From 204a308be0f741726b9a620d88fbc22b22124c81 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Fri, 29 Dec 2023 18:55:37 +0000
Subject: Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.
---
 wqflask/utility/authentication_tools.py | 150 --------------------------------
 1 file changed, 150 deletions(-)
 delete mode 100644 wqflask/utility/authentication_tools.py

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
deleted file mode 100644
index 5d00d600..00000000
--- a/wqflask/utility/authentication_tools.py
+++ /dev/null
@@ -1,150 +0,0 @@
-import json
-import requests
-
-from flask import g
-from wqflask.database import database_connection
-from base import webqtlConfig
-
-from utility.redis_tools import (get_redis_conn,
-                                 get_resource_info,
-                                 get_resource_id,
-                                 add_resource)
-from utility.tools import get_setting, GN_PROXY_URL
-
-Redis = get_redis_conn()
-
-def check_resource_availability(dataset, user_id, trait_id=None):
-    # At least for now assume temporary entered traits are accessible
-    if type(dataset) == str or dataset.type == "Temp":
-        return webqtlConfig.DEFAULT_PRIVILEGES
-
-    resource_id = get_resource_id(dataset, trait_id)
-
-    # ZS: This should never be false, but it's technically possible if
-    # a non-Temp dataset somehow had a type other than
-    # Publish/ProbeSet/Geno
-    if resource_id:
-        resource_info = get_resource_info(resource_id)
-
-        # If resource isn't already in redis, add it with default
-        # privileges
-        if not resource_info:
-            resource_info = add_new_resource(dataset, trait_id)
-
-    # Check if super-user - we should probably come up with some
-    # way to integrate this into the proxy
-    if user_id in Redis.smembers("super_users"):
-        return webqtlConfig.SUPER_PRIVILEGES
-
-    response = None
-    the_url = f"{GN_PROXY_URL}available?resource={resource_id}&user={user_id}"
-    try:
-        response = json.loads(requests.get(the_url).content)
-    except:
-        response = resource_info['default_mask']
-
-    return response
-
-
-def add_new_resource(dataset, trait_id=None):
-    resource_ob = {
-        'owner_id': "none",  # webqtlConfig.DEFAULT_OWNER_ID,
-        'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
-        'group_masks': {}
-    }
-
-    if dataset.type == "Publish":
-        group_code = get_group_code(dataset)
-        if group_code is None:
-            group_code = ""
-        resource_ob['name'] = group_code + "_" + str(trait_id)
-        resource_ob['data'] = {
-            'dataset': dataset.id,
-            'trait': trait_id
-        }
-        resource_ob['type'] = 'dataset-publish'
-    elif dataset.type == "Geno":
-        resource_ob['name'] = dataset.name
-        resource_ob['data'] = {
-            'dataset': dataset.id
-        }
-        resource_ob['type'] = 'dataset-geno'
-    else:
-        resource_ob['name'] = dataset.name
-        resource_ob['data'] = {
-            'dataset': dataset.id
-        }
-        resource_ob['type'] = 'dataset-probeset'
-
-    resource_info = add_resource(resource_ob, update=False)
-
-    return resource_info
-
-
-def get_group_code(dataset):
-    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-        cursor.execute(
-            "SELECT InbredSetCode FROM InbredSet WHERE Name=%s",
-            (dataset.group.name,)
-        )
-        if results := cursor.fetchone():
-            return results[0]
-        return ""
-
-
-def check_admin(resource_id=None):
-    the_url = GN_PROXY_URL + "available?resource={}&user={}".format(
-        resource_id, g.user_session.user_id)
-    try:
-        response = json.loads(requests.get(the_url).content)['admin']
-    except:
-        resource_info = get_resource_info(resource_id)
-        response = resource_info['default_mask']['admin']
-
-    if type(response) is list:
-        if 'edit-admins' in response:
-            return 'edit_admins'
-        elif 'edit-access' in response:
-            return 'edit-access'
-
-    return response
-
-
-def check_owner(dataset=None, trait_id=None, resource_id=None):
-    if resource_id:
-        resource_info = get_resource_info(resource_id)
-        if g.user_session.user_id == resource_info['owner_id']:
-            return resource_id
-    else:
-        resource_id = get_resource_id(dataset, trait_id)
-        if resource_id:
-            resource_info = get_resource_info(resource_id)
-            if g.user_session.user_id == resource_info['owner_id']:
-                return resource_id
-
-    return False
-
-
-def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
-    if not resource_id:
-        if dataset.type == "Temp":
-            return "not-admin"
-        else:
-            resource_id = get_resource_id(dataset, trait_id)
-
-    try:
-        user_id = g.user_session.user_id.encode('utf-8')
-    except:
-        user_id = g.user_session.user_id
-
-    if user_id in Redis.smembers("super_users"):
-        return "owner"
-
-    resource_info = get_resource_info(resource_id)
-    if resource_info:
-        if user_id == resource_info['owner_id']:
-            return "owner"
-        else:
-            return check_admin(resource_id)
-
-    return "not-admin"
-- 
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