Jkmarx/update management command argparse (#2607)

* Update management command, argparse.

* Move for consistency.

* Add tests for `create_workflow_engine`

* Add tests for `create_galaxy_instance`

refinery/core/management/commands/create_workflowengine.py

@@ -16,29 +16,34 @@
 
 
 class Command(BaseCommand):
-    args = "<Galaxy instance ID> <Group name>"
     help = "Creates a %s workflow engine with the specified Galaxy instance " \
            "and group." % Site.objects.get_current().name
     """
     Name: handle
     Description:
     main program; run the command
     """
+    def add_arguments(self, parser):
+        parser.add_argument('galaxy_instance_id', type=int)
+        parser.add_argument('group_name')
+
     def handle(self, *args, **options):
         """This function creates a workflow engine and assigns it to the
         specified group
         """
         try:
-            instance = Instance.objects.get(id=args[0])
-        except IndexError:
+            instance = Instance.objects.get(id=options["galaxy_instance_id"])
+        except KeyError:
             raise CommandError("Please provide a Galaxy instance ID")
         except Instance.DoesNotExist:
             raise CommandError(
-                "Unable to retrieve Galaxy instance with id '%d'" % args[0])
+                "Unable to retrieve Galaxy instance with id '%s'" %
+                options["galaxy_instance_id"]
+            )
         # get *manager* group for indicated group
         try:
-            group_name = args[1]
-        except IndexError:
+            group_name = options["group_name"]
+        except KeyError:
             raise CommandError("Please provide a group name")
         try:
             manager_group = ExtendedGroup.objects.get(

refinery/core/management/commands/set_up_site_name.py

@@ -14,6 +14,9 @@ class Command(BaseCommand):
     Description:
     main program; run the command
     """
+    def add_arguments(self, parser):
+        parser.add_argument('refinery_instance_name')
+        parser.add_argument('refinery_base_url')
 
     def handle(self, *args, **options):
         try:
@@ -26,10 +29,6 @@ def handle(self, *args, **options):
         else:
             set_up_site_name(refinery_instance_name, refinery_base_url)
 
-    def add_arguments(self, parser):
-        parser.add_argument('refinery_instance_name')
-        parser.add_argument('refinery_base_url')
-
 
 def set_up_site_name(refinery_instance_name, refinery_base_url):
     """Set up the site name

refinery/core/tests.py

@@ -2267,3 +2267,31 @@ def test_import_annotations(self):
         neo4j interactions """
         with mock.patch.object(ImportAnnotationsCommand, "handle"):
             call_command("import_annotations", "-c")
+
+    def test_create_workflow_engine(self):
+        galaxy_instance = GalaxyInstanceFactory()
+        call_command(
+            "create_workflowengine",
+            str(galaxy_instance.id),
+            ExtendedGroup.objects.public_group().name
+        )
+        self.assertIsNotNone(
+            WorkflowEngine.objects.get(instance=galaxy_instance)
+        )
+
+    def test_create_workflow_engine_bad_galaxy_instance(self):
+        with self.assertRaises(CommandError):
+            call_command(
+                "create_workflowengine",
+                str(123),
+                ExtendedGroup.objects.public_group().name
+            )
+
+    def test_create_workflow_engine_bad_group_name(self):
+        galaxy_instance = GalaxyInstanceFactory()
+        with self.assertRaises(CommandError):
+            call_command(
+                "create_workflowengine",
+                str(galaxy_instance.id),
+                "non-existent group name"
+            )

refinery/galaxy_connector/management/commands/create_galaxy_instance.py

@@ -10,14 +10,11 @@
 
 
 class Command(BaseCommand):
-    args = "<base_url> <api_key>"
     help = "Creates a new Galaxy instance."
 
     def add_arguments(self, parser):
-        parser.add_argument(
-            '--file_name',
-            action='store'
-        )
+        parser.add_argument('base_url')
+        parser.add_argument('api_key')
         parser.add_argument(
             '--description',
             action='store',
@@ -42,31 +39,40 @@ def add_arguments(self, parser):
     """
     def handle(self, *args, **options):
         try:
-            base_url = args[0]
+            base_url = options['base_url']
         except IndexError:
             raise CommandError("Please provide a base URL for Galaxy instance")
         try:
-            api_key = args[1]
+            api_key = options['api_key']
         except IndexError:
             raise CommandError("Please provide an API key")
         instance_count = Instance.objects.filter(
-            base_url__exact=base_url).count()
+            base_url__exact=base_url
+        ).count()
+
         if instance_count > 0:
-            self.stdout.write("Instance with URL '%s' already exists" %
-                              base_url)
-            logger.error("Instance with URL '%s' already exists", base_url)
+            aready_exists_message = "Instance with URL '{}' already " \
+                                 "exists".format(base_url)
+            self.stdout.write(aready_exists_message)
+            logger.info(aready_exists_message)
             return
+
         instance = Instance.objects.create(base_url=base_url,
                                            api_key=api_key,
                                            data_url=options['data_url'],
                                            api_url=options['api_url'],
                                            description=options['description'])
         if instance is not None:
-            self.stdout.write("Instance '%s -- %s' created" %
-                              base_url, api_key)
-            logger.info("Instance '%s -- %s' created", base_url, api_key)
+            creation_message = "Instance '{} -- {}' created".format(
+                base_url,
+                api_key
+            )
+            self.stdout.write(creation_message)
+            logger.info(creation_message)
         else:
-            self.stdout.write("Unable to create instance '%s -- %s'" %
-                              base_url, api_key)
-            logger.error("Unable to create instance '%s -- %s'",
-                         base_url, api_key)
+            error_message = "Unable to create instance '{} -- {}'".format(
+                base_url,
+                api_key
+            )
+            self.stdout.write(error_message)
+            logger.error(error_message)

refinery/galaxy_connector/tests.py

@@ -1,11 +1,13 @@
 import uuid
 
+from django.core.management import call_command
 from django.test import TestCase
 
 from bioblend import galaxy
 import mock
 
 from factory_boy.django_model_factories import GalaxyInstanceFactory
+from galaxy_connector.models import Instance
 
 
 class GalaxyInstanceTests(TestCase):
@@ -100,3 +102,21 @@ def test_no_history_files_if_history_content_entry_isnt_a_file(self):
             self.GALAXY_HISTORY_ID
         )
         self.assertEqual(len(history_file_list), 0)
+
+
+class TestManagementCommands(TestCase):
+    def test_create_galaxy_instance(self):
+        fake_api_key = str(uuid.uuid4())
+        fake_galaxy_url = "http://www.example.com/galaxy",
+        call_command(
+            "create_galaxy_instance",
+            fake_galaxy_url,
+            fake_api_key
+        )
+
+        self.assertIsNotNone(
+            Instance.objects.get(
+                base_url=fake_galaxy_url,
+                api_key=fake_api_key
+            )
+        )