diff options
Diffstat (limited to 'gn3/commands.py')
| -rw-r--r-- | gn3/commands.py | 32 |
1 files changed, 26 insertions, 6 deletions
diff --git a/gn3/commands.py b/gn3/commands.py index 7d42ced..29e3df2 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -1,5 +1,8 @@ """Procedures used to work with the various bio-informatics cli commands""" +import os +import sys +import json import subprocess from datetime import datetime @@ -7,6 +10,8 @@ from typing import Dict from typing import List from typing import Optional from typing import Tuple +from typing import Union +from typing import Sequence from uuid import uuid4 from redis.client import Redis # Used only in type hinting @@ -46,10 +51,20 @@ def compose_rqtl_cmd(rqtl_wrapper_cmd: str, return cmd +def compose_pcorrs_command( + primary_trait: str, control_traits: Tuple[str, ...], method: str, + target_database: str, criteria: int = 500): + rundir = os.path.abspath(".") + return ( + f"{sys.executable}", f"{rundir}/scripts/partial_correlations.py", + primary_trait, ",".join(control_traits), f'"{method}"', + f"{target_database}", f"--criteria={criteria}") + def queue_cmd(conn: Redis, job_queue: str, - cmd: str, - email: Optional[str] = None) -> 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: @@ -68,17 +83,22 @@ Returns the name of the specific redis hash for the specific task. 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": cmd, "result": "", "status": "queued"}.items(): + for key, value in { + "cmd": json.dumps(cmd), "result": "", "status": "queued", + "env": json.dumps(env)}.items(): conn.hset(name=unique_id, key=key, value=value) if email: conn.hset(name=unique_id, key="email", value=email) return unique_id -def run_cmd(cmd: str, success_codes: Tuple = (0,)) -> Dict: +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""" - results = subprocess.run(cmd, capture_output=True, shell=True, - check=False) + 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') |