Populations: Hook population creation to auth system.

2 files changed, 77 insertions, 37 deletions

diff --git a/uploader/population/models.py b/uploader/population/models.py
index 782bc9f..c6c77ae 100644
--- a/uploader/population/models.py
+++ b/uploader/population/models.py
@@ -44,33 +44,32 @@ def population_genetic_types(conn) -> tuple:
         return tuple(row["GeneticType"] for row in cursor.fetchall())
 
 
-def save_population(conn: mdb.Connection, population_details: dict) -> dict:
+def save_population(cursor: mdb.cursors.Cursor, population_details: dict) -> dict:
     """Save the population details to the db."""
-    with conn.cursor(cursorclass=DictCursor) as cursor:
-        #TODO: Handle FamilyOrder here
-        cursor.execute(
-            "INSERT INTO InbredSet("
-            "InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
-            "public, MappingMethodId, GeneticType, Family, MenuOrderId, "
-            "InbredSetCode, Description"
-            ") "
-            "VALUES ("
-            "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, "
-            "%(FullName)s, %(public)s, %(MappingMethodId)s, %(GeneticType)s, "
-            "%(Family)s, %(MenuOrderId)s, %(InbredSetCode)s, %(Description)s"
-            ")",
-            {
-                "MenuOrderId": 0,
-                "InbredSetId": 0,
-                "public": 2,
-                **population_details
-            })
-        new_id = cursor.lastrowid
-        cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s",
-                       (new_id, new_id))
-        return {
-            **population_details,
-            "Id": new_id,
-            "InbredSetId": new_id,
-            "population_id": new_id
-        }
+    #TODO: Handle FamilyOrder here
+    cursor.execute(
+        "INSERT INTO InbredSet("
+        "InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
+        "public, MappingMethodId, GeneticType, Family, MenuOrderId, "
+        "InbredSetCode, Description"
+        ") "
+        "VALUES ("
+        "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, "
+        "%(FullName)s, %(public)s, %(MappingMethodId)s, %(GeneticType)s, "
+        "%(Family)s, %(MenuOrderId)s, %(InbredSetCode)s, %(Description)s"
+        ")",
+        {
+            "MenuOrderId": 0,
+            "InbredSetId": 0,
+            "public": 2,
+            **population_details
+        })
+    new_id = cursor.lastrowid
+    cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s",
+                   (new_id, new_id))
+    return {
+        **population_details,
+        "Id": new_id,
+        "InbredSetId": new_id,
+        "population_id": new_id
+    }
diff --git a/uploader/population/views.py b/uploader/population/views.py
index f9041be..af0a043 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -2,7 +2,10 @@
 import re
 import json
 import base64
+import traceback
 
+from MySQLdb.cursors import DictCursor
+from pymonad.either import Left, Right, Either
 from flask import (flash,
                    request,
                    url_for,
@@ -15,6 +18,7 @@ from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
 from uploader.db_utils import database_connection
 from uploader.genotypes.views import genotypesbp
+from uploader.oauth2.client import oauth2_get, oauth2_post
 from uploader.species.models import (all_species,
                                      species_by_id,
                                      order_species_by_family)
@@ -91,7 +95,8 @@ def valid_population_name(population_name: str) -> bool:
 @require_login
 def create_population(species_id: int):
     """Create a new population."""
-    with database_connection(app.config["SQL_URI"]) as conn:
+    with (database_connection(app.config["SQL_URI"]) as conn,
+          conn.cursor(cursorclass=DictCursor) as cursor):
         species = species_by_id(conn, species_id)
 
         if request.method == "GET":
@@ -151,10 +156,7 @@ def create_population(species_id: int):
                                     species_id=species["SpeciesId"],
                                     error_values=values))
 
-        # TODO: Setup auth
-        # 1. Create new resource in gn-auth and add this population to it
-        # 2. Assign active user the "resource-creator" rights to the new resource
-        new_population = save_population(conn, {
+        new_population = save_population(cursor, {
             "SpeciesId": species["SpeciesId"],
             "Name": population_name,
             "InbredSetName": population_fullname,
@@ -166,9 +168,48 @@ def create_population(species_id: int):
             "GeneticType": request.form.get("population_genetic_type") or None
         })
 
-        return redirect(url_for("species.populations.view_population",
-                                species_id=species["SpeciesId"],
-                                population_id=new_population["InbredSetId"]))
+        def __select_inbredset_resource_category__(categories) -> Either:
+            from uploader.debug import __pk__
+            _cat = tuple(
+                category for category in categories
+                if category["resource_category_key"] == "inbredset-group")
+            if len(_cat) == 0:
+                return Left("Could not find appropriate category key.")
+            if len(_cat) > 1:
+                return Left(
+                    f"Invalid categories — Expected one, got {{len(_cat)}}")
+            return Right(_cat[0])
+
+        def __handle_error__(error):
+            error_format = (
+                "\n\nThere was an error creating the population:\n\t%s\n\n")
+            if issubclass(type(error), Exception):
+                app.logger.debug(error_format, traceback.format_exc())
+                raise error
+            app.logger.debug(error_format, error)
+            raise Exception(error)
+
+        return oauth2_get(
+            "auth/resource/categories"
+        ).then(
+            __select_inbredset_resource_category__
+        ).then(
+            lambda category: oauth2_post(
+                "auth/resource/create",
+                json={
+                    "resource_name": f"Population — {population_name}",
+                    "resource_category": category["resource_category_id"],
+                    "public": "on"
+                })
+        ).then(
+            lambda resp: flash("Successfully created resource.",
+                               "alert-success") or resp
+        ).either(
+            __handle_error__,
+            lambda _success: redirect(url_for(
+                "species.populations.view_population",
+                species_id=species["SpeciesId"],
+                population_id=new_population["InbredSetId"])))
 
 
 @popbp.route("/<int:species_id>/populations/<int:population_id>",