diff options
Diffstat (limited to 'uploader/expression_data')
| -rw-r--r-- | uploader/expression_data/dbinsert.py | 6 | ||||
| -rw-r--r-- | uploader/expression_data/views.py | 12 |
2 files changed, 9 insertions, 9 deletions
diff --git a/uploader/expression_data/dbinsert.py b/uploader/expression_data/dbinsert.py index 6d8ce80..7040698 100644 --- a/uploader/expression_data/dbinsert.py +++ b/uploader/expression_data/dbinsert.py @@ -94,7 +94,7 @@ def select_platform(): job = jobs.job(rconn, jobs.jobsnamespace(), job_id) if job: filename = job["filename"] - filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}" + filepath = f"{app.config['UPLOADS_DIRECTORY']}/{filename}" if os.path.exists(filepath): default_species = 1 gchips = genechips() @@ -367,7 +367,7 @@ def insert_data(): assert form.get("datasetid"), "dataset" filename = form["filename"] - filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}" + filepath = f"{app.config['UPLOADS_DIRECTORY']}/{filename}" redisurl = app.config["REDIS_URL"] if os.path.exists(filepath): with Redis.from_url(redisurl, decode_responses=True) as rconn: @@ -377,7 +377,7 @@ def insert_data(): form["species"], form["genechipid"], form["datasetid"], app.config["SQL_URI"], redisurl, app.config["JOBS_TTL_SECONDS"]), - redisurl, f"{app.config['UPLOAD_FOLDER']}/job_errors") + redisurl, f"{app.config['UPLOADS_DIRECTORY']}/job_errors") return redirect(url_for("dbinsert.insert_status", job_id=job["jobid"])) return render_error(f"File '{filename}' no longer exists.") diff --git a/uploader/expression_data/views.py b/uploader/expression_data/views.py index 7629f3e..0e9b072 100644 --- a/uploader/expression_data/views.py +++ b/uploader/expression_data/views.py @@ -11,7 +11,6 @@ from werkzeug.utils import secure_filename from gn_libs.mysqldb import database_connection from flask import (flash, request, - url_for, redirect, Blueprint, current_app as app) @@ -19,6 +18,7 @@ from flask import (flash, from quality_control.errors import InvalidValue, DuplicateHeading from uploader import jobs +from uploader.flask_extensions import url_for from uploader.datautils import order_by_family from uploader.ui import make_template_renderer from uploader.authorisation import require_login @@ -162,7 +162,7 @@ def upload_file(species_id: int, population_id: int): species=species, population=population) - upload_dir = app.config["UPLOAD_FOLDER"] + upload_dir = app.config["UPLOADS_DIRECTORY"] request_errors = errors(request) if request_errors: for error in request_errors: @@ -225,7 +225,7 @@ def parse_file(species_id: int, population_id: int): _errors = True if filename: - filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename) + filepath = os.path.join(app.config["UPLOADS_DIRECTORY"], filename) if not os.path.exists(filepath): flash("Selected file does not exist (any longer)", "alert-danger") _errors = True @@ -241,7 +241,7 @@ def parse_file(species_id: int, population_id: int): species_id, filepath, filetype,# type: ignore[arg-type] app.config["JOBS_TTL_SECONDS"]), redisurl, - f"{app.config['UPLOAD_FOLDER']}/job_errors") + f"{app.config['UPLOADS_DIRECTORY']}/job_errors") return redirect(url_for("species.populations.expression-data.parse_status", species_id=species_id, @@ -263,7 +263,7 @@ def parse_status(species_id: int, population_id: int, job_id: str): return render_template("no_such_job.html", job_id=job_id), 400 error_filename = jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors") + job_id, f"{app.config['UPLOADS_DIRECTORY']}/job_errors") if os.path.exists(error_filename): stat = os.stat(error_filename) if stat.st_size > 0: @@ -345,7 +345,7 @@ def fail(species_id: int, population_id: int, job_id: str): if job: error_filename = jobs.error_filename( - job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors") + job_id, f"{app.config['UPLOADS_DIRECTORY']}/job_errors") if os.path.exists(error_filename): stat = os.stat(error_filename) if stat.st_size > 0: |