Merge c8af43a into 03410c1

microsetta_private_api/admin/admin_impl.py

@@ -144,14 +144,14 @@ def create_kits(body, token_info):
     number_of_kits = body['number_of_kits']
     number_of_samples = body['number_of_samples']
     kit_prefix = body.get('kit_id_prefix', None)
-    projects = body['projects']
+    project_ids = body['project_ids']
 
     with Transaction() as t:
         admin_repo = AdminRepo(t)
 
         try:
             kits = admin_repo.create_kits(number_of_kits, number_of_samples,
-                                          kit_prefix, projects)
+                                          kit_prefix, project_ids)
         except KeyError:
             return jsonify(code=422, message="Unable to create kits"), 422
         else:

microsetta_private_api/admin/tests/test_admin.py

@@ -378,13 +378,13 @@ def test_create_kits_fail_nonexistent_project(self):
             admin_repo = AdminRepo(t)
 
             with self.assertRaisesRegex(KeyError, "does not exist"):
-                admin_repo.create_kits(5, 3, '', ['foo', 'bar'])
+                admin_repo.create_kits(5, 3, '', [10000, 10001])
 
     def test_create_kits_success_not_microsetta(self):
         with Transaction() as t:
             admin_repo = AdminRepo(t)
             non_tmi = admin_repo.create_kits(5, 3, '',
-                                             ['Project - lm3eáqç(>?'])
+                                             [33])
             self.assertEqual(['created', ], list(non_tmi.keys()))
             self.assertEqual(len(non_tmi['created']), 5)
             for obj in non_tmi['created']:
@@ -406,7 +406,7 @@ def test_create_kits_success_is_microsetta(self):
         with Transaction() as t:
             admin_repo = AdminRepo(t)
             tmi = admin_repo.create_kits(4, 2, 'foo',
-                                         ['American Gut Project'])
+                                         [1])
             self.assertEqual(['created', ], list(tmi.keys()))
             self.assertEqual(len(tmi['created']), 4)
             for obj in tmi['created']:

microsetta_private_api/api/microsetta_private_api.yaml

@@ -1246,14 +1246,14 @@ paths:
                     type: integer
                   kit_id_prefix:
                     type: string
-                  projects:
+                  project_ids:
                     type: array
                     items:
                       type: string
                 required:
                   - number_of_kits
                   - number_of_samples
-                  - projects
+                  - project_ids
       responses:
         '201':
           description: Kit identifiers and associated samples were successfully created

microsetta_private_api/repo/admin_repo.py

@@ -647,7 +647,7 @@ def _generate_random_kit_name(self, name_length, prefix):
         return prefix + '_' + rand_name
 
     def create_kits(self, number_of_kits, number_of_samples, kit_prefix,
-                    projects):
+                    project_ids):
         """Create kits each with the same number of samples
 
         Parameters
@@ -658,24 +658,29 @@ def create_kits(self, number_of_kits, number_of_samples, kit_prefix,
             Number of samples that each kit will contain
         kit_prefix : str or None
             A prefix to put on to the kit IDs, this is optional.
-        projects : list of str
-            Project names the samples are to be associated with
+        project_ids : list of int
+            Project ids the samples are to be associated with
         """
+        # int ids come in as strings ...
+        project_ids = [int(x) for x in project_ids]
+
         with self._transaction.cursor() as cur:
             # get existing projects
             query = f"""
-                    SELECT {p.DB_PROJ_NAME_KEY}, project_id,
+                    SELECT project_id,
                     {p.IS_MICROSETTA_KEY}
                     FROM barcodes.project;"""
 
             cur.execute(query)
-            known_projects = {prj: (id_, tmi)
-                              for prj, id_, tmi in cur.fetchall()}
+            projects_tmi = {id_: bool(tmi) for id_, tmi in cur.fetchall()}
             is_tmi = False
-            for name in projects:
-                if name not in known_projects:
-                    raise KeyError("%s does not exist" % name)
-                if known_projects[name][1]:
+            for input_proj_id in project_ids:
+                if input_proj_id not in projects_tmi:
+                    raise KeyError("Project id %s does not exist" %
+                                   input_proj_id)
+                # if *any* of the projects the kits will be associate with are
+                # microsetta projects, set is_tmi to true
+                if projects_tmi[input_proj_id]:
                     is_tmi = True
 
             # get existing kits to test for conflicts
@@ -717,8 +722,7 @@ def create_kits(self, number_of_kits, number_of_samples, kit_prefix,
             # create barcode project associations
             barcode_projects = []
             for barcode in new_barcodes:
-                for project in projects:
-                    prj_id = known_projects[project][0]
+                for prj_id in project_ids:
                     barcode_projects.append((barcode, prj_id))
 
             # create shipping IDs