Merge pull request #120 from wasade/get_create_project

Allow an admin to create a new project

microsetta_private_api/admin/admin_impl.py

@@ -105,6 +105,23 @@ def validate_admin_access(token_info):
             raise Unauthorized()
 
 
+def create_project(body, token_info):
+    validate_admin_access(token_info)
+
+    project_name = body['project_name']
+    is_microsetta = body['is_microsetta']
+
+    if len(project_name) == 0:
+        return jsonify(code=400, message="No project name provided"), 400
+
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        admin_repo.create_project(project_name, is_microsetta)
+        t.commit()
+
+    return {}, 201
+
+
 def create_kits(body, token_info):
     validate_admin_access(token_info)
 

microsetta_private_api/admin/tests/test_admin.py

@@ -118,6 +118,29 @@ def test_search_barcode(self):
             diag = admin_repo.retrieve_diagnostics_by_barcode('NotABarcode :D')
             self.assertIsNone(diag)
 
+    def test_create_project(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            with t.cursor() as cur:
+                cur.execute("SELECT project "
+                            "FROM barcodes.project "
+                            "WHERE project = 'doesnotexist'")
+                self.assertEqual(len(cur.fetchall()), 0)
+
+                admin_repo.create_project('doesnotexist', True)
+                cur.execute("SELECT project, is_microsetta "
+                            "FROM barcodes.project "
+                            "WHERE project = 'doesnotexist'")
+                obs = cur.fetchall()
+                self.assertEqual(obs, [('doesnotexist', True), ])
+
+                admin_repo.create_project('doesnotexist2', False)
+                cur.execute("SELECT project, is_microsetta "
+                            "FROM barcodes.project "
+                            "WHERE project = 'doesnotexist2'")
+                obs = cur.fetchall()
+                self.assertEqual(obs, [('doesnotexist2', False), ])
+
     def test_create_kits(self):
         with Transaction() as t:
             admin_repo = AdminRepo(t)

microsetta_private_api/api/microsetta_private_api.yaml

@@ -1068,6 +1068,36 @@ paths:
         '404':
           $ref: '#/components/responses/404NotFound'
 
+  '/admin/create/project':
+    post:
+      operationId: microsetta_private_api.admin.admin_impl.create_project
+      tags:
+        - Admin
+      summary: Create a project which kits can be associated too
+      description: Create a project which kits can be associated too
+      requestBody:
+        content:
+          application/json:
+            schema:
+              type: "object"
+              properties:
+                project_name:
+                  type: string
+                is_microsetta:
+                  type: boolean
+
+              required:
+                - project_name
+                - is_microsetta
+
+      responses:
+        '201':
+          description: Project successfully created
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '422':
+          $ref: '#/components/responses/422UnprocessableEntity'
+
   '/admin/create/kits':
     post:
       operationId: microsetta_private_api.admin.admin_impl.create_kits

microsetta_private_api/db/patches/0056.sql

@@ -0,0 +1,10 @@
+ALTER TABLE barcodes.project ADD COLUMN is_microsetta BOOLEAN;
+UPDATE barcodes.project SET is_microsetta='no' WHERE is_microsetta IS NULL;
+UPDATE barcodes.project SET is_microsetta='yes' WHERE project in ('American Gut Project',
+                                                                  'British Gut Project',
+                                                                  'Daklapak W1',
+                                                                  'canadian gut',
+                                                                  'TMI - Daklapack W1',
+                                                                  'TMI - Daklapack W2');
+ALTER TABLE barcodes.project ALTER COLUMN is_microsetta SET NOT NULL;
+ALTER TABLE barcodes.project ADD CONSTRAINT project_unique UNIQUE (project);

microsetta_private_api/repo/admin_repo.py

@@ -127,6 +127,31 @@ def retrieve_diagnostics_by_barcode(self, sample_barcode, grab_kit=True):
 
             return diagnostic
 
+    def create_project(self, project_name, is_microsetta):
+        """Create a project entry in the database
+
+        Parameters
+        ----------
+        project_name : str
+            The name of the project to create
+        is_microsetta : bool
+            If the project is part of The Microsetta Initiative
+        """
+        if is_microsetta:
+            tmi = 'yes'
+        else:
+            tmi = 'no'
+
+        with self._transaction.cursor() as cur:
+            cur.execute("SELECT MAX(project_id) + 1 "
+                        "FROM barcodes.project")
+            id_ = cur.fetchone()[0]
+
+            cur.execute("INSERT INTO barcodes.project "
+                        "(project_id, project, is_microsetta) "
+                        "VALUES (%s, %s, %s)", [id_, project_name, tmi])
+        return True
+
     def _generate_random_kit_name(self, name_length, prefix):
         if prefix is None:
             prefix = 'tmi'
@@ -153,21 +178,18 @@ def create_kits(self, number_of_kits, number_of_samples, kit_prefix,
         projects : list of str
             Project names the samples are to be associated with
         """
-        TMI_PROJECTS = {'The Microsetta Initiative', 'American Gut Project',
-                        'British Gut Project'}
-        if len(TMI_PROJECTS & set(projects)) > 0:
-            is_tmi = True
-        else:
-            is_tmi = False
-
         with self._transaction.cursor() as cur:
             # get existing projects
-            cur.execute("SELECT project, project_id "
+            cur.execute("SELECT project, project_id, is_microsetta "
                         "FROM barcodes.project")
-            known_projects = {prj.lower(): id_ for prj, id_ in cur.fetchall()}
+            known_projects = {prj: (id_, tmi)
+                              for prj, id_, tmi in cur.fetchall()}
+            is_tmi = False
             for name in projects:
-                if name.lower() not in known_projects:
+                if name not in known_projects:
                     raise KeyError("%s does not exist" % name)
+                if known_projects[name][1]:
+                    is_tmi = True
 
             # get existing kits to test for conflicts
             cur.execute("""SELECT kit_id FROM barcodes.kit""")
@@ -209,7 +231,7 @@ def create_kits(self, number_of_kits, number_of_samples, kit_prefix,
             barcode_projects = []
             for barcode in new_barcodes:
                 for project in projects:
-                    prj_id = known_projects[project.lower()]
+                    prj_id = known_projects[project][0]
                     barcode_projects.append((barcode, prj_id))
 
             # create shipping IDs