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"""Endpoints for running the gemma cmd"""
import os
import redis
from flask import Blueprint
from flask import current_app
from flask import jsonify
from flask import request
from gn3.commands import queue_cmd
from gn3.commands import run_cmd
from gn3.computations.gemma import generate_hash_of_string
from gn3.computations.gemma import generate_pheno_txt_file
from gn3.computations.gemma import generate_gemma_computation_cmd
gemma = Blueprint("gemma", __name__)
@gemma.route("/version")
def get_version():
"""Display the installed version of gemma-wrapper"""
gemma_cmd = current_app.config['APP_DEFAULTS'].get('GEMMA_WRAPPER_CMD')
return jsonify(
run_cmd(f"{gemma_cmd} -v | head -n 1"))
# This is basically extracted from genenetwork2
# wqflask/wqflask/marker_regression/gemma_ampping.py
@gemma.route("/run", methods=["POST"])
def run_gemma():
"""Generates a command for generating K-Values and then later, generate a GWA
command that contains markers. These commands are queued; and the expected
file output is returned.
"""
data = request.get_json()
app_defaults = current_app.config.get('APP_DEFAULTS')
__hash = generate_hash_of_string("".join(data.get("values")))
gemma_kwargs = {
"geno_filename": os.path.join(app_defaults.get("GENODIR"), "bimbam",
f"{data.get('genofile_name')}.txt"),
"trait_filename": generate_pheno_txt_file(
tmpdir=app_defaults.get("TMPDIR"),
values=data.get("values"),
# Generate this file on the fly!
trait_filename=(f"{data.get('dataset_groupname')}_"
f"{data.get('trait_name')}_"
f"{__hash}.txt"))}
k_computation_cmd = generate_gemma_computation_cmd(
gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
gemma_kwargs=gemma_kwargs,
output_file=(f"{app_defaults.get('TMPDIR')}/gn2/"
f"{data.get('dataset_name')}_K_"
f"{__hash}.json"))
if data.get("covariates"):
gemma_kwargs["c"] = os.path.join(app_defaults.get("GENODIR"),
"bimbam",
data.get("covariates"))
gemma_kwargs["lmm"] = data.get("lmm", 9)
gwa_cmd = generate_gemma_computation_cmd(
gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
gemma_kwargs=gemma_kwargs,
output_file=(f"{data.get('dataset_name')}_GWA_"
f"{__hash}.txt"))
if not all([k_computation_cmd, gwa_cmd]):
return jsonify(status=128,
error="Unable to generate cmds for computation!"), 500
return jsonify(
unique_id=queue_cmd(conn=redis.Redis(),
email=data.get("email"),
cmd=f"{k_computation_cmd} && {gwa_cmd}"),
status="queued",
output_file=(f"{data.get('dataset_name')}_GWA_"
f"{__hash}.txt"))
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