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"""Procedures used to work with the various bio-informatics cli
commands"""
import subprocess
from datetime import datetime
from typing import Dict
from typing import List
from typing import Optional
from uuid import uuid4
from redis.client import Redis # Used only in type hinting
from gn3.exceptions import RedisConnectionError
def compose_gemma_cmd(gemma_wrapper_cmd: str = "gemma-wrapper",
gemma_wrapper_kwargs: Optional[Dict] = None,
gemma_kwargs: Optional[Dict] = None,
gemma_args: Optional[List] = None) -> str:
"""Compose a valid GEMMA command given the correct values"""
cmd = f"{gemma_wrapper_cmd} --json"
if gemma_wrapper_kwargs:
cmd += " " # Add extra space between commands
cmd += " ".join(
[f"--{key} {val}" for key, val in gemma_wrapper_kwargs.items()])
cmd += " -- "
if gemma_kwargs:
cmd += " ".join([f"-{key} {val}" for key, val in gemma_kwargs.items()])
if gemma_args:
cmd += " "
cmd += " ".join([f"{arg}" for arg in gemma_args])
return cmd
def compose_rqtl_cmd(rqtl_wrapper_cmd: str,
rqtl_wrapper_kwargs: Dict,
rqtl_wrapper_bool_kwargs: list) -> str:
"""Compose a valid R/qtl command given the correct input"""
# Add kwargs with values
cmd = f"Rscript { rqtl_wrapper_cmd } " + " ".join(
[f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
# Add boolean kwargs (kwargs that are either on or off, like --interval)
if rqtl_wrapper_bool_kwargs:
cmd += " "
cmd += " ".join([f"--{val}" for val in rqtl_wrapper_bool_kwargs])
return cmd
def queue_cmd(conn: Redis,
job_queue: str,
cmd: str,
email: Optional[str] = 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": 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)
return unique_id
def run_cmd(cmd: str) -> 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)
out = str(results.stdout, 'utf-8')
if results.returncode < 0: # Error!
out = str(results.stderr, 'utf-8')
return {"code": results.returncode, "output": out}
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