diff options
Diffstat (limited to 'gn3/api/rqtl.py')
| -rw-r--r-- | gn3/api/rqtl.py | 75 |
1 files changed, 50 insertions, 25 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index e029d8d..eb49f8b 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -1,5 +1,7 @@ """Endpoints for running the rqtl cmd""" + import os +import uuid from pathlib import Path from flask import Blueprint @@ -7,30 +9,40 @@ from flask import current_app from flask import jsonify from flask import request -from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, \ - process_rqtl_pairscan, process_perm_output -from gn3.fs_helpers import assert_paths_exist, get_tmpdir +from gn3.computations.rqtl import ( + generate_rqtl_cmd, + process_rqtl_mapping, + process_rqtl_pairscan, + process_perm_output, +) +from gn3.computations.streaming import run_process, enable_streaming +from gn3.fs_helpers import assert_path_exists, get_tmpdir rqtl = Blueprint("rqtl", __name__) + @rqtl.route("/compute", methods=["POST"]) -def compute(): +@enable_streaming +def compute(stream_output_file): """Given at least a geno_file and pheno_file, generate and -run the rqtl_wrapper script and return the results as JSON + run the rqtl_wrapper script and return the results as JSON """ - genofile = request.form['geno_file'] - phenofile = request.form['pheno_file'] - - assert_paths_exist([genofile, phenofile]) - - # Split kwargs by those with values and boolean ones that just convert to True/False + genofile = request.form["geno_file"] + phenofile = request.form["pheno_file"] + assert_path_exists(genofile) + assert_path_exists(phenofile) kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control"] boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"] all_kwargs = kwargs + boolean_kwargs - rqtl_kwargs = {"geno": genofile, "pheno": phenofile, "outdir": current_app.config.get("TMPDIR")} + rqtl_kwargs = { + "geno": genofile, + "pheno": phenofile, + "outdir": current_app.config.get("TMPDIR"), + } rqtl_bool_kwargs = [] + for kwarg in all_kwargs: if kwarg in request.form: if kwarg in kwargs: @@ -38,30 +50,43 @@ run the rqtl_wrapper script and return the results as JSON if kwarg in boolean_kwargs: rqtl_bool_kwargs.append(kwarg) - outdir = os.path.join(get_tmpdir(),"gn3") + outdir = os.path.join(get_tmpdir(), "gn3") if not os.path.isdir(outdir): os.mkdir(outdir) rqtl_cmd = generate_rqtl_cmd( rqtl_wrapper_cmd=str( - Path(__file__).absolute().parent.parent.parent.joinpath( - 'scripts/rqtl_wrapper.R')), + Path(__file__) + .absolute() + .parent.parent.parent.joinpath("scripts/rqtl_wrapper.R") + ), rqtl_wrapper_kwargs=rqtl_kwargs, - rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs + rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs, ) rqtl_output = {} - if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"), - "gn3", rqtl_cmd.get('output_file'))): - os.system(rqtl_cmd.get('rqtl_cmd')) + run_id = request.args.get("id", str(uuid.uuid4())) + if not os.path.isfile( + os.path.join( + current_app.config.get("TMPDIR"), "gn3", rqtl_cmd.get("output_file") + ) + ): + pass + run_process(rqtl_cmd.get("rqtl_cmd").split(), stream_output_file, run_id) if "pairscan" in rqtl_bool_kwargs: - rqtl_output['results'] = process_rqtl_pairscan(rqtl_cmd.get('output_file'), genofile) + rqtl_output["results"] = process_rqtl_pairscan( + rqtl_cmd.get("output_file"), genofile + ) else: - rqtl_output['results'] = process_rqtl_mapping(rqtl_cmd.get('output_file')) - - if int(rqtl_kwargs['nperm']) > 0: - rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = \ - process_perm_output(rqtl_cmd.get('output_file')) + rqtl_output["results"] = process_rqtl_mapping(rqtl_cmd.get("output_file")) + if int(rqtl_kwargs["nperm"]) > 0: + # pylint: disable=C0301 + perm_output_file = f"PERM_{rqtl_cmd.get('output_file')}" + ( + rqtl_output["perm_results"], + rqtl_output["suggestive"], + rqtl_output["significant"], + ) = process_perm_output(perm_output_file) return jsonify(rqtl_output) |