diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/wgcna.py | 25 | ||||
| -rw-r--r-- | gn3/app.py | 2 | ||||
| -rw-r--r-- | gn3/computations/wgcna.py | 48 | ||||
| -rw-r--r-- | gn3/settings.py | 2 |
4 files changed, 77 insertions, 0 deletions
diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py new file mode 100644 index 0000000..fa044cf --- /dev/null +++ b/gn3/api/wgcna.py @@ -0,0 +1,25 @@ +"""endpoint to run wgcna analysis""" +from flask import Blueprint +from flask import request +from flask import current_app +from flask import jsonify + +from gn3.computations.wgcna import call_wgcna_script + +wgcna = Blueprint("wgcna", __name__) + + +@wgcna.route("/run_wgcna", methods=["POST"]) +def run_wgcna(): + """run wgcna:output should be a json with a the data""" + + wgcna_data = request.json + + wgcna_script = current_app.config["WGCNA_RSCRIPT"] + + results = call_wgcna_script(wgcna_script, wgcna_data) + + if results.get("data") is None: + return jsonify(results), 401 + + return jsonify(results), 200 @@ -13,6 +13,7 @@ from gn3.api.general import general from gn3.api.heatmaps import heatmaps from gn3.api.correlation import correlation from gn3.api.data_entry import data_entry +from gn3.api.wgcna import wgcna def create_app(config: Union[Dict, str, None] = None) -> Flask: """Create a new flask object""" @@ -42,4 +43,5 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask: app.register_blueprint(heatmaps, url_prefix="/api/heatmaps") app.register_blueprint(correlation, url_prefix="/api/correlation") app.register_blueprint(data_entry, url_prefix="/api/dataentry") + app.register_blueprint(wgcna, url_prefix="/api/wgcna") return app diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py new file mode 100644 index 0000000..436a888 --- /dev/null +++ b/gn3/computations/wgcna.py @@ -0,0 +1,48 @@ +"""module contains code to preprocess and call wgcna script""" + +import os +import json +import uuid +from gn3.settings import TMPDIR + +from gn3.commands import run_cmd + + +def dump_wgcna_data(request_data: dict): + """function to dump request data to json file""" + filename = f"{str(uuid.uuid4())}.json" + + temp_file_path = os.path.join(TMPDIR, filename) + + with open(temp_file_path, "w") as output_file: + json.dump(request_data, output_file) + + return temp_file_path + + +def compose_wgcna_cmd(rscript_path: str, temp_file_path: str): + """function to componse wgcna cmd""" + # (todo):issue relative paths to abs paths + cmd = f"Rscript ./scripts/{rscript_path} {temp_file_path}" + return cmd + + +def call_wgcna_script(rscript_path: str, request_data: dict): + """function to call wgcna script""" + generated_file = dump_wgcna_data(request_data) + cmd = compose_wgcna_cmd(rscript_path, generated_file) + + try: + + run_cmd_results = run_cmd(cmd) + + with open(generated_file, "r") as outputfile: + + if run_cmd_results["code"] != 0: + return run_cmd_results + return { + "data": json.load(outputfile), + **run_cmd_results + } + except Exception as error: + raise error diff --git a/gn3/settings.py b/gn3/settings.py index 9d7bba3..150d96d 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -25,6 +25,8 @@ GN2_BASE_URL = "http://www.genenetwork.org/" # biweight script BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R" +# wgcna script +WGCNA_RSCRIPT = "wgcna_analysis.R" # qtlreaper command REAPER_COMMAND = "{}/bin/qtlreaper".format(os.environ.get("GUIX_ENVIRONMENT")) |