Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/add_rqtl_pairscan

1 files changed, 153 insertions, 0 deletions

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
new file mode 100644
index 00000000..c8c2caad
--- /dev/null
+++ b/scripts/authentication/group.py
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+"""A script for adding users to a specific group.
+
+Example:
+
+Assuming there are no groups and 'test@bonfacemunyoki.com' does not
+exist in Redis:
+
+.. code-block:: bash
+   python group.py -g "editors" -m "test@bonfacemunyoki.com"
+
+results in::
+
+   Successfully created the group: 'editors'
+   Data: '{"admins": [], "members": []}'
+
+If 'me@bonfacemunyoki.com' exists in 'users' in Redis and we run:
+
+.. code-block:: bash
+   python group.py -g "editors" -m "me@bonfacemunyoki.com"
+
+now results in::
+
+   No new group was created.
+   Updated Data: {'admins': [], 'members': ['me@bonfacemunyoki.com']}
+
+"""
+
+import argparse
+import datetime
+import redis
+import json
+import uuid
+
+from typing import Dict, Optional, Set
+
+
+def create_group_data(users: Dict, target_group: str,
+                      members: Optional[str] = None,
+                      admins: Optional[str] = None) -> Dict:
+    """Return a dictionary that contains the following keys: "key",
+    "field", and "value" that can be used in a redis hash as follows:
+    HSET key field value
+
+    The "field" return value is a unique-id that is used to
+    distinguish the groups.
+
+    Parameters:
+
+    - `users`: a list of users for example:
+
+    {'8ad942fe-490d-453e-bd37-56f252e41603':
+    '{"email_address": "me@test.com",
+      "full_name": "John Doe",
+      "organization": "Genenetwork",
+      "password": {"algorithm": "pbkdf2",
+                   "hashfunc": "sha256",
+                    "salt": "gJrd1HnPSSCmzB5veMPaVk2ozzDlS1Z7Ggcyl1+pciA=",
+                    "iterations": 100000, "keylength": 32,
+                    "created_timestamp": "2021-09-22T11:32:44.971912",
+                    "password": "edcdaa60e84526c6"},
+                    "user_id": "8ad942fe", "confirmed": 1,
+                    "registration_info": {
+                        "timestamp": "2021-09-22T11:32:45.028833",
+                        "ip_address": "127.0.0.1",
+                        "user_agent": "Mozilla/5.0"}}'}
+
+    - `target_group`: the group name that will be stored inside the
+      "groups" hash in Redis.
+
+    - `members`: a comma-separated list of values that contain members
+      of the `target_group` e.g. "me@test1.com, me@test2.com,
+      me@test3.com"
+
+    - `admins`: a comma-separated list of values that contain
+      administrators of the `target_group` e.g. "me@test1.com,
+      me@test2.com, me@test3.com"
+
+    """
+    # Emails
+    _members: Set = set("".join(members.split()).split(",")
+                        if members else [])
+    _admins: Set = set("".join(admins.split()).split(",")
+                       if admins else [])
+
+    # Unique IDs
+    member_ids: Set = set()
+    admin_ids: Set = set()
+
+    for user_id, user_details in users.items():
+        _details = json.loads(user_details)
+        if _details.get("email_address") in _members:
+            member_ids.add(user_id)
+        if _details.get("email_address") in _admins:
+            admin_ids.add(user_id)
+
+    timestamp: str = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+    return {"key": "groups",
+            "field": str(uuid.uuid4()),
+            "value": json.dumps({
+                "name": target_group,
+                "admins": list(admin_ids),
+                "members": list(member_ids),
+                "changed_timestamp": timestamp,
+            })}
+
+
+if __name__ == "__main__":
+    # Initialising the parser CLI arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-g", "--group-name",
+                        help="This is the name of the GROUP mask")
+    parser.add_argument("-m", "--members",
+                        help="Members of the GROUP mask")
+    parser.add_argument("-a", "--admins",
+                        help="Admins of the GROUP mask")
+    args = parser.parse_args()
+
+    if not args.group_name:
+        exit("\nExiting. Please specify a group name to use!\n")
+
+    members = args.members if args.members else None
+    admins = args.admins if args.admins else None
+
+    REDIS_CONN = redis.Redis(decode_responses=True)
+    USERS = REDIS_CONN.hgetall("users")
+
+    if not any([members, admins]):
+        exit("\nExiting. Please provide a value for "
+             "MEMBERS(-m) or ADMINS(-a)!\n")
+
+    data = create_group_data(
+        users=USERS,
+        target_group=args.group_name,
+        members=members,
+        admins=admins)
+
+    if not REDIS_CONN.hget("groups", data.get("field")):
+        updated_data = json.loads(data["value"])
+        timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        updated_data["created_timestamp"] = timestamp
+        data["value"] = json.dumps(updated_data)
+
+    created_p = REDIS_CONN.hset(data.get("key", ""),
+                                data.get("field", ""),
+                                data.get("value", ""))
+
+    groups = json.loads(REDIS_CONN.hget("groups",
+                                        data.get("field")))  # type: ignore
+    if created_p:
+        exit(f"\nSuccessfully created the group: '{args.group_name}'\n"
+             f"`HGETALL groups {args.group_name}`: {groups}\n")
+    exit("\nNo new group was created.\n"
+         f"`HGETALL groups {args.group_name}`: {groups}\n")