Bugfix: Fix bugs that were preventing creation of geno resource

Fix the bugs that were causing the creation of a genotype resource via
API to fail.

3 files changed, 36 insertions, 18 deletions

diff --git a/gn_auth/auth/authorisation/resources/genotypes/models.py b/gn_auth/auth/authorisation/resources/genotypes/models.py
index c64922e..e8dca9b 100644
--- a/gn_auth/auth/authorisation/resources/genotypes/models.py
+++ b/gn_auth/auth/authorisation/resources/genotypes/models.py
@@ -68,9 +68,10 @@ def attach_resources_data(
     return __attach_data__(cursor.fetchall(), resources)
 
 
-def insert_and_link_data_to_resource(
+def insert_and_link_data_to_resource(# pylint: disable=[too-many-arguments]
         cursor,
         resource_id: uuid.UUID,
+        group_id: uuid.UUID,
         species_id: int,
         population_id: int,
         dataset_id: int,
@@ -81,6 +82,7 @@ def insert_and_link_data_to_resource(
     """Link the genotype identifier data to the genotype resource."""
     params = {
         "resource_id": str(resource_id),
+        "group_id": str(group_id),
         "data_link_id": str(uuid.uuid4()),
         "species_id": species_id,
         "population_id": population_id,
@@ -93,12 +95,13 @@ def insert_and_link_data_to_resource(
         "INSERT INTO linked_genotype_data "
         "VALUES ("
         ":data_link_id,"
+        ":group_id,"
         ":species_id,"
         ":population_id,"
         ":dataset_id,"
         ":dataset_name,"
         ":dataset_fullname,"
-        ":dataset_shortname,"
+        ":dataset_shortname"
         ")",
         params)
     cursor.execute(
diff --git a/gn_auth/auth/authorisation/resources/genotypes/views.py b/gn_auth/auth/authorisation/resources/genotypes/views.py
index 4908ff3..2beed58 100644
--- a/gn_auth/auth/authorisation/resources/genotypes/views.py
+++ b/gn_auth/auth/authorisation/resources/genotypes/views.py
@@ -1,10 +1,18 @@
 """Genotype-resources-specific views."""
-from flask import jsonify, Blueprint
+import uuid
+
 from pymonad.either import Left, Right
+from flask import jsonify, Blueprint, current_app as app
 
 from gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.requests import request_json
+
+from gn_auth.auth.authorisation.resources.base import ResourceCategory
 from gn_auth.auth.authorisation.resources.request_utils import check_form
+from gn_auth.auth.authorisation.resources.groups.models import user_group
+
 from gn_auth.auth.authentication.oauth2.resource_server import require_oauth
+
 from gn_auth.auth.authorisation.resources.models import create_resource
 from gn_auth.auth.authorisation.resources.common import (
     assign_resource_owner_role)
@@ -14,16 +22,19 @@ from .models import insert_and_link_data_to_resource
 
 genobp = Blueprint("genotypes", __name__)
 
-@genobp.route("/create", methods=["POST"])
+@genobp.route("genotypes/create", methods=["POST"])
 @require_oauth("profile group resource")
 def create_geno_resource():
     """Create a new genotype resource."""
     with (require_oauth.acquire("profile group resource") as _token,
           db.connection(app.config["AUTH_DB"]) as conn,
           db.cursor(conn) as cursor):
+        cursor.execute("SELECT * FROM resource_categories "
+                       "WHERE resource_category_key='genotype'")
+        row = cursor.fetchone()
 
         return check_form(
-            request.form,
+            request_json(),
             "species_id",
             "population_id",
             "dataset_id",
@@ -31,33 +42,37 @@ def create_geno_resource():
             "dataset_fullname",
             "dataset_shortname"
         ).then(
-            lambda form: user_group(conn, _token.user).either(
-                lambda err: Left(err),
+            lambda form: user_group(conn, _token.user).maybe(
+                Left("No user group found!"),
                 lambda group: Right({"formdata": form, "group": group}))
         ).then(
             lambda fdgrp: {
                 **fdgrp,
                 "resource": create_resource(
                     cursor,
-                    f"Geno — {fdgrp['formdata']['dataset_fullname']}",
+                    f"Genotype — {fdgrp['formdata']['dataset_fullname']}",
+                    ResourceCategory(uuid.UUID(row["resource_category_id"]),
+                                     row["resource_category_key"],
+                                     row["resource_category_description"]),
                     _token.user,
                     fdgrp["group"],
-                    fdgrp["formdata"].get("public", "on") // "on")}
+                    fdgrp["formdata"].get("public", "on") == "on")}
         ).then(
             lambda fdgrpres: {
                 **fdgrpres,
                 "owner_role": assign_resource_owner_role(
                     cursor,
-                    fdgrpres["resource"],
-                    _token.user)}
+                    fdgrpres["resource"].resource_id,
+                    _token.user.user_id)}
         ).then(
             lambda fdgrpres: insert_and_link_data_to_resource(
                 cursor,
                 fdgrpres["resource"].resource_id,
-                fdgrpres["resource"]["species_id"],
-                fdgrpres["resource"]["population_id"],
-                fdgrpres["resource"]["dataset_id"],
-                fdgrpres["resource"]["dataset_name"],
-                fdgrpres["resource"]["dataset_fullname"],
-                fdgrpres["resource"]["dataset_shortname"])
+                fdgrpres["group"].group_id,
+                fdgrpres["formdata"]["species_id"],
+                fdgrpres["formdata"]["population_id"],
+                fdgrpres["formdata"]["dataset_id"],
+                fdgrpres["formdata"]["dataset_name"],
+                fdgrpres["formdata"]["dataset_fullname"],
+                fdgrpres["formdata"]["dataset_shortname"])
         ).either(lambda error: (jsonify(error), 400), jsonify)
diff --git a/gn_auth/auth/authorisation/resources/request_utils.py b/gn_auth/auth/authorisation/resources/request_utils.py
index 03d3c3b..5fe6a29 100644
--- a/gn_auth/auth/authorisation/resources/request_utils.py
+++ b/gn_auth/auth/authorisation/resources/request_utils.py
@@ -7,7 +7,7 @@ def check_form(form, *fields) -> Either:
     """Check form for errors"""
     def __check_field__(errors, field):
         if not bool(form.get(field)):
-            return errors + (f"Missing `{field}` value.")
+            return errors + (f"Missing `{field}` value.",)
         return errors
 
     errors = reduce(__check_field__, fields, tuple())