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-rw-r--r--gn3/api/correlation.py65
-rw-r--r--gn3/commands.py32
-rw-r--r--gn3/responses/__init__.py0
-rw-r--r--gn3/responses/pcorrs_responses.py24
-rwxr-xr-xscripts/partial_correlations.py59
-rw-r--r--sheepdog/worker.py16
6 files changed, 150 insertions, 46 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 00b3ad5..14c029c 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -1,17 +1,22 @@
"""Endpoints for running correlations"""
+import sys
import json
from functools import reduce
+import redis
from flask import jsonify
from flask import Blueprint
from flask import request
-from flask import make_response
+from flask import current_app
-from gn3.computations.correlations import compute_all_sample_correlation
-from gn3.computations.correlations import compute_all_lit_correlation
-from gn3.computations.correlations import compute_tissue_correlation
-from gn3.computations.correlations import map_shared_keys_to_values
+from gn3.settings import SQL_URI
+from gn3.commands import queue_cmd, compose_pcorrs_command
from gn3.db_utils import database_connector
+from gn3.responses.pcorrs_responses import build_response
+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_entry
correlation = Blueprint("correlation", __name__)
@@ -93,7 +98,7 @@ def compute_tissue_corr(corr_method="pearson"):
def partial_correlation():
"""API endpoint for partial correlations."""
def trait_fullname(trait):
- return f"{trait['dataset']}::{trait['name']}"
+ return f"{trait['dataset']}::{trait['trait_name']}"
def __field_errors__(args):
def __check__(acc, field):
@@ -107,37 +112,29 @@ def partial_correlation():
if request_data is None:
return ("No request data",)
- return reduce(__field_errors__(args), fields, errors)
-
- class OutputEncoder(json.JSONEncoder):
- """
- Class to encode output into JSON, for objects which the default
- json.JSONEncoder class does not have default encoding for.
- """
- def default(self, o):
- if isinstance(o, bytes):
- return str(o, encoding="utf-8")
- return json.JSONEncoder.default(self, o)
-
- def __build_response__(data):
- status_codes = {"error": 400, "not-found": 404, "success": 200}
- response = make_response(
- json.dumps(data, cls=OutputEncoder),
- status_codes[data["status"]])
- response.headers["Content-Type"] = "application/json"
- return response
-
- args = request.get_json()
+ return reduce(__field_errors__(request_data), fields, errors)
+
+ args = json.loads(request.get_json())
request_errors = __errors__(
args, ("primary_trait", "control_traits", "target_db", "method"))
if request_errors:
- return __build_response__({
+ return build_response({
"status": "error",
"messages": request_errors,
"error_type": "Client Error"})
- conn, _cursor_object = database_connector()
- corr_results = partial_correlations_entry(
- conn, trait_fullname(args["primary_trait"]),
- tuple(trait_fullname(trait) for trait in args["control_traits"]),
- args["method"], int(args.get("criteria", 500)), args["target_db"])
- return __build_response__(corr_results)
+ return build_response({
+ "status": "success",
+ "results": queue_cmd(
+ conn=redis.Redis(),
+ 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))),
+ job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+ env = {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI})})
+
+@correlation.route("/partial/<job_id>", methods=["GET"])
+def partial_correlation_results():
+ raise Exception("Not implemented!!")
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')
diff --git a/gn3/responses/__init__.py b/gn3/responses/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/gn3/responses/__init__.py
diff --git a/gn3/responses/pcorrs_responses.py b/gn3/responses/pcorrs_responses.py
new file mode 100644
index 0000000..d6fd9d7
--- /dev/null
+++ b/gn3/responses/pcorrs_responses.py
@@ -0,0 +1,24 @@
+"""Functions and classes that deal with responses and conversion to JSON."""
+import json
+
+from flask import make_response
+
+class OutputEncoder(json.JSONEncoder):
+ """
+ Class to encode output into JSON, for objects which the default
+ json.JSONEncoder class does not have default encoding for.
+ """
+ def default(self, o):
+ if isinstance(o, bytes):
+ return str(o, encoding="utf-8")
+ return json.JSONEncoder.default(self, o)
+
+def build_response(data):
+ """Build the responses for the API"""
+ status_codes = {
+ "error": 400, "not-found": 404, "success": 200, "exception": 500}
+ response = make_response(
+ json.dumps(data, cls=OutputEncoder),
+ status_codes[data["status"]])
+ response.headers["Content-Type"] = "application/json"
+ return response
diff --git a/scripts/partial_correlations.py b/scripts/partial_correlations.py
new file mode 100755
index 0000000..ee442df
--- /dev/null
+++ b/scripts/partial_correlations.py
@@ -0,0 +1,59 @@
+import sys
+import json
+import traceback
+from argparse import ArgumentParser
+
+from gn3.db_utils import database_connector
+from gn3.responses.pcorrs_responses import OutputEncoder
+from gn3.computations.partial_correlations import partial_correlations_entry
+
+def process_cli_arguments():
+ parser = ArgumentParser()
+ parser.add_argument(
+ "primary_trait",
+ help="The primary trait's full name",
+ type=str)
+ parser.add_argument(
+ "control_traits",
+ help="A comma-separated list of traits' full names",
+ type=str)
+ parser.add_argument(
+ "method",
+ help="The correlation method to use",
+ type=str)
+ parser.add_argument(
+ "target_database",
+ help="The target database to run the partial correlations against",
+ type=str)
+ parser.add_argument(
+ "--criteria",
+ help="Number of results to return",
+ type=int, default=500)
+ return parser.parse_args()
+
+def cleanup_string(the_str):
+ return the_str.strip('"\t\n\r ')
+
+def run_partial_corrs(args):
+ try:
+ conn, _cursor_object = database_connector()
+ return partial_correlations_entry(
+ conn, cleanup_string(args.primary_trait),
+ tuple(cleanup_string(args.control_traits).split(",")),
+ cleanup_string(args.method), args.criteria,
+ cleanup_string(args.target_database))
+ except Exception as exc:
+ print(traceback.format_exc(), file=sys.stderr)
+ return {
+ "status": "exception",
+ "message": traceback.format_exc()
+ }
+
+def enter():
+ args = process_cli_arguments()
+ print(json.dumps(
+ run_partial_corrs(process_cli_arguments()),
+ cls = OutputEncoder))
+
+if __name__ == "__main__":
+ enter()
diff --git a/sheepdog/worker.py b/sheepdog/worker.py
index 4e3610e..4e7f9e7 100644
--- a/sheepdog/worker.py
+++ b/sheepdog/worker.py
@@ -5,9 +5,12 @@ import time
import redis
import redis.connection
-# Enable importing from one dir up since gn3 isn't installed as a globally
-sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+# Enable importing from one dir up: put as first to override any other globally
+# accessible GN3
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+def update_status(conn, cmd_id, status):
+ conn.hset(name=f"{cmd_id}", key="status", value=f"{status}")
def run_jobs(conn):
"""Process the redis using a redis connection, CONN"""
@@ -17,13 +20,14 @@ def run_jobs(conn):
if bool(cmd_id):
cmd = conn.hget(name=cmd_id, key="cmd")
if cmd and (conn.hget(cmd_id, "status") == b"queued"):
- result = run_cmd(cmd.decode("utf-8"))
+ update_status(conn, cmd_id, "running")
+ result = run_cmd(
+ cmd.decode("utf-8"), env=conn.hget(name=cmd_id, key="env"))
conn.hset(name=cmd_id, key="result", value=result.get("output"))
if result.get("code") == 0: # Success
- conn.hset(name=cmd_id, key="status", value="success")
+ update_status(conn, cmd_id, "success")
else:
- conn.hset(name=cmd_id, key="status", value="error")
-
+ update_status(conn, cmd_id, "error")
if __name__ == "__main__":
redis_conn = redis.Redis()