feat: Implement Subject vs Object refactor #158
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Add new Subject concept to separate facts (Objects) from decision scopes (Subjects). Changes: - Database: Add sx_instance_seq sequence and polymorphic ORM classes (subject_template, subject_instance, subject_instance_lineage) - Config: Add subject templates for accession, analysis_bundle, report, and generic subject kinds - Helper Functions: Create bloom_lims/subjecting.py with create_subject, add_subject_members, list_subjects_for_object, etc. - Actions: Add create-subject-and-anchor action to core.json - UI: Display subject relationships in euid_details.html - Tests: Add test_subject_model.py with 12 passing tests - Docs: Add Subjects vs Objects section to README.md Subjects are logical aggregates that decisions apply to, spanning multiple objects. They have stable, deterministic keys and support idempotent creation.
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| bob.session.commit() | ||
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| # Create anchor relationship | ||
| link_subject_anchor(bob, subject.euid, anchor_euid) | ||
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In create_subject, the subject is committed before creating the anchor lineage and the return value of link_subject_anchor is ignored. If anchor_euid is invalid or the lineage insert fails (e.g., FK error), this function still returns a new subject EUID even though the subject has no anchor, leaving orphaned “decision scopes” that violate the model’s invariants and will surface in UI queries. Consider checking the link result and rolling back (or deleting) the subject when the anchor relationship cannot be created, or move the commit until after the link succeeds.
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Add new Subject concept to separate facts (Objects) from decision scopes (Subjects).
Changes:
Subjects are logical aggregates that decisions apply to, spanning multiple objects. They have stable, deterministic keys and support idempotent creation.