"""General API endpoints. Put endpoints that can't be grouped together nicely here.""" from flask import Blueprint from flask import current_app from flask import jsonify from flask import request from gn3.fs_helpers import extract_uploaded_file from gn3.commands import run_cmd general = Blueprint("general", __name__) @general.route("/metadata/upload/", methods=["POST"], strict_slashes=False) def upload_metadata_with_no_token(): """Extract uploaded file to a some TMPDIR/TOKEN/ with a TTL(Time To Live). The TTL is set in the metadata file. If none is provided, the default is 1 week. Generate a TOKEN """ file_ = request.files.get("file") if not file_: return jsonify(status=128, error="Please provide a file!"), 400 status = 201 results = extract_uploaded_file( gzipped_file=file_, target_dir=current_app.config["TMPDIR"], token=None) if results.get("status") > 0: status = 500 return jsonify(results), status @general.route("/metadata/upload/<token>", methods=["POST"], strict_slashes=False) def upload_metadata(token): """Extract uploaded file to a some TMPDIR/TOKEN/ with a TTL(Time To Live). The TTL is set in the metadata file. If none is provided, the default is 1 week. """ file_ = request.files.get("file") if not file_: return jsonify(status=128, error="Please provide a file!"), 400 status = 201 results = extract_uploaded_file( gzipped_file=file_, target_dir=current_app.config["TMPDIR"], token=token) if results.get("status") > 0: status = 500 return jsonify(results), status @general.route("/qtl/run/<geno_filestr>/<pheno_filestr>", methods=["POST"], strict_slashes=False) def run_r_qtl(geno_filestr, pheno_filestr): """Run r_qtl command using the written rqtl_wrapper program """ rqtl_wrapper = current_app.config["RQTL_WRAPPER"] cmd = (f"Rscript {rqtl_wrapper} " f"{geno_filestr} {pheno_filestr}") return jsonify(run_cmd(cmd)), 201