diff options
| -rw-r--r-- | qc_app/default_settings.py | 2 | ||||
| -rw-r--r-- | tests/conftest.py | 2 | ||||
| -rw-r--r-- | tests/test_instance_dir/config.py | 2 | ||||
| -rw-r--r-- | tests/uploader/test_parse.py | 2 | ||||
| -rw-r--r-- | uploader/expression_data/dbinsert.py | 6 | ||||
| -rw-r--r-- | uploader/expression_data/views.py | 10 | ||||
| -rw-r--r-- | uploader/population/rqtl2.py | 6 | ||||
| -rw-r--r-- | uploader/samples/views.py | 4 |
8 files changed, 17 insertions, 17 deletions
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( |