add unit test for cubids bids-version

Author: tien-tong

cubids/cli.py

@@ -43,7 +43,7 @@ def _parse_validate():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -119,7 +119,7 @@ def _parse_bids_version():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -188,7 +188,7 @@ def _parse_group():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -255,7 +255,7 @@ def _parse_apply():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -351,7 +351,7 @@ def _parse_datalad_save():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -393,7 +393,7 @@ def _parse_undo():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -617,7 +617,7 @@ def _parse_remove_metadata_fields():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -663,7 +663,7 @@ def _parse_print_metadata_fields():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )

cubids/cubids.py

@@ -1346,9 +1346,10 @@ def get_all_metadata_fields(self):
                         metadata = json.loads(content)
                     found_fields.update(metadata.keys())
                 except json.JSONDecodeError as e:
-                    print(f"Error decoding JSON in {json_file}: {e}")
+                    warnings.warn(f"Error decoding JSON in {json_file}: {e}")
                 except Exception as e:
-                    print(f"Unexpected error with file {json_file}: {e}")
+                    warnings.warn(f"Unexpected error with file {json_file}: {e}")
+
         return sorted(found_fields)
 
     def remove_metadata_fields(self, fields_to_remove):

cubids/tests/test_bond.py

@@ -9,6 +9,7 @@
 import numpy as np
 import pandas as pd
 import pytest
+from packaging.version import Version
 
 from cubids.cubids import CuBIDS
 from cubids.metadata_merge import merge_json_into_json, merge_without_overwrite
@@ -22,7 +23,15 @@
     file_hash,
     get_data,
 )
-from cubids.validator import build_validator_call, parse_validator_output, run_validator
+from cubids.validator import (
+    build_validator_call,
+    parse_validator_output,
+    run_validator,
+    get_bids_validator_version,
+    extract_summary_info,
+    update_dataset_description,
+    bids_validator_version,
+)
 
 COMPLETE_KEY_GROUPS = [
     "acquisition-HASC55AP_datatype-dwi_suffix-dwi",
@@ -1028,6 +1037,47 @@ def test_validator(tmp_path):
     assert isinstance(parsed, pd.DataFrame)
 
 
+def bids_validator_version(tmp_path):
+    """Test validator.bids_validator_version."""
+    # Get the BIDS validator version
+    validator_version = get_bids_validator_version()
+    # Extract schemaVersion
+    summary_info = extract_summary_info(decoded)
+
+
+def test_bids_version(tmp_path):
+    """Test workflows.bids_version."""
+    data_root = get_data(tmp_path)
+    bids_dir = Path(data_root) / "complete"
+
+    # Ensure the test directory exists
+    assert bids_dir.exists()
+
+    # test the validator in valid dataset
+    call = build_validator_call(bids_dir)
+    ret = run_validator(call)
+
+    assert ret.returncode == 0
+
+    decoded = ret.stdout.decode("UTF-8")
+
+    # Get the BIDS validator version
+    validator_version = Version(get_bids_validator_version()["ValidatorVersion"])
+    # Extract schemaVersion
+    schema_version = Version(extract_summary_info(decoded)["SchemaVersion"])
+
+    # Set baseline versions to compare against
+    min_validator_version = Version("2.0.0")
+    min_schema_version = Version("0.11.3")
+
+    assert (
+        validator_version >= min_validator_version
+    ), f"Validator version {validator_version} is less than minimum {min_validator_version}"
+    assert (
+        schema_version >= min_schema_version
+    ), f"Schema version {schema_version} is less than minimum {min_schema_version}"
+
+
 def test_docker():
     """Verify that docker is installed and the user has permission to run docker images.
 

cubids/validator.py

@@ -7,6 +7,7 @@
 import pathlib
 import re
 import subprocess
+import warnings
 
 import pandas as pd
 
@@ -249,7 +250,7 @@ def update_dataset_description(path, new_info):
             )
             print("Changes saved with DataLad.")
         except subprocess.CalledProcessError as e:
-            print(f"Error running DataLad save: {e}")
+            warnings.warn(f"Error running DataLad save: {e}")
 
 
 def bids_validator_version(output, path, write=False):

docs/installation.rst

@@ -51,7 +51,7 @@ We can accomplish this using the following command:
 
     $ conda install deno
 
-The new schema ``bids-validator`` doesn't need to be installed 
+The new schema-based ``bids-validator`` doesn't need to be installed 
 and will be implemented automatically when `cubids validate` is called
 
 

pyproject.toml

@@ -86,6 +86,7 @@ cubids-copy-exemplars = "cubids.cli:_enter_copy_exemplars"
 cubids-undo = "cubids.cli:_enter_undo"
 bids-sidecar-merge = "cubids.cli:_enter_bids_sidecar_merge"
 cubids-validate = "cubids.cli:_enter_validate"
+cubids-bids-version = "cubids.cli:_enter_bids_version"
 cubids-datalad-save = "cubids.cli:_enter_datalad_save"
 cubids-print-metadata-fields = "cubids.cli:_enter_print_metadata_fields"
 cubids-remove-metadata-fields = "cubids.cli:_enter_remove_metadata_fields"