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-rw-r--r--uploader/expression_data/views.py39
1 files changed, 19 insertions, 20 deletions
diff --git a/uploader/expression_data/views.py b/uploader/expression_data/views.py
index c5a75e7..88c4528 100644
--- a/uploader/expression_data/views.py
+++ b/uploader/expression_data/views.py
@@ -105,15 +105,14 @@ def index():
if not bool(request.args.get("species_id")):
return render_template("expression-data/index.html",
species=order_by_family(all_species(conn)),
- activelink="genotypes")
+ activelink="expression-data")
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
- flash(f"Could not find species with ID '{request.args.get('species_id')}'!",
- "alert-danger")
+ flash("Could not find species selected!", "alert-danger")
return redirect(url_for("species.populations.expression-data.index"))
- return redirect(url_for("species.populations.expression-data.select_population",
- species_id=species["SpeciesId"]))
- return render_template()
+ return redirect(url_for(
+ "species.populations.expression-data.select_population",
+ species_id=species["SpeciesId"]))
@exprdatabp.route("<int:species_id>/populations/expression-data/select-population",
@@ -124,7 +123,7 @@ def select_population(species_id: int):
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
- flash("Invalid species provided!", "alert-danger")
+ flash("No such species!", "alert-danger")
return redirect(url_for("species.populations.expression-data.index"))
if not bool(request.args.get("population_id")):
@@ -133,12 +132,12 @@ def select_population(species_id: int):
populations=order_by_family(
populations_by_species(conn, species_id),
order_key="FamilyOrder"),
- activelink="genotypes")
+ activelink="expression-data")
population = population_by_species_and_id(
conn, species_id, request.args.get("population_id"))
if not bool(population):
- flash("Invalid population selected!", "alert-danger")
+ flash("No such population!", "alert-danger")
return redirect(url_for(
"species.populations.expression-data.select_population",
species_id=species_id))
@@ -202,34 +201,34 @@ def data_review():
@require_login
def parse_file(species_id: int, population_id: int):
"""Trigger file parsing"""
- errors = False
+ _errors = False
filename = request.args.get("filename")
filetype = request.args.get("filetype")
species = with_db_connection(lambda con: species_by_id(con, species_id))
if not bool(species):
flash("No such species.", "alert-danger")
- errors = True
+ _errors = True
if filename is None:
flash("No file provided", "alert-danger")
- errors = True
+ _errors = True
if filetype is None:
flash("No filetype provided", "alert-danger")
- errors = True
+ _errors = True
if filetype not in ("average", "standard-error"):
flash("Invalid filetype provided", "alert-danger")
- errors = True
+ _errors = True
if filename:
filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename)
if not os.path.exists(filepath):
flash("Selected file does not exist (any longer)", "alert-danger")
- errors = True
+ _errors = True
- if errors:
+ if _errors:
return redirect(url_for("species.populations.expression-data.upload_file"))
redisurl = app.config["REDIS_URL"]
@@ -272,7 +271,7 @@ def parse_status(species_id: int, population_id: int, job_id: str):
progress = float(job["percent"])
status = job["status"]
filename = job.get("filename", "uploaded file")
- errors = jsonpickle.decode(
+ _errors = jsonpickle.decode(
job.get("errors", jsonpickle.encode(tuple())))
if status in ("success", "aborted"):
return redirect(url_for("species.populations.expression-data.results",
@@ -293,7 +292,7 @@ def parse_status(species_id: int, population_id: int, job_id: str):
progress = progress,
message = job.get("message", ""),
job_name = f"Parsing '{filename}'",
- errors=errors,
+ errors=_errors,
species=with_db_connection(
lambda conn: species_by_id(conn, species_id)),
population=with_db_connection(
@@ -313,13 +312,13 @@ def results(species_id: int, population_id: int, job_id: uuid.UUID):
if job:
filename = job["filename"]
- errors = jsonpickle.decode(job.get("errors", jsonpickle.encode(tuple())))
+ _errors = jsonpickle.decode(job.get("errors", jsonpickle.encode(tuple())))
app.jinja_env.globals.update(
isinvalidvalue=isinvalidvalue,
isduplicateheading=isduplicateheading)
return render_template(
"expression-data/parse-results.html",
- errors=errors,
+ errors=_errors,
job_name = f"Parsing '{filename}'",
user_aborted = job.get("user_aborted"),
job_id=job["jobid"],