Add integration tests for EEG BIDS import

python/lib/candidate.py

@@ -125,8 +125,8 @@ def create_candidate(self, db, participants_info):
             if 'project' in row and row['project'].lower() not in ("null", ""):
                 # search project id in Project table by its full name
                 project_info = db.pselect(
-                    "SELECT ProjectID FROM Project WHERE Name = %s",
-                    [row['project'], ]
+                    "SELECT ProjectID FROM Project WHERE Name = %s OR Alias = %s",
+                    [row['project'], row['project']]
                 )
                 if len(project_info) > 0:
                     self.project_id = project_info[0]['ProjectID']

python/loris_eeg_chunker/edf_to_chunks.py

@@ -39,8 +39,8 @@ def load_channels(exclude):
             eog=None,
             misc=None,
             exclude=(),
-            preload=False,
-            infer_types=False
+            infer_types=False,
+            file_type=mne_edf.FileType.EDF,
         )
         channel_names = edf_info['ch_names']
 

python/tests/integration/scripts/test_import_bids_dataset.py

@@ -0,0 +1,77 @@
+from lib.db.queries.candidate import try_get_candidate_with_psc_id
+from lib.db.queries.config import set_config_with_setting_name
+from lib.db.queries.session import try_get_session_with_cand_id_visit_label
+from tests.util.database import get_integration_database_session
+from tests.util.file_system import assert_files_exist
+from tests.util.run_integration_script import run_integration_script
+
+
+def test_import_eeg_bids_dataset():
+    db = get_integration_database_session()
+
+    # Enable EEG chunking.
+    set_config_with_setting_name(db, 'useEEGBrowserVisualizationComponents', 'true')
+    db.commit()
+
+    process = run_integration_script([
+        'bids_import.py',
+        '--createcandidate', '--createsession',
+        '--directory', '/data/loris/incoming/Face13',
+    ])
+
+    # Check the return code.
+    assert process.returncode == 0
+
+    # Check that the candidate and sessions are present in the database.
+    candidate = try_get_candidate_with_psc_id(db, 'OTT166')
+    assert candidate is not None
+    session = try_get_session_with_cand_id_visit_label(db, candidate.cand_id, 'V1')
+    assert session is not None
+
+    # TODO: Add EEG-specific database checks once the EEG-specific ORM models have been created.
+
+    # Check that the BIDS files have been copied.
+    assert_files_exist('/data/loris/bids_imports', {
+        'Face13_BIDSVersion_1.1.0': {
+            'dataset_description.json': None,
+            'participants.tsv': None,
+            'README': None,
+            'sub-OTT166': {
+                'ses-V1': {
+                    'eeg': {
+                        'sub-OTT166_ses-V1_task-faceO_channels.tsv': None,
+                        'sub-OTT166_ses-V1_task-faceO_eeg.edf': None,
+                        'sub-OTT166_ses-V1_task-faceO_eeg.json': None,
+                        'sub-OTT166_ses-V1_task-faceO_electrodes.tsv': None,
+                        'sub-OTT166_ses-V1_task-faceO_events.tsv': None,
+                    }
+                }
+            }
+        }
+    })
+
+    # Check that the chunk files have been created.
+    assert_files_exist('/data/loris/bids_imports', {
+        'Face13_BIDSVersion_1.1.0_chunks': {
+            'sub-OTT166_ses-V1_task-faceO_eeg.chunks': {
+                'index.json': None,
+                'raw': {
+                    '0': {
+                        str(i): {
+                            '0': {
+                                '0.buf': None,
+                                '1.buf': None,
+                            }
+                        } for i in range(0, 128)
+                    },
+                    '1': {
+                        str(i): {
+                            '0': {
+                                f'{j}.buf': None for j in range(0, 58)
+                            }
+                        } for i in range(0, 128)
+                    }
+                }
+            }
+        }
+    })

python/tests/integration/scripts/test_run_dicom_archive_loader.py

@@ -2,7 +2,7 @@
 from lib.db.queries.mri_upload import get_mri_upload_with_patient_name
 from lib.exitcode import GETOPT_FAILURE, INVALID_PATH, SELECT_FAILURE, SUCCESS
 from tests.util.database import get_integration_database_session
-from tests.util.file_system import check_file_tree
+from tests.util.file_system import assert_files_exist
 from tests.util.run_integration_script import run_integration_script
 
 
@@ -73,7 +73,7 @@ def test_successful_run_on_valid_tarchive_path():
     assert process.stderr == ""
 
     # Check that the expected files have been created
-    assert check_file_tree('/data/loris/assembly_bids', {
+    assert_files_exist('/data/loris/assembly_bids', {
         'sub-300001': {
             'ses-V2': {
                 'anat': {

python/tests/integration/scripts/test_run_nifti_insertion.py

@@ -18,7 +18,7 @@
     UNKNOWN_PROTOCOL,
 )
 from tests.util.database import get_integration_database_session
-from tests.util.file_system import check_file_tree
+from tests.util.file_system import assert_files_exist
 from tests.util.run_integration_script import run_integration_script
 
 
@@ -388,7 +388,7 @@ def test_nifti_mri_protocol_violated_scans_features():
     assert file_json_data is not None and file_json_data.value == f'{file_base_rel_path}.json'
     assert file_pic_data is None
 
-    assert check_file_tree('/data/loris/', {
+    assert_files_exist('/data/loris', {
         'assembly_bids': {
             'sub-400184': {
                 'ses-V3': {
@@ -549,7 +549,7 @@ def test_nifti_mri_violations_log_exclude_features():
     assert file_bvec_data is not None and file_bvec_data.value == f'{file_base_rel_path}.bvec'
     assert file_pic_data is None
 
-    assert check_file_tree('/data/loris/', {
+    assert_files_exist('/data/loris', {
         'assembly_bids': {
             'sub-400184': {
                 'ses-V3': {
@@ -634,7 +634,7 @@ def test_dwi_insertion_with_mri_violations_log_warning():
     assert file_bvec_data is not None and file_bvec_data.value == f'{file_base_rel_path}.bvec'
     assert file_pic_data is not None
 
-    assert check_file_tree('/data/loris/', {
+    assert_files_exist('/data/loris', {
         'assembly_bids': {
             'sub-400184': {
                 'ses-V3': {

python/tests/util/file_system.py

@@ -9,20 +9,17 @@
 """
 
 
-def check_file_tree(path: str, file_tree: FileTree):
+def assert_files_exist(path: str, file_tree: FileTree):
     """
-    Check that a path has at least all the directories and files of a file tree.
+    Assert that all the directories and files specified in a path exist.
     """
 
     if file_tree is None:
-        return os.path.isfile(path)
+        assert os.path.isfile(path)
+        return
 
-    if not os.path.isdir(path):
-        return False
+    assert os.path.isdir(path)
 
     for sub_dir_name, sub_file_tree in file_tree.items():
         sub_dir_path = os.path.join(path, sub_dir_name)
-        if not check_file_tree(sub_dir_path, sub_file_tree):
-            return False
-
-    return True
+        assert_files_exist(sub_dir_path, sub_file_tree)