Merge pull request #417 from UW-GAC/feature/dar-history

Add a view showing history for a DAR

primed/dbgap/tables.py

@@ -237,7 +237,10 @@ class dbGaPDataAccessRequestTable(tables.Table):
         verbose_name=" dbGaP application",
         linkify=lambda record: record.dbgap_data_access_snapshot.dbgap_application.get_absolute_url(),
     )
-    dbgap_dar_id = tables.columns.Column(verbose_name="DAR")
+    dbgap_dar_id = tables.columns.Column(
+        verbose_name="DAR",
+        linkify=("dbgap:dars:history", {"dbgap_dar_id": tables.A("dbgap_dar_id")}),
+    )
     dbgap_dac = tables.columns.Column(verbose_name="DAC")
     dbgap_accession = dbGaPAccessionColumn(
         accessor="get_dbgap_accession",
@@ -273,22 +276,11 @@ class Meta:
         attrs = {"class": "table table-sm"}
 
 
-class dbGaPDataAccessRequestBySnapshotTable(tables.Table):
+class dbGaPDataAccessRequestBySnapshotTable(dbGaPDataAccessRequestTable):
     """Class to render a table of dbGaPDataAccessRequest objects for a specific dbGaPDataAccessSnapshot."""
 
-    dbgap_dar_id = tables.columns.Column(verbose_name="DAR")
-    dbgap_dac = tables.columns.Column(verbose_name="DAC")
-    dbgap_accession = dbGaPAccessionColumn(
-        accessor="get_dbgap_accession",
-        verbose_name="Accession",
-        order_by=(
-            "dbgap_phs",
-            "original_version",
-            "original_participant_set",
-        ),
-    )
-    dbgap_consent_abbreviation = tables.columns.Column(verbose_name="Consent")
-    dbgap_current_status = tables.columns.Column(verbose_name="Current status")
+    dbgap_data_access_snapshot__dbgap_application__dbgap_project_id = None
+    dbgap_data_access_snapshot__created = None
     matching_workspaces = tables.columns.Column(
         accessor="get_dbgap_workspaces", orderable=False, default=" "
     )
@@ -326,6 +318,29 @@ def render_matching_workspaces(self, value, record):
         return html
 
 
+class dbGaPDataAccessRequestHistoryTable(dbGaPDataAccessRequestTable):
+    """Class to render a table of dbGaPDataAccessRequest history by dbgap_dar_id."""
+
+    dbgap_dar_id = tables.columns.Column(
+        verbose_name="DAR",
+        linkify=False,
+    )
+
+    class Meta:
+        model = models.dbGaPDataAccessRequest
+        fields = (
+            "dbgap_dar_id",
+            "dbgap_data_access_snapshot__created",
+            "dbgap_current_status",
+            "dbgap_data_access_snapshot__dbgap_application__dbgap_project_id",
+            "dbgap_dac",
+            "dbgap_accession",
+            "dbgap_consent_abbreviation",
+        )
+        order_by = ("-dbgap_data_access_snapshot__created",)
+        attrs = {"class": "table table-sm"}
+
+
 class dbGaPDataAccessRequestSummaryTable(tables.Table):
     """Table intended to show a summary of data access requests, grouped by DAC and current status."""
 

primed/dbgap/tests/test_tables.py

@@ -611,6 +611,53 @@ def test_ordering(self):
         self.assertEqual(table.data[3], instance_1)
 
 
+class dbGaPDataAccessRequestHistoryTest(TestCase):
+    model = models.dbGaPDataAccessRequest
+    model_factory = factories.dbGaPDataAccessRequestFactory
+    table_class = tables.dbGaPDataAccessRequestHistoryTable
+
+    def test_row_count_with_no_objects(self):
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(len(table.rows), 0)
+
+    def test_row_count_with_one_object(self):
+        self.model_factory.create()
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(len(table.rows), 1)
+
+    def test_row_count_with_two_objects(self):
+        self.model_factory.create_batch(2)
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(len(table.rows), 2)
+
+    def test_ordering(self):
+        """Instances are ordered alphabetically by dbgap_application and dbgap_dar_id."""
+        dbgap_snapshot_1 = factories.dbGaPDataAccessSnapshotFactory.create(
+            created=timezone.now() - timedelta(weeks=5),
+        )
+        instance_1 = self.model_factory.create(
+            dbgap_data_access_snapshot=dbgap_snapshot_1,
+        )
+        dbgap_snapshot_2 = factories.dbGaPDataAccessSnapshotFactory.create(
+            created=timezone.now() - timedelta(weeks=4)
+        )
+        instance_2 = self.model_factory.create(
+            dbgap_dar_id=instance_1.dbgap_dar_id,
+            dbgap_data_access_snapshot=dbgap_snapshot_2,
+        )
+        dbgap_snapshot_3 = factories.dbGaPDataAccessSnapshotFactory.create(
+            created=timezone.now() - timedelta(weeks=3)
+        )
+        instance_3 = self.model_factory.create(
+            dbgap_dar_id=instance_1.dbgap_dar_id,
+            dbgap_data_access_snapshot=dbgap_snapshot_3,
+        )
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(table.data[0], instance_3)
+        self.assertEqual(table.data[1], instance_2)
+        self.assertEqual(table.data[2], instance_1)
+
+
 class dbGaPDataAccessRequestBySnapshotTableTest(TestCase):
     model = models.dbGaPDataAccessRequest
     model_factory = factories.dbGaPDataAccessRequestFactory

primed/dbgap/tests/test_views.py

@@ -3670,7 +3670,7 @@ def setUp(self):
 
     def get_url(self, *args):
         """Get the url for the view being tested."""
-        return reverse("dbgap:dbgap_applications:dars", args=args)
+        return reverse("dbgap:dars:current", args=args)
 
     def get_view(self):
         """Return the view being tested."""
@@ -3751,6 +3751,120 @@ def test_export(self):
         )
 
 
+class dbGaPDataAccessRequestHistoryTest(TestCase):
+    def setUp(self):
+        """Set up test class."""
+        self.factory = RequestFactory()
+        # Create a user with both view and edit permission.
+        self.user = User.objects.create_user(username="test", password="test")
+        self.user.user_permissions.add(
+            Permission.objects.get(
+                codename=AnVILProjectManagerAccess.STAFF_VIEW_PERMISSION_CODENAME
+            )
+        )
+
+    def get_url(self, *args):
+        """Get the url for the view being tested."""
+        return reverse("dbgap:dars:history", args=args)
+
+    def get_view(self):
+        """Return the view being tested."""
+        return views.dbGaPDataAccessRequestHistory.as_view()
+
+    def test_view_redirect_not_logged_in(self):
+        "View redirects to login view when user is not logged in."
+        # Need a client for redirects.
+        response = self.client.get(self.get_url(1))
+        self.assertRedirects(
+            response,
+            resolve_url(settings.LOGIN_URL) + "?next=" + self.get_url(1),
+        )
+
+    def test_status_code_with_user_permission(self):
+        """Returns successful response code."""
+        instance = factories.dbGaPDataAccessRequestFactory.create()
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(instance.dbgap_dar_id))
+        self.assertEqual(response.status_code, 200)
+
+    def test_access_without_user_permission(self):
+        """Raises permission denied if user has no permissions."""
+        user_no_perms = User.objects.create_user(
+            username="test-none", password="test-none"
+        )
+        request = self.factory.get(self.get_url(1))
+        request.user = user_no_perms
+        with self.assertRaises(PermissionDenied):
+            self.get_view()(request, 1)
+
+    def test_dbgap_dar_id_does_not_exist(self):
+        """Raises permission denied if user has no permissions."""
+        request = self.factory.get(self.get_url(1))
+        request.user = self.user
+        with self.assertRaises(Http404):
+            self.get_view()(request, 1)
+
+    def test_table_class(self):
+        """The table is the correct class."""
+        instance = factories.dbGaPDataAccessRequestFactory.create()
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(instance.dbgap_dar_id))
+        self.assertIn("table", response.context_data)
+        self.assertIsInstance(
+            response.context_data["table"], tables.dbGaPDataAccessRequestHistoryTable
+        )
+
+    def test_one_dars(self):
+        """Table displays two dars."""
+        dar = factories.dbGaPDataAccessRequestFactory.create(dbgap_dar_id=1)
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(1))
+        self.assertEqual(len(response.context_data["table"].rows), 1)
+        self.assertIn(dar, response.context_data["table"].data)
+
+    def test_two_dars(self):
+        """Table displays two dars."""
+        dar_1 = factories.dbGaPDataAccessRequestFactory.create(dbgap_dar_id=1)
+        dar_2 = factories.dbGaPDataAccessRequestFactory.create(dbgap_dar_id=1)
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(1))
+        self.assertEqual(len(response.context_data["table"].rows), 2)
+        self.assertIn(dar_1, response.context_data["table"].data)
+        self.assertIn(dar_2, response.context_data["table"].data)
+
+    def test_matching_dbgap_dar_id(self):
+        """Only DARs with the same dbgap_dar_id are in the table."""
+        dar_1 = factories.dbGaPDataAccessRequestFactory.create(dbgap_dar_id=1)
+        dar_2 = factories.dbGaPDataAccessRequestFactory.create(dbgap_dar_id=2)
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(1))
+        self.assertEqual(len(response.context_data["table"].rows), 1)
+        self.assertIn(dar_1, response.context_data["table"].data)
+        self.assertNotIn(dar_2, response.context_data["table"].data)
+
+    def test_table_ordering(self):
+        """DARs from the most recent snapshot appear first."""
+        old_snapshot = factories.dbGaPDataAccessSnapshotFactory.create(
+            created=timezone.now() - timedelta(weeks=5),
+            is_most_recent=False,
+        )
+        dar_1 = factories.dbGaPDataAccessRequestFactory.create(
+            dbgap_dar_id=1, dbgap_data_access_snapshot=old_snapshot
+        )
+        new_snapshot = factories.dbGaPDataAccessSnapshotFactory.create(
+            created=timezone.now() - timedelta(weeks=1),
+            is_most_recent=True,
+        )
+        dar_2 = factories.dbGaPDataAccessRequestFactory.create(
+            dbgap_dar_id=1, dbgap_data_access_snapshot=new_snapshot
+        )
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(1))
+        self.assertEqual(len(response.context_data["table"].rows), 2)
+        self.assertEqual(dar_2, response.context_data["table"].rows[0].record)
+        self.assertEqual(dar_1, response.context_data["table"].rows[1].record)
+
+
 class dbGaPApplicationAuditTest(TestCase):
     """Tests for the dbGaPApplicationAudit view."""
 

primed/dbgap/urls.py

@@ -41,6 +41,17 @@
     "dbgap_data_access_snapshots",
 )
 
+data_access_request_patterns = (
+    [
+        path("current/", views.dbGaPDataAccessRequestList.as_view(), name="current"),
+        path(
+            "history/<int:dbgap_dar_id>",
+            views.dbGaPDataAccessRequestHistory.as_view(),
+            name="history",
+        ),
+    ],
+    "dars",
+)
 dbgap_application_patterns = (
     [
         path("", views.dbGaPApplicationList.as_view(), name="list"),
@@ -50,7 +61,7 @@
             views.dbGaPDataAccessSnapshotCreateMultiple.as_view(),
             name="update_dars",
         ),
-        path("dars/", views.dbGaPDataAccessRequestList.as_view(), name="dars"),
+        # path("dars/", views.dbGaPDataAccessRequestList.as_view(), name="dars"),
         path(
             "<int:dbgap_project_id>/",
             views.dbGaPApplicationDetail.as_view(),
@@ -93,6 +104,7 @@
 urlpatterns = [
     path("studies/", include(dbgap_study_accession_patterns)),
     path("applications/", include(dbgap_application_patterns)),
+    path("dars/", include(data_access_request_patterns)),
     path("workspaces/", include(dbgap_workspace_patterns)),
     path("records/", include(records_patterns)),
 ]

primed/dbgap/views.py

@@ -517,6 +517,41 @@ def get_table_data(self):
         )
 
 
+class dbGaPDataAccessRequestHistory(
+    AnVILConsortiumManagerStaffViewRequired, ExportMixin, SingleTableView
+):
+    """View to show the history of a given DAR."""
+
+    model = models.dbGaPDataAccessRequest
+    table_class = tables.dbGaPDataAccessRequestHistoryTable
+    template_name = "dbgap/dbgapdataaccessrequest_history.html"
+
+    def get_dbgap_dar_id(self):
+        return self.kwargs.get("dbgap_dar_id")
+
+    def get(self, request, *args, **kwargs):
+        self.dbgap_dar_id = self.get_dbgap_dar_id()
+        return super().get(request, *args, **kwargs)
+
+    def get_table_data(self):
+        qs = self.get_queryset().filter(
+            dbgap_dar_id=self.dbgap_dar_id,
+        )
+        if not qs.count():
+            raise Http404("No DARs found matching the query.")
+        return qs
+
+    def get_table_kwargs(self):
+        return {
+            "order_by": "-dbgap_data_access_snapshot__created",
+        }
+
+    def get_context_data(self, **kwargs):
+        context = super().get_context_data(**kwargs)
+        context["dbgap_dar_id"] = self.dbgap_dar_id
+        return context
+
+
 class dbGaPApplicationAudit(AnVILConsortiumManagerStaffViewRequired, DetailView):
     """View to show audit results for a `dbGaPApplication`."""
 

primed/templates/dbgap/dbgapdataaccessrequest_history.html

@@ -0,0 +1,15 @@
+{% extends "anvil_consortium_manager/base.html" %}
+{% load render_table from django_tables2 %}
+
+{% block title %}dbGaP DAR history{% endblock %}
+
+{% block content %}
+<h1>dbGaP DAR history: {{ dbgap_dar_id }}</h1>
+
+<p>
+    The table below shows all snapshots that have a record of this DAR.
+</p>
+
+{% render_table table %}
+
+{% endblock content %}

primed/templates/dbgap/dbgapdataaccessrequest_list.html

@@ -7,7 +7,7 @@
 <h1>Current dbGaP data access requests</h1>
 
 <div class="container text-end">
-    <a class="btn btn-secondary" href="{% url 'dbgap:dbgap_applications:dars' %}?_export=tsv" role="button">Export <i class="bi bi-download ms-1"></i></a>
+    <a class="btn btn-secondary" href="{% url 'dbgap:dars:current' %}?_export=tsv" role="button">Export <i class="bi bi-download ms-1"></i></a>
 </div>
 
 {% render_table table %}

primed/templates/dbgap/nav_items.html

@@ -18,7 +18,7 @@
       <a class="dropdown-item" href="{% url 'dbgap:dbgap_applications:list' %}">List dbGaP applications</a>
     </li>
     <li>
-      <a class="dropdown-item" href="{% url 'dbgap:dbgap_applications:dars' %}">List all current DARs</a>
+      <a class="dropdown-item" href="{% url 'dbgap:dars:current' %}">List all current DARs</a>
     </li>
   {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_edit %}
       <li>