"""Procedures used to work with the various bio-informatics cli
commands"""
import os
import sys
import json
import shlex
import pickle
import logging
import tempfile
import subprocess
from datetime import datetime
from typing import Any
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 flask import Flask, current_app
from redis.client import Redis # Used only in type hinting
from pymonad.either import Either, Left, Right
from gn3.debug import __pk__
from gn3.chancy import random_string
from gn3.exceptions import RedisConnectionError
logger = logging.getLogger(__name__)
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
rscript = os.environ.get("RSCRIPT", "Rscript")
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 compose_pcorrs_command_for_selected_traits(
prefix_cmd: Tuple[str, ...], target_traits: Tuple[str, ...]) -> Tuple[
str, ...]:
"""Build command for partial correlations against selected traits."""
return prefix_cmd + ("against-traits", ",".join(target_traits))
def compose_pcorrs_command_for_database(
prefix_cmd: Tuple[str, ...], target_database: str,
criteria: int = 500) -> Tuple[str, ...]:
"""Build command for partial correlations against an entire dataset."""
return prefix_cmd + (
"against-db", f"{target_database}", "--criteria", str(criteria),
"--textdir", current_app.config["TEXTDIR"])
def compose_pcorrs_command(
primary_trait: str, control_traits: Tuple[str, ...], method: str,
**kwargs):
"""Compose the command to run partias correlations"""
def __parse_method__(method):
mthd = method.lower().replace("'", "")
if "pearsons" in mthd:
return "pearsons"
if "spearmans" in mthd:
return "spearmans"
# pylint: disable=[broad-exception-raised]
raise Exception(
f"Invalid method '{method}'")
prefix_cmd = (
f"{sys.executable}", "-m", "scripts.partial_correlations",
primary_trait, ",".join(control_traits), __parse_method__(method),
current_app.config["SQL_URI"])
if (
kwargs.get("target_database") is not None
and kwargs.get("target_traits") is None):
return compose_pcorrs_command_for_database(prefix_cmd, **kwargs)
if (
kwargs.get("target_database") is None
and kwargs.get("target_traits") is not None):
return compose_pcorrs_command_for_selected_traits(prefix_cmd, **kwargs)
# pylint: disable=[broad-exception-raised]
raise Exception(
"Invalid state: I don't know what command to generate!")
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_sample_corr_cmd(method, this_trait_data, target_dataset_data):
"Run the sample correlations in an external process, returning the results."
with tempfile.TemporaryDirectory() as tempdir:
traitfile = f"{tempdir}/traitfile_{random_string(10)}"
targetfile = f"{tempdir}/targetdb_{random_string(10)}"
destfile = f"{tempdir}/corrs_{random_string(10)}"
with open(traitfile, "wb") as trtfl:
pickle.dump(this_trait_data, trtfl)
with open(targetfile, "wb") as targfl:
pickle.dump(target_dataset_data, targfl)
subprocess.run(
["python3", "-m", "scripts.sample_correlations", method,
traitfile, targetfile, destfile],
check=True)
with open(destfile, "rb") as dstfl:
correlation_results = pickle.load(dstfl)
return correlation_results
def run_cmd(cmd: str, success_codes: Tuple = (0,), env: Optional[str] = None) -> Dict:
"""Run CMD and return the CMD's status code and output as a dict"""
try:
parsed_cmd = json.loads(cmd)
except json.decoder.JSONDecodeError as _jderr:
parsed_cmd = shlex.split(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')
logger.debug("Command output: %s", out)
return {"code": results.returncode, "output": out}
def compute_job_queue(app: Flask) -> str:
"""Use the app configurations to compute the job queue"""
app_env = app.config["APPLICATION_ENVIRONMENT"]
job_queue = app.config["REDIS_JOB_QUEUE"]
if bool(app_env):
return f"{app_env}::{job_queue}"
return job_queue
def run_async_cmd(
conn: Redis, job_queue: str, cmd: Union[str, Sequence[str]],
options: Optional[Dict[str, Any]] = None,
log_level: str = "info") -> str:
"""A utility function to call `gn3.commands.queue_cmd` function and run the
worker in the `one-shot` mode."""
email = options.get("email") if options else None
env = options.get("env") if options else None
cmd_id = queue_cmd(conn, job_queue, cmd, email, env)
worker_command = [
sys.executable,
"-m", "sheepdog.worker",
"--queue-name", job_queue,
"--log-level", log_level
]
logging.debug("Launching the worker: %s", worker_command)
subprocess.Popen( # pylint: disable=[consider-using-with]
worker_command)
return cmd_id
def monadic_run_cmd(cmd) -> Either:
"""Run a given command and return it's results as an Either monad"""
result = ""
try:
result = subprocess.run(cmd,
capture_output=True,
check=True).stdout.decode()
# This command does not exist
except FileNotFoundError as excpt:
return Left({
"command": cmd,
"error": str(excpt),
})
except subprocess.CalledProcessError as excpt:
return Left({
"command": cmd,
"error": str(excpt),
})
return Right(result)
