models.CharField(max_length=15, unique=True)
     """The short name of the Research Center."""
 
-    full_name = models.CharField(max_length=255)
+    full_name = models.CharField(max_length=255, unique=True)
     """The full name of the Research Center."""
 
     history = HistoricalRecords()
@@ -56,6 +56,30 @@ def get_absolute_url(self):
         return reverse("gregor_anvil:research_centers:detail", args=[self.pk])
 
 
+class PartnerGroup(TimeStampedModel, models.Model):
+    """A model to track Partner Groups"""
+
+    short_name = models.CharField(max_length=15, unique=True)
+    """The short name of the Partner Group"""
+
+    full_name = models.CharField(max_length=255, unique=True)
+    """The full name of the Partner Group"""
+
+    history = HistoricalRecords()
+
+    def __str__(self):
+        """String method.
+
+        Returns:
+        A string showing the short_name of the object.
+        """
+        return self.short_name
+
+    def get_absolute_url(self):
+        """Return the absolute url for this object."""
+        return reverse("gregor_anvil:partner_groups:detail", args=[self.pk])
+
+
 class UploadWorkspace(TimeStampedModel, BaseWorkspaceData):
     """A model to track additional data about an upload workspace."""
 

gregor_django/gregor_anvil/tables.py

@@ -1,6 +1,7 @@
 import django_tables2 as tables
 from anvil_consortium_manager.adapters.workspace import workspace_adapter_registry
 from anvil_consortium_manager.models import Account, Workspace
+from django.utils.html import format_html
 
 from . import models
 
@@ -33,6 +34,16 @@ class Meta:
         fields = ("full_name", "short_name")
 
 
+class PartnerGroupTable(tables.Table):
+    """A table for PartnerGroups."""
+
+    full_name = tables.Column(linkify=True)
+
+    class Meta:
+        model = models.PartnerGroup
+        fields = ("full_name", "short_name")
+
+
 class ConsentGroupTable(tables.Table):
     """A table for `ConsentGroups`."""
 
@@ -46,7 +57,54 @@ class Meta:
         )
 
 
-class UploadWorkspaceTable(tables.Table):
+class WorkspaceSharedWithConsortiumTable(tables.Table):
+    """Table including a column to indicate if a workspace is shared with PRIMED_ALL."""
+
+    is_shared = tables.columns.Column(
+        accessor="pk",
+        verbose_name="Shared with GREGoR?",
+        orderable=False,
+    )
+
+    def render_is_shared(self, record):
+        is_shared = record.workspacegroupsharing_set.filter(
+            group__name="GREGOR_ALL"
+        ).exists()
+        if is_shared:
+            icon = "check-circle-fill"
+            color = "green"
+            value = format_html(
+                """<i class="bi bi-{}" style="color: {};"></i>""".format(icon, color)
+            )
+        else:
+            value = ""
+        return value
+
+
+class DefaultWorkspaceTable(WorkspaceSharedWithConsortiumTable, tables.Table):
+    """Class to use for default workspace tables in GREGoR."""
+
+    name = tables.Column(linkify=True, verbose_name="Workspace")
+    billing_project = tables.Column(linkify=True)
+    number_groups = tables.Column(
+        verbose_name="Number of groups shared with",
+        empty_values=(),
+        orderable=False,
+        accessor="workspacegroupsharing_set__count",
+    )
+
+    class Meta:
+        model = Workspace
+        fields = (
+            "name",
+            "billing_project",
+            "number_groups",
+            "is_shared",
+        )
+        order_by = ("name",)
+
+
+class UploadWorkspaceTable(WorkspaceSharedWithConsortiumTable, tables.Table):
     """A table for Workspaces that includes fields from UploadWorkspace."""
 
     name = tables.columns.Column(linkify=True)
@@ -58,10 +116,11 @@ class Meta:
             "uploadworkspace__research_center",
             "uploadworkspace__consent_group",
             "uploadworkspace__version",
+            "is_shared",
         )
 
 
-class TemplateWorkspaceTable(tables.Table):
+class TemplateWorkspaceTable(WorkspaceSharedWithConsortiumTable, tables.Table):
     """A table for Workspaces that includes fields from TemplateWorkspace."""
 
     name = tables.columns.Column(linkify=True)
@@ -71,6 +130,7 @@ class Meta:
         fields = (
             "name",
             "templateworkspace__intended_use",
+            "is_shared",
         )
 
 

gregor_django/gregor_anvil/tests/factories.py

@@ -28,6 +28,17 @@ class Meta:
         django_get_or_create = ["short_name"]
 
 
+class PartnerGroupFactory(DjangoModelFactory):
+    """A factory for the PartnerGroup model."""
+
+    short_name = Faker("word")
+    full_name = Faker("company")
+
+    class Meta:
+        model = models.PartnerGroup
+        django_get_or_create = ["short_name"]
+
+
 class UploadWorkspaceFactory(DjangoModelFactory):
     """A factory for the UploadWorkspace model."""