diff --git a/qc_app/default_settings.py b/qc_app/default_settings.py
index 7a9da0f..7bb0bf8 100644
--- a/qc_app/default_settings.py
+++ b/qc_app/default_settings.py
@@ -7,7 +7,7 @@ import os
LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING")
SECRET_KEY = b"<Please! Please! Please! Change This!>"
-UPLOAD_FOLDER = "/tmp/qc_app_files"
+UPLOADS_DIRECTORY = "/tmp/qc_app_files"
REDIS_URL = "redis://"
JOBS_TTL_SECONDS = 1209600 # 14 days
GNQC_REDIS_PREFIX="GNQC"
diff --git a/tests/conftest.py b/tests/conftest.py
index a716c52..2009aab 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -183,7 +183,7 @@ def redis_conn_with_completed_job_some_errors(redis_url, redis_ttl, jobs_prefix,
def uploads_dir(client): # pylint: disable=[redefined-outer-name]
"""Returns the configured, uploads directory, creating it if it does not
exist."""
- the_dir = client.application.config["UPLOAD_FOLDER"]
+ the_dir = client.application.config["UPLOADS_DIRECTORY"]
if not os.path.exists(the_dir):
os.mkdir(the_dir)
diff --git a/tests/test_instance_dir/config.py b/tests/test_instance_dir/config.py
index 2ee569b..f04b3df 100644
--- a/tests/test_instance_dir/config.py
+++ b/tests/test_instance_dir/config.py
@@ -6,6 +6,6 @@ import os
LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING")
SECRET_KEY = b"<Please! Please! Please! Change This!>"
-UPLOAD_FOLDER = "/tmp/qc_app_files"
+UPLOADS_DIRECTORY = "/tmp/qc_app_files"
REDIS_URL = "redis://"
JOBS_TTL_SECONDS = 600 # 10 minutes
diff --git a/tests/uploader/test_parse.py b/tests/uploader/test_parse.py
index 20c75b7..56e1b41 100644
--- a/tests/uploader/test_parse.py
+++ b/tests/uploader/test_parse.py
@@ -50,7 +50,7 @@ def test_parse_with_existing_uploaded_file(
assert the_job["command"] == " ".join([
sys.executable, "-m", "scripts.validate_file", db_url, redis_url,
jobs_prefix, job_id, "--redisexpiry", str(redis_ttl), str(speciesid),
- filetype, f"{client.application.config['UPLOAD_FOLDER']}/{filename}"])
+ filetype, f"{client.application.config['UPLOADS_DIRECTORY']}/{filename}"])
@pytest.mark.parametrize(
"filename,uri,error_msgs",
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 0b318b7..0e9b072 100644
--- a/uploader/expression_data/views.py
+++ b/uploader/expression_data/views.py
@@ -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:
diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py
index 97d4854..bb5066e 100644
--- a/uploader/population/rqtl2.py
+++ b/uploader/population/rqtl2.py
@@ -134,7 +134,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
try:
app.logger.debug("Files in the form: %s", request.files)
the_file = save_file(request.files["rqtl2_bundle_file"],
- Path(app.config["UPLOAD_FOLDER"]))
+ Path(app.config["UPLOADS_DIRECTORY"]))
except AssertionError:
app.logger.debug(traceback.format_exc())
flash("Please provide a valid R/qtl2 zip bundle.",
@@ -185,7 +185,7 @@ def trigger_rqtl2_bundle_qc(
"rqtl2-bundle-file": str(rqtl2bundle.absolute()),
"original-filename": originalfilename})}),
redisuri,
- f"{app.config['UPLOAD_FOLDER']}/job_errors")
+ f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
return jobid
@@ -895,7 +895,7 @@ def confirm_bundle_details(species_id: int, population_id: int):
})
}),
redisuri,
- f"{app.config['UPLOAD_FOLDER']}/job_errors")
+ f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
return redirect(url_for("expression-data.rqtl2.rqtl2_processing_status",
jobid=jobid))
diff --git a/uploader/samples/views.py b/uploader/samples/views.py
index ee002ba..1c0569d 100644
--- a/uploader/samples/views.py
+++ b/uploader/samples/views.py
@@ -138,7 +138,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma
try:
samples_file = save_file(request.files["samples_file"],
- Path(app.config["UPLOAD_FOLDER"]))
+ Path(app.config["UPLOADS_DIRECTORY"]))
except AssertionError:
flash("You need to provide a file with the samples data.",
"alert-error")
@@ -176,7 +176,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma
},
external_id=session.logged_in_user_id()),
_jobs_db,
- Path(f"{app.config['UPLOAD_FOLDER']}/job_errors").absolute(),
+ Path(f"{app.config['UPLOADS_DIRECTORY']}/job_errors").absolute(),
loglevel=logging.getLevelName(
app.logger.getEffectiveLevel()).lower())
return redirect(
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