📦️ Restore bids-validator installation in containerized C-PAC images (#2170)

Author: shnizzedy

.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile

@@ -29,7 +29,8 @@ FROM neurodebian:jammy-non-free
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 Ubuntu Jammy base image"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
-ARG DEBIAN_FRONTEND=noninteractive
+ARG BIDS_VALIDATOR_VERSION=1.14.6 \
+    DEBIAN_FRONTEND=noninteractive
 ENV TZ=America/New_York \
     PATH=$PATH:/.local/bin \
     PYTHONPATH=$PYTHONPATH:/.local/lib/python3.10/site-packages
@@ -61,7 +62,10 @@ RUN groupadd -r c-pac \
     && echo $TZ > /etc/timezone \
     && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
     && dpkg-reconfigure --frontend=noninteractive locales \
-    && update-locale LANG="en_US.UTF-8"
+    && update-locale LANG="en_US.UTF-8" \
+    # # install bids-validator
+    && curl -fsSL https://raw.githubusercontent.com/tj/n/master/bin/n | bash -s lts \
+    && npm install -g "bids-validator@${BIDS_VALIDATOR_VERSION}"
 
 COPY --from=c-pac_templates /cpac_templates /cpac_templates
 COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global

CHANGELOG.md

@@ -29,6 +29,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Disabled variant image builds.
 - Made orientation configurable (was hard-coded as "RPI").
 
+### Fixed
+
+- Restored `bids-validator` functionality.
+
 ### Removed
 
 - Variant image recipes.

CPAC/utils/tests/test_bids_utils.py

@@ -1,5 +1,7 @@
 """Tests for bids_utils"""
 import os
+from subprocess import run
+
 import pytest
 import yaml
 from CPAC.utils.bids_utils import bids_gen_cpac_sublist, \
@@ -45,7 +47,12 @@ def _prefix_entities(paths, path):
             ])), 'w')
 
 
-@pytest.mark.parametrize('only_one_anat', [True, False])
+def test_bids_validator() -> None:
+    """Test subprocess call to `bids-validator`."""
+    run(["bids-validator", "--version"], check=True)
+
+
+@pytest.mark.parametrize("only_one_anat", [True, False])
 def test_create_cpac_data_config_only_one_anat(tmp_path, only_one_anat):
     """Function to test 'only_one_anat' parameter of
     'create_cpac_data_config' function"""

CPAC/utils/versioning/dependencies.py

@@ -119,9 +119,12 @@ def requirements() -> dict:
 
 
 REPORTED = dict(sorted({
-    **cli_version('ldd --version', formatting=first_line),
-    'Python': sys.version.replace('\n', ' ').replace('  ', ' '),
-    **cli_version('3dECM -help', delimiter='_',
-                  formatting=lambda _: last_line(_).split('{')[-1].rstrip('}'))
+    **cli_version("bids-validator --version", dependency="bids-validator",
+                  in_result=False, formatting=first_line),
+    **cli_version("ldd --version", formatting=first_line),
+    "Python": sys.version.replace("\n", " ").replace("  ", " "),
+    **cli_version("3dECM -help", delimiter="_",
+                  formatting=lambda _: last_line(_).split("{")[-1].rstrip("}"))
 }.items(), key=_version_sort))
+
 REQUIREMENTS = requirements()