From 3ed0705fd3861f4f29e05a6329508db6f9af3599 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Tue, 23 Jan 2024 08:40:39 -0500
Subject: [PATCH] Remove `--ignore_subject_consistency` param from `cubids
 validate` (#276)

* Remove `--ignore_subject_consistency` param.

* Simplify command.

* Fix style issues.
---
 cubids/cli.py       | 10 ----------
 cubids/cubids.py    |  2 +-
 cubids/validator.py | 11 +++++------
 cubids/workflows.py | 12 +-----------
 4 files changed, 7 insertions(+), 28 deletions(-)

diff --git a/cubids/cli.py b/cubids/cli.py
index 40c2eca8..a55cecb0 100644
--- 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/cubids.py b/cubids/cubids.py
index 6fdba68b..842215e0 100644
--- a/cubids/cubids.py
+++ b/cubids/cubids.py
@@ -150,7 +150,7 @@ def datalad_undo_last_commit(self):
         Uses git reset --hard to revert to the previous commit.
         """
         if not self.is_datalad_clean():
-            raise Exception("Untracked changes present. " "Run clear_untracked_changes first")
+            raise Exception("Untracked changes present. Run clear_untracked_changes first")
         reset_proc = subprocess.run(["git", "reset", "--hard", "HEAD~1"], cwd=self.path)
         reset_proc.check_returncode()
 
diff --git a/cubids/validator.py b/cubids/validator.py
index 40a130b8..3f670041 100644
--- a/cubids/validator.py
+++ b/cubids/validator.py
@@ -11,15 +11,14 @@
 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"]
+    # CuBIDS automatically ignores subject consistency.
+    command = ["bids-validator", "--verbose", "--json", "--ignoreSubjectConsistency"]
 
     if ignore_headers:
         command.append("--ignoreNiftiHeaders")
-    if ignore_subject:
-        command.append("--ignoreSubjectConsistency")
 
     command.append(path)
 
@@ -39,7 +38,7 @@ def build_subject_paths(bids_dir):
     subjects = glob.glob(bids_dir)
 
     if len(subjects) < 1:
-        raise ValueError("Couldn't find any subjects " "in the specified directory:\n" + bids_dir)
+        raise ValueError("Couldn't find any subjects in the specified directory:\n" + bids_dir)
 
     subjects_dict = {}
 
@@ -94,7 +93,7 @@ def parse_issue(issue_dict):
         return_dict["files"] = [
             get_nested(x, "file", "relativePath") for x in issue_dict.get("files", "")
         ]
-        return_dict["type"] = issue_dict.get("key" "")
+        return_dict["type"] = issue_dict.get("key", "")
         return_dict["severity"] = issue_dict.get("severity", "")
         return_dict["description"] = issue_dict.get("reason", "")
         return_dict["code"] = issue_dict.get("code", "")
diff --git a/cubids/workflows.py b/cubids/workflows.py
index eea9bfa5..37793981 100644
--- 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")