Girder Plugin adding models and resources to handle BIDS format

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = CHANGELOG.md
+ignore-words-list = nin, notIn

.github/workflows/test_and_release.yml

@@ -0,0 +1,92 @@
+name: Test and Release
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      # Install and run pre-commit
+      - run: |
+          pip install pre-commit
+          pre-commit install
+          pre-commit run --all-files
+
+  pytest:
+    name: Pytest ${{ matrix.config.name }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.config.os }}
+
+    services:
+      mongo:
+        image: mongo:7
+        ports:
+          - 27017:27017
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+        config:
+          - { name: "Linux", os: ubuntu-latest }
+
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install system dependencies
+        if: matrix.config.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libsdl2-ttf-2.0-0 \
+            libsdl2-2.0-0
+
+      - name: Install and Run Tests
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[dev]"
+          python -m pytest -s tests
+
+  release:
+    needs: [pre-commit, pytest]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+    environment: release
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+      contents: write # IMPORTANT: mandatory for making GitHub Releases
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Python Semantic Release
+        id: release
+        uses: python-semantic-release/python-semantic-release@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,81 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+exclude: ^.cruft.json|.copier-answers.yml$
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.19.1"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v5.0.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.4.2"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.11.9"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+        args: ["--line-length", "120"]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.23"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
+    rev: v9.20.0
+    hooks:
+      - id: commitlint
+        stages: [commit-msg]
+        additional_dependencies: ["@commitlint/config-conventional"]

.prettierignore

@@ -0,0 +1 @@
+CHANGELOG.md

README.md

@@ -1,23 +1,36 @@
 # GirderBIDS
 
-Girder plugin to import a BIDS database
+A Girder plugin providing support for working with datasets in the Brain Imaging
+Data Structure (BIDS) format. The project includes:
+
+- A Girder plugin for managing and handling BIDS datasets within Girder.
+- A command-line interface (CLI) for validating and importing BIDS datasets into
+  a Girder instance (with or without the plugin).
 
 ## 1. Setup
 
 ### Ubuntu 22.04:
+
 ```bash
-pip install -r requirements.txt
+pip install ".[cli]"
 ```
 
 ### MacOS
+
 ```bash
 curl -fsSL https://deno.land/install.sh | sh
 deno compile -ERWN -o bids-validator jsr:@bids/validator
-pip install girder girder-client fire
+pip install ".[cli]"
 ```
 
 ### Windows
-Not currently supported.
+
+BIDS Validation is not supported but you can still use the plugin and the
+importer (without validation)
+
+```bash
+pip install ".[cli]"
+```
 
 ## 2. Build girder front
 
@@ -28,11 +41,15 @@ girder build
 ```
 
 ### MacOS
-Install npm using Homebrew : 
+
+Install npm using Homebrew :
+
 ```bash
 brew install node
 ```
+
 Add the following environment variable:
+
 ```bash
 export NODE_OPTIONS=--openssl-legacy-provider
 ```
@@ -44,6 +61,7 @@ girder build
 ## 3. Install mongodb
 
 ### Ubuntu 22.04
+
 To set up MongoDB 4.4 on Ubuntu 22.04 execute the following commands :
 
 ```bash
@@ -61,7 +79,9 @@ chown -R mongodb:mongodb /var/lib/mongodb/*
 ```
 
 ### MacOS
+
 Add MongoDB 4.4:
+
 ```bash
 brew tap mongodb/brew
 brew install mongodb-community@4.4
@@ -74,7 +94,8 @@ brew services start mongodb-community@4.4
 girder serve
 ```
 
-You can specify a database other than "girder" by creating a girder.cfg with following content:
+You can specify a database other than "girder" by creating a girder.cfg with
+following content:
 
 ```
 [database]
@@ -88,14 +109,23 @@ GIRDER_CONFIG=./girder.cfg girder serve
 ```
 
 ## 4. Create admin account with "Register" on localhost:8080
+
 ## 5. Login and create API key
+
 ## 6. Create assetstore on localhost:8080
-## 7. Create a Collection and a Folder in the collection, copy the ID of the created Folder
+
+## 7. Create a Collection copy the ID of the created collection
 
 ## 8. Import BIDS database
 
 ```bash
-python tools/bids-importer.py  --bids_dir ... --girder_api_url http://localhost:8080/api/v1  --girder_api_key ... --girder_folder_id ...
+bids-importer --bids_dir ... --api_url http://localhost:8080/api/v1  --api_key ... --location_id ...
 ```
 
-If you want to ignore the validation step, pass `--ignore_validation` on the command-line.
+If you want to ignore the validation step, pass `--ignore_validation` on the
+command-line. If you need to upload the dataset directly under a collection or a
+user, pass `--location_type {collection / user / folder}` (default is `folder`).
+If you want to import the BIDS Dataset using the Girder Plugin, pass
+`--use_plugin` on the command-line. If you want to copy BIDS JSON to Girder
+metadata, pass `--extract_metadata` on the command-line (works only for
+`dataset_description.json` and JSON sidecars).

bids_plugin/__init__.py

@@ -0,0 +1,17 @@
+from typing import Any
+
+from girder import plugin
+from girder.utility.model_importer import ModelImporter
+
+from .api import BIDSDatasetResource, BIDSFolderResource, BIDSItemResource
+from .models import BIDSDatasetModel, BIDSFolderModel, BIDSItemModel
+
+
+class BIDSPlugin(plugin.GirderPlugin):
+    def load(self, info: dict[str, Any]) -> None:
+        ModelImporter.registerModel("bids_dataset", BIDSDatasetModel, plugin="bids_plugin")
+        info["apiRoot"].bids_dataset = BIDSDatasetResource()
+        ModelImporter.registerModel("bids_folder", BIDSFolderModel, plugin="bids_plugin")
+        info["apiRoot"].bids_folder = BIDSFolderResource()
+        ModelImporter.registerModel("bids_item", BIDSItemModel, plugin="bids_plugin")
+        info["apiRoot"].bids_item = BIDSItemResource()

bids_plugin/api/__init__.py

@@ -0,0 +1,5 @@
+from .bids_dataset import BIDSDatasetResource
+from .bids_folder import BIDSFolderResource
+from .bids_item import BIDSItemResource
+
+__all__ = ["BIDSDatasetResource", "BIDSFolderResource", "BIDSItemResource"]