From c6500c6285a9344d613e6df2416366fdd124ad98 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 12 Sep 2024 10:52:05 +0200
Subject: [PATCH] use validator

---
 .github/workflows/docker.yml |  4 ++--
 Dockerfile                   |  9 +++++++--
 code/_parsers.py             | 14 ++++++++++----
 code/main.py                 | 11 +++++++++++
 makefile                     |  2 +-
 5 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index bd57d80..2ebe1be 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -34,9 +34,9 @@ jobs:
         -   name: Run simple commands
             run: |
                 docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} --help
-                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . . participant view tfce --verbose 3
+                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant view tfce --verbose 3
                 docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant copy tfce --verbose 3
-                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo segment --help
+                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant segment --help
         -   name: Save docker image
             run: |
                 mkdir -p ${{ env.IMAGE }}
diff --git a/Dockerfile b/Dockerfile
index d8d223c..2101ffb 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -16,9 +16,10 @@ ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/MCR-${MCR_V
     MATLABCMD="/opt/MCR-${MCR_VERSION}/v93/toolbox/matlab" \
     XAPPLRESDIR="/opt//opt/MCR-${MCR_VERSION}/v93/x11/app-defaults" \
     MCRROOT="/opt/MCR-${MCR_VERSION}/v93" \
-    CAT_VERSION=".8.1_r2042_R${MCR_VERSION}"
+    CAT_VERSION=".8.1_r2042_R${MCR_VERSION}" \
+    DENO_INSTALL="/root/.deno"
 ENV SPMROOT="/opt/CAT12${CAT_VERSION}" \
-    PATH="/opt/CAT12${CAT_VERSION}:$PATH" \
+    PATH="$DENO_INSTALL/bin:/opt/CAT12${CAT_VERSION}:$PATH" \
     STANDALONE="/opt/CAT12${CAT_VERSION}/standalone"
 
 RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
@@ -64,6 +65,10 @@ RUN echo "Downloading standalone CAT12 ..." \
     # Test
     && /opt/CAT12${CAT_VERSION}/spm12 function exit
 
+## Install BIDS validator
+RUN curl -fsSL https://deno.land/install.sh | sh && \
+    deno install -Agf -n bids-validator jsr:@bids/validator@1.14.12
+
 # transfer code and set permission
 RUN mkdir -p /code
 COPY ./code/requirements.txt /code
diff --git a/code/_parsers.py b/code/_parsers.py
index 726cbc8..8342c9e 100644
--- a/code/_parsers.py
+++ b/code/_parsers.py
@@ -64,7 +64,7 @@ def _add_common_arguments(parser: ArgumentParser) -> ArgumentParser:
         nargs="+",
         required=False,
     )
-    parser = _add_versbose(parser)
+    parser = _add_verbose(parser)
     parser.add_argument(
         "--bids_filter_file",
         help="""
@@ -73,6 +73,12 @@ def _add_common_arguments(parser: ArgumentParser) -> ArgumentParser:
         """,
         required=False,
     )
+    parser.add_argument(
+        "--skip_validation",
+        help="Do not run the bids validation.",
+        action="store_true",
+        required=False,
+    )
     return parser
 
 
@@ -90,7 +96,7 @@ def _add_target(parser, with_all=False):
     return parser
 
 
-def _add_versbose(parser):
+def _add_verbose(parser):
     parser.add_argument(
         "--verbose",
         help="""
@@ -127,7 +133,7 @@ def common_parser(
         formatter_class=parser.formatter_class,
     )
     view_parser = _add_target(view_parser)
-    view_parser = _add_versbose(view_parser)
+    view_parser = _add_verbose(view_parser)
 
     copy_parser = subparsers.add_parser(
         "copy",
@@ -135,7 +141,7 @@ def common_parser(
         formatter_class=parser.formatter_class,
     )
     copy_parser = _add_target(copy_parser, with_all=True)
-    copy_parser = _add_versbose(copy_parser)
+    copy_parser = _add_verbose(copy_parser)
 
     segment_parser = subparsers.add_parser(
         "segment",
diff --git a/code/main.py b/code/main.py
index 89db21e..df3ad9f 100644
--- a/code/main.py
+++ b/code/main.py
@@ -85,6 +85,9 @@ def main():
         )
         sys.exit(EXIT_CODES["DATAERR"]["Value"])
 
+    if not args.skip_validation:
+        run_validation(bids_dir)
+
     layout_in = get_dataset_layout(bids_dir)
 
     output_dir = output_dir / f"CAT12_{__version__}"
@@ -231,5 +234,13 @@ def copy_files(layout_in, output_dir, subjects):
             progress.update(copy_loop, advance=1)
 
 
+def run_validation(bids_dir):
+    """Run bids validator."""
+    try:
+        subprocess.run(f"bids-validator {bids_dir}", shell=True, check=True)
+    except subprocess.CalledProcessError:
+        sys.exit(EXIT_CODES["DATAERR"]["Value"])
+
+
 if __name__ == "__main__":
     main()
diff --git a/makefile b/makefile
index d955088..5ef4fa9 100644
--- a/makefile
+++ b/makefile
@@ -14,7 +14,7 @@ copy:
 	docker run --rm -it cat12 . /foo participant copy tfce --verbose 3
 
 segment: tests/data/MoAEpilot
-	docker run --rm -it -v $${PWD}/tests/data/MoAEpilot:/data cat12 /data /data/derivatives participant segment --verbose 3 --type segment
+	docker run --rm -it -v $${PWD}/tests/data/MoAEpilot:/data cat12 /data /data/derivatives participant segment --verbose 3 --type default
 
 simple: tests/data/MoAEpilot
 	docker run --rm -it -v $${PWD}/tests/data/MoAEpilot:/data cat12 /data /data/derivatives participant segment --verbose 3 --type simple