[ISSUE-10] Implement domestication planner/service with approvals#77
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| metadata = { | ||
| "source_stage": "domestication", | ||
| "source_part_identity": job.part_identity, | ||
| "insert_identities": [job.part_identity], |
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The domestication product metadata only records identities and never provides an implementation_identity, and this service also does not create an sbol2.Implementation for the new plasmid. When this generated product is later selected by AssemblyLvl1Stage, AssemblyService._implementation_from_plasmid_record raises because it requires either metadata implementation_identity or an implementation in the source document. That makes domesticated products non-consumable in downstream assembly for runs where no pre-existing part plasmid is available.
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Summary
- Fixed the domestication SBOL service to preserve all source roles by assigning the full roles list once, rather than overwriting per-loop iteration. src/buildcompiler/sbol/domestication.pyL43-L44
- Added generation and registration of an
sbol2.Implementationfor each domesticated product, wired itsbuiltfield to the generated component, and recordedimplementation_identityin product metadata for downstream assembly resolution. src/buildcompiler/sbol/domestication.pyL46-L56 - Corrected
IndexedPlasmid.identityto use the canonical identity from the created SBOL component, ensuring consistency between metadata/implementation references and stored product identity. src/buildcompiler/sbol/domestication.pyL64-L71 - Extended the domestication service unit test to verify role preservation and implementation creation/resolution behavior. tests/unit/sbol/test_domestication_service.pyL12-L40
Testing
- ✅
pytest tests/unit/sbol/test_domestication_service.py - ✅
pytest tests/unit/planning/test_domestication_planner.py tests/unit/sbol/test_domestication_service.py tests/unit/stages/test_domestication_stage.py
Committed on the current branch as:
58ccf8c - Fix domestication SBOL implementation metadata and role copying
Also created a follow-up PR message via make_pr summarizing these changes on top of the original PR.
| for role in component.roles: | ||
| product_component.roles = role |
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Assigning product_component.roles = role inside the loop overwrites prior values, so only the last source role is retained. If a source part carries multiple ontology roles, the generated domesticated SBOL object silently drops all but one role, which can break downstream logic that depends on preserved role annotations.
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I checked the branch state, and this issue is already fixed in the current HEAD commit (b50b13f), so there was nothing additional to patch.
What I verified
- ✅
git status --short(clean working tree; no pending changes) - ✅
git log --oneline -n 5(includesb50b13f Fix domestication SBOL implementation metadata and role copying)
Because no new code changes were required, I did not create a new commit and did not call make_pr (per your workflow rules).
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Motivation
Description
src/buildcompiler/planning/domestication.pyintroducingSequenceEditProposal,DomesticationPlan, andDomesticationPlannerwhich validates part roles, requires a usable DNA sequence, and detects internal BsaI motifs (GGTCTC/GAGACC) as non-mutating proposals.src/buildcompiler/sbol/domestication.pywithDomesticationJob,DomesticationSbolResult, andDomesticationServicethat emits a minimal generatedIndexedPlasmidproduct, attaches provenance (source part, backbone, reagents, and proposals), and adds SBOL objects to the target document without writing files.src/buildcompiler/stages/domestication.pythat resolves the source part, produces structuredMissingBuildInputblockers for missing backbone/reagents, enforces a hard approval gate viaRequiredApprovalfor proposed sequence edits, and indexes generated products viainventory.add_generated_product()withinsert_identitiesset to the source part identity.src/buildcompiler/planning/__init__.py,src/buildcompiler/sbol/__init__.py, andsrc/buildcompiler/stages/__init__.py, and kept changes lightweight (no Opentrons/PUDU/SBOLInventory dependencies at runtime of core imports).domestication_sequence_editand stable approval id convention isdomestication-edit:<part_identity>; sequence edits are represented asSequenceEditProposalrecords surfaced inStageResult.protocol_artifactsandRequiredApproval.metadata.Testing
tests/unit/planning/test_domestication_planner.py(planner role/sequence/bsai detection),tests/unit/sbol/test_domestication_service.py(product/provenance), andtests/unit/stages/test_domestication_stage.py(missing backbone/reagent blockers, approval gating, protocol-mode behavior, approved-process success).python -c "from buildcompiler.api.options import BuildOptions"— succeeded.python -c "from buildcompiler.inventory import Inventory, CompatibilitySelector"— succeeded.python -c "from buildcompiler.stages import AssemblyLvl1Stage"— succeeded.python -c "from buildcompiler.domain import StageResult, MissingBuildInput, RequiredApproval, ApprovalStatus"— succeeded.python -c "from buildcompiler.stages import DomesticationStage"— succeeded.python -c "from buildcompiler.sbol import DomesticationService"— succeeded.python -c "from buildcompiler.planning import DomesticationPlanner"— succeeded.uv run pytest tests/unit/planning/test_domestication.py tests/unit/sbol/test_domestication_service.py tests/unit/stages/test_domestication.py— failed in this environment due to network/Git fetch of optionalSBOLInventorydependency (403), souvvirtualenv provisioning could not complete.pytest tests/unit/planning/test_domestication_planner.py tests/unit/sbol/test_domestication_service.py tests/unit/stages/test_domestication_stage.py— succeeded (these targeted tests passed).pytest tests/unit/domain tests/unit/api tests/unit/inventory tests/unit/planning tests/unit/sbol tests/unit/stages— succeeded; all unit suites report53 passed.ruff check . && ruff format --check .— failed due to pre-existing unrelated lint issues in legacy files and notebooks (these are outside this PR scope).uv-based environment setup failed due to network restrictions fetching an optional dependency and is a CI/environment issue rather than code failure.Codex Task