diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/correlation.py | 41 | ||||
| -rw-r--r-- | gn3/commands.py | 36 |
2 files changed, 46 insertions, 31 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index 3aadcb9..1667302 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -16,8 +16,6 @@ from gn3.computations.correlations import map_shared_keys_to_values from gn3.computations.correlations import compute_tissue_correlation from gn3.computations.correlations import compute_all_lit_correlation from gn3.computations.correlations import compute_all_sample_correlation -from gn3.computations.partial_correlations import ( - partial_correlations_with_target_traits) correlation = Blueprint("correlation", __name__) @@ -124,16 +122,25 @@ def partial_correlation(): "messages": request_errors, "error_type": "Client Error"}) - if with_target_db: - with redis.Redis() as conn: - queueing_results = run_async_cmd( + with redis.Redis() as conn: + if with_target_db: + command = compose_pcorrs_command( + trait_fullname(args["primary_trait"]), + tuple( + trait_fullname(trait) for trait in args["control_traits"]), + args["method"], target_database=args["target_db"], + criteria = int(args.get("criteria", 500))) + else: + command = compose_pcorrs_command( + trait_fullname(args["primary_trait"]), + tuple( + trait_fullname(trait) for trait in args["control_traits"]), + args["method"], target_traits=tuple( + trait_fullname(trait) for trait in args["target_traits"])) + + queueing_results = run_async_cmd( conn=conn, - cmd=compose_pcorrs_command( - trait_fullname(args["primary_trait"]), - tuple( - trait_fullname(trait) for trait in args["control_traits"]), - args["method"], args["target_db"], - int(args.get("criteria", 500))), + cmd=command, job_queue=current_app.config.get("REDIS_JOB_QUEUE"), env = {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI}) return build_response({ @@ -141,15 +148,3 @@ def partial_correlation(): "results": queueing_results, "queued": True }) - - with database_connector() as conn: - results = partial_correlations_with_target_traits( - conn, - trait_fullname(args["primary_trait"]), - tuple( - trait_fullname(trait) for trait in args["control_traits"]), - args["method"], - tuple( - trait_fullname(trait) for trait in args["target_traits"])) - - return build_response({"status": "success", "results": results}) diff --git a/gn3/commands.py b/gn3/commands.py index 9684eeb..b1b3fc7 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -1,6 +1,5 @@ """Procedures used to work with the various bio-informatics cli commands""" -import os import sys import json import subprocess @@ -51,15 +50,36 @@ def compose_rqtl_cmd(rqtl_wrapper_cmd: str, 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}", f"--criteria={criteria}") + def compose_pcorrs_command( primary_trait: str, control_traits: Tuple[str, ...], method: str, - target_database: str, criteria: int = 500): + **kwargs): """Compose the command to run partias correlations""" - 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}") + print(f"KWARGS: {kwargs}") + prefix_cmd = ( + f"{sys.executable}", "-m", "scripts.partial_correlations", + primary_trait, ",".join(control_traits), f'"{method}"') + 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) + raise Exception("Invalid state: I don't know what command to generate!") def queue_cmd(conn: Redis, job_queue: str, @@ -111,5 +131,5 @@ def run_async_cmd( """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(["python3", "sheepdog/worker.py"]) # pylint: disable=[consider-using-with] + subprocess.Popen([f"{sys.executable}", "-m", "sheepdog.worker"]) # pylint: disable=[consider-using-with] return cmd_id |