[SPRINT-02-02] Split collection pulling from SBOL document indexing

[Gonza10V]

Motivation

• Decouple SynBioHub network fetching from SBOL document indexing to make collection indexing reusable for local sbol2.Document objects and easier to test and debug.
• Preserve existing constructor behavior that accepts SynBioHub URIs while avoiding hidden network pulls when indexing local documents.
• Improve separation of concerns to make indexing helpers individually testable and to clarify failure modes (fetch vs indexing).

Description

• Added pull_collection_uris(self, uris: list[str]) -> sbol2.Document to perform SynBioHub pull operations and raise a RuntimeError with URI context on fetch failure. (changed file: src/buildcompiler/buildcompiler.py).
• Added index_sbol_document(self, doc: sbol2.Document, source: str = "local") to perform SBOL scanning/classification without invoking sbh.pull, and changed _index_collections into a compatibility wrapper that calls pull_collection_uris then index_sbol_document. (changed file: src/buildcompiler/buildcompiler.py).
• Extracted smaller indexing helpers _index_implementation, _index_strain_module, _index_plasmid_or_backbone_definition, and _index_reagent_implementation and updated _index_document_objects signature to accept a source parameter; preserved existing list-based runtime state (indexed_plasmids, indexed_backbones, restriction_enzyme_implementations, ligase_implementations). (changed file: src/buildcompiler/buildcompiler.py).
• Fixed an undefined-variable bug in _get_abstract_design by iterating self.sbol_doc.componentDefinitions.
• Added targeted unit tests that exercise local-document indexing and the pull-then-index compatibility behavior. (changed file: tests/test_buildcompiler.py).

Testing

• Ran pytest -k "index or collection or synbiohub" and observed all selected tests passed: 16 passed, 107 deselected.
• Ran ruff check src/buildcompiler/buildcompiler.py tests/test_buildcompiler.py and the checks passed for the modified files.
• Attempted the broader integration command uv run python -m unittest discover -s tests, which failed in this environment due to an external git dependency fetch error for SBOLInventory (HTTP 403), so full test discovery could not complete here.
• Verified that local document indexing path does not call sbh.pull and that pull failures surface with URI context while indexing failures remain distinct via the new unit tests (tests/test_buildcompiler.py).

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[chatgpt-codex-connector]

Index component definitions from the input document

index_sbol_document accepts an arbitrary SBOL document, but _index_document_objects iterates self.sbol_doc.componentDefinitions instead of source_doc.componentDefinitions. In the new local-indexing flow (where the passed doc is not already merged into self.sbol_doc), plasmid/backbone definitions in that document are skipped, and related implementations can later fail object resolution. This makes local document indexing silently incomplete unless callers do an extra manual merge step.

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