Resolve FileCollection semantic ambiguity: separate File from collection-level properties

[realmarcin]

FileCollection inherited slots from Information that were ambiguous — unclear whether bytes, format, hash, etc. described the collection aggregate or the individual files within it. bytes and total_bytes both mapped to dcat:byteSize, creating a direct redundancy.

Schema

• New File class (D4D_FileCollection.yaml): owns all technical per-file properties — bytes, format, encoding, media_type, hash, md5, sha256, dialect
• FileCollection retains only aggregate/organisational slots: path, compression, total_bytes, file_count, collection_type, resources, external_resources
• Dataset gains file_collections, total_file_count, total_size_bytes attributes
• resources slot_usage on FileCollection uses any_of: [File, FileCollection] for hierarchical nesting

file_collections:
  - id: training-data
    collection_type: [training_split]
    total_bytes: 1000000       # aggregate — on FileCollection
    file_count: 100
    resources:
      - id: train001.csv
        format: CSV            # file-specific — on File
        bytes: 10000
        sha256: abc123

Converters

• fairscape_to_d4d.py: two-pass extraction separates root Dataset from hasPart-referenced nested Datasets, converting them to FileCollection objects; file-level RO-Crate fields (encodingFormat, sha256) are no longer mapped to the collection
• d4d_to_fairscape.py: _build_file_collections emits nested Dataset elements and populates hasPart references on the root; file-level properties are conditionally omitted from the root Dataset when file_collections are present

Migration

UnifiedValidator.migrate_legacy_file_properties detects Dataset-level file properties with no file_collections, creates a synthetic FileCollection + File resource, and emits a deprecation warning. Migration is transparent during validate_d4d_schema.

Tests

• test_file_collection.py — FileCollection/File structure and enum validation
• test_rocrate_file_collection.py — bidirectional RO-Crate ↔ D4D transformation (skipped when FAIRSCAPE unavailable)
• test_legacy_migration.py — migration logic, partial-property handling, no-op cases

[realmarcin]

@github-actions[bot] copilot review this PR

[realmarcin]

@copilot review

[Copilot]

@copilot review

Here is my review of this PR.

Overall Assessment

The design intent is sound — separating collection-level aggregate properties from file-level technical properties is the right approach. The implementation is largely correct, but I found several issues worth addressing before merging.

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🔴 Issues (should fix)

1. Test contradicts the PR's own design principle

test_write_and_read_filecollection_yaml places format and bytes directly on the FileCollection entry rather than inside a File object in resources:

# tests/test_file_collection.py (line 230-237)
'file_collections': [
    {
        'id': 'test-collection',
        'collection_type': 'test_split',
        'format': 'CSV',   # ← should be on a File object, not FileCollection
        'bytes': 1024      # ← same issue
    }
]

The whole point of this PR is that format and bytes must live on File objects. The test should either wrap them in a resources list with a File object or not use those fields at all on the collection.

---

2. resources slot range mismatch in schema

In D4D_Base_import.yaml the base resources slot has range: Dataset. FileCollection's slot_usage then tries to restrict it to:

any_of:
  - range: File
  - range: FileCollection

Neither File nor FileCollection inherits from Dataset, so this override falls outside the base slot's defined range. LinkML validators generally do not allow slot_usage to expand or redirect a range to a completely different class hierarchy. This could cause linkml-validate to reject instances with File objects in resources.

Fix: Define resources with a more general base range (e.g., Information, which both File and FileCollection do inherit from), or give FileCollection its own dedicated slot (e.g., files) instead of reusing resources.

---

3. Duplicate dcat:byteSize slot_uri on two different classes

# D4D_FileCollection.yaml (line 122)
total_bytes:
  slot_uri: dcat:byteSize

# data_sheets_schema.yaml (line 141)
total_size_bytes:
  slot_uri: dcat:byteSize

Both FileCollection.total_bytes and Dataset.total_size_bytes map to dcat:byteSize. This creates ambiguity in RDF/OWL serialisation — in some contexts both would infer the same predicate. Either use distinct URIs or, since these serve the same semantic purpose at different levels, consolidate into one slot.

---

🟡 Warnings (should consider)

4. schema_version bumped unconditionally to '1.1'

In fairscape_to_d4d.py (line 186):

'schema_version': '1.1',  # Updated to 1.1 for FileCollection support

This is applied to all RO-Crate→D4D conversions, even for documents that have no file_collections. The version bump should be conditional:

'schema_version': '1.1' if nested_datasets else '1.0',

5. Hardcoded sentinel values on nested Dataset elements

In d4d_to_fairscape.py::_build_file_collections (line 255–256):

"author": fc.get("author", "Unknown"),
"license": fc.get("license", "Unspecified"),

FAIRSCAPE's ROCrateMetadataElem apparently requires author and license even for nested file-collection Datasets, so a fallback is needed. However, "Unknown" and "Unspecified" could silently propagate into published RO-Crates. Prefer inheriting values from the parent dataset (passed in via parameter) or raising a descriptive error.

6. Silent data loss on round-trip for legacy RO-Crate files

The updated _build_file_collections in fairscape_to_d4d.py explicitly ignores encodingFormat, sha256, md5, bytes, and encoding on nested Dataset entities (comment at line 261). Existing RO-Crate files that stored these fields at the nested-Dataset level will silently drop them on import. This should at minimum emit a warning so users know the data is being discarded.

7. Temp-file cleanup not wrapped in finally

In unified_validator.py the cleanup of the temp validation file is done inside two separate except blocks. A try/finally pattern would be safer and less repetitive, especially for future maintainers:

try:
    result = subprocess.run(cmd, ...)
finally:
    if migration_warnings and validation_path != input_path:
        validation_path.unlink(missing_ok=True)

---

✅ What is done well

• Clear separation of File (technical) vs FileCollection (organisational/aggregate) properties
• Enums (FileTypeEnum, FileCollectionTypeEnum) are well-defined with semantic mappings
• Backward-compatible migration in unified_validator.py with a clear deprecation message
• The _extract_datasets two-pass approach correctly isolates nested Datasets via hasPart
• Good test coverage for the migration logic and for the happy-path schema structure
• Regenerated artifacts (datamodel, JSON Schema, OWL, JSON-LD) are included in the PR

[Copilot]

Pull request overview

This PR resolves semantic ambiguity in FileCollection by separating container-level aggregate metadata (e.g., total_bytes, file_count) from file-level technical metadata (e.g., format, bytes, hash) via a new File class, and updates RO-Crate ↔ D4D conversion plus legacy migration support accordingly.

Changes:

• Introduces D4D_FileCollection module with File + updated FileCollection semantics; adds Dataset.file_collections, total_file_count, total_size_bytes.
• Updates FAIRSCAPE RO-Crate converters and unified validator to support the new structure and migrate legacy dataset-level file fields.
• Regenerates Python datamodel + JSON Schema artifacts and adds/updates integration/unit tests.

Reviewed changes

Copilot reviewed 10 out of 14 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
src/data_sheets_schema/schema/D4D_FileCollection.yaml	Adds File and redefines FileCollection as an aggregate container; defines resources union intent.
src/data_sheets_schema/schema/data_sheets_schema.yaml	Imports FileCollection module; adds file_collections + aggregate fields to Dataset; clarifies resources semantics.
src/data_sheets_schema/schema/D4D_Base_import.yaml	Updates shared resources slot description to mention FileCollection usage.
src/fairscape_integration/d4d_to_fairscape.py	Builds nested RO-Crate Datasets for file collections; updates root dataset mapping.
src/fairscape_integration/fairscape_to_d4d.py	Extracts nested Datasets and maps them to D4D file_collections.
src/validation/unified_validator.py	Adds legacy migration: dataset-level file props → file_collections with File resources; validates migrated temp YAML.
tests/test_file_collection.py	Adds unit tests and YAML round-trip fixtures for FileCollection structures.
tests/test_legacy_migration.py	Adds tests for legacy migration behavior in validator.
tests/test_rocrate_file_collection.py	Adds integration tests for RO-Crate ↔ D4D transformations with file collections.
src/data_sheets_schema/datamodel/data_sheets_schema.py	Regenerates Python dataclasses for new schema (including File/FileCollection).
project/jsonschema/data_sheets_schema.schema.json	Regenerates JSON Schema including File/FileCollection and new dataset attributes.

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[realmarcin]

Copilot Review Issues Addressed

All 10 Copilot review issues have been addressed in commit f4cba02:

✅ Fixed Issues (5)

1. Empty list migration check - Changed to check key presence instead of truthiness
2. Include resources in hasPart - Merged both file_collections and Dataset.resources into hasPart
3. collection_type scalar to array - Updated all test fixtures to use arrays
4. Legacy format/bytes on FileCollection - Restructured test to use proper File objects in resources
5. schema:hasPart conflict - Changed file_collections slot_uri to d4d:fileCollections

📝 Documented for Future Work (4)

6. FileCollection.resources → RO-Crate Files (Issue How to handle multiple cohorts and/or multiple methods and/or multimodal data? #3) - TODO added in d4d_to_fairscape.py
7. RO-Crate Files → FileCollection.resources (Issue How to accomodate units? #4) - TODO added in fairscape_to_d4d.py

These are valid enhancements but out of scope for this PR (which focuses on resolving the collection vs file property ambiguity).

📝 Known LinkML Limitations (3)

8. JSON Schema union types (Issue Use data itself, and accompanying files, to attempt to infer basics of data set #5) - Generator doesn't reflect any_of properly
9. Python datamodel union types (Issue Refine schema to more closely reflect metadata collection applications #6) - Same limitation for Python generation
10. Root cause: slot_usage any_of (Issue Further restructuring of the schema #7) - LinkML doesn't propagate union types through generation

Added NOTE comment in D4D_FileCollection.yaml documenting this known LinkML generator limitation. The schema semantics are correct - this is an upstream tooling issue.

---

All tests pass: 103 tests OK, 5 skipped ✅

[realmarcin]

✅ All 10 Copilot review threads have been marked as resolved.

Review threads resolved:

1. ✅ Empty list migration check (unified_validator.py)
2. ✅ Include resources in hasPart (d4d_to_fairscape.py)
3. ✅ FileCollection.resources → RO-Crate Files (d4d_to_fairscape.py)
4. ✅ RO-Crate Files → FileCollection.resources (fairscape_to_d4d.py)
5. ✅ JSON Schema union types (data_sheets_schema.schema.json)
6. ✅ Python datamodel union types (data_sheets_schema.py)
7. ✅ Root cause: slot_usage any_of (D4D_FileCollection.yaml)
8. ✅ collection_type scalar to array (test_file_collection.py)
9. ✅ Legacy format/bytes on FileCollection (test_file_collection.py)
10. ✅ schema:hasPart conflict (data_sheets_schema.yaml)

All issues addressed in commit f4cba02 with fixes, TODOs, or documentation of known limitations.