diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/general.py | 2 | ||||
| -rw-r--r-- | gn3/api/rqtl2.py | 16 | ||||
| -rw-r--r-- | gn3/db/probesets.py | 3 |
3 files changed, 12 insertions, 9 deletions
diff --git a/gn3/api/general.py b/gn3/api/general.py index fcaf21b..8b57f23 100644 --- a/gn3/api/general.py +++ b/gn3/api/general.py @@ -91,7 +91,7 @@ def stream(): output_file = os.path.join(current_app.config.get("TMPDIR"), f"{run_id}.txt") seek_position = int(request.args.get("peak", 0)) - with open(output_file) as file_handler: + with open(output_file, encoding="utf-8") as file_handler: # read to the last position default to 0 file_handler.seek(seek_position) return jsonify({"data": file_handler.readlines(), diff --git a/gn3/api/rqtl2.py b/gn3/api/rqtl2.py index ffa8755..cacd3e0 100644 --- a/gn3/api/rqtl2.py +++ b/gn3/api/rqtl2.py @@ -1,7 +1,6 @@ """ File contains endpoints for rqlt2""" import subprocess -import uuid import os from flask import current_app from flask import jsonify @@ -10,6 +9,7 @@ from flask import request rqtl2 = Blueprint("rqtl2", __name__) + @rqtl2.route("/compute", methods=["GET"]) def compute(): """Endpoint for computing QTL analysis using R/QTL2""" @@ -19,11 +19,11 @@ def compute(): f"{run_id}.txt") # this should be computed locally not via files rscript_cmd = ( - f"Rscript ./scripts/rqtl2_wrapper.R " - f"-i /home/kabui/r_playground/meta_grav.json " - f"-d /home/kabui/r_playground " - f"-o /home/kabui/r_playground/rqtl_output.json " - f"--nperm 100 --threshold 1 --cores 0" + "Rscript ./scripts/rqtl2_wrapper.R " + "-i /home/kabui/r_playground/meta_grav.json " + "-d /home/kabui/r_playground " + "-o /home/kabui/r_playground/rqtl_output.json " + "--nperm 100 --threshold 1 --cores 0" ) process = subprocess.Popen( rscript_cmd, shell=True, @@ -33,7 +33,7 @@ def compute(): for line in iter(process.stdout.readline, b""): # these allow endpoint stream to read the file since # no read and write file same tiem - with open(output_file, "a+") as file_handler: + with open(output_file, "a+", encoding="utf-8") as file_handler: file_handler.write(line.decode("utf-8")) process.stdout.close() process.wait() @@ -53,7 +53,7 @@ def stream(identifier="output"): output_file = os.path.join(current_app.config.get("TMPDIR"), f"{identifier}.txt") seek_position = int(request.args.get("peak", 0)) - with open(output_file) as file_handler: + with open(output_file, encoding="utf-8") as file_handler: # read to the last position default to 0 file_handler.seek(seek_position) return jsonify({"data": file_handler.readlines(), diff --git a/gn3/db/probesets.py b/gn3/db/probesets.py index 82045b4..e725add 100644 --- a/gn3/db/probesets.py +++ b/gn3/db/probesets.py @@ -8,6 +8,9 @@ from gn3.db_utils import Connection as DBConnection from .query_tools import mapping_to_query_columns + +# pylint: disable = line-too-long + @dataclass(frozen=True) class Probeset: # pylint: disable=[too-many-instance-attributes] """Data Type that represents a Probeset""" |