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FIX: allow multiple inspections of the same dataset #37

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FIX: allow multiple inspections of the same dataset #37

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60 changes: 31 additions & 29 deletions qkay/qkay.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ class User(UserMixin, db.Document):
password = db.StringField()
is_admin = db.BooleanField(default=False)
dataset_list = db.ListField()
current_dataset = db.StringField()
current_inspection_param = db.ListField()
meta = {"collection": "users"}

def set_password(self, password):
Expand Down Expand Up @@ -687,18 +687,18 @@ def display_report_non_anonymized(username, report_name):
display report sub-<subject_number>
"""
user = User.objects(username=username).first()
dataset = user.current_dataset
dataset = user.current_inspection_param[0]
dataset_path = str(Dataset.objects(name=dataset).values_list("path_dataset")[0])

app.logger.debug("Searching recursively for a report named %s under %s.", report_name, dataset_path)

mriqc_report = ""
path_mriqc_report = glob.glob(os.path.join(dataset_path, "**", "sub-" + report_name), recursive=True)
if len(path_mriqc_report) == 0:
app.logger.error("No report named %s was found in the children of %s.","sub-" + report_name, dataset_path)
app.logger.error("No report named %s was found in the children of %s.", "sub-" + report_name, dataset_path)
else:
path_mriqc_report = path_mriqc_report[0]
# Modify the html to adapt it to Q'kay
# Modify the html to adapt it to Q'kay
mriqc_report = modify_mriqc_report(path_mriqc_report)

return render_template(
Expand All @@ -722,48 +722,50 @@ def info_user(username):
"""
display user's panel
"""
list_inspections_assigned = Inspection.objects(username=username).values_list(
"dataset"
)
dataset_names = Inspection.objects(username=username).values_list("dataset")
blind_values = Inspection.objects(username=username).values_list("blind")
rate_all_values = Inspection.objects(username=username).values_list("rate_all")
randomize_values = Inspection.objects(username=username).values_list("randomize")

route_list = [
"/index-" + username + "/" + str(name) for name in list_inspections_assigned
]
"/index-" + username + "/" + str(dataset_names) + "-" + str(blind_values) + "-" + str(rate_all_values) + "-" + str(randomize_values)
for dataset_names, blind_values, rate_all_values, randomize_values in zip(dataset_names, blind_values, rate_all_values, randomize_values)]

if request.method == "POST":
pass
if current_user.is_admin:
return render_template(
op.relpath("./templates/user_panel_admin_version.html", template_folder),
list_inspections_assigned=list_inspections_assigned,
number_inspections=len(list_inspections_assigned),
list_inspections_assigned=dataset_names,
number_inspections=len(dataset_names),
username=username,
route_list=route_list,
)
else:
return render_template(
op.relpath("./templates/user_panel.html", template_folder),
list_inspections_assigned=list_inspections_assigned,
number_inspections=len(list_inspections_assigned),
list_inspections_assigned=dataset_names,
number_inspections=len(dataset_names),
username=username,
route_list=route_list,
)


@app.route("/index-<username>/<dataset>", methods=["POST", "GET"])
@app.route("/index-<username>/<dataset>-<blind>-<rateall>-<randomize>", methods=["POST", "GET"])
@login_required
def display_index_inspection(username, dataset):
def display_index_inspection(username, dataset,blind,rateall,randomize):
"""
display interactive list of files to grade
"""
user = User.objects(username=username).first()
user.current_dataset = dataset
user.current_inspection_param = [dataset, blind, rateall, randomize]
user.save()
path_index = "./templates/index.html"

app.logger.debug("Searching for inspection matching dataset %s and username %s.", dataset, username)

# Find in the inspection which reports have been rated
current_inspection = Inspection.objects(Q(dataset=dataset) & Q(username=username))
current_inspection = Inspection.objects(Q(dataset=dataset) & Q(username=username) & Q(rate_all=(rateall == "True")) & Q(blind=(blind == "True")) & Q(randomize=(randomize == "True")))
array_rated = (
np.array(
current_inspection.values_list("index_rated_reports")[0], dtype=np.int8
Expand All @@ -777,7 +779,7 @@ def display_index_inspection(username, dataset):
op.relpath(path_index, template_folder),
array_rated=array_rated,
index_list=names_files,
url_index="/index-" + str(username) + "/" + str(dataset),
url_index="/index-" + str(username) + "/" + str(dataset)+"-"+str(blind) + "-"+str(rateall)+"-"+str(randomize),
url_home="/" + str(username),
)

Expand Down Expand Up @@ -819,28 +821,28 @@ def create_dataset():
selected_datasets = request.form.getlist("datasets[]")
for d in selected_datasets:
dataset_path = op.join("/datasets", d)
app.logger.debug("Searching recursively for dataset_description.json under %s.", dataset_path)
app.logger.debug("Searching recursively for dataset_description.json under %s.", dataset_path)

# Get dataset name from the data_description.json file if it exists
# otherwise, use the folder name
desc_file = ""
desc_files = glob.glob(os.path.join(dataset_path, "**", "dataset_description.json"), recursive=True)
if len(desc_files) > 1:
app.logger.warning("More than one dataset_description.json was found!: %s .", desc_files)
app.logger.warning("More than one dataset_description.json was found!: %s .", desc_files)

desc_file = desc_files[0]
app.logger.debug("dataset_description.json found at %s.", desc_file)
app.logger.debug("dataset_description.json found at %s.", desc_file)
if desc_file:
with open(desc_file, "r") as file:
data_description = json.load(file)
dataset_name = data_description["Name"]
app.logger.info("The dataset name %s was assigned based on the name in %s", dataset_name, desc_file)
app.logger.info("The dataset name %s was assigned based on the name in %s", dataset_name, desc_file)
# If the name of the dataset is the default MRIQC value, use the folder name instead
if dataset_name == "MRIQC - MRI Quality Control":
app.logger.info("The dataset name is the default of MRIQC which is not informative, using folder name instead: %s.", d)
app.logger.info("The dataset name is the default of MRIQC which is not informative, using folder name instead: %s.", d)
dataset_name = d
else:
app.logger.info("No dataset_description.json found, assigning dataset name to folder name: %s.", d)
app.logger.info("No dataset_description.json found, assigning dataset name to folder name: %s.", d)
dataset_name = d

dataset = Dataset(name=dataset_name, path_dataset=dataset_path)
Expand Down Expand Up @@ -968,20 +970,20 @@ def receive_report():
"""
request_data = request.get_json()
username = current_user.username
dataset = current_user.current_dataset
current_inspection = Inspection.objects(Q(dataset=dataset) & Q(username=username))
current_inspection_param = current_user.current_inspection_param
current_inspection = Inspection.objects(Q(dataset=current_inspection_param[0]) & Q(username=username) & Q(rate_all=(current_inspection_param[2] == "True")) & Q(blind=(current_inspection_param[1] == "True")) & Q(randomize=(current_inspection_param[3] == "True")))
shuffled_names = current_inspection.values_list("names_shuffled")
index_rated = np.array(current_inspection.values_list("index_rated_reports"))
report = Rating()
report = report.from_json(json.dumps(request_data))
report.dataset = dataset
report.dataset = current_inspection_param[0]
report.rater_id = username
report.save()
ind_name = np.where(np.array(shuffled_names[0]) == str(report.subject) + ".html")
index_rated[0][ind_name] = True
current_inspection.update_one(set__index_rated_reports=index_rated[0].tolist())
app.logger.info("Report %s has been rated by user %s.", report.subject, username)
return redirect("/index-" + username + "/" + dataset, code=307)
return redirect("/index-" + username + "/" + current_inspection_param[0], code=307)


if __name__ == "__main__":
Expand Down