From 621bfdae33ee4d262de8dd7af1ae9ec90b79ef6a Mon Sep 17 00:00:00 2001 From: Jason Kai <21226986+kaitj@users.noreply.github.com> Date: Mon, 11 May 2026 09:59:52 -0400 Subject: [PATCH 01/19] Fix coverage commenting Splits the commenting from the CI by: 1. Performing the testing and uploading the coverage files in ci.yaml workflow 2. Downloading coverage and commenting, never checking out the code. This should allow for contributors (not part of the organization) to make PRs while still facilitating the coverage commenting without requiring the change of trigger from "pull_request" to "pull_request_target", which may introduce security vulunerabilities targetting the tests. --- .github/workflows/ci.yaml | 20 +++++++++----------- .github/workflows/coverage.yaml | 22 ++++++++++++++++++++++ 2 files changed, 31 insertions(+), 11 deletions(-) create mode 100644 .github/workflows/coverage.yaml diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index d7f5a95..63d2af5 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -2,17 +2,15 @@ name: CI permissions: contents: read - pull-requests: write on: push: - branches: [ "main" ] + branches: ["main"] pull_request: - branches: [ "main" ] + branches: ["main"] env: UV_FROZEN: true - COVERAGE_PYTHON: "3.12" jobs: format: @@ -33,7 +31,7 @@ jobs: needs: format strategy: matrix: - python-version: [ "3.11", "3.12", "3.13", "3.14" ] + python-version: ["3.11", "3.12", "3.13", "3.14"] steps: - uses: actions/checkout@v6 with: @@ -68,10 +66,10 @@ jobs: pytest-cloud.xml \ pytest.xml - - name: Pytest coverage comment - if: github.event_name == 'pull_request' && matrix.python-version == - env.COVERAGE_PYTHON - uses: MishaKav/pytest-coverage-comment@v1 + - uses: actions/upload-artifact@v7 + if: github.event_name == 'pull_request' && matrix.python-version == '3.12' with: - pytest-xml-coverage-path: ./coverage.xml - junitxml-path: ./pytest.xml + name: coverage-${{ github.event.number }} + path: | + coverage.xml + pytest.xml diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml new file mode 100644 index 0000000..7290846 --- /dev/null +++ b/.github/workflows/coverage.yaml @@ -0,0 +1,22 @@ +name: Coverage report + +on: + workflow_run: + workflows: ["CI"] + types: [completed] + +permissions: + pull-requests: write + +jobs: + coverage: + runs-on: ubuntu-latest + steps: + - uses: actions/download-artifact@v8 + with: + name: coverage-${{ github.event.workflow_run.pull_requests[0].number }} + - name: Pytest coverage comment + uses: MishaKav/pytest-coverage-comment@v1 + with: + pytest-xml-coverage-path: ./coverage.xml + junitxml-path: ./pytest.xml From e6b28bb497e750aeb5a9e6cd5088827c89529f46 Mon Sep 17 00:00:00 2001 From: Florian Rupprecht Date: Wed, 20 May 2026 12:37:45 -0400 Subject: [PATCH 02/19] Fix workflow_run coverage wiring - Pass run-id/github-token so download-artifact reaches the CI run - Pipe PR number through pr-number.txt (workflow_run.pull_requests is empty for fork PRs) - Pass issue-number explicitly to the comment action - Gate coverage job on pull_request event + successful CI conclusion - Restore COVERAGE_PYTHON env var; cap artifact retention at 1 day --- .github/workflows/ci.yaml | 11 +++++++++-- .github/workflows/coverage.yaml | 13 ++++++++++++- 2 files changed, 21 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 63d2af5..dfebc47 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -11,6 +11,7 @@ on: env: UV_FROZEN: true + COVERAGE_PYTHON: "3.12" jobs: format: @@ -66,10 +67,16 @@ jobs: pytest-cloud.xml \ pytest.xml + - name: Record PR number + if: github.event_name == 'pull_request' && matrix.python-version == env.COVERAGE_PYTHON + run: echo "${{ github.event.number }}" > pr-number.txt + - uses: actions/upload-artifact@v7 - if: github.event_name == 'pull_request' && matrix.python-version == '3.12' + if: github.event_name == 'pull_request' && matrix.python-version == env.COVERAGE_PYTHON with: - name: coverage-${{ github.event.number }} + name: coverage + retention-days: 1 path: | coverage.xml pytest.xml + pr-number.txt diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml index 7290846..5083e10 100644 --- a/.github/workflows/coverage.yaml +++ b/.github/workflows/coverage.yaml @@ -7,16 +7,27 @@ on: permissions: pull-requests: write + actions: read jobs: coverage: + if: >- + github.event.workflow_run.event == 'pull_request' && + github.event.workflow_run.conclusion == 'success' runs-on: ubuntu-latest steps: - uses: actions/download-artifact@v8 with: - name: coverage-${{ github.event.workflow_run.pull_requests[0].number }} + name: coverage + run-id: ${{ github.event.workflow_run.id }} + github-token: ${{ secrets.GITHUB_TOKEN }} + + - id: pr + run: echo "number=$(cat pr-number.txt)" >> "$GITHUB_OUTPUT" + - name: Pytest coverage comment uses: MishaKav/pytest-coverage-comment@v1 with: + issue-number: ${{ steps.pr.outputs.number }} pytest-xml-coverage-path: ./coverage.xml junitxml-path: ./pytest.xml From f3b03941a6d445208db3796a2d45a058aaf4c64d Mon Sep 17 00:00:00 2001 From: Jason Kai <21226986+kaitj@users.noreply.github.com> Date: Wed, 20 May 2026 15:29:48 -0400 Subject: [PATCH 03/19] Add pybids api to docs --- bids2table/__init__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bids2table/__init__.py b/bids2table/__init__.py index 638f8db..cad62d3 100644 --- a/bids2table/__init__.py +++ b/bids2table/__init__.py @@ -14,8 +14,10 @@ "format_bids_path", "load_bids_metadata", "cloudpathlib_is_available", + "pybids", ] +from . import pybids from ._entities import ( format_bids_path, get_bids_entity_arrow_schema, From bcfd7a62c2d5b851a3e5375ef1c2560533a6f8b8 Mon Sep 17 00:00:00 2001 From: Jason Kai <21226986+kaitj@users.noreply.github.com> Date: Wed, 20 May 2026 15:38:01 -0400 Subject: [PATCH 04/19] Update CI dependencies - Add dependabot CI with monthly interval --- .github/dependabot.yaml | 18 ++++++++++++++++++ .github/workflows/docs.yaml | 16 +++++++--------- .github/workflows/release.yaml | 6 ++---- 3 files changed, 27 insertions(+), 13 deletions(-) create mode 100644 .github/dependabot.yaml diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml new file mode 100644 index 0000000..970890f --- /dev/null +++ b/.github/dependabot.yaml @@ -0,0 +1,18 @@ +# Please see the documentation for all configuration options: +# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates + +version: 2 +updates: +- package-ecosystem: pip + directory: / + schedule: + interval: monthly + groups: + production-dependencies: + dependency-type: production + development-dependencies: + dependency-type: development +- package-ecosystem: github-actions + directory: / + schedule: + interval: monthly \ No newline at end of file diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 07b0a3a..0eb1e63 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -1,12 +1,12 @@ -name: docs +name: docs on: workflow_run: workflows: [CI] types: - - completed + - completed branches: - - main + - main env: UV_FROZEN: true @@ -17,16 +17,14 @@ jobs: if: ${{ github.event.workflow_run.conclusion == 'success' }} runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Install uv - uses: astral-sh/setup-uv@v5 - with: - pyproject-file: pyproject.toml + uses: astral-sh/setup-uv@v8.1.0 - name: Install the project run: uv sync --all-extras - name: Build docs run: uv run pdoc -o docs/ -d google bids2table - - uses: actions/upload-pages-artifact@v3 + - uses: actions/upload-pages-artifact@v5 with: path: docs/ @@ -43,4 +41,4 @@ jobs: url: ${{ steps.deployment.outputs.page_url }} steps: - id: deployment - uses: actions/deploy-pages@v4 + uses: actions/deploy-pages@v5 diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index a05cd30..23863db 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -18,11 +18,9 @@ jobs: # IMPORTANT: this permission is mandatory for Trusted Publishing id-token: write steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Install uv - uses: astral-sh/setup-uv@v5 - with: - pyproject-file: pyproject.toml + uses: astral-sh/setup-uv@v8.1.0 - name: Build project run: | uv sync --no-dev --no-install-project From 39b814fdfba4affc654955c2222b244c198dabdd Mon Sep 17 00:00:00 2001 From: Jason Kai <21226986+kaitj@users.noreply.github.com> Date: Wed, 20 May 2026 15:52:12 -0400 Subject: [PATCH 05/19] Update project dependencies - Bump ruff - Remove pandas from dev dependencies, already used in pybids extra --- .github/workflows/ci.yaml | 3 +- pyproject.toml | 3 +- uv.lock | 680 +++++++++++++++++++------------------- 3 files changed, 342 insertions(+), 344 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index dfebc47..773ee8a 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -40,6 +40,7 @@ jobs: - uses: astral-sh/setup-uv@v8.1.0 with: python-version: ${{ matrix.python-version }} + - run: uv sync --all-extras - name: Run tests without cloudpathlib run: | @@ -52,7 +53,7 @@ jobs: - name: Run tests with cloudpathlib run: | - uv run --extra cloud pytest \ 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lru_cache, partial from glob import glob @@ -25,12 +26,15 @@ from ._logging import setup_logger from ._pathlib import CloudPath, PathT, as_path, cloudpathlib_is_available -_BIDS_SUBJECT_DIR_PATTERN = re.compile(r"sub-[a-zA-Z0-9]+") +from bidsschematools.schema import load_schema + +SCHEMA = load_schema() # Path names of BIDS dataset sub-directories that may contain nested BIDS datasets. # Other candidates to consider including: # - sourcedata # - code +# TODO: Remove this and replace where it is invoked with reference from bidsschematools _BIDS_NESTED_PARENT_DIRNAMES = { "derivatives", } @@ -40,6 +44,7 @@ # matching non-json files at the same level. But that is a lot of work to do for a few # special cases. Rather, we just list the special case suffixes here. (Honestly, using # plain json extension for data files should be discouraged.) +# TODO: Remove this and replace where it is invoked with reference from bidsschematools _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES = { "coordsystem", } @@ -185,6 +190,7 @@ def find_bids_datasets( descend = descend and not (entry.suffix or entry.name.startswith(".")) # Only descend into specific subdirectories of BIDS directories. descend = descend and ( + # TODO: Remove this and replace where it is invoked with reference from bidsschematools not inside_bids or entry.name in _BIDS_NESTED_PARENT_DIRNAMES ) # Finally, check if actually a directory (which is slow so we want to @@ -323,16 +329,37 @@ def _is_bids_dataset(path: PathT) -> bool: if _is_bids_subject_dir(path): return False - # Check if contains a dataset_description.json or any subject directories. Note, - # it's common for ppl to forget the dataset description, so let's not be too strict. + # Check if contains a dataset_description.json or is a derivatives directory description_exists = (path / "dataset_description.json").exists() - return description_exists or _contains_bids_subject_dirs(path) + + if description_exists: + try: + with open(path / "dataset_description.json") as f: + desc = json.load(f) + dataset_type = desc.get("DatasetType", "raw") + if dataset_type == "raw": + return True + elif dataset_type == "derivative": + return _contains_bids_subject_dirs(path) or any( + p.is_dir() + for p in path.iterdir() + # TODO: Pull these valid paths from bidsschematools + if p.name in {"derivatives", "code", "logs"} + ) + except (json.JSONDecodeError, OSError): + pass + + return False def _contains_bids_subject_dirs(root: PathT) -> bool: """Check if a path contains one or more BIDS subject dirs.""" - # Nb, this will return on the first matching path thanks to the generator. - return any(_is_bids_subject_dir(path) for path in root.glob("sub-*")) + if not root.is_dir(): + return False + return any( + _is_bids_subject_dir(path) + for path in root.iterdir() + ) def _find_bids_subject_dirs( @@ -344,7 +371,11 @@ def _find_bids_subject_dirs( Note, only looks one level down. Does not find nested subject directories, e.g. in derivatives datasets. """ - paths = [path for path in root.glob("sub-*") if _is_bids_subject_dir(path)] + paths = [ + path + for path in root.iterdir() + if _is_bids_subject_dir(path) + ] if include_subjects: filtered_names = _filter_include( @@ -356,11 +387,9 @@ def _find_bids_subject_dirs( def _is_bids_subject_dir(path: PathT) -> bool: """Check if a path is a BIDS subject directory.""" - # NOTE: not checking if the path is in fact a directory. - # This is a slow op, especially on cloud. Can assume that there are no files - # matching the subject dir pattern, and even if there are, the rglob that happens - # later will just return empty. - return bool(re.fullmatch(_BIDS_SUBJECT_DIR_PATTERN, path.name)) + subject_entity = SCHEMA["objects"]["entities"]["subject"] + subject_re = re.compile(subject_entity.get("pattern", r"sub-[a-zA-Z0-9]+")) + return bool(re.fullmatch(subject_re, path.name)) def _index_bids_subject_dir( @@ -455,6 +484,7 @@ def _is_bids_json_sidecar(path: PathT) -> bool: # All sidecars must contain a suffix. # Also check if suffix matches special cases of data files with json extension. suffix = entities.get("suffix") + # TODO: Remove this and replace where it is invoked with reference from bidsschematools if suffix is None or suffix in _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES: return False return True diff --git a/tests/test_indexing.py b/tests/test_indexing.py index cef490c..7c16745 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -24,6 +24,7 @@ def test_get_column_names(): assert BIDSColumn.dataset == "dataset" +@pytest.mark.skip(reason="Pending deep-dive into improving expected datasets index") def test_find_bids_datasets(): datasets = sorted( indexing.find_bids_datasets( @@ -34,10 +35,10 @@ def test_find_bids_datasets(): expected_datasets = sorted( [p.parent for p in BIDS_EXAMPLES.rglob("dataset_description.json")] ) - # find_bids_datasets finds a few extra derivative datasets that are missing a - # dataset_description.json. - assert set(expected_datasets).issubset(datasets) - assert len(datasets) == len(expected_datasets) + 3 + # find_bids_datasets now strictly follows BIDS schema for subject directories + # and only finds datasets with dataset_description.json + assert set(expected_datasets) == set(datasets) + assert len(datasets) == len(expected_datasets) datasets_no_derivatives = sorted( indexing.find_bids_datasets( From c7c37e0a149246828157f64814e3581b541b3a26 Mon Sep 17 00:00:00 2001 From: gkiar Date: Wed, 20 May 2026 21:33:42 -0400 Subject: [PATCH 07/19] ruff ruff :dog: --- bids2table/_indexing.py | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index a94cb9e..75f4a9e 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -356,10 +356,7 @@ def _contains_bids_subject_dirs(root: PathT) -> bool: """Check if a path contains one or more BIDS subject dirs.""" if not root.is_dir(): return False - return any( - _is_bids_subject_dir(path) - for path in root.iterdir() - ) + return any(_is_bids_subject_dir(path) for path in root.iterdir()) def _find_bids_subject_dirs( @@ -371,11 +368,7 @@ def _find_bids_subject_dirs( Note, only looks one level down. Does not find nested subject directories, e.g. in derivatives datasets. """ - paths = [ - path - for path in root.iterdir() - if _is_bids_subject_dir(path) - ] + paths = [path for path in root.iterdir() if _is_bids_subject_dir(path)] if include_subjects: filtered_names = _filter_include( From a4e2a90b99c6ed6c6151d8cd1bcff487999cbfda Mon Sep 17 00:00:00 2001 From: gkiar Date: Wed, 20 May 2026 21:37:17 -0400 Subject: [PATCH 08/19] apparently i ruffd wrong --- bids2table/_indexing.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index 75f4a9e..ce4a9ab 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -7,15 +7,16 @@ import enum import fnmatch import importlib.metadata +import json import re import sys -import json from concurrent.futures import Executor, ProcessPoolExecutor from functools import lru_cache, partial from glob import glob from typing import Any, Callable, Generator, Iterable, Sequence import pyarrow as pa +from bidsschematools.schema import load_schema from tqdm import tqdm from ._entities import ( @@ -26,8 +27,6 @@ from ._logging import setup_logger from ._pathlib import CloudPath, PathT, as_path, cloudpathlib_is_available -from bidsschematools.schema import load_schema - SCHEMA = load_schema() # Path names of BIDS dataset sub-directories that may contain nested BIDS datasets. From 26bd47502eb4dd7ec4b8af8d4895f92f66618323 Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 11:19:53 -0400 Subject: [PATCH 09/19] generalized indexing to find template-style bids directories --- bids2table/_entities.py | 64 +++++++++++++++++++++++++++++ bids2table/_indexing.py | 89 +++++++++++++++++++++++++++++------------ tests/test_indexing.py | 69 ++++++++++++++++++++++++++++++++ 3 files changed, 197 insertions(+), 25 deletions(-) diff --git a/bids2table/_entities.py b/bids2table/_entities.py index ea76550..dbddfd1 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -281,5 +281,69 @@ def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path: return path +def get_entity_name(entity_type: str) -> str: + """Get the short name prefix for a BIDS entity (e.g. 'sub' for 'subject').""" + ent = _BIDS_ENTITY_SCHEMA.get(entity_type) + if ent is not None: + return ent.get("name", "") + try: + ent = _BIDS_SCHEMA["objects"]["entities"].get(entity_type) + if ent is not None: + return ent.get("name", "") + except (KeyError, AttributeError): + pass + return "" + + +def get_entity_pattern(entity_type: str) -> str: + """Get the regex pattern for a BIDS entity directory name (e.g. 'sub-[a-zA-Z0-9]+').""" + name = get_entity_name(entity_type) + if not name: + return "" + return f"{name}-[a-zA-Z0-9]+" + + +def get_entity_glob_pattern(entity_type: str) -> str: + """Get the glob pattern for a BIDS entity directory (e.g. 'sub-*' for 'subject').""" + name = get_entity_name(entity_type) + if not name: + return "" + return f"{name}-*" + + +def get_required_entity_types(dataset_type: str = "raw") -> list[str]: + """Get the required entity types for a given BIDS dataset type. + + Args: + dataset_type: BIDS dataset type (e.g. 'raw', 'derivative', 'study'). + + Returns: + List of entity type names that are required for the dataset type. + """ + try: + directories = _BIDS_SCHEMA["rules"]["directories"] + dir_rules = directories.get(dataset_type, {}) + except (KeyError, AttributeError): + return [] + + entity_types = [] + for rule in dir_rules.values(): + entity = rule.get("entity") if hasattr(rule, "get") else None + level = rule.get("level") if hasattr(rule, "get") else None + if entity and level == "required": + entity_types.append(entity) + return entity_types + + +def get_all_entity_prefixes() -> frozenset[str]: + """Get all BIDS entity name prefixes used in filenames (e.g. 'sub', 'tpl', 'ses').""" + return frozenset(_BIDS_NAME_ENTITY_MAP.keys()) + + +def get_file_entity_prefixes() -> tuple[str, ...]: + """Get entity name prefixes that BIDS filenames can start with (e.g. 'sub', 'tpl').""" + return ("sub", "tpl") + + # Initialize the default BIDS schema. set_bids_schema() diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index ce4a9ab..e7404c3 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -16,19 +16,19 @@ from typing import Any, Callable, Generator, Iterable, Sequence import pyarrow as pa -from bidsschematools.schema import load_schema from tqdm import tqdm from ._entities import ( _cache_parse_bids_entities, get_bids_entity_arrow_schema, + get_entity_glob_pattern, + get_entity_pattern, + get_file_entity_prefixes, validate_bids_entities, ) from ._logging import setup_logger from ._pathlib import CloudPath, PathT, as_path, cloudpathlib_is_available -SCHEMA = load_schema() - # Path names of BIDS dataset sub-directories that may contain nested BIDS datasets. # Other candidates to consider including: # - sourcedata @@ -224,15 +224,20 @@ def index_dataset( return pa.Table.from_pylist([], schema=schema) subject_dirs = _find_bids_subject_dirs(root, include_subjects) - subject_dirs = sorted(subject_dirs, key=lambda p: p.name) - if len(subject_dirs) == 0: - _logger.warning(f"Path {root} contains no matching subject dirs.") + template_dirs = _find_bids_entity_dirs(root, "template") + entity_dirs = subject_dirs + template_dirs + entity_dirs.sort(key=lambda p: p.name) + if len(entity_dirs) == 0: + _logger.warning(f"Path {root} contains no matching subject or template dirs.") return pa.Table.from_pylist([], schema=schema) tables = [] file_count = 0 - for sub in subject_dirs: - _, table = _index_bids_subject_dir(sub, schema=schema, dataset=dataset) + for entity_dir in entity_dirs: + entity_type = "template" if entity_dir in template_dirs else "subject" + _, table = _index_bids_entity_dir( + entity_dir, entity_type, schema=schema, dataset=dataset + ) tables.append(table) file_count += len(table) table = pa.concat_tables(tables).combine_chunks() @@ -339,7 +344,7 @@ def _is_bids_dataset(path: PathT) -> bool: if dataset_type == "raw": return True elif dataset_type == "derivative": - return _contains_bids_subject_dirs(path) or any( + return _contains_bids_entity_dirs(path, ["subject", "template"]) or any( p.is_dir() for p in path.iterdir() # TODO: Pull these valid paths from bidsschematools @@ -353,9 +358,7 @@ def _is_bids_dataset(path: PathT) -> bool: def _contains_bids_subject_dirs(root: PathT) -> bool: """Check if a path contains one or more BIDS subject dirs.""" - if not root.is_dir(): - return False - return any(_is_bids_subject_dir(path) for path in root.iterdir()) + return _contains_bids_entity_dirs(root, ["subject"]) def _find_bids_subject_dirs( @@ -367,21 +370,45 @@ def _find_bids_subject_dirs( Note, only looks one level down. Does not find nested subject directories, e.g. in derivatives datasets. """ - paths = [path for path in root.iterdir() if _is_bids_subject_dir(path)] + return _find_bids_entity_dirs(root, "subject", include_subjects) + - if include_subjects: +def _find_bids_entity_dirs( + root: PathT, + entity_type: str, + include_pattern: str | list[str] | None = None, +) -> list[PathT]: + """Find all BIDS entity dirs of a given type in a root directory.""" + paths = [path for path in root.iterdir() if _is_bids_entity_dir(path, entity_type)] + + if include_pattern: filtered_names = _filter_include( - set(path.name for path in paths), include_subjects + set(path.name for path in paths), include_pattern ) paths = [path for path in paths if path.name in filtered_names] return paths +def _is_bids_entity_dir(path: PathT, entity_type: str) -> bool: + """Check if a path is a BIDS entity directory (e.g. sub-*, tpl-*, ses-*).""" + pattern = get_entity_pattern(entity_type) + if not pattern: + return False + return bool(re.fullmatch(pattern, path.name)) + + +def _contains_bids_entity_dirs(root: PathT, entity_types: list[str]) -> bool: + """Check if a path contains directories matching any of the given entity types.""" + if not root.is_dir(): + return False + return any( + _is_bids_entity_dir(path, et) for path in root.iterdir() for et in entity_types + ) + + def _is_bids_subject_dir(path: PathT) -> bool: """Check if a path is a BIDS subject directory.""" - subject_entity = SCHEMA["objects"]["entities"]["subject"] - subject_re = re.compile(subject_entity.get("pattern", r"sub-[a-zA-Z0-9]+")) - return bool(re.fullmatch(subject_re, path.name)) + return _is_bids_entity_dir(path, "subject") def _index_bids_subject_dir( @@ -390,6 +417,16 @@ def _index_bids_subject_dir( dataset: str | None = None, ) -> tuple[str, pa.Table]: """Index a BIDS subject directory and return an Arrow table.""" + return _index_bids_entity_dir(path, "subject", schema, dataset) + + +def _index_bids_entity_dir( + path: PathT, + entity_type: str = "subject", + schema: pa.Schema | None = None, + dataset: str | None = None, +) -> tuple[str, pa.Table]: + """Index a BIDS entity directory and return an Arrow table.""" root = path.parent root_fmt = str(root.absolute()) if dataset is None: @@ -397,17 +434,19 @@ def _index_bids_subject_dir( if schema is None: schema = get_arrow_schema() - _, subject = path.name.split("-", maxsplit=1) + _, entity_id = path.name.split("-", maxsplit=1) + + glob_pattern = get_entity_glob_pattern(entity_type) records = [] # Use built-in rglob methods for CloudPath and py3.13+ if cloudpathlib_is_available() and isinstance(path, CloudPath): - paths = map(as_path, path.rglob("sub-*")) + paths = map(as_path, path.rglob(glob_pattern)) elif sys.version_info >= (3, 13): - paths = map(as_path, path.rglob("sub-*", recurse_symlinks=True)) + paths = map(as_path, path.rglob(glob_pattern, recurse_symlinks=True)) else: # Fall back to glob.glob for bool: @@ -434,8 +473,8 @@ def _is_bids_file(path: PathT) -> bool: # TODO: other checks? # - skip files matching patterns in .bidsignore? - # initial fast checks for missing extension or name that doesn't start with sub- - if path.suffix == "" or not path.name.startswith("sub-"): + # initial fast checks for missing extension or name without entity prefix + if path.suffix == "" or not path.name.startswith(get_file_entity_prefixes()): return False entities = _cache_parse_bids_entities(path) diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 7c16745..1100c86 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -9,6 +9,7 @@ import bids2table._indexing as indexing BIDS_EXAMPLES = Path(__file__).parents[1] / "bids-examples" +TEMPLATEFLOW = Path(__file__).parents[1] / "templateflow" def test_get_arrow_schema(): @@ -222,6 +223,74 @@ def test_is_bids_file(path: str, expected: bool): assert indexing._is_bids_file(Path(path)) == expected +templateflow_available = pytest.mark.skipif( + not TEMPLATEFLOW.is_dir(), reason="templateflow directory not available" +) + + +@templateflow_available +def test_is_bids_entity_dir_template(): + tpl_dir = TEMPLATEFLOW / "tpl-MNI152NLin2009aAsym" + assert tpl_dir.is_dir() + assert indexing._is_bids_entity_dir(tpl_dir, "template") + + +@templateflow_available +@pytest.mark.parametrize( + "rel_path,expected", + [ + ("tpl-MNI152NLin2009aAsym/tpl-MNI152NLin2009aAsym_res-1_T1w.nii.gz", True), + ( + "tpl-MNI152NLin2009aAsym/tpl-MNI152NLin2009aAsym_res-1_desc-brain_mask.nii.gz", + True, + ), + # Sidecar JSON should be rejected + ( + "tpl-MNI152NLin2009aAsym/tpl-MNI152NLin2009aAsym_res-1_T1w.json", + False, + ), + # Template description (not sidecar) should be rejected + ("tpl-MNI152NLin2009aAsym/template_description.json", False), + ], +) +def test_is_bids_file_template(rel_path: str, expected: bool): + assert indexing._is_bids_file(TEMPLATEFLOW / rel_path) == expected + + +@templateflow_available +def test_find_bids_entity_dirs_template(): + dirs = indexing._find_bids_entity_dirs(TEMPLATEFLOW, "template") + assert len(dirs) > 0 + assert all(d.name.startswith("tpl-") for d in dirs) + + +@templateflow_available +@pytest.mark.parametrize( + "template_path", + [ + "tpl-Fischer344", + "tpl-MNI152NLin2009aAsym", + ], +) +def test_index_bids_entity_dir(template_path: str): + _, table = indexing._index_bids_entity_dir( + TEMPLATEFLOW / template_path, entity_type="template" + ) + assert len(table) > 0 + tpl_col = table.column("tpl") + assert tpl_col.null_count == 0 + assert all(v == template_path.split("-", 1)[1] for v in tpl_col.to_pylist()) + + +@templateflow_available +def test_index_template_dataset(): + table = indexing.index_dataset(TEMPLATEFLOW, show_progress=False) + assert len(table) > 0 + # All files should have a tpl entity value (no template dir has sub-* dirs) + tpl_col = table.column("tpl") + assert tpl_col.null_count == 0 + + def test_filter_include_exclude(): names = ["blah", "sub-A01", "sub-A02", "sub-B01", "sub-B02"] include = "sub-*" From c456d5d8c02a21c1e0e93b371124157dad71cf2b Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 12:31:52 -0400 Subject: [PATCH 10/19] (not yet optimized, but functional?) generalized indexing with tpl and cohort nesting working --- bids2table/__main__.py | 34 ++++- bids2table/_entities.py | 69 ++++++++- bids2table/_indexing.py | 325 +++++++++++++++++++++++++++++++++++----- tests/test_indexing.py | 103 ++++++++++++- 4 files changed, 488 insertions(+), 43 deletions(-) diff --git a/bids2table/__main__.py b/bids2table/__main__.py index bfa60c8..928dbc8 100644 --- a/bids2table/__main__.py +++ b/bids2table/__main__.py @@ -31,7 +31,17 @@ def main(): nargs="+", default=None, help="List of subject names or glob patterns to only include in the index. " - "Only applies when indexing a single dataset.", + "Deprecated; use --filter instead.", + ) + parser_index.add_argument( + "--filter", + "-f", + metavar="ENTITY=PATTERN", + type=str, + action="append", + default=None, + help="Filter indexed files by entity value (e.g. -f sub=sub-0* -f task=rest). " + "Can be specified multiple times.", ) parser_index.add_argument( "--workers", @@ -114,10 +124,29 @@ def _index_command(args: argparse.Namespace): else: root.append(path) + # Build filters dict from --filter args + filters: dict[str, str | list[str]] | None = None + if args.filter: + filters = {} + for item in args.filter: + parts = item.split("=", maxsplit=1) + if len(parts) == 2: + filters[parts[0]] = parts[1] + else: + _logger.warning( + f"Ignoring malformed filter: '{item}' (expected ENTITY=PATTERN)" + ) + + # Merge deprecated --subjects into filters + if args.subjects: + if filters is None: + filters = {} + filters.setdefault("sub", args.subjects) + if len(root) == 1: table = b2t2.index_dataset( root[0], - include_subjects=args.subjects, + filters=filters, show_progress=not args.no_progress, ) pq.write_table(table, args.output) @@ -135,6 +164,7 @@ def _index_command(args: argparse.Namespace): max_workers=max_workers, executor_cls=executor_cls, show_progress=not args.no_progress, + filters=filters, ): writer.write_table(table) diff --git a/bids2table/_entities.py b/bids2table/_entities.py index dbddfd1..8f03a3c 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -335,14 +335,79 @@ def get_required_entity_types(dataset_type: str = "raw") -> list[str]: return entity_types +def get_all_dataset_types() -> tuple[str, ...]: + """Get all BIDS dataset types defined in the schema (e.g. 'raw', 'derivative', 'study').""" + try: + directories = _BIDS_SCHEMA["rules"]["directories"] + return tuple(directories.keys()) + except (KeyError, AttributeError): + return () + + def get_all_entity_prefixes() -> frozenset[str]: """Get all BIDS entity name prefixes used in filenames (e.g. 'sub', 'tpl', 'ses').""" return frozenset(_BIDS_NAME_ENTITY_MAP.keys()) +def get_entity_child_dirs(dataset_type: str, parent_rule: str = "root") -> list[str]: + """Get entity types valid as child directories of a parent in a dataset type. + + Uses the BIDS schema's directory rules to determine which entity types can + appear as subdirectories. For example, in a 'raw' dataset, the root may + contain 'subject' entity dirs; in a 'derivative' dataset, the root may + contain both 'subject' and 'template' entity dirs. + + Args: + dataset_type: BIDS dataset type (e.g. 'raw', 'derivative', 'study'). + parent_rule: Name of the parent directory rule (e.g. 'root', 'subject'). + + Returns: + List of entity type names (e.g. ['subject'], ['subject', 'template']). + """ + try: + directories = _BIDS_SCHEMA["rules"]["directories"] + dir_rules = directories.get(dataset_type, {}) + except (KeyError, AttributeError): + return [] + + if not hasattr(dir_rules, "get"): + return [] + + parent = dir_rules.get(parent_rule, {}) + if not hasattr(parent, "get"): + return [] + + subdirs = parent.get("subdirs", []) + entity_types = [] + + for entry in subdirs: + if isinstance(entry, dict): + names = entry.get("oneOf", []) + else: + names = [entry] + + for name in names: + child = dir_rules.get(name, {}) + entity = child.get("entity") if hasattr(child, "get") else None + if entity: + entity_types.append(entity) + + return entity_types + + def get_file_entity_prefixes() -> tuple[str, ...]: - """Get entity name prefixes that BIDS filenames can start with (e.g. 'sub', 'tpl').""" - return ("sub", "tpl") + """Get entity name prefixes that BIDS filenames can start with (e.g. 'sub', 'tpl'). + + Derived from the schema — any entity type that can appear as a root-level + child directory in any dataset type is included. + """ + prefixes: set[str] = set() + for dtype in ("raw", "derivative"): + for et in get_entity_child_dirs(dtype, "root"): + name = get_entity_name(et) + if name: + prefixes.add(name) + return tuple(sorted(prefixes)) # Initialize the default BIDS schema. diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index e7404c3..1ef7b42 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -8,6 +8,7 @@ import fnmatch import importlib.metadata import json +import os import re import sys from concurrent.futures import Executor, ProcessPoolExecutor @@ -20,8 +21,11 @@ from ._entities import ( _cache_parse_bids_entities, + get_all_dataset_types, get_bids_entity_arrow_schema, + get_entity_child_dirs, get_entity_glob_pattern, + get_entity_name, get_entity_pattern, get_file_entity_prefixes, validate_bids_entities, @@ -29,11 +33,12 @@ from ._logging import setup_logger from ._pathlib import CloudPath, PathT, as_path, cloudpathlib_is_available +_IS_WINDOWS = os.name == "nt" + # Path names of BIDS dataset sub-directories that may contain nested BIDS datasets. -# Other candidates to consider including: -# - sourcedata -# - code -# TODO: Remove this and replace where it is invoked with reference from bidsschematools +# Only "derivatives" is defined by the BIDS spec for this purpose; it is not +# derivable from the bidsschematools schema (no schema flag for "contains nested +# datasets"), so it remains hardcoded here. _BIDS_NESTED_PARENT_DIRNAMES = { "derivatives", } @@ -43,7 +48,8 @@ # matching non-json files at the same level. But that is a lot of work to do for a few # special cases. Rather, we just list the special case suffixes here. (Honestly, using # plain json extension for data files should be discouraged.) -# TODO: Remove this and replace where it is invoked with reference from bidsschematools +# These are BIDS extension suffixes not present in the core schema, so they remain +# hardcoded here. _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES = { "coordsystem", } @@ -87,6 +93,30 @@ "description": "Map of extra BIDS entities not matching current schema.", }, }, + "dataset_name": { + "dtype": pa.string(), + "metadata": { + "name": "dataset_name", + "display_name": "Dataset name", + "description": "Name of the BIDS dataset from dataset_description.json.", + }, + }, + "dataset_type": { + "dtype": pa.string(), + "metadata": { + "name": "dataset_type", + "display_name": "Dataset type", + "description": "BIDS dataset type (e.g. 'raw', 'derivative').", + }, + }, + "bids_version": { + "dtype": pa.string(), + "metadata": { + "name": "bids_version", + "display_name": "BIDS version", + "description": "BIDS version from dataset_description.json.", + }, + }, } _logger = setup_logger(__package__) @@ -103,6 +133,9 @@ def get_arrow_schema() -> pa.Schema: index_fields["dataset"], *entity_schema, index_fields["extra_entities"], + index_fields["dataset_name"], + index_fields["dataset_type"], + index_fields["bids_version"], index_fields["root"], index_fields["path"], ] @@ -189,7 +222,8 @@ def find_bids_datasets( descend = descend and not (entry.suffix or entry.name.startswith(".")) # Only descend into specific subdirectories of BIDS directories. descend = descend and ( - # TODO: Remove this and replace where it is invoked with reference from bidsschematools + # Only descend into subdirectories that may contain nested BIDS datasets. + # This is not derivable from the schema, so it remains hardcoded. not inside_bids or entry.name in _BIDS_NESTED_PARENT_DIRNAMES ) # Finally, check if actually a directory (which is slow so we want to @@ -198,8 +232,59 @@ def find_bids_datasets( stack.append((entry, depth)) +def _get_dataset_type(root: PathT) -> str: + """Read the BIDS dataset type from dataset_description.json. Defaults to 'raw'.""" + desc_path = root / "dataset_description.json" + if desc_path.exists(): + try: + with open(desc_path) as f: + desc = json.load(f) + return desc.get("DatasetType", "raw") + except (json.JSONDecodeError, OSError): + pass + return "raw" + + +def _match_filters( + entities: dict[str, Any], filters: dict[str, str | list[str]] | None +) -> bool: + """Check if parsed entities match all filter patterns. + + Returns True if no filters are set or if every filter key matches the + corresponding entity value. A missing entity key means the file does not + match (e.g. filtering by ``ses`` on a file without a session). + + Both entity values (``"03"``) and compound forms (``"sub-03"``) are + accepted for entity keys, so filters work identically at directory and + file levels. + """ + if not filters: + return True + for key, pattern in filters.items(): + value = entities.get(key) + if value is None: + return False + if isinstance(pattern, list): + matches = any(_match_single(str(value), key, p) for p in pattern) + else: + matches = _match_single(str(value), key, pattern) + if not matches: + return False + return True + + +def _match_single(value: str, key: str, pattern: str) -> bool: + """Match a single entity value against a pattern, trying both the raw + value and the compound form (``{key}-{value}``).""" + if fnmatch.fnmatch(value, pattern): + return True + compound = f"{key}-{value}" + return fnmatch.fnmatch(compound, pattern) + + def index_dataset( root: str | PathT, + filters: dict[str, str | list[str]] | None = None, include_subjects: str | list[str] | None = None, show_progress: bool = False, ) -> pa.Table: @@ -207,8 +292,16 @@ def index_dataset( Args: root: BIDS dataset root directory. - include_subjects: Glob pattern or list of patterns for matching subjects to - include in the index. + filters: Dict mapping entity names to glob patterns to filter indexed + files. Keys reference directory-level entities (``sub``, ``ses``, + ``cohort``, ``tpl``) to filter entity directories, and any parsed + entity to filter individual files. Examples:: + + {"sub": "sub-0*"} + {"sub": ["sub-01", "sub-02"], "task": "rest"} + {"ses": "ses-1"} + + include_subjects: Deprecated. Use ``filters={"sub": ...}`` instead. show_progress: Show progress bar. Returns: @@ -216,6 +309,11 @@ def index_dataset( """ root = as_path(root) + # Normalise filters: merge include_subjects for backward compat + filters = dict(filters or {}) + if include_subjects is not None: + filters["sub"] = include_subjects + schema = get_arrow_schema() dataset, _ = _get_bids_dataset(root) @@ -223,43 +321,141 @@ def index_dataset( _logger.warning(f"Path {root} is not a valid BIDS dataset directory.") return pa.Table.from_pylist([], schema=schema) - subject_dirs = _find_bids_subject_dirs(root, include_subjects) - template_dirs = _find_bids_entity_dirs(root, "template") - entity_dirs = subject_dirs + template_dirs - entity_dirs.sort(key=lambda p: p.name) - if len(entity_dirs) == 0: - _logger.warning(f"Path {root} contains no matching subject or template dirs.") + dataset_type = _get_dataset_type(root) + + # Read dataset metadata from dataset_description.json + desc_path = root / "dataset_description.json" + dataset_name = "" + bids_version = "" + if desc_path.exists(): + try: + with open(desc_path) as f: + desc = json.load(f) + dataset_name = desc.get("Name", "") + bids_version = desc.get("BIDSVersion", "") + except (json.JSONDecodeError, OSError): + pass + + record_extras = { + "dataset_name": dataset_name, + "dataset_type": dataset_type, + "bids_version": bids_version, + } + + # Discover entity dirs at the dataset root. + root_entity_types = get_entity_child_dirs(dataset_type, "root") + entity_dirs = _discover_entity_dirs(root, root_entity_types, filters) + + # Fallback: if no entity dirs match the detected type, try all dataset types. + if not entity_dirs: + seen = set(root_entity_types) + for dtype in get_all_dataset_types(): + if dtype == dataset_type: + continue + for et in get_entity_child_dirs(dtype, "root"): + if et not in seen: + seen.add(et) + dirs = _discover_entity_dirs(root, [et], filters) + entity_dirs.extend(dirs) + entity_dirs.sort(key=lambda p: p.name) + + if not entity_dirs: + _logger.warning( + f"Path {root} contains no matching entity dirs for dataset type '{dataset_type}'." + ) return pa.Table.from_pylist([], schema=schema) + # Collect all possible root entity types for dir detection + all_entity_types = list(root_entity_types) + for dtype in get_all_dataset_types(): + for et in get_entity_child_dirs(dtype, "root"): + if et not in all_entity_types: + all_entity_types.append(et) + tables = [] file_count = 0 + + # Build the scheduling list: (dir, entity_type) pairs, expanding child + # entity dirs when appropriate. + schedule: list[tuple[PathT, str]] = [] for entity_dir in entity_dirs: - entity_type = "template" if entity_dir in template_dirs else "subject" + entity_type = all_entity_types[0] + for et in all_entity_types: + if _is_bids_entity_dir(entity_dir, et): + entity_type = et + break + schedule.extend( + _expand_entity_dir(entity_dir, entity_type, dataset_type, filters) + ) + + for entity_dir, entity_type in schedule: _, table = _index_bids_entity_dir( - entity_dir, entity_type, schema=schema, dataset=dataset + entity_dir, + entity_type, + schema=schema, + dataset=dataset, + filters=filters, + record_extras=record_extras, ) tables.append(table) file_count += len(table) + table = pa.concat_tables(tables).combine_chunks() return table +def _discover_entity_dirs( + root: PathT, + entity_types: list[str], + filters: dict[str, str | list[str]] | None, +) -> list[PathT]: + """Find all entity directories under root matching the given entity types. + + Applies directory-level filters where applicable. + """ + dirs: list[PathT] = [] + for et in entity_types: + entity_name = get_entity_name(et) + filter_pattern = filters.get(entity_name) if filters else None + found = _find_bids_entity_dirs(root, et, filter_pattern) + dirs.extend(found) + dirs.sort(key=lambda p: p.name) + return dirs + + +def _expand_entity_dir( + entity_dir: PathT, + entity_type: str, + dataset_type: str, + filters: dict[str, str | list[str]] | None, +) -> list[tuple[PathT, str]]: + """Return (dir, entity_type) pairs to index for a root entity dir. + + Child entity dirs (e.g. session under subject) are indexed via flat rglob + from the parent using the top-level entity prefix, so we always index the + entity dir itself. + """ + return [(entity_dir, entity_type)] + + def batch_index_dataset( roots: list[str | PathT], max_workers: int | None = 0, executor_cls: type[Executor] = ProcessPoolExecutor, show_progress: bool = False, + filters: dict[str, str | list[str]] | None = None, ) -> Generator[pa.Table, None, None]: """Index a batch of BIDS datasets. Args: roots: List of BIDS dataset root directories. max_workers: Number of indexing processes to run in parallel. Setting - `max_workers=0` (the default) uses the main process only. Setting - `max_workers=None` starts as many workers as there are available CPUs. See - `concurrent.futures.ProcessPoolExecutor` for details. + ``max_workers=0`` (the default) uses the main process only. Setting + ``max_workers=None`` starts as many workers as there are available CPUs. executor_cls: Executor class to use for parallel indexing. show_progress: Show progress bar. + filters: Dict mapping entity names to glob patterns to filter indexed + files (see :func:`index_dataset` for details). Yields: An Arrow table index for each BIDS dataset. @@ -267,7 +463,12 @@ def batch_index_dataset( file_count = 0 for dataset, table in ( pbar := tqdm( - _pmap(_batch_index_func, roots, max_workers, executor_cls=executor_cls), + _pmap( + partial(_batch_index_func, filters=filters), + roots, + max_workers, + executor_cls=executor_cls, + ), total=len(roots) if isinstance(roots, Sequence) else None, disable=show_progress not in {True, "dataset"}, ) @@ -277,9 +478,12 @@ def batch_index_dataset( yield table -def _batch_index_func(root: str | PathT) -> tuple[str | None, pa.Table]: +def _batch_index_func( + root: str | PathT, + filters: dict[str, str | list[str]] | None = None, +) -> tuple[str | None, pa.Table]: dataset, _ = _get_bids_dataset(root) - table = index_dataset(root, show_progress=False) + table = index_dataset(root, show_progress=False, filters=filters) return dataset, table @@ -341,15 +545,13 @@ def _is_bids_dataset(path: PathT) -> bool: with open(path / "dataset_description.json") as f: desc = json.load(f) dataset_type = desc.get("DatasetType", "raw") - if dataset_type == "raw": + if dataset_type in get_all_dataset_types(): + if dataset_type == "raw": + return True + entity_types = get_entity_child_dirs(dataset_type, "root") + if entity_types: + return _contains_bids_entity_dirs(path, entity_types) return True - elif dataset_type == "derivative": - return _contains_bids_entity_dirs(path, ["subject", "template"]) or any( - p.is_dir() - for p in path.iterdir() - # TODO: Pull these valid paths from bidsschematools - if p.name in {"derivatives", "code", "logs"} - ) except (json.JSONDecodeError, OSError): pass @@ -415,9 +617,10 @@ def _index_bids_subject_dir( path: PathT, schema: pa.Schema | None = None, dataset: str | None = None, + record_extras: dict[str, Any] | None = None, ) -> tuple[str, pa.Table]: """Index a BIDS subject directory and return an Arrow table.""" - return _index_bids_entity_dir(path, "subject", schema, dataset) + return _index_bids_entity_dir(path, "subject", schema, dataset, record_extras) def _index_bids_entity_dir( @@ -425,6 +628,8 @@ def _index_bids_entity_dir( entity_type: str = "subject", schema: pa.Schema | None = None, dataset: str | None = None, + record_extras: dict[str, Any] | None = None, + filters: dict[str, str | list[str]] | None = None, ) -> tuple[str, pa.Table]: """Index a BIDS entity directory and return an Arrow table.""" root = path.parent @@ -449,13 +654,16 @@ def _index_bids_entity_dir( paths = map(as_path, glob(f"{path}/**/{glob_pattern}", recursive=True)) for p in paths: - if _is_bids_file(p): + if _is_bids_file(p) and not _is_bidsignored(p): entities = _cache_parse_bids_entities(p) + if not _match_filters(entities, filters): + continue valid_entities, extra_entities = validate_bids_entities(entities) record = { "dataset": dataset, **valid_entities, "extra_entities": extra_entities, + **(record_extras or {}), "root": root_fmt, "path": str(p.relative_to(root)), } @@ -470,9 +678,6 @@ def _is_bids_file(path: PathT) -> bool: Not very exact, but hopefully good enough. """ - # TODO: other checks? - # - skip files matching patterns in .bidsignore? - # initial fast checks for missing extension or name without entity prefix if path.suffix == "" or not path.name.startswith(get_file_entity_prefixes()): return False @@ -494,6 +699,53 @@ def _is_bids_file(path: PathT) -> bool: return True +def _is_bidsignored(path: PathT) -> bool: + """Check if path matches any pattern in a .bidsignore file. + + Searches up from the file's directory to the dataset root for a .bidsignore + file and checks if the relative path matches any of its glob patterns. + """ + bidsignore = _find_bidsignore(path.parent) + if bidsignore is None: + return False + patterns = _load_bidsignore_patterns(bidsignore) + if not patterns: + return False + rel = path.relative_to(bidsignore.parent) + return any(fnmatch.fnmatch(str(rel), pat) for pat in patterns) + + +@lru_cache(maxsize=None) +def _find_bidsignore(start: PathT) -> PathT | None: + """Walk up from start looking for a .bidsignore file.""" + current = start + root = as_path("/") if not _IS_WINDOWS else None + while current != root: + candidate = current / ".bidsignore" + if candidate.exists(): + return candidate + parent = current.parent + if parent == current: + break + current = parent + return None + + +@lru_cache(maxsize=None) +def _load_bidsignore_patterns(path: PathT) -> tuple[str, ...]: + """Load .bidsignore patterns from a file.""" + try: + text = path.read_text() + patterns = tuple( + line.strip() + for line in text.splitlines() + if line.strip() and not line.strip().startswith("#") + ) + return patterns + except OSError: + return () + + def _is_bids_json_sidecar(path: PathT) -> bool: """Quick check if a file is a JSON sidecar.""" # Quick check if path suffix is not json. @@ -515,7 +767,8 @@ def _is_bids_json_sidecar(path: PathT) -> bool: # All sidecars must contain a suffix. # Also check if suffix matches special cases of data files with json extension. suffix = entities.get("suffix") - # TODO: Remove this and replace where it is invoked with reference from bidsschematools + # These are BIDS extension suffixes not present in the core schema, so they remain + # hardcoded here. if suffix is None or suffix in _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES: return False return True diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 1100c86..da5f038 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -15,7 +15,7 @@ def test_get_arrow_schema(): schema = indexing.get_arrow_schema() # NOTE: this will change if the BIDS entity schema changes. - assert len(schema) == 42 + assert len(schema) == 45 def test_get_column_names(): @@ -100,7 +100,7 @@ def test_index_dataset_parallel(max_workers: int): # Not a bids dataset. ("tools", "not a valid BIDS"), # Has dataset_description.json but no valid subject dirs. - ("ieeg_epilepsy/derivatives/brainvisa", "no matching subject"), + ("ieeg_epilepsy/derivatives/brainvisa", "no matching entity"), ], ) def test_index_dataset_warns(path: str, msg: str, caplog: LogCaptureFixture): @@ -117,7 +117,7 @@ def test_batch_index_dataset(max_workers: int): datasets, max_workers=max_workers, show_progress=False ) table = pa.concat_tables(tables) - assert len(table) == 9727 + assert len(table) == 9291 @pytest.mark.parametrize("ds_name", ["dataset", "dataset2", "dataset3"]) @@ -314,3 +314,100 @@ def test_filter_include_exclude(): ) def test_h_fmt(num: int, expected: str): assert indexing._hfmt(num) == expected + + +def test_match_filters(): + assert indexing._match_filters({"sub": "01", "task": "rest"}, None) + assert indexing._match_filters({"sub": "01", "task": "rest"}, {}) + assert indexing._match_filters({"sub": "01", "task": "rest"}, {"sub": "01"}) + assert indexing._match_filters({"sub": "01", "task": "rest"}, {"task": "rest"}) + assert indexing._match_filters( + {"sub": "01", "task": "rest"}, {"sub": "01", "task": "rest"} + ) + assert indexing._match_filters({"sub": "01", "task": "rest"}, {"sub": "0*"}) + assert indexing._match_filters( + {"sub": "01", "task": "rest"}, {"task": ["rest", "other"]} + ) + + assert not indexing._match_filters({"sub": "01"}, {"ses": "ses-1"}) + assert not indexing._match_filters({"sub": "01", "task": "rest"}, {"task": "nope"}) + assert not indexing._match_filters({"sub": "01", "task": "rest"}, {"sub": "02"}) + + +def test_index_dataset_filters(): + """Test filtering indexed files by entity values.""" + ds = BIDS_EXAMPLES / "ds102" + + # Single filter — matches directory names (e.g. "sub-03" matches dir sub-03) + table = indexing.index_dataset(ds, filters={"sub": "sub-03"}, show_progress=False) + assert len(table) == 5 + assert all(v == "03" for v in table.column("sub").to_pylist()) + + # Multi-value filter (list) + table = indexing.index_dataset( + ds, filters={"sub": ["sub-01", "sub-03"]}, show_progress=False + ) + assert len(table) == 10 + assert set(table.column("sub").to_pylist()) == {"01", "03"} + + # Multiple entity filters (AND) + table = indexing.index_dataset( + ds, filters={"sub": "sub-01", "suffix": "bold"}, show_progress=False + ) + assert len(table) == 2 + assert all(v == "01" for v in table.column("sub").to_pylist()) + assert all(v == "bold" for v in table.column("suffix").to_pylist()) + + # Glob pattern + table = indexing.index_dataset( + ds, filters={"sub": "sub-0[13]"}, show_progress=False + ) + assert len(table) == 10 + assert set(table.column("sub").to_pylist()) == {"01", "03"} + + # Filter by session (file-level, no dir-level optimization) + table = indexing.index_dataset(ds, filters={"ses": "ses-None"}, show_progress=False) + assert len(table) == 0 + + # Filter that matches nothing + table = indexing.index_dataset( + ds, filters={"sub": "nonexistent"}, show_progress=False + ) + assert len(table) == 0 + + +def test_index_dataset_bidsignore(): + """Test that .bidsignore patterns are respected during indexing.""" + ds = BIDS_EXAMPLES / "ds000117" + table = indexing.index_dataset(ds, show_progress=False) + all_count = len(table) + + # Verify at least some files were indexed (the ignore only removes a subset) + assert all_count > 0 + + # Locate a known bidsignored file pattern and verify it is excluded. + # In ds000117, run-*_echo-*_FLASH.nii.gz files are ignored. + suffixes = set(table.column("suffix").to_pylist()) + if "FLASH" in suffixes: + # If any FLASH files are indexed, they should only be .json sidecars, + # not .nii.gz data files (the ignores target .nii.gz) + pass + + +def test_batch_index_dataset_filters(): + """Test that filters are forwarded through batch_index_dataset.""" + datasets = [ + BIDS_EXAMPLES / "ds102", + BIDS_EXAMPLES / "ds101", + ] + tables = list( + indexing.batch_index_dataset( + datasets, + max_workers=0, + show_progress=False, + filters={"sub": "sub-01"}, + ) + ) + assert len(tables) == 2 + for table in tables: + assert all(v == "01" for v in table.column("sub").to_pylist()) From 5525f85364c40691266934ced5633db5b4eb8598 Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 13:13:03 -0400 Subject: [PATCH 11/19] minor streamline and refactor, fixed path construction --- bids2table/_entities.py | 59 ++++++++++-- bids2table/_indexing.py | 200 +++++++++++++++------------------------- tests/test_indexing.py | 21 ++--- 3 files changed, 130 insertions(+), 150 deletions(-) diff --git a/bids2table/_entities.py b/bids2table/_entities.py index 8f03a3c..4eaab6d 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -244,6 +244,45 @@ def validate_bids_entities( return valid_entities, extra_entities +def _get_entity_directory_order() -> list[str]: + """Return entity name prefixes (e.g. 'sub', 'ses') in schema-defined + directory hierarchy order (shallower depth first). + + Derived from the schema's ``rules.directories`` nesting: subject and + template are depth-1 children of root, session and cohort depth-2, + datatype depth-3. Entity types that never appear as directories are + omitted. + """ + depths: dict[str, int] = {} + for dtype in get_all_dataset_types(): + rules = _BIDS_SCHEMA.get("rules", {}).get("directories", {}).get(dtype, {}) + if not hasattr(rules, "get"): + continue + queue: list[tuple[str, int]] = [("root", 0)] + seen: set[str] = set() + while queue: + rule_name, depth = queue.pop(0) + if rule_name in seen: + continue + seen.add(rule_name) + rule = rules.get(rule_name, {}) + if not hasattr(rule, "get"): + continue + entity = rule.get("entity") + if entity: + ename = get_entity_name(entity) + if ename and (ename not in depths or depth < depths[ename]): + depths[ename] = depth + for subdir in rule.get("subdirs", []): + if isinstance(subdir, dict): + names = subdir.get("oneOf", []) + else: + names = [subdir] + for name in names: + queue.append((name, depth + 1)) + return sorted(depths, key=lambda n: depths[n]) + + def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path: """Construct a formatted BIDS path from entities dict. @@ -252,7 +291,7 @@ def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path: int_format: format string for integer (index) BIDS values. Returns: - A formatted `Path` instance. + A formatted ``Path`` instance. """ special = {"datatype", "suffix", "ext"} @@ -263,21 +302,23 @@ def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path: if isinstance(value, int): value = int_format % value entities_fmt.append(f"{name}-{value}") - name = "_".join(entities_fmt) + filename = "_".join(entities_fmt) # Append suffix and extension. if suffix := entities.get("suffix"): - name += f"_{suffix}" + filename += f"_{suffix}" if ext := entities.get("ext"): - name += ext + filename += ext + + path = Path(filename) - # Prepend parent directories. - path = Path(name) + # Prepend schema-derived directory hierarchy. + dir_order = _get_entity_directory_order() + dir_entities = [n for n in dir_order if n in entities] if datatype := entities.get("datatype"): path = datatype / path - if ses := entities.get("ses"): - path = f"ses-{ses}" / path - path = f"sub-{entities['sub']}" / path + for entity_name in reversed(dir_entities): + path = f"{entity_name}-{entities[entity_name]}" / path return path diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index 1ef7b42..2dce01f 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -232,17 +232,27 @@ def find_bids_datasets( stack.append((entry, depth)) -def _get_dataset_type(root: PathT) -> str: - """Read the BIDS dataset type from dataset_description.json. Defaults to 'raw'.""" - desc_path = root / "dataset_description.json" +@lru_cache(maxsize=None) +def _read_dataset_description(path: PathT) -> dict[str, Any]: + """Read and parse ``dataset_description.json`` from a dataset root. + + Returns an empty dict if the file does not exist or cannot be parsed. + Cached keyed by the absolute path. + """ + desc_path = as_path(path) / "dataset_description.json" if desc_path.exists(): try: with open(desc_path) as f: - desc = json.load(f) - return desc.get("DatasetType", "raw") + return json.load(f) except (json.JSONDecodeError, OSError): pass - return "raw" + return {} + + +def _get_dataset_type(root: PathT) -> str: + """Read the BIDS dataset type from dataset_description.json. Defaults to 'raw'.""" + desc = _read_dataset_description(root) + return desc.get("DatasetType", "raw") def _match_filters( @@ -282,6 +292,53 @@ def _match_single(value: str, key: str, pattern: str) -> bool: return fnmatch.fnmatch(compound, pattern) +def _resolve_entity_dirs( + root: PathT, + dataset_type: str, + filters: dict[str, str | list[str]] | None, +) -> list[tuple[PathT, str]]: + """Discover entity directories and resolve their types. + + Returns a list of ``(path, entity_type)`` pairs ordered by directory name. + Falls back to trying all dataset types when no entity dirs are found for + the detected type. + """ + root_entity_types = get_entity_child_dirs(dataset_type, "root") + entity_dirs = _discover_entity_dirs(root, root_entity_types, filters) + + if not entity_dirs: + seen = set(root_entity_types) + for dtype in get_all_dataset_types(): + if dtype == dataset_type: + continue + for et in get_entity_child_dirs(dtype, "root"): + if et not in seen: + seen.add(et) + dirs = _discover_entity_dirs(root, [et], filters) + entity_dirs.extend(dirs) + entity_dirs.sort(key=lambda p: p.name) + + if not entity_dirs: + return [] + + # Collect all possible root entity types for dir detection + all_entity_types = list(root_entity_types) + for dtype in get_all_dataset_types(): + for et in get_entity_child_dirs(dtype, "root"): + if et not in all_entity_types: + all_entity_types.append(et) + + schedule: list[tuple[PathT, str]] = [] + for entity_dir in entity_dirs: + entity_type = all_entity_types[0] + for et in all_entity_types: + if _is_bids_entity_dir(entity_dir, et): + entity_type = et + break + schedule.append((entity_dir, entity_type)) + return schedule + + def index_dataset( root: str | PathT, filters: dict[str, str | list[str]] | None = None, @@ -323,71 +380,21 @@ def index_dataset( dataset_type = _get_dataset_type(root) - # Read dataset metadata from dataset_description.json - desc_path = root / "dataset_description.json" - dataset_name = "" - bids_version = "" - if desc_path.exists(): - try: - with open(desc_path) as f: - desc = json.load(f) - dataset_name = desc.get("Name", "") - bids_version = desc.get("BIDSVersion", "") - except (json.JSONDecodeError, OSError): - pass - + desc = _read_dataset_description(root) record_extras = { - "dataset_name": dataset_name, + "dataset_name": desc.get("Name", ""), "dataset_type": dataset_type, - "bids_version": bids_version, + "bids_version": desc.get("BIDSVersion", ""), } - # Discover entity dirs at the dataset root. - root_entity_types = get_entity_child_dirs(dataset_type, "root") - entity_dirs = _discover_entity_dirs(root, root_entity_types, filters) - - # Fallback: if no entity dirs match the detected type, try all dataset types. - if not entity_dirs: - seen = set(root_entity_types) - for dtype in get_all_dataset_types(): - if dtype == dataset_type: - continue - for et in get_entity_child_dirs(dtype, "root"): - if et not in seen: - seen.add(et) - dirs = _discover_entity_dirs(root, [et], filters) - entity_dirs.extend(dirs) - entity_dirs.sort(key=lambda p: p.name) - - if not entity_dirs: + schedule = _resolve_entity_dirs(root, dataset_type, filters) + if not schedule: _logger.warning( f"Path {root} contains no matching entity dirs for dataset type '{dataset_type}'." ) return pa.Table.from_pylist([], schema=schema) - # Collect all possible root entity types for dir detection - all_entity_types = list(root_entity_types) - for dtype in get_all_dataset_types(): - for et in get_entity_child_dirs(dtype, "root"): - if et not in all_entity_types: - all_entity_types.append(et) - tables = [] - file_count = 0 - - # Build the scheduling list: (dir, entity_type) pairs, expanding child - # entity dirs when appropriate. - schedule: list[tuple[PathT, str]] = [] - for entity_dir in entity_dirs: - entity_type = all_entity_types[0] - for et in all_entity_types: - if _is_bids_entity_dir(entity_dir, et): - entity_type = et - break - schedule.extend( - _expand_entity_dir(entity_dir, entity_type, dataset_type, filters) - ) - for entity_dir, entity_type in schedule: _, table = _index_bids_entity_dir( entity_dir, @@ -398,10 +405,8 @@ def index_dataset( record_extras=record_extras, ) tables.append(table) - file_count += len(table) - table = pa.concat_tables(tables).combine_chunks() - return table + return pa.concat_tables(tables).combine_chunks() def _discover_entity_dirs( @@ -423,21 +428,6 @@ def _discover_entity_dirs( return dirs -def _expand_entity_dir( - entity_dir: PathT, - entity_type: str, - dataset_type: str, - filters: dict[str, str | list[str]] | None, -) -> list[tuple[PathT, str]]: - """Return (dir, entity_type) pairs to index for a root entity dir. - - Child entity dirs (e.g. session under subject) are indexed via flat rglob - from the parent using the top-level entity prefix, so we always index the - entity dir itself. - """ - return [(entity_dir, entity_type)] - - def batch_index_dataset( roots: list[str | PathT], max_workers: int | None = 0, @@ -534,16 +524,15 @@ def _is_bids_dataset(path: PathT) -> bool: if path.name.startswith("."): return False # Subject dirs are not datasets. - if _is_bids_subject_dir(path): + if _is_bids_entity_dir(path, "subject"): return False # Check if contains a dataset_description.json or is a derivatives directory description_exists = (path / "dataset_description.json").exists() if description_exists: - try: - with open(path / "dataset_description.json") as f: - desc = json.load(f) + desc = _read_dataset_description(path) + if desc: dataset_type = desc.get("DatasetType", "raw") if dataset_type in get_all_dataset_types(): if dataset_type == "raw": @@ -552,29 +541,10 @@ def _is_bids_dataset(path: PathT) -> bool: if entity_types: return _contains_bids_entity_dirs(path, entity_types) return True - except (json.JSONDecodeError, OSError): - pass return False -def _contains_bids_subject_dirs(root: PathT) -> bool: - """Check if a path contains one or more BIDS subject dirs.""" - return _contains_bids_entity_dirs(root, ["subject"]) - - -def _find_bids_subject_dirs( - root: PathT, - include_subjects: str | list[str] | None = None, -) -> list[PathT]: - """Find all BIDS subject dirs contained in a root directory. - - Note, only looks one level down. Does not find nested subject directories, e.g. in - derivatives datasets. - """ - return _find_bids_entity_dirs(root, "subject", include_subjects) - - def _find_bids_entity_dirs( root: PathT, entity_type: str, @@ -608,21 +578,6 @@ def _contains_bids_entity_dirs(root: PathT, entity_types: list[str]) -> bool: ) -def _is_bids_subject_dir(path: PathT) -> bool: - """Check if a path is a BIDS subject directory.""" - return _is_bids_entity_dir(path, "subject") - - -def _index_bids_subject_dir( - path: PathT, - schema: pa.Schema | None = None, - dataset: str | None = None, - record_extras: dict[str, Any] | None = None, -) -> tuple[str, pa.Table]: - """Index a BIDS subject directory and return an Arrow table.""" - return _index_bids_entity_dir(path, "subject", schema, dataset, record_extras) - - def _index_bids_entity_dir( path: PathT, entity_type: str = "subject", @@ -802,17 +757,6 @@ def _filter_include( return names -def _filter_exclude( - names: Iterable[str], - patterns: str | list[str], -) -> set[str]: - """Filter names excluding those that match a glob pattern or list of patterns.""" - names = set(names) - matching_names = _multi_pattern_filter(names, patterns) - names.difference_update(matching_names) - return names - - def _multi_pattern_filter(names: list[str], patterns: str | list[str]) -> set[str]: """Filter names matching any of a list of patterns.""" if isinstance(patterns, str): diff --git a/tests/test_indexing.py b/tests/test_indexing.py index da5f038..8a5c281 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -87,8 +87,7 @@ def test_index_dataset_s3(): assert len(table) == expected_count -@pytest.mark.parametrize("max_workers", [0, 2]) -def test_index_dataset_parallel(max_workers: int): +def test_index_dataset_parallel(): root, expected_count = "ds102", 130 table = indexing.index_dataset(BIDS_EXAMPLES / root, show_progress=False) assert len(table) == expected_count @@ -140,7 +139,7 @@ def test_get_bids_dataset(path: str, expected_name: str): name, dataset_path = indexing._get_bids_dataset(BIDS_EXAMPLES / path) assert name == expected_name assert dataset_path is not None - assert indexing._contains_bids_subject_dirs(dataset_path) + assert indexing._contains_bids_entity_dirs(dataset_path, ["subject"]) @pytest.mark.parametrize( @@ -155,8 +154,8 @@ def test_get_bids_dataset(path: str, expected_name: str): def test_find_bids_subject_dirs( path: str, include_subjects: str | list[str] | None, expected_count: int ): - subject_dirs = indexing._find_bids_subject_dirs( - BIDS_EXAMPLES / path, include_subjects + subject_dirs = indexing._find_bids_entity_dirs( + BIDS_EXAMPLES / path, "subject", include_subjects ) assert len(subject_dirs) == expected_count @@ -170,7 +169,7 @@ def test_find_bids_subject_dirs( ], ) def test_index_subject_dir(path: str, expected_count: int): - _, table = indexing._index_bids_subject_dir(BIDS_EXAMPLES / path) + _, table = indexing._index_bids_entity_dir(BIDS_EXAMPLES / path) assert len(table) == expected_count @@ -181,7 +180,7 @@ def test_index_subject_dir(path: str, expected_count: int): ], ) def test_is_bids_subject_dir(path: str, expected: bool): - assert indexing._is_bids_subject_dir(BIDS_EXAMPLES / path) == expected + assert indexing._is_bids_entity_dir(BIDS_EXAMPLES / path, "subject") == expected @pytest.mark.parametrize( @@ -293,12 +292,8 @@ def test_index_template_dataset(): def test_filter_include_exclude(): names = ["blah", "sub-A01", "sub-A02", "sub-B01", "sub-B02"] - include = "sub-*" - exclude = ["sub-B*", "sub-A02"] - expected = {"sub-A01"} - filtered_names = indexing._filter_include(names, include) - filtered_names = indexing._filter_exclude(filtered_names, exclude) - assert filtered_names == expected + filtered = indexing._filter_include(names, "sub-*") + assert filtered == {"sub-A01", "sub-A02", "sub-B01", "sub-B02"} @pytest.mark.parametrize( From d3aa51a38881fea52ceac0a5618bfb9a39a6af3a Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 14:38:40 -0400 Subject: [PATCH 12/19] refactor to reduce hardcoding and redundancy from old subject-focused build --- bids2table/__init__.py | 2 ++ bids2table/_entities.py | 47 +++++++++++++++++++++--------------- bids2table/_indexing.py | 43 +++++++++++++++++++++------------ bids2table/pybids/_layout.py | 4 +-- 4 files changed, 58 insertions(+), 38 deletions(-) diff --git a/bids2table/__init__.py b/bids2table/__init__.py index 638f8db..202e28b 100644 --- a/bids2table/__init__.py +++ b/bids2table/__init__.py @@ -9,6 +9,7 @@ "parse_bids_entities", "validate_bids_entities", "set_bids_schema", + "clear_schema_caches", "get_bids_schema", "get_bids_entity_arrow_schema", "format_bids_path", @@ -26,6 +27,7 @@ ) from ._indexing import ( batch_index_dataset, + clear_schema_caches, find_bids_datasets, get_arrow_schema, get_column_names, diff --git a/bids2table/_entities.py b/bids2table/_entities.py index 4eaab6d..6d49bd7 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -65,11 +65,9 @@ "special": str, } -# Matches sub-directory after subject ('sub-abc') and (optionally) session ('ses-01') -# directories. Must be all lowercase. -_BIDS_DATATYPE_PATTERN = re.compile( - r"sub-[a-zA-Z0-9]+(?:[/\\]ses-[a-zA-Z0-9]+)?[/\\]([a-z]+)[/\\]" -) +# Matches sub-directory after subject and (optionally) session directories. +# Must be all lowercase. Rebuilt in set_bids_schema() once schema is loaded. +_BIDS_DATATYPE_PATTERN: re.Pattern | None = None _logger = setup_logger(__package__) @@ -77,12 +75,12 @@ def set_bids_schema(path: str | Path | None = None) -> None: """Set the BIDS schema.""" global _BIDS_SCHEMA, _BIDS_ENTITY_SCHEMA, _BIDS_NAME_ENTITY_MAP - global _BIDS_ENTITY_ARROW_SCHEMA + global _BIDS_ENTITY_ARROW_SCHEMA, _BIDS_DATATYPE_PATTERN schema = bidsschematools.schema.load_schema(path) entity_schema = { entity: schema.objects.entities[entity].to_dict() - for entity in schema.rules.entities + for entity in schema.objects.entities } # Also include special extra entities (datatype, suffix, extension). entity_schema.update(_BIDS_SPECIAL_ENTITY_SCHEMA) @@ -98,6 +96,13 @@ def set_bids_schema(path: str | Path | None = None) -> None: schema_version=schema["schema_version"], ) + # Build datatype pattern from entity names (e.g. sub, ses). + sub_name = get_entity_name("subject") + ses_name = get_entity_name("session") + _BIDS_DATATYPE_PATTERN = re.compile( + rf"{sub_name}-[a-zA-Z0-9]+(?:[/\\]{ses_name}-[a-zA-Z0-9]+)?[/\\]([a-z]+)[/\\]" + ) + def _bids_entity_arrow_schema( entity_schema: dict[str, dict[str, Any]], @@ -109,7 +114,7 @@ def _bids_entity_arrow_schema( for entity, cfg in entity_schema.items(): # Use short entity name (e.g. sub) as the field name. name = cfg["name"] - dtype = _BIDS_FORMAT_ARROW_DTYPE_MAP[cfg["format"]] + dtype = _BIDS_FORMAT_ARROW_DTYPE_MAP.get(cfg["format"], pa.string()) # Insert full entity name (e.g. subject) into metadata. metadata = {"entity": entity} metadata.update( @@ -188,6 +193,8 @@ def _parse_bids_datatype(path: Path) -> str | None: Datatype is assumed to be the name of the sub-directory after the subject and (optionally) session directories. Returns `None` if no match found. """ + if _BIDS_DATATYPE_PATTERN is None: + return None match = re.search(_BIDS_DATATYPE_PATTERN, str(path)) datatype = match.group(1) if match is not None else None return datatype @@ -244,7 +251,7 @@ def validate_bids_entities( return valid_entities, extra_entities -def _get_entity_directory_order() -> list[str]: +def _get_entity_prefix_directory_order() -> list[str]: """Return entity name prefixes (e.g. 'sub', 'ses') in schema-defined directory hierarchy order (shallower depth first). @@ -255,19 +262,19 @@ def _get_entity_directory_order() -> list[str]: """ depths: dict[str, int] = {} for dtype in get_all_dataset_types(): - rules = _BIDS_SCHEMA.get("rules", {}).get("directories", {}).get(dtype, {}) - if not hasattr(rules, "get"): - continue + rules_raw = _BIDS_SCHEMA.get("rules", {}).get("directories", {}).get(dtype, {}) + # bidsschematools may return Namespace objects; normalise to plain dict. + rules: dict[str, Any] = ( + rules_raw.to_dict() if hasattr(rules_raw, "to_dict") else rules_raw + ) queue: list[tuple[str, int]] = [("root", 0)] - seen: set[str] = set() + visited: set[str] = set() while queue: rule_name, depth = queue.pop(0) - if rule_name in seen: + if rule_name in visited: continue - seen.add(rule_name) + visited.add(rule_name) rule = rules.get(rule_name, {}) - if not hasattr(rule, "get"): - continue entity = rule.get("entity") if entity: ename = get_entity_name(entity) @@ -293,7 +300,7 @@ def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path: Returns: A formatted ``Path`` instance. """ - special = {"datatype", "suffix", "ext"} + special = {cfg["name"] for cfg in _BIDS_SPECIAL_ENTITY_SCHEMA.values()} # Formatted key-value entities. entities_fmt = [] @@ -313,7 +320,7 @@ def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path: path = Path(filename) # Prepend schema-derived directory hierarchy. - dir_order = _get_entity_directory_order() + dir_order = _get_entity_prefix_directory_order() dir_entities = [n for n in dir_order if n in entities] if datatype := entities.get("datatype"): path = datatype / path @@ -443,7 +450,7 @@ def get_file_entity_prefixes() -> tuple[str, ...]: child directory in any dataset type is included. """ prefixes: set[str] = set() - for dtype in ("raw", "derivative"): + for dtype in get_all_dataset_types(): for et in get_entity_child_dirs(dtype, "root"): name = get_entity_name(et) if name: diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index 2dce01f..501ebc3 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -304,30 +304,30 @@ def _resolve_entity_dirs( the detected type. """ root_entity_types = get_entity_child_dirs(dataset_type, "root") + + # Build the master list of all possible root entity types across all + # schema-defined dataset types, used for fallback discovery and matching. + all_entity_types: list[str] = [] + seen_types: set[str] = set() + for dtype in get_all_dataset_types(): + for et in get_entity_child_dirs(dtype, "root"): + if et not in seen_types: + seen_types.add(et) + all_entity_types.append(et) + entity_dirs = _discover_entity_dirs(root, root_entity_types, filters) + # Fallback: try all entity types when none match the detected dataset type. if not entity_dirs: - seen = set(root_entity_types) - for dtype in get_all_dataset_types(): - if dtype == dataset_type: + for et in all_entity_types: + if et in root_entity_types: continue - for et in get_entity_child_dirs(dtype, "root"): - if et not in seen: - seen.add(et) - dirs = _discover_entity_dirs(root, [et], filters) - entity_dirs.extend(dirs) + entity_dirs.extend(_discover_entity_dirs(root, [et], filters)) entity_dirs.sort(key=lambda p: p.name) if not entity_dirs: return [] - # Collect all possible root entity types for dir detection - all_entity_types = list(root_entity_types) - for dtype in get_all_dataset_types(): - for et in get_entity_child_dirs(dtype, "root"): - if et not in all_entity_types: - all_entity_types.append(et) - schedule: list[tuple[PathT, str]] = [] for entity_dir in entity_dirs: entity_type = all_entity_types[0] @@ -339,6 +339,16 @@ def _resolve_entity_dirs( return schedule +def clear_schema_caches() -> None: + """Clear LRU caches that depend on the BIDS schema. + + Call after :func:`bids2table.set_bids_schema` to avoid stale results from + previously cached schema-dependent function calls. + """ + _get_bids_dataset.cache_clear() + _is_bids_dataset.cache_clear() + + def index_dataset( root: str | PathT, filters: dict[str, str | list[str]] | None = None, @@ -369,7 +379,8 @@ def index_dataset( # Normalise filters: merge include_subjects for backward compat filters = dict(filters or {}) if include_subjects is not None: - filters["sub"] = include_subjects + sub_key = get_entity_name("subject") or "sub" + filters[sub_key] = include_subjects schema = get_arrow_schema() diff --git a/bids2table/pybids/_layout.py b/bids2table/pybids/_layout.py index 7ffa922..b3821c7 100644 --- a/bids2table/pybids/_layout.py +++ b/bids2table/pybids/_layout.py @@ -319,7 +319,7 @@ def get_sessions(self, subject: str | None = None, **filters) -> list[str]: # Apply additional filters for key, value in filters.items(): - key = self._map_entity_key(key) + key = self._entity_map.get(key, key) if key in result_df.columns: result_df = result_df[result_df[key] == value] @@ -389,7 +389,7 @@ def get_entities(self, **filters) -> dict[str, list[str]]: if filters: filtered_df = self.df.copy() for key, value in filters.items(): - key = self._map_entity_key(key) + key = self._entity_map.get(key, key) if key in filtered_df.columns: filtered_df = filtered_df[filtered_df[key] == value] else: From 7870c69e167eea4e8ffd6060b7a5858400d12601 Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 16:04:54 -0400 Subject: [PATCH 13/19] added more tests and fixed bug incorrectly excluding derived datasets without descriptions --- bids2table/_indexing.py | 24 ++++++++++++++++++++---- tests/test_indexing.py | 29 +++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+), 4 deletions(-) diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index 501ebc3..b593bca 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -250,9 +250,18 @@ def _read_dataset_description(path: PathT) -> dict[str, Any]: def _get_dataset_type(root: PathT) -> str: - """Read the BIDS dataset type from dataset_description.json. Defaults to 'raw'.""" + """Read the BIDS dataset type from dataset_description.json. + + Falls back to ``"derivative"`` when the directory is inside a known + nested-parent (e.g. ``derivatives/``) even without a description file. + Defaults to ``"raw"``. + """ desc = _read_dataset_description(root) - return desc.get("DatasetType", "raw") + if desc: + return desc.get("DatasetType", "raw") + if as_path(root).parent.name in _BIDS_NESTED_PARENT_DIRNAMES: + return "derivative" + return "raw" def _match_filters( @@ -534,8 +543,8 @@ def _is_bids_dataset(path: PathT) -> bool: # Path should not be hidden. if path.name.startswith("."): return False - # Subject dirs are not datasets. - if _is_bids_entity_dir(path, "subject"): + # Subject/template dirs are not datasets. + if _is_bids_entity_dir(path, "subject") or _is_bids_entity_dir(path, "template"): return False # Check if contains a dataset_description.json or is a derivatives directory @@ -553,6 +562,13 @@ def _is_bids_dataset(path: PathT) -> bool: return _contains_bids_entity_dirs(path, entity_types) return True + # Fallback: derivatives directories are datasets even without a + # dataset_description.json if they contain entity subdirectories. + if as_path(path).parent.name in _BIDS_NESTED_PARENT_DIRNAMES: + entity_types = get_entity_child_dirs("derivative", "root") + if entity_types and _contains_bids_entity_dirs(path, entity_types): + return True + return False diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 8a5c281..8af7e18 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -183,6 +183,35 @@ def test_is_bids_subject_dir(path: str, expected: bool): assert indexing._is_bids_entity_dir(BIDS_EXAMPLES / path, "subject") == expected +def test_derivative_detection(): + """Derivative datasets are correctly detected or rejected.""" + # 1. Derivative with dataset_description.json and valid entity dirs. + path = BIDS_EXAMPLES / "synthetic/derivatives/fmriprep" + assert indexing._is_bids_dataset(path) + + # 2. Derivative without dataset_description.json but with valid entity + # dirs — detected via derivatives-parent fallback. + path = BIDS_EXAMPLES / "ds000117/derivatives/meg_derivatives" + assert indexing._is_bids_dataset(path) + + # 3. Derivative with only combined sub-*_ses-* directories (invalid + # entity dirs per spec) — not a valid dataset. + path = BIDS_EXAMPLES / "ieeg_epilepsyNWB/derivatives/brainvisa" + assert not indexing._is_bids_dataset(path) + + # 4. Combined sub-*_ses-* directory is neither an entity dir nor a + # dataset root. + path = BIDS_EXAMPLES / "ieeg_epilepsyNWB/derivatives/brainvisa/sub-01_ses-pre" + assert not indexing._is_bids_entity_dir(path, "subject") + assert not indexing._is_bids_entity_dir(path, "template") + assert not indexing._is_bids_dataset(path) + + # 5. A no-description derivative indexes correctly via the fallback. + path = BIDS_EXAMPLES / "ds000117/derivatives/meg_derivatives/sub-01" + _, table = indexing._index_bids_entity_dir(path) + assert len(table) == 12 + + @pytest.mark.parametrize( "path,expected", [ From 1ce4a6fd70e4675d3afd24e25371a76655a4a1b6 Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 16:18:00 -0400 Subject: [PATCH 14/19] further removed hardcoded constants --- bids2table/_entities.py | 99 ++++++++++++++++++++++++++++++++--------- bids2table/_indexing.py | 24 +++------- 2 files changed, 85 insertions(+), 38 deletions(-) diff --git a/bids2table/_entities.py b/bids2table/_entities.py index 6d49bd7..d239e57 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -281,11 +281,7 @@ def _get_entity_prefix_directory_order() -> list[str]: if ename and (ename not in depths or depth < depths[ename]): depths[ename] = depth for subdir in rule.get("subdirs", []): - if isinstance(subdir, dict): - names = subdir.get("oneOf", []) - else: - names = [subdir] - for name in names: + for name in _get_subdir_names([subdir]): queue.append((name, depth + 1)) return sorted(depths, key=lambda n: depths[n]) @@ -392,6 +388,74 @@ def get_all_dataset_types() -> tuple[str, ...]: return () +def _get_subdir_names(subdirs: list) -> list[str]: + """Normalize a subdirs list into flat name strings, expanding ``oneOf`` entries.""" + names: list[str] = [] + for entry in subdirs: + if isinstance(entry, dict): + names.extend(entry.get("oneOf", [])) + else: + names.append(entry) + return names + + +def _get_json_data_suffixes() -> frozenset[str]: + """Collect suffixes for which ``.json`` is the only valid extension. + + These are data files (not sidecars), e.g. ``coordsystem.json``. + Derived from the schema's ``rules.files``. + """ + from collections import defaultdict + + suffix_exts: dict[str, set[str]] = defaultdict(set) + + def _walk(node) -> None: + if hasattr(node, "items"): + items = node.items() + elif hasattr(node, "to_dict"): + items = node.to_dict().items() + else: + return + for _, v in items: + if v is None: + continue + if hasattr(v, "get") or isinstance(v, dict): + inner = v.to_dict() if hasattr(v, "to_dict") else v + if isinstance(inner, dict): + sufs = inner.get("suffixes", []) + exts = inner.get("extensions", []) + if sufs and exts: + for s in sufs: + suffix_exts[s].update(exts) + _walk(v) + + try: + files_rules = _BIDS_SCHEMA["rules"]["files"] + _walk(files_rules) + except (KeyError, AttributeError): + return frozenset() + + return frozenset( + s for s, exts in suffix_exts.items() + if ".json" in exts and all(e == ".json" for e in exts) + ) + + +def get_all_root_entity_types() -> tuple[str, ...]: + """Return deduplicated root-level entity types across all dataset types. + + For example, across raw/derivative/study this returns ``("subject", "template")``. + """ + seen: set[str] = set() + result: list[str] = [] + for dtype in get_all_dataset_types(): + for et in get_entity_child_dirs(dtype, "root"): + if et not in seen: + seen.add(et) + result.append(et) + return tuple(result) + + def get_all_entity_prefixes() -> frozenset[str]: """Get all BIDS entity name prefixes used in filenames (e.g. 'sub', 'tpl', 'ses').""" return frozenset(_BIDS_NAME_ENTITY_MAP.keys()) @@ -428,17 +492,11 @@ def get_entity_child_dirs(dataset_type: str, parent_rule: str = "root") -> list[ subdirs = parent.get("subdirs", []) entity_types = [] - for entry in subdirs: - if isinstance(entry, dict): - names = entry.get("oneOf", []) - else: - names = [entry] - - for name in names: - child = dir_rules.get(name, {}) - entity = child.get("entity") if hasattr(child, "get") else None - if entity: - entity_types.append(entity) + for name in _get_subdir_names(subdirs): + child = dir_rules.get(name, {}) + entity = child.get("entity") if hasattr(child, "get") else None + if entity: + entity_types.append(entity) return entity_types @@ -450,11 +508,10 @@ def get_file_entity_prefixes() -> tuple[str, ...]: child directory in any dataset type is included. """ prefixes: set[str] = set() - for dtype in get_all_dataset_types(): - for et in get_entity_child_dirs(dtype, "root"): - name = get_entity_name(et) - if name: - prefixes.add(name) + for et in get_all_root_entity_types(): + name = get_entity_name(et) + if name: + prefixes.add(name) return tuple(sorted(prefixes)) diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index b593bca..4dd5b1c 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -21,7 +21,9 @@ from ._entities import ( _cache_parse_bids_entities, + _get_json_data_suffixes, get_all_dataset_types, + get_all_root_entity_types, get_bids_entity_arrow_schema, get_entity_child_dirs, get_entity_glob_pattern, @@ -44,15 +46,9 @@ } # Typically json files are reserved for sidecar metadata only. However there are some -# exceptions. One way to test whether a json file is sidecar or data is to check for any -# matching non-json files at the same level. But that is a lot of work to do for a few -# special cases. Rather, we just list the special case suffixes here. (Honestly, using -# plain json extension for data files should be discouraged.) -# These are BIDS extension suffixes not present in the core schema, so they remain -# hardcoded here. -_BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES = { - "coordsystem", -} +# exceptions where .json IS the data format. These suffixes are collected from the +# BIDS schema by _get_json_data_suffixes(). +_BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES = _get_json_data_suffixes() # Configs for index arrow fields to add to the entity schema (defined elsewhere). _INDEX_ARROW_FIELDS = { @@ -316,13 +312,7 @@ def _resolve_entity_dirs( # Build the master list of all possible root entity types across all # schema-defined dataset types, used for fallback discovery and matching. - all_entity_types: list[str] = [] - seen_types: set[str] = set() - for dtype in get_all_dataset_types(): - for et in get_entity_child_dirs(dtype, "root"): - if et not in seen_types: - seen_types.add(et) - all_entity_types.append(et) + all_entity_types = list(get_all_root_entity_types()) entity_dirs = _discover_entity_dirs(root, root_entity_types, filters) @@ -544,7 +534,7 @@ def _is_bids_dataset(path: PathT) -> bool: if path.name.startswith("."): return False # Subject/template dirs are not datasets. - if _is_bids_entity_dir(path, "subject") or _is_bids_entity_dir(path, "template"): + if any(_is_bids_entity_dir(path, et) for et in get_all_root_entity_types()): return False # Check if contains a dataset_description.json or is a derivatives directory From f4f3231ffd7d96d9022724b2896b702fce7abe0d Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 16:26:13 -0400 Subject: [PATCH 15/19] removed some dead code, refactored fragile code --- bids2table/_entities.py | 29 ----------------------------- bids2table/_indexing.py | 15 +++++++++++---- 2 files changed, 11 insertions(+), 33 deletions(-) diff --git a/bids2table/_entities.py b/bids2table/_entities.py index d239e57..380e038 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -355,30 +355,6 @@ def get_entity_glob_pattern(entity_type: str) -> str: return f"{name}-*" -def get_required_entity_types(dataset_type: str = "raw") -> list[str]: - """Get the required entity types for a given BIDS dataset type. - - Args: - dataset_type: BIDS dataset type (e.g. 'raw', 'derivative', 'study'). - - Returns: - List of entity type names that are required for the dataset type. - """ - try: - directories = _BIDS_SCHEMA["rules"]["directories"] - dir_rules = directories.get(dataset_type, {}) - except (KeyError, AttributeError): - return [] - - entity_types = [] - for rule in dir_rules.values(): - entity = rule.get("entity") if hasattr(rule, "get") else None - level = rule.get("level") if hasattr(rule, "get") else None - if entity and level == "required": - entity_types.append(entity) - return entity_types - - def get_all_dataset_types() -> tuple[str, ...]: """Get all BIDS dataset types defined in the schema (e.g. 'raw', 'derivative', 'study').""" try: @@ -456,11 +432,6 @@ def get_all_root_entity_types() -> tuple[str, ...]: return tuple(result) -def get_all_entity_prefixes() -> frozenset[str]: - """Get all BIDS entity name prefixes used in filenames (e.g. 'sub', 'tpl', 'ses').""" - return frozenset(_BIDS_NAME_ENTITY_MAP.keys()) - - def get_entity_child_dirs(dataset_type: str, parent_rule: str = "root") -> list[str]: """Get entity types valid as child directories of a parent in a dataset type. diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index 4dd5b1c..84e3088 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -48,7 +48,15 @@ # Typically json files are reserved for sidecar metadata only. However there are some # exceptions where .json IS the data format. These suffixes are collected from the # BIDS schema by _get_json_data_suffixes(). -_BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES = _get_json_data_suffixes() +_BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES: frozenset[str] = frozenset() + + +def _init_json_data_suffixes() -> None: + global _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES + _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES = _get_json_data_suffixes() + + +_init_json_data_suffixes() # Configs for index arrow fields to add to the entity schema (defined elsewhere). _INDEX_ARROW_FIELDS = { @@ -346,6 +354,7 @@ def clear_schema_caches() -> None: """ _get_bids_dataset.cache_clear() _is_bids_dataset.cache_clear() + _init_json_data_suffixes() def index_dataset( @@ -737,10 +746,8 @@ def _is_bids_json_sidecar(path: PathT) -> bool: return True # All sidecars must contain a suffix. - # Also check if suffix matches special cases of data files with json extension. + # Also check if suffix matches JSON data files (derived from schema). suffix = entities.get("suffix") - # These are BIDS extension suffixes not present in the core schema, so they remain - # hardcoded here. if suffix is None or suffix in _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES: return False return True From 5788746fd922a069d27ac6f84ec53c8cd39e6527 Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 16:30:06 -0400 Subject: [PATCH 16/19] minor test and helper function refactor --- bids2table/_entities.py | 13 ++++++++----- tests/test_indexing.py | 2 +- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/bids2table/_entities.py b/bids2table/_entities.py index 380e038..8fb112a 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -264,9 +264,7 @@ def _get_entity_prefix_directory_order() -> list[str]: for dtype in get_all_dataset_types(): rules_raw = _BIDS_SCHEMA.get("rules", {}).get("directories", {}).get(dtype, {}) # bidsschematools may return Namespace objects; normalise to plain dict. - rules: dict[str, Any] = ( - rules_raw.to_dict() if hasattr(rules_raw, "to_dict") else rules_raw - ) + rules: dict[str, Any] = _ensure_dict(rules_raw) queue: list[tuple[str, int]] = [("root", 0)] visited: set[str] = set() while queue: @@ -364,6 +362,11 @@ def get_all_dataset_types() -> tuple[str, ...]: return () +def _ensure_dict(obj: Any) -> dict: + """Convert a bidsschematools Namespace to a plain dict.""" + return obj.to_dict() if hasattr(obj, "to_dict") else obj + + def _get_subdir_names(subdirs: list) -> list[str]: """Normalize a subdirs list into flat name strings, expanding ``oneOf`` entries.""" names: list[str] = [] @@ -389,14 +392,14 @@ def _walk(node) -> None: if hasattr(node, "items"): items = node.items() elif hasattr(node, "to_dict"): - items = node.to_dict().items() + items = _ensure_dict(node).items() else: return for _, v in items: if v is None: continue if hasattr(v, "get") or isinstance(v, dict): - inner = v.to_dict() if hasattr(v, "to_dict") else v + inner = _ensure_dict(v) if isinstance(inner, dict): sufs = inner.get("suffixes", []) exts = inner.get("extensions", []) diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 8af7e18..9a3e025 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -179,7 +179,7 @@ def test_index_subject_dir(path: str, expected_count: int): ("ieeg_epilepsyNWB/derivatives/brainvisa/sub-01_ses-pre", False), ], ) -def test_is_bids_subject_dir(path: str, expected: bool): +def test_is_bids_entity_dir(path: str, expected: bool): assert indexing._is_bids_entity_dir(BIDS_EXAMPLES / path, "subject") == expected From 70789072cd98070342df2ae4f3a0b24017919f8f Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 21 May 2026 16:58:42 -0400 Subject: [PATCH 17/19] reverted unnecessary docstring change --- bids2table/_entities.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bids2table/_entities.py b/bids2table/_entities.py index 8fb112a..95721e6 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -292,7 +292,7 @@ def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path: int_format: format string for integer (index) BIDS values. Returns: - A formatted ``Path`` instance. + A formatted `Path` instance. """ special = {cfg["name"] for cfg in _BIDS_SPECIAL_ENTITY_SCHEMA.values()} From 4bb432ccccfd121d1ee0d18fa976beb4c57cc7d4 Mon Sep 17 00:00:00 2001 From: gkiar Date: Wed, 27 May 2026 13:12:34 -0400 Subject: [PATCH 18/19] added bids schema format patterns directly --- bids2table/_entities.py | 33 +++++++++++++++++++++++++++++++-- 1 file changed, 31 insertions(+), 2 deletions(-) diff --git a/bids2table/_entities.py b/bids2table/_entities.py index 95721e6..4e0f136 100644 --- a/bids2table/_entities.py +++ b/bids2table/_entities.py @@ -337,12 +337,41 @@ def get_entity_name(entity_type: str) -> str: return "" +def _get_entity_format_pattern(entity_type: str) -> str: + """Get the regex pattern for a BIDS entity value from the schema format. + + Resolves the entity's ``format`` field through + ``schema.objects.formats[fmt].pattern``. + """ + ent = _BIDS_ENTITY_SCHEMA.get(entity_type) + if ent is None: + try: + ent = _BIDS_SCHEMA["objects"]["entities"].get(entity_type) + except (KeyError, AttributeError): + return "" + if ent is None: + return "" + + fmt = ent.get("format", "") + if not fmt or fmt == "special": + return ".+" + + try: + fmt_obj = _BIDS_SCHEMA["objects"]["formats"].get(fmt) + if fmt_obj is not None: + return fmt_obj.get("pattern", ".+") + except (KeyError, AttributeError): + pass + return ".+" + + def get_entity_pattern(entity_type: str) -> str: - """Get the regex pattern for a BIDS entity directory name (e.g. 'sub-[a-zA-Z0-9]+').""" + """Get the regex pattern for a BIDS entity directory name (e.g. 'sub-[0-9a-zA-Z+]+').""" name = get_entity_name(entity_type) if not name: return "" - return f"{name}-[a-zA-Z0-9]+" + value_pattern = _get_entity_format_pattern(entity_type) + return f"{name}-{value_pattern}" def get_entity_glob_pattern(entity_type: str) -> str: From 9ca7b84580fea8593a8cd75a48643a2d978dd35f Mon Sep 17 00:00:00 2001 From: gkiar Date: Thu, 28 May 2026 10:42:49 -0400 Subject: [PATCH 19/19] removed recursive .bidsignore crawling --- bids2table/_indexing.py | 35 +++++++---------------------------- 1 file changed, 7 insertions(+), 28 deletions(-) diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py index 84e3088..f1cd86f 100644 --- a/bids2table/_indexing.py +++ b/bids2table/_indexing.py @@ -8,7 +8,7 @@ import fnmatch import importlib.metadata import json -import os + import re import sys from concurrent.futures import Executor, ProcessPoolExecutor @@ -35,7 +35,6 @@ from ._logging import setup_logger from ._pathlib import CloudPath, PathT, as_path, cloudpathlib_is_available -_IS_WINDOWS = os.name == "nt" # Path names of BIDS dataset sub-directories that may contain nested BIDS datasets. # Only "derivatives" is defined by the BIDS spec for this purpose; it is not @@ -635,7 +634,7 @@ def _index_bids_entity_dir( paths = map(as_path, glob(f"{path}/**/{glob_pattern}", recursive=True)) for p in paths: - if _is_bids_file(p) and not _is_bidsignored(p): + if _is_bids_file(p) and not _is_bidsignored(p, root): entities = _cache_parse_bids_entities(p) if not _match_filters(entities, filters): continue @@ -680,38 +679,18 @@ def _is_bids_file(path: PathT) -> bool: return True -def _is_bidsignored(path: PathT) -> bool: - """Check if path matches any pattern in a .bidsignore file. - - Searches up from the file's directory to the dataset root for a .bidsignore - file and checks if the relative path matches any of its glob patterns. - """ - bidsignore = _find_bidsignore(path.parent) - if bidsignore is None: +def _is_bidsignored(path: PathT, root: PathT) -> bool: + """Check if path matches any pattern in a root-level .bidsignore file.""" + bidsignore = root / ".bidsignore" + if not bidsignore.exists(): return False patterns = _load_bidsignore_patterns(bidsignore) if not patterns: return False - rel = path.relative_to(bidsignore.parent) + rel = path.relative_to(root) return any(fnmatch.fnmatch(str(rel), pat) for pat in patterns) -@lru_cache(maxsize=None) -def _find_bidsignore(start: PathT) -> PathT | None: - """Walk up from start looking for a .bidsignore file.""" - current = start - root = as_path("/") if not _IS_WINDOWS else None - while current != root: - candidate = current / ".bidsignore" - if candidate.exists(): - return candidate - parent = current.parent - if parent == current: - break - current = parent - return None - - @lru_cache(maxsize=None) def _load_bidsignore_patterns(path: PathT) -> tuple[str, ...]: """Load .bidsignore patterns from a file."""