Run the collaborator audit as part of the run_dbgap_audit command

primed/dbgap/management/commands/run_dbgap_audit.py

@@ -4,7 +4,7 @@
 from django.template.loader import render_to_string
 from django.urls import reverse
 
-from ...audit import access_audit
+from ...audit import access_audit, collaborator_audit
 
 
 class Command(BaseCommand):
@@ -17,36 +17,44 @@ def add_arguments(self, parser):
             help="""Email to which to send access reports that need action or have errors.""",
         )
 
-    def handle(self, *args, **options):
+    def run_access_audit(self, *args, **options):
         self.stdout.write("Running dbGaP access audit... ", ending="")
-        data_access_audit = access_audit.dbGaPAccessAudit()
-        data_access_audit.run_audit()
+        audit = access_audit.dbGaPAccessAudit()
+        audit.run_audit()
+        self._handle_audit_results(audit, reverse("dbgap:audit:access:all"), **options)
+
+    def run_collaborator_audit(self, *args, **options):
+        self.stdout.write("Running dbGaP collaborator audit... ", ending="")
+        audit = collaborator_audit.dbGaPCollaboratorAudit()
+        audit.run_audit()
+        self._handle_audit_results(audit, reverse("dbgap:audit:collaborators:all"), **options)
 
+    def _handle_audit_results(self, audit, url, **options):
         # Report errors and needs access.
-        audit_ok = data_access_audit.ok()
+        audit_ok = audit.ok()
         # Construct the url for handling errors.
-        url = "https://" + Site.objects.get_current().domain + reverse("dbgap:audit:access:all")
+        url = "https://" + Site.objects.get_current().domain + url
         if audit_ok:
             self.stdout.write(self.style.SUCCESS("ok!"))
         else:
             self.stdout.write(self.style.ERROR("problems found."))
 
         # Print results
-        self.stdout.write("* Verified: {}".format(len(data_access_audit.verified)))
-        self.stdout.write("* Needs action: {}".format(len(data_access_audit.needs_action)))
-        self.stdout.write("* Errors: {}".format(len(data_access_audit.errors)))
+        self.stdout.write("* Verified: {}".format(len(audit.verified)))
+        self.stdout.write("* Needs action: {}".format(len(audit.needs_action)))
+        self.stdout.write("* Errors: {}".format(len(audit.errors)))
 
         if not audit_ok:
             self.stdout.write(self.style.ERROR(f"Please visit {url} to resolve these issues."))
 
             # Send email if requested and there are problems.
             email = options["email"]
-            subject = "dbGaP access audit - problems found"
+            subject = "{} - problems found".format(audit.__class__.__name__)
             html_body = render_to_string(
                 "primed_anvil/email_audit_report.html",
                 context={
-                    "title": "dbGaP access audit",
-                    "data_access_audit": data_access_audit,
+                    "title": "dbGaP collaborator audit",
+                    "data_access_audit": audit,
                     "url": url,
                 },
             )
@@ -58,3 +66,7 @@ def handle(self, *args, **options):
                 fail_silently=False,
                 html_message=html_body,
             )
+
+    def handle(self, *args, **options):
+        self.run_access_audit(*args, **options)
+        self.run_collaborator_audit(*args, **options)

primed/dbgap/tests/test_commands.py

@@ -2,7 +2,10 @@
 
 from io import StringIO
 
-from anvil_consortium_manager.tests.factories import GroupGroupMembershipFactory
+from anvil_consortium_manager.tests.factories import (
+    AccountFactory,
+    GroupGroupMembershipFactory,
+)
 from django.contrib.sites.models import Site
 from django.core import mail
 from django.core.management import call_command
@@ -14,46 +17,70 @@
 class RunDbGaPAuditTest(TestCase):
     """Tests for the run_dbgap_audit command"""
 
-    def test_command_output_no_records(self):
+    def test_no_dbgap_applications(self):
         """Test command output."""
         out = StringIO()
         call_command("run_dbgap_audit", "--no-color", stdout=out)
-        self.assertIn("Running dbGaP access audit... ok!", out.getvalue())
-        self.assertIn("* Verified: 0", out.getvalue())
-        self.assertIn("* Needs action: 0", out.getvalue())
-        self.assertIn("* Errors: 0", out.getvalue())
+        expected_string = "\n".join(
+            [
+                "Running dbGaP access audit... ok!",
+                "* Verified: 0",
+                "* Needs action: 0",
+                "* Errors: 0",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
+        expected_string = "\n".join(
+            [
+                "Running dbGaP collaborator audit... ok!",
+                "* Verified: 0",
+                "* Needs action: 0",
+                "* Errors: 0",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
         # Zero messages have been sent by default.
         self.assertEqual(len(mail.outbox), 0)
 
-    def test_command_run_audit_one_instance_verified(self):
+    def test_access_audit_one_instance_verified(self):
         """Test command output with one verified instance."""
         # Create a workspace and matching DAR.
         factories.dbGaPWorkspaceFactory.create()
         factories.dbGaPApplicationFactory.create()
         out = StringIO()
         call_command("run_dbgap_audit", "--no-color", stdout=out)
-        self.assertIn("Running dbGaP access audit... ok!", out.getvalue())
-        self.assertIn("* Verified: 1", out.getvalue())
-        self.assertIn("* Needs action: 0", out.getvalue())
-        self.assertIn("* Errors: 0", out.getvalue())
+        expected_string = "\n".join(
+            [
+                "Running dbGaP access audit... ok!",
+                "* Verified: 1",
+                "* Needs action: 0",
+                "* Errors: 0",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
         # Zero messages have been sent by default.
         self.assertEqual(len(mail.outbox), 0)
 
-    def test_command_run_audit_one_instance_needs_action(self):
+    def test_access_audit_one_instance_needs_action(self):
         """Test command output with one needs_action instance."""
         # Create a workspace and matching DAR.
         dbgap_workspace = factories.dbGaPWorkspaceFactory.create()
         factories.dbGaPDataAccessRequestForWorkspaceFactory.create(dbgap_workspace=dbgap_workspace)
         out = StringIO()
         call_command("run_dbgap_audit", "--no-color", stdout=out)
-        self.assertIn("Running dbGaP access audit... problems found.", out.getvalue())
-        self.assertIn("* Verified: 0", out.getvalue())
-        self.assertIn("* Needs action: 1", out.getvalue())
-        self.assertIn("* Errors: 0", out.getvalue())
+        expected_string = "\n".join(
+            [
+                "Running dbGaP access audit... problems found.",
+                "* Verified: 0",
+                "* Needs action: 1",
+                "* Errors: 0",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
         # Zero messages have been sent by default.
         self.assertEqual(len(mail.outbox), 0)
 
-    def test_command_run_audit_one_instance_error(self):
+    def test_access_audit_one_instance_error(self):
         """Test command output with one error instance."""
         # Create a workspace and matching DAR.
         dbgap_workspace = factories.dbGaPWorkspaceFactory.create()
@@ -64,14 +91,19 @@ def test_command_run_audit_one_instance_error(self):
         )
         out = StringIO()
         call_command("run_dbgap_audit", "--no-color", stdout=out)
-        self.assertIn("Running dbGaP access audit... problems found.", out.getvalue())
-        self.assertIn("* Verified: 0", out.getvalue())
-        self.assertIn("* Needs action: 0", out.getvalue())
-        self.assertIn("* Errors: 1", out.getvalue())
+        expected_string = "\n".join(
+            [
+                "Running dbGaP access audit... problems found.",
+                "* Verified: 0",
+                "* Needs action: 0",
+                "* Errors: 1",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
         # Zero messages have been sent by default.
         self.assertEqual(len(mail.outbox), 0)
 
-    def test_command_run_audit_one_instance_verified_email(self):
+    def test_access_audit_one_instance_verified_email(self):
         """No email is sent when there are no errors."""
         # Create a workspace and matching DAR.
         factories.dbGaPWorkspaceFactory.create()
@@ -82,24 +114,29 @@ def test_command_run_audit_one_instance_verified_email(self):
         # Zero messages have been sent by default.
         self.assertEqual(len(mail.outbox), 0)
 
-    def test_command_run_audit_one_instance_needs_action_email(self):
+    def test_access_audit_one_instance_needs_action_email(self):
         """Email is sent for one needs_action instance."""
         # Create a workspace and matching DAR.
         dbgap_workspace = factories.dbGaPWorkspaceFactory.create()
         factories.dbGaPDataAccessRequestForWorkspaceFactory.create(dbgap_workspace=dbgap_workspace)
         out = StringIO()
         call_command("run_dbgap_audit", "--no-color", email="[email protected]", stdout=out)
-        self.assertIn("Running dbGaP access audit... problems found.", out.getvalue())
-        self.assertIn("* Verified: 0", out.getvalue())
-        self.assertIn("* Needs action: 1", out.getvalue())
-        self.assertIn("* Errors: 0", out.getvalue())
+        expected_string = "\n".join(
+            [
+                "Running dbGaP access audit... problems found.",
+                "* Verified: 0",
+                "* Needs action: 1",
+                "* Errors: 0",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
         # One message has been sent by default.
         self.assertEqual(len(mail.outbox), 1)
         email = mail.outbox[0]
         self.assertEqual(email.to, ["[email protected]"])
-        self.assertEqual(email.subject, "dbGaP access audit - problems found")
+        self.assertEqual(email.subject, "dbGaPAccessAudit - problems found")
 
-    def test_command_run_audit_one_instance_error_email(self):
+    def test_access_audit_one_instance_error_email(self):
         """Test command output with one error instance."""
         # Create a workspace and matching DAR.
         dbgap_workspace = factories.dbGaPWorkspaceFactory.create()
@@ -110,17 +147,22 @@ def test_command_run_audit_one_instance_error_email(self):
         )
         out = StringIO()
         call_command("run_dbgap_audit", "--no-color", email="[email protected]", stdout=out)
-        self.assertIn("Running dbGaP access audit... problems found.", out.getvalue())
-        self.assertIn("* Verified: 0", out.getvalue())
-        self.assertIn("* Needs action: 0", out.getvalue())
-        self.assertIn("* Errors: 1", out.getvalue())
+        expected_string = "\n".join(
+            [
+                "Running dbGaP access audit... problems found.",
+                "* Verified: 0",
+                "* Needs action: 0",
+                "* Errors: 1",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
         # One message has been sent by default.
         self.assertEqual(len(mail.outbox), 1)
         email = mail.outbox[0]
         self.assertEqual(email.to, ["[email protected]"])
-        self.assertEqual(email.subject, "dbGaP access audit - problems found")
+        self.assertEqual(email.subject, "dbGaPAccessAudit - problems found")
 
-    def test_different_domain(self):
+    def test_access_audit_different_domain(self):
         """Test command output when a different domain is specified."""
         site = Site.objects.create(domain="foobar.com", name="test")
         site.save()
@@ -132,6 +174,126 @@ def test_different_domain(self):
             self.assertIn("Running dbGaP access audit... problems found.", out.getvalue())
             self.assertIn("https://foobar.com", out.getvalue())
 
-    def test_command_collaborator_audit(self):
-        """run_dbgap_audit runs an audit on collaborators."""
-        self.fail()
+    def test_collaborator_audit_one_instance_verified(self):
+        """Test command output with one verified instance."""
+        # Create a workspace and matching DAR.
+        factories.dbGaPApplicationFactory.create()
+        # Verified no access for PI.
+        out = StringIO()
+        call_command("run_dbgap_audit", "--no-color", stdout=out)
+        expected_string = "\n".join(
+            [
+                "Running dbGaP collaborator audit... ok!",
+                "* Verified: 1",
+                "* Needs action: 0",
+                "* Errors: 0",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
+        # Zero messages have been sent by default.
+        self.assertEqual(len(mail.outbox), 0)
+
+    def test_collaborator_audit_one_instance_needs_action(self):
+        """Test command output with one needs_action instance."""
+        application = factories.dbGaPApplicationFactory.create()
+        AccountFactory.create(user=application.principal_investigator)
+        out = StringIO()
+        call_command("run_dbgap_audit", "--no-color", stdout=out)
+        expected_string = "\n".join(
+            [
+                "Running dbGaP collaborator audit... problems found.",
+                "* Verified: 0",
+                "* Needs action: 1",
+                "* Errors: 0",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
+        # Zero messages have been sent by default.
+        self.assertEqual(len(mail.outbox), 0)
+
+    def test_collaborator_audit_one_instance_error(self):
+        """Test command output with one error instance."""
+        application = factories.dbGaPApplicationFactory.create()
+        GroupGroupMembershipFactory(
+            parent_group=application.anvil_access_group,
+        )
+        out = StringIO()
+        call_command("run_dbgap_audit", "--no-color", stdout=out)
+        expected_string = "\n".join(
+            [
+                "Running dbGaP collaborator audit... problems found.",
+                "* Verified: 1",  # PI - no linked account, verified no access.
+                "* Needs action: 0",
+                "* Errors: 1",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
+        # Zero messages have been sent by default.
+        self.assertEqual(len(mail.outbox), 0)
+
+    def test_collaborator_audit_one_instance_verified_email(self):
+        """No email is sent when there are no errors."""
+        factories.dbGaPApplicationFactory.create()
+        # Verified no access for PI.
+        out = StringIO()
+        call_command("run_dbgap_audit", "--no-color", email="[email protected]", stdout=out)
+        self.assertIn("Running dbGaP collaborator audit... ok!", out.getvalue())
+        # Zero messages have been sent by default.
+        self.assertEqual(len(mail.outbox), 0)
+
+    def test_collaborator_audit_one_instance_needs_action_email(self):
+        """Email is sent for one needs_action instance."""
+        # Create a workspace and matching DAR.
+        application = factories.dbGaPApplicationFactory.create()
+        AccountFactory.create(user=application.principal_investigator)
+        out = StringIO()
+        call_command("run_dbgap_audit", "--no-color", email="[email protected]", stdout=out)
+        expected_string = "\n".join(
+            [
+                "Running dbGaP collaborator audit... problems found.",
+                "* Verified: 0",
+                "* Needs action: 1",
+                "* Errors: 0",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
+        # One message has been sent by default.
+        self.assertEqual(len(mail.outbox), 1)
+        email = mail.outbox[0]
+        self.assertEqual(email.to, ["[email protected]"])
+        self.assertEqual(email.subject, "dbGaPCollaboratorAudit - problems found")
+
+    def test_collaborator_audit_one_instance_error_email(self):
+        """Test command output with one error instance."""
+        application = factories.dbGaPApplicationFactory.create()
+        GroupGroupMembershipFactory(
+            parent_group=application.anvil_access_group,
+        )
+        out = StringIO()
+        call_command("run_dbgap_audit", "--no-color", email="[email protected]", stdout=out)
+        expected_string = "\n".join(
+            [
+                "Running dbGaP collaborator audit... problems found.",
+                "* Verified: 1",  # PI - no linked account, verified no access.
+                "* Needs action: 0",
+                "* Errors: 1",
+            ]
+        )
+        self.assertIn(expected_string, out.getvalue())
+        # One message has been sent by default.
+        self.assertEqual(len(mail.outbox), 1)
+        email = mail.outbox[0]
+        self.assertEqual(email.to, ["[email protected]"])
+        self.assertEqual(email.subject, "dbGaPCollaboratorAudit - problems found")
+
+    def test_collaborator_audit_different_domain(self):
+        """Test command output when a different domain is specified."""
+        site = Site.objects.create(domain="foobar.com", name="test")
+        site.save()
+        with self.settings(SITE_ID=site.id):
+            application = factories.dbGaPApplicationFactory.create()
+            AccountFactory.create(user=application.principal_investigator)
+            out = StringIO()
+            call_command("run_dbgap_audit", "--no-color", stdout=out)
+            self.assertIn("Running dbGaP collaborator audit... problems found.", out.getvalue())
+            self.assertIn("https://foobar.com", out.getvalue())