From c5f7be71fb9164065753ea00da86b2104c85248b Mon Sep 17 00:00:00 2001 From: Peyman Najafi Date: Fri, 21 Jun 2024 17:08:54 +0200 Subject: [PATCH] Adding thorough testing (#38) * Adding thorough testing * Using pytest fixture * Changing the pytest fixture names * Activating the person test * deleting age * adding second dataset * adding file and fiel boundle * add seek to file open * modifying text files * fixing path prefix * use tempfile * using pathlib for abs path * not cheking hash for windows --- test/bids_examples_ds005.jsonld | 5654 +++++++++++++++++++++++ test/bids_examples_eeg_rest_fmri.jsonld | 1967 ++++++++ test/test_thorough_bids_example.py | 169 + 3 files changed, 7790 insertions(+) create mode 100644 test/bids_examples_ds005.jsonld create mode 100644 test/bids_examples_eeg_rest_fmri.jsonld create mode 100644 test/test_thorough_bids_example.py diff --git a/test/bids_examples_ds005.jsonld b/test/bids_examples_ds005.jsonld new file mode 100644 index 0000000..a3793d4 --- /dev/null +++ b/test/bids_examples_ds005.jsonld @@ -0,0 +1,5654 @@ +{ + "@context": { + "@vocab": "https://openminds.ebrains.eu/vocab/" + }, + "@graph": [ + { + "@id": "_:000000", + "@type": "https://openminds.ebrains.eu/core/SubjectState", + "age": { + "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "unit": { + "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + }, + "value": 28 + }, + "internalIdentifier": "Studied state sub-01", + "lookupLabel": "Studied state sub-01" + }, + { + "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year", + "@type": "https://openminds.ebrains.eu/controlledTerms/UnitOfMeasurement", + "name": "year" + }, + { + "@id": "_:000002", + "@type": "https://openminds.ebrains.eu/core/Subject", + "biologicalSex": { + "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + }, + "internalIdentifier": "sub-01", + "lookupLabel": "sub-01", + "species": { + "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + }, + "studiedState": [ + { + "@id": "_:000000" + } + ] + }, + { + "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male", + "@type": "https://openminds.ebrains.eu/controlledTerms/BiologicalSex", + "definition": "Biological sex that produces sperm cells (spermatozoa).", + "description": "A male organism typically has the capacity to produce relatively small, usually mobile gametes (reproductive cells), called sperm cells (or spermatozoa). 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], + "fullName": "EEG, fMRI and NODDI at rest'", + "hasVersion": [ + { + "@id": "_:000086" + } + ], + "shortName": "EEG, fMRI and NODDI at rest'" + } + ] +} diff --git a/test/test_thorough_bids_example.py b/test/test_thorough_bids_example.py new file mode 100644 index 0000000..9360221 --- /dev/null +++ b/test/test_thorough_bids_example.py @@ -0,0 +1,169 @@ +import bids2openminds.converter +import os +from openminds import Collection +import pytest +from tempfile import mkdtemp +import pathlib +import shutil +import platform + + +dataset_labels = ["eeg_rest_fmri", "ds005"] + + +@pytest.fixture(scope="session") +def load_collections(): + collections = {} + tempdir = mkdtemp() + for dataset_label in dataset_labels: + test_standard_name = "bids_examples_" + dataset_label + ".jsonld" + test_standard_path = os.path.join("test", test_standard_name) + + test_dataset = os.path.join("bids-examples", dataset_label) + prefix = pathlib.Path(test_dataset).absolute().as_uri()+"/" + + with open(test_standard_path, "r") as file: + template_data = file.read() + actual_data = template_data.replace( + "PREFIX", prefix) + + with open(tempdir+test_standard_name, "w") as file: + file.write(actual_data) + + reference_collection = Collection() + reference_collection.load(tempdir+test_standard_name) + + bids2openminds.converter.convert(test_dataset, save_output=True) + generated_collection = Collection() + generated_collection.load(os.path.join( + test_dataset, "openminds.jsonld")) + + collections[dataset_label] = ( + reference_collection, generated_collection) + + shutil.rmtree(tempdir) + return collections + + +def detect_type(collection, type): + type_IRI = "https://openminds.ebrains.eu/core/" + type + items_list = [] + for item in collection: + if item.type_ == type_IRI: + items_list.append(item) + return items_list if items_list else [] + + +def find_lookup_label(lookup_label, items): + for item in items: + if item.lookup_label == lookup_label: + return item + return None + + +def find_name(name, items): + for item in items: + if item.name == name: + return item + return None + + +def find_person(given_name, family_name, persons): + for person in persons: + if person.given_name == given_name and person.family_name == family_name: + return person + return None + + +@pytest.mark.parametrize("dataset_label", dataset_labels) +def test_subject(load_collections, dataset_label): + reference_collection, generated_collection = load_collections[dataset_label] + generated_subjects = detect_type(generated_collection, "Subject") + reference_subjects = detect_type(reference_collection, "Subject") + + assert len(generated_subjects) == len(reference_subjects) + + for reference_subject in reference_subjects: + generated_subject = find_lookup_label( + reference_subject.lookup_label, generated_subjects) + assert generated_subject is not None + + +@pytest.mark.parametrize("dataset_label", dataset_labels) +def test_subject_state(load_collections, dataset_label): + reference_collection, generated_collection = load_collections[dataset_label] + generated_subjects_states = detect_type( + generated_collection, "SubjectState") + reference_subjects_states = detect_type( + reference_collection, "SubjectState") + + assert len(generated_subjects_states) == len(reference_subjects_states) + + for reference_subject_state in reference_subjects_states: + generated_subject_state = find_lookup_label( + reference_subject_state.lookup_label, generated_subjects_states) + assert generated_subject_state is not None + + +@pytest.mark.parametrize("dataset_label", dataset_labels) +def test_person(load_collections, dataset_label): + reference_collection, generated_collection = load_collections[dataset_label] + generated_persons = detect_type(generated_collection, "Person") + reference_persons = detect_type(reference_collection, "Person") + + assert len(generated_persons) == len(reference_persons) + + for reference_person in reference_persons: + generated_person = find_person( + reference_person.given_name, reference_person.family_name, generated_persons) + assert generated_person is not None + + +@pytest.mark.parametrize("dataset_label", dataset_labels) +def test_dataset_version(load_collections, dataset_label): + reference_collection, generated_collection = load_collections[dataset_label] + generated_dataset_version = detect_type( + generated_collection, "DatasetVersion")[0] + reference_dataset_version = detect_type( + reference_collection, "DatasetVersion")[0] + + assert len(generated_dataset_version.experimental_approaches) == len( + reference_dataset_version.experimental_approaches) + assert generated_dataset_version.short_name == reference_dataset_version.short_name + assert len(generated_dataset_version.techniques or []) == len( + reference_dataset_version.techniques or []) + + +@pytest.mark.parametrize("dataset_label", dataset_labels) +def test_file(load_collections, dataset_label): + reference_collection, generated_collection = load_collections[dataset_label] + generated_files = detect_type(generated_collection, "File") + reference_files = detect_type(reference_collection, "File") + + assert len(generated_files) == len(reference_files) + for refrence_file in reference_files: + generated_file = find_name(refrence_file.name, generated_files) + assert generated_file is not None + assert generated_file.iri.value == refrence_file.iri.value + if generated_file.format is None: + assert refrence_file.format is None + else: + assert generated_file.format.id == refrence_file.format.id + if platform.system() != 'Windows': + assert generated_file.hashes[0].digest == refrence_file.hashes[0].digest + + +@pytest.mark.parametrize("dataset_label", dataset_labels) +def test_file_bundle(load_collections, dataset_label): + reference_collection, generated_collection = load_collections[dataset_label] + generated_file_bundles = detect_type(generated_collection, "FileBundle") + reference_file_bundles = detect_type(reference_collection, "FileBundle") + + assert len(generated_file_bundles) == len(reference_file_bundles) + for refrence_file_bundle in reference_file_bundles: + generated_file_bundle = find_name( + refrence_file_bundle.name, generated_file_bundles) + assert generated_file_bundle is not None + if refrence_file_bundle.is_part_of.type_ == "https://openminds.ebrains.eu/core/FileBundle": + assert generated_file_bundle.is_part_of.type_ == "https://openminds.ebrains.eu/core/FileBundle" + assert refrence_file_bundle.is_part_of.name == generated_file_bundle.is_part_of.name