added validator check

Author: bendhouseart

petdeface/petdeface.py

@@ -31,10 +31,12 @@
     from mideface import ApplyMideface
     from mideface import Mideface
     from pet import WeightedAverage
+    from utils import run_validator
 except ModuleNotFoundError:
     from .mideface import ApplyMideface
     from .mideface import Mideface
     from .pet import WeightedAverage
+    from .utils import run_validator
 
 
 # collect version from pyproject.toml
@@ -207,6 +209,10 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
     else:
         args = args
 
+    # first check to see if the dataset is bids valid
+    if not args.skip_bids_validator:
+        run_validator(args.bids_dir)
+
     if not check_valid_fs_license() and not locate_freesurfer_license().exists():
         raise Exception("You need a valid FreeSurfer license to proceed!")
 

petdeface/utils.py

@@ -0,0 +1,50 @@
+import subprocess
+from pathlib import Path
+import json
+import sys
+
+
+class InvalidBIDSDataset(Exception):
+    def __init__(self, message, errors):
+        super().__init__(message)
+        self.errors = errors
+        print(f"{message}\n{errors}")
+
+
+def deno_validator_installed():
+    get_help = subprocess.run(
+        "bids-validator-deno --help", shell=True, capture_output=True
+    )
+    if get_help.returncode == 0:
+        return True
+    else:
+        return False
+
+
+def run_validator(bids_path):
+    bids_path = Path(bids_path)
+    if bids_path.exists():
+        pass
+    else:
+        raise FileNotFoundError(bids_path)
+    if deno_validator_installed():
+        command = f"bids-validator-deno {bids_path.resolve()} --ignoreWarnings --json --no-color"
+        run_validator = subprocess.run(command, shell=True, capture_output=True)
+        json_output = json.loads(run_validator.stdout.decode("utf-8"))
+        # since we've ignored warnings any issue in issue is an error
+        issues = json_output.get("issues").get("issues")
+        formatted_errors = ""
+        for issue in issues:
+            formatted_errors += "\n" + json.dumps(issue, indent=4)
+        if formatted_errors != "":
+            raise InvalidBIDSDataset(
+                message=f"Dataset at {bids_path} is invalid, see:",
+                errors=formatted_errors,
+            )
+
+    else:
+        raise Exception(
+            f"bids-validator-deno not found"
+            + "\nskip validation with --skip_bids_validator"
+            + "\nor install with pip install bids-validator-deno"
+        )

poetry.lock

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "petdeface"
-version = "0.2.2"
+version = "0.2.3"
 description = "A nipype PET and MR defacing pipeline for BIDS datasets utilizing FreeSurfer's MiDeFace."
 authors = ["Martin Nørgaard <[email protected]>", "Anthony Galassi <[email protected]>", "Murat Bilgel <[email protected]>"]
 license = "MIT"
@@ -20,6 +20,7 @@ setuptools = "^68.1.2"
 petutils = "^0.0.1"
 niworkflows = "^1.11.0"
 niftifixer = {git = "https://github.com/openneuropet/nifti_fixer.git"}
+bids-validator-deno = "^2.0.5"
 
 
 [tool.poetry.group.dev.dependencies]