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FIX: Dataset creation when description absent #44

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FIX: Dataset creation when description absent #44

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40 changes: 28 additions & 12 deletions qkay/qkay.py
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Original file line number Diff line number Diff line change
Expand Up @@ -820,26 +820,42 @@ def create_dataset():

# 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)

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)

desc_file = desc_files[0]
app.logger.debug("dataset_description.json found at %s.", desc_file)
if desc_file:
app.logger.warning(
"More than one dataset_description.json was found!: %s .",
desc_files,
)

if desc_files:
desc_file = desc_files[0]
app.logger.debug(
"dataset_description.json found at %s.", 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)
# If the name of the dataset is the default MRIQC value, use the folder name instead
app.logger.info(
"The dataset name %s was assigned based on the name in %s",
dataset_name,
desc_file,
)
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)
existing_dataset = Dataset.objects(name=dataset_name).first()
if not dataset.validate_dataset():
Expand Down
30 changes: 30 additions & 0 deletions test/test_create_dataset.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
import sys
import glob
import json
import os
from importlib.machinery import SourceFileLoader


def test_dataset_creation_without_description(tmp_path):
dataset_dir = tmp_path / "ds1"
dataset_dir.mkdir()
(dataset_dir / "sub-001.html").write_text("<html></html>")

sys.path.append('qkay')
mod = SourceFileLoader('qkay_module', 'qkay/qkay.py').load_module()
Dataset = mod.Dataset

dataset_path = str(dataset_dir)
desc_files = glob.glob(os.path.join(dataset_path, '**', 'dataset_description.json'), recursive=True)
if desc_files:
with open(desc_files[0]) as f:
data_description = json.load(f)
dataset_name = data_description.get('Name', dataset_dir.name)
if dataset_name == 'MRIQC - MRI Quality Control':
dataset_name = dataset_dir.name
else:
dataset_name = dataset_dir.name

dataset = Dataset(name=dataset_name, path_dataset=dataset_path)
assert dataset.validate_dataset() is True
assert dataset.name == dataset_dir.name