Creating behavioral protocol (openMetadataInitiative#52)

* protocol

* deling with no task

* behavioral_protocol

* adding test for behavioral_protocols

* adding behavioral_protocol_number to test_bids_examples.py

bids2openminds/converter.py

@@ -21,8 +21,6 @@ def convert(input_path, save_output=False, output_path=None, multiple_files=Fals
 
  subjects_id = bids_layout.get_subjects()
 
- tasks = bids_layout.get_task()
-
  # imprting the dataset description file containing some of the
  dataset_description_path = utility.table_filter(layout_df, "description")
 
@@ -31,11 +29,14 @@ def convert(input_path, save_output=False, output_path=None, multiple_files=Fals
  [subjects_dict, subject_state_dict, subjects_list] = main.create_subjects(
  subjects_id, layout_df, bids_layout, collection)
 
+ behavioral_protocols, behavioral_protocols_dict = main.create_behavioral_protocol(
+ bids_layout, collection)
+
  [files_list, file_repository] = main.create_file(
  layout_df, input_path, collection)
 
  dataset_version = main.create_dataset_version(
- bids_layout, dataset_description, layout_df, subjects_list, file_repository, collection)
+ bids_layout, dataset_description, layout_df, subjects_list, file_repository, behavioral_protocols, collection)
 
  dataset = main.create_dataset(
  dataset_description, dataset_version, collection)

bids2openminds/main.py

@@ -72,6 +72,26 @@ def create_persons(dataset_description, collection):
  return openminds_list
 
 
+def create_behavioral_protocol(layout, collection):
+ behavioral_protocols_dict = {}
+ behavioral_protocols = []
+ tasks = layout.get_tasks()
+
+ if not tasks:
+ return None, None
+
+ for task in tasks:
+
+ behavioral_protocol = omcore.BehavioralProtocol(name=task,
+ internal_identifier=task,
+ description="To be defined")
+ behavioral_protocols.append(behavioral_protocol)
+ behavioral_protocols_dict[task] = behavioral_protocol
+ collection.add(behavioral_protocol)
+
+ return behavioral_protocols, behavioral_protocols_dict
+
+
 def create_techniques(layout_df):
  suffixs = layout_df["suffix"].unique().tolist()
  techniques = []
@@ -126,7 +146,7 @@ def create_openminds_age(data_subject):
  return None
 
 
-def create_dataset_version(bids_layout, dataset_description, layout_df, studied_specimens, file_repository, collection):
+def create_dataset_version(bids_layout, dataset_description, layout_df, studied_specimens, file_repository, behavioral_protocols, collection):
 
  # Fetch the dataset type from dataset description file
 
@@ -179,6 +199,7 @@ def create_dataset_version(bids_layout, dataset_description, layout_df, studied_
  techniques=techniques,
  how_to_cite=how_to_cite,
  repository=file_repository,
+ behavioral_protocols=behavioral_protocols
  # other_contributions=other_contribution # needs to be a Contribution object
  # version_identifier
  )

test/test_bids_examples.py

@@ -4,18 +4,18 @@
 import bids2openminds.converter
 
 
-# Dataset information in following order dataset_label, dataset_subject_number, dataset_subject_state_number, dataset_person_number, dataset_files_number
-example_dataset = [("ds003", 13, 13, 2, 58),
- ("ds000247", 6, 10, 5, 202),
+# Dataset information in following order dataset_label, dataset_subject_number, dataset_subject_state_number, dataset_person_number, dataset_files_number, dataset_behavioral_protocol_number
+example_dataset = [("ds003", 13, 13, 2, 58, 1),
+ ("ds000247", 6, 10, 5, 202, 2),
  # The authors list in 'eeg_cbm' contains non person entities 2 is not correct name (issue raied #43)
- ("eeg_cbm", 20, 20, 2, 104),
- ("asl001", 1, 1, 2, 8),
+ ("eeg_cbm", 20, 20, 2, 104, 1),
+ ("asl001", 1, 1, 2, 8, 0),
  # Number of files in 'eeg_rest_fmri' is not correct as it doesn't contain files in derivated (issue raied #42)
- ("eeg_rest_fmri", 3, 3, 6, 46)]
+ ("eeg_rest_fmri", 3, 3, 6, 46, 1)]
 
 
-@pytest.mark.parametrize("dataset_label, dataset_subject_number, dataset_subject_state_number, dataset_person_number, dataset_files_number", example_dataset)
-def test_example_datasets(dataset_label, dataset_subject_number, dataset_subject_state_number, dataset_person_number, dataset_files_number):
+@pytest.mark.parametrize("dataset_label, dataset_subject_number, dataset_subject_state_number, dataset_person_number, dataset_files_number, dataset_behavioral_protocol_number", example_dataset)
+def test_example_datasets(dataset_label, dataset_subject_number, dataset_subject_state_number, dataset_person_number, dataset_files_number, dataset_behavioral_protocol_number):
  test_dir = os.path.join("bids-examples", dataset_label)
  bids2openminds.converter.convert(test_dir, save_output=True)
  c = Collection()
@@ -25,6 +25,7 @@ def test_example_datasets(dataset_label, dataset_subject_number, dataset_subject
  subject_state_number = 0
  person_number = 0
  files_number = 0
+ behavioral_protocol_number = 0
 
  for item in c:
  match item.type_:
@@ -36,8 +37,11 @@ def test_example_datasets(dataset_label, dataset_subject_number, dataset_subject
  person_number += 1
  case "https://openminds.ebrains.eu/core/File":
  files_number += 1
+ case "https://openminds.ebrains.eu/core/BehavioralProtocol":
+ behavioral_protocol_number += 1
 
  assert dataset_subject_number == subject_number
  assert dataset_subject_state_number == subject_state_number
  assert dataset_person_number == person_number
  assert dataset_files_number == files_number
+ assert dataset_behavioral_protocol_number == behavioral_protocol_number

test/test_task.py

@@ -0,0 +1,25 @@
+import pytest
+from bids import BIDSLayout
+from openminds import Collection
+import os
+from bids2openminds.main import create_behavioral_protocol
+
+(datasets, tasks) = ("ds002", ("deterministicclassification",
+ "mixedeventrelatedprobe", "probabilisticclassification"))
+
+
+@pytest.fixture
+def creating_behavioral_protocols():
+ c = Collection()
+ test_dir = os.path.join("bids-examples", datasets)
+ bids_layout = BIDSLayout(test_dir)
+ _, behavioral_protocols_dict = create_behavioral_protocol(
+ bids_layout, c)
+ return behavioral_protocols_dict
+
+
+def test_behavioral_protocols(creating_behavioral_protocols):
+ assert len(tasks) == len(creating_behavioral_protocols)
+ for item in creating_behavioral_protocols:
+ assert item in tasks
+ assert creating_behavioral_protocols[item].internal_identifier == item