Provide option to run locally installed bids-validator (#380)

* provide option to run local installation of bids validator

* added detail in help section of parsing function of validate command, to --local-validator arg

* added docstrings to edited functions

* fixed linting issue

Author: gabridele

cubids/cli.py

@@ -63,6 +63,13 @@ def _is_file(path, parser):
 
 
 def _parse_validate():
+    """Create the parser for the "cubids validate" command.
+
+    Returns:
+    -------
+    parser : argparse.ArgumentParser
+        The parser object for the "cubids validate" command.
+    """
     parser = argparse.ArgumentParser(
         description="cubids-validate: Wrapper around the official BIDS Validator",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -123,6 +130,13 @@ def _parse_validate():
         nargs="+",
         required=False,
     )
+    parser.add_argument(
+        "--local-validator",
+        action="store_true",
+        default=False,
+        help="Lets user run a locally installed BIDS validator. Default is set to False ",
+        required=False,
+    )
     return parser
 
 

cubids/validator.py

@@ -14,11 +14,27 @@
 logger = logging.getLogger("cubids-cli")
 
 
-def build_validator_call(path, ignore_headers=False):
-    """Build a subprocess command to the bids validator."""
-    # New schema BIDS validator doesn't have option to ignore subject consistency.
-    # Build the deno command to run the BIDS validator.
-    command = ["deno", "run", "-A", "jsr:@bids/validator", path, "--verbose", "--json"]
+def build_validator_call(path, local_validator=False, ignore_headers=False):
+    """Build a subprocess command to the bids validator.
+
+    Parameters
+    ----------
+    path : :obj:`str`
+        Path to the BIDS dataset.
+    local_validator : :obj:`bool`
+        If provided, use the local bids-validator.
+    ignore_headers : :obj:`bool`
+        If provided, ignore NIfTI headers.
+
+    Returns
+    -------
+    command : :obj:`list`
+        List of strings to pass to subprocess.run().
+    """
+    if local_validator:
+        command = ["bids-validator", path, "--verbose", "--json"]
+    else:
+        command = ["deno", "run", "-A", "jsr:@bids/validator", path, "--verbose", "--json"]
 
     if ignore_headers:
         command.append("--ignoreNiftiHeaders")

cubids/workflows.py

@@ -39,6 +39,7 @@ def validate(
     container,
     sequential,
     sequential_subjects,
+    local_validator,
     ignore_nifti_headers,
 ):
     """Run the bids validator.
@@ -55,6 +56,8 @@ def validate(
         Run the validator sequentially.
     sequential_subjects : :obj:`list` of :obj:`str`
         Filter the sequential run to only include the listed subjects.
+    local_validator : :obj:`bool`
+        Use the local bids validator.
     ignore_nifti_headers : :obj:`bool`
         Ignore NIfTI headers when validating.
     """
@@ -75,6 +78,7 @@ def validate(
             # run on full dataset
             call = build_validator_call(
                 str(bids_dir),
+                local_validator,
                 ignore_nifti_headers,
             )
             ret = run_validator(call)
@@ -154,7 +158,7 @@ def validate(
 
                     # run the validator
                     nifti_head = ignore_nifti_headers
-                    call = build_validator_call(tmpdirname, nifti_head)
+                    call = build_validator_call(tmpdirname, local_validator, nifti_head)
                     ret = run_validator(call)
                     # parse output
                     if ret.returncode != 0: