From a112c99cae0c5422a38e3a35e843a82db764316a Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 7 Aug 2023 08:40:50 +0300
Subject: Add missing modules

Copy over missing modules and functions to completely disconnect
gn-auth from GN3.
---
 gn_auth/commands.py | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 gn_auth/commands.py

(limited to 'gn_auth/commands.py')

diff --git a/gn_auth/commands.py b/gn_auth/commands.py
new file mode 100644
index 0000000..d6f6f56
--- /dev/null
+++ b/gn_auth/commands.py
@@ -0,0 +1,64 @@
+"""Procedures used to work with the various bio-informatics cli
+commands"""
+import sys
+import json
+import subprocess
+from uuid import uuid4
+from datetime import datetime
+from typing import Dict, Optional, Tuple, Union, Sequence
+
+
+from redis.client import Redis
+
+def queue_cmd(conn: Redis,
+              job_queue: str,
+              cmd: Union[str, Sequence[str]],
+              email: Optional[str] = None,
+              env: Optional[dict] = None) -> str:
+    """Given a command CMD; (optional) EMAIL; and a redis connection CONN, queue
+it in Redis with an initial status of 'queued'.  The following status codes
+are supported:
+
+    queued:  Unprocessed; Still in the queue
+    running: Still running
+    success: Successful completion
+    error:   Erroneous completion
+
+Returns the name of the specific redis hash for the specific task.
+
+    """
+    if not conn.ping():
+        raise RedisConnectionError
+    unique_id = ("cmd::"
+                 f"{datetime.now().strftime('%Y-%m-%d%H-%M%S-%M%S-')}"
+                 f"{str(uuid4())}")
+    conn.rpush(job_queue, unique_id)
+    for key, value in {
+            "cmd": json.dumps(cmd), "result": "", "status": "queued"}.items():
+        conn.hset(name=unique_id, key=key, value=value)
+    if email:
+        conn.hset(name=unique_id, key="email", value=email)
+    if env:
+        conn.hset(name=unique_id, key="env", value=json.dumps(env))
+    return unique_id
+
+def run_cmd(cmd: str, success_codes: Tuple = (0,), env: str = None) -> Dict:
+    """Run CMD and return the CMD's status code and output as a dict"""
+    parsed_cmd = json.loads(cmd)
+    parsed_env = (json.loads(env) if env is not None else None)
+    results = subprocess.run(
+        parsed_cmd, capture_output=True, shell=isinstance(parsed_cmd, str),
+        check=False, env=parsed_env)
+    out = str(results.stdout, 'utf-8')
+    if results.returncode not in success_codes:  # Error!
+        out = str(results.stderr, 'utf-8')
+    return {"code": results.returncode, "output": out}
+
+def run_async_cmd(
+        conn: Redis, job_queue: str, cmd: Union[str, Sequence[str]],
+        email: Optional[str] = None, env: Optional[dict] = None) -> str:
+    """A utility function to call `gn3.commands.queue_cmd` function and run the
+    worker in the `one-shot` mode."""
+    cmd_id = queue_cmd(conn, job_queue, cmd, email, env)
+    subprocess.Popen([f"{sys.executable}", "-m", "sheepdog.worker"]) # pylint: disable=[consider-using-with]
+    return cmd_id
-- 
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