Remove --ignore_subject_consistency param.

PennLINC · Jan 17, 2024 · e91b612 · e91b612
1 parent 8e90140
commit e91b612
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Showing 3 changed files with 5 additions and 24 deletions.
diff --git a/cubids/cli.py b/cubids/cli.py
@@ -61,16 +61,6 @@ def _parse_validate():
         help="Disregard NIfTI header content during validation",
         required=False,
     )
-    parser.add_argument(
-        "--ignore_subject_consistency",
-        action="store_true",
-        default=True,
-        help=(
-            "Skip checking that any given file for one "
-            "subject is present for all other subjects"
-        ),
-        required=False,
-    )
     parser.add_argument(
         "--sequential-subjects",
         action="store",

diff --git a/cubids/validator.py b/cubids/validator.py
@@ -11,15 +11,16 @@
 logger = logging.getLogger("cubids-cli")
 
 
-def build_validator_call(path, ignore_headers=False, ignore_subject=True):
+def build_validator_call(path, ignore_headers=False):
     """Build a subprocess command to the bids validator."""
     # build docker call
     command = ["bids-validator", "--verbose", "--json"]
 
     if ignore_headers:
         command.append("--ignoreNiftiHeaders")
-    if ignore_subject:
-        command.append("--ignoreSubjectConsistency")
+
+    # CuBIDS automatically ignores subject consistency.
+    command.append("--ignoreSubjectConsistency")
 
     command.append(path)
 

diff --git a/cubids/workflows.py b/cubids/workflows.py
@@ -37,7 +37,6 @@ def validate(
     sequential,
     sequential_subjects,
     ignore_nifti_headers,
-    ignore_subject_consistency,
 ):
     """Run the bids validator.
 
@@ -49,7 +48,6 @@ def validate(
     sequential
     sequential_subjects
     ignore_nifti_headers
-    ignore_subject_consistency
     """
     # check status of output_prefix, absolute or relative?
     abs_path_output = True
@@ -69,7 +67,6 @@ def validate(
             call = build_validator_call(
                 str(bids_dir),
                 ignore_nifti_headers,
-                ignore_subject_consistency,
             )
             ret = run_validator(call)
 
@@ -148,8 +145,7 @@ def validate(
 
                     # run the validator
                     nifti_head = ignore_nifti_headers
-                    subj_consist = ignore_subject_consistency
-                    call = build_validator_call(tmpdirname, nifti_head, subj_consist)
+                    call = build_validator_call(tmpdirname, nifti_head)
                     ret = run_validator(call)
                     # parse output
                     if ret.returncode != 0:
@@ -228,9 +224,6 @@ def validate(
         if ignore_nifti_headers:
             cmd.append("--ignore_nifti_headers")
 
-        if ignore_subject_consistency:
-            cmd.append("--ignore_subject_consistency")
-
     elif container_type == "singularity":
         cmd = [
             "singularity",
@@ -250,9 +243,6 @@ def validate(
         if ignore_nifti_headers:
             cmd.append("--ignore_nifti_headers")
 
-        if ignore_subject_consistency:
-            cmd.append("--ignore_subject_consistency")
-
         if sequential:
             cmd.append("--sequential")