feat: add schema and entity helper utilities - #107
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effigies
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| _FORMAT_RE: dict[str, str] = { | ||
| "label": "[a-zA-Z0-9]+", | ||
| "index": "[0-9]+", | ||
| "special": ".+", | ||
| } |
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Note that label and index are found in schema.objects.formats. Label should support plus (+) characters.
https://github.com/bids-standard/bids-specification/blob/bb1df92/src/schema/objects/formats.yaml#L21
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Thanks! These are now derived from the schema with the "special" fallback and stored as part of the adapter in 219b02f instead of the hardcoded regex pattern mapping.
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Add `rules` field to BIDSSchemaAdapter storing `schema["rules"].to_dict()`
so downstream helpers can query directories, files, and tabular data
without re-loading the schema. The `Namespace` cannot be pickled
(circular references), so the dict representation is used with
`hash=False` to keep adapter hashing stable (similar to entities).
Add three schema helper functions:
- get_dataset_types(adapter) — returns dataset type keys ("study", "raw", "derivative")
- get_json_data_suffixes(adapter) — derives JSON data file suffixes from
rules.files/tabular_data, replacing the previously hardcoded {"coordsystem"}
- get_entity_directory_order(adapter) — BFS over rules.directories to return
depth-ordered deque of entity prefixes (e.g. sub, tpl, ses, cohort)
All helpers accept the adapter (not spec) to ensure the queried rules
correspond to the same schema spec used to build the adapter, avoiding
repeated load_schema calls.
Add schema-driven helper functions for querying BIDS entity metadata, replacing hardcoded entity assumptions. New functions in _entities.py: - get_entity_name() — map entity type to short prefix (e.g. "subject" -> "sub") - get_entity_regex() — compiled regex for prefix-value matching - get_entity_glob_pattern() — glob pattern for entity discovery - get_root_entity_types() — root-level directory entity prefixes - get_file_entity_prefixes() — non-directory, non-special entity prefixes Unknown entity types return None and log a warning instead of raising, matching the graceful degradation pattern used throughout bids2table. get_file_entity_prefixes excludes all directory entities via get_entity_directory_order() (not just root-level ones), so ses, cohort, and future directory entities are also filtered out. Adds a module-scoped adapter fixture to conftest.py so tests load the BIDS schema once instead of repeatedly.
Extract label and index format patterns from schema.objects.formats
instead of hardcoding them. This ensures regex patterns stay in sync
with the BIDS schema version.
The adapter now carries a `format_patterns` dict with only the
entity-relevant formats ("label", "index"). "special" is added as a
fallback since it is not defined in the BIDS schema.
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This PR
Phase 1 of the generalized entities refactor (supersedes #86). Adds a schema-driven helper function for querying BIDS entities in order to replace hard coded entity assumptions in downstream phases.
_schema.py — 3 new functions:
_entities.py — 5 new functions:
All three entity lookup functions gracefully handle unknown entities by returning None and logging a warning.
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