Index

A

activity_identity (buildcompiler.sbol.assembly.AssemblySbolResult attribute) (buildcompiler.sbol.transformation.TransformationSbolResult attribute) adapters (buildcompiler.api.compiler.BuildCompiler attribute) (buildcompiler.execution.context.BuildContext attribute) add_edge() (buildcompiler.reporting.graph.BuildGraph method) add_generated_product() (buildcompiler.inventory.inventory.Inventory method) add_node() (buildcompiler.reporting.graph.BuildGraph method) add_object_to_doc() (in module buildcompiler.sbol2build) allow_large_expansion (buildcompiler.api.options.CombinatorialOptions attribute) allow_large_order_search (buildcompiler.api.options.Lvl2SearchOptions attribute) allow_reagent_purchase (buildcompiler.api.options.ReagentOptions attribute) allow_sequence_domestication_edits (buildcompiler.api.options.DomesticationOptions attribute) ALWAYS_REFRESH (buildcompiler.sbol.resolver.PullPolicy attribute) append_extracts_to_doc() (in module buildcompiler.sbol2build) approval_count (buildcompiler.reporting.report.StageReportSection attribute) ApprovalOptions (class in buildcompiler.api.options) approvals (buildcompiler.api.options.BuildOptions attribute) ApprovalStatus (class in buildcompiler.domain.approvals) APPROVED (buildcompiler.domain.approvals.ApprovalStatus attribute) approved (buildcompiler.planning.domestication.SequenceEditProposal attribute)

approved_approval_ids (buildcompiler.api.options.ApprovalOptions attribute) approved_processes (buildcompiler.api.options.ApprovalOptions attribute) artifacts (buildcompiler.sbol.domestication.DomesticationSbolResult attribute) (buildcompiler.sbol.transformation.TransformationSbolResult attribute) ASSEMBLED (buildcompiler.domain.material_state.MaterialState attribute) Assembly (class in buildcompiler.sbol2build) ASSEMBLY_LVL1 (buildcompiler.domain.build_stage.BuildStage attribute) assembly_lvl1() (buildcompiler.buildcompiler.BuildCompiler method) (in module buildcompiler.api.compiler) ASSEMBLY_LVL2 (buildcompiler.domain.build_stage.BuildStage attribute) assembly_lvl2() (buildcompiler.buildcompiler.BuildCompiler method) (in module buildcompiler.api.compiler) assembly_plan_RDF_to_JSON() (in module buildcompiler.robotutils) assembly_route_to_pudu_json() (in module buildcompiler.adapters.pudu.assembly_json) assembly_routes_to_pudu_json() (in module buildcompiler.adapters.pudu.assembly_json) AssemblyJob (class in buildcompiler.sbol.assembly) AssemblyLvl1Stage (class in buildcompiler.stages.assembly_lvl1) AssemblyLvl2Stage (class in buildcompiler.stages.assembly_lvl2) AssemblySbolResult (class in buildcompiler.sbol.assembly) AssemblyService (class in buildcompiler.sbol.assembly) AUTOMATED (buildcompiler.api.options.ProtocolMode attribute)

B

backbone (buildcompiler.inventory.compatibility.Lvl1Route attribute) (buildcompiler.inventory.compatibility.Lvl2Route attribute) (buildcompiler.sbol.assembly.AssemblyJob attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) backbone_digestion() (in module buildcompiler.sbol2build) backbone_identity (buildcompiler.planning.domestication.DomesticationPlan attribute) bacterial_transformation() (in module buildcompiler.transformation) BLOCKED (buildcompiler.domain.status.StageStatus attribute) build_document (buildcompiler.domain.build_result.FullBuildResult attribute) (buildcompiler.execution.context.BuildContext attribute) build_graph() (in module buildcompiler.reporting.graph) build_report() (in module buildcompiler.reporting.report) build_summary() (in module buildcompiler.reporting.summary) BuildCompiler (class in buildcompiler.api.compiler) (class in buildcompiler.buildcompiler) buildcompiler.adapters.opentrons.simulation module buildcompiler.adapters.protocols module buildcompiler.adapters.pudu.assembly_json module buildcompiler.adapters.pudu.plating_json module buildcompiler.adapters.pudu.transformation_json module buildcompiler.api.compiler module buildcompiler.api.options module buildcompiler.buildcompiler module buildcompiler.constants module buildcompiler.domain.approvals module buildcompiler.domain.build_request module buildcompiler.domain.build_result module buildcompiler.domain.build_stage module buildcompiler.domain.design module buildcompiler.domain.material_state module buildcompiler.domain.missing_input module buildcompiler.domain.plasmid module buildcompiler.domain.reagent module buildcompiler.domain.status module buildcompiler.domain.warnings module buildcompiler.execution.context module buildcompiler.execution.executor module

buildcompiler.inventory.compatibility module buildcompiler.inventory.inventory module buildcompiler.inventory.selector module buildcompiler.planning.classifier module buildcompiler.planning.combinatorial module buildcompiler.planning.domestication module buildcompiler.planning.full_build_planner module buildcompiler.planning.models module buildcompiler.planning.validation module buildcompiler.plasmid module buildcompiler.reporting.graph module buildcompiler.reporting.report module buildcompiler.reporting.summary module buildcompiler.robotutils module buildcompiler.sbol.assembly module buildcompiler.sbol.domestication module buildcompiler.sbol.resolver module buildcompiler.sbol.transformation module buildcompiler.sbol2build module buildcompiler.stages.assembly_lvl1 module buildcompiler.stages.assembly_lvl2 module buildcompiler.stages.domestication module buildcompiler.stages.transformation module buildcompiler.transformation module BuildContext (class in buildcompiler.execution.context) BuildGraph (class in buildcompiler.reporting.graph) BuildGraphEdge (class in buildcompiler.reporting.graph) BuildGraphNode (class in buildcompiler.reporting.graph) BuildOptions (class in buildcompiler.api.options) BuildPlan (class in buildcompiler.planning.models) BuildReport (class in buildcompiler.reporting.report) BuildRequest (class in buildcompiler.domain.build_request) BuildStage (class in buildcompiler.domain.build_stage) BuildStatus (class in buildcompiler.domain.status) BuildSummary (class in buildcompiler.reporting.summary) BuildWarning (class in buildcompiler.domain.warnings)

C

candidates_tried (buildcompiler.domain.missing_input.MissingBuildInput attribute) chassis_display_id (buildcompiler.api.options.TransformationOptions attribute) (buildcompiler.sbol.transformation.TransformationJob attribute) chassis_identity (buildcompiler.api.options.TransformationOptions attribute) (buildcompiler.sbol.transformation.TransformationJob attribute) chemical_transformation() (buildcompiler.sbol2build.Transformation method) classify_non_combinatorial() (in module buildcompiler.planning.classifier) classify_part_role() (in module buildcompiler.planning.validation) code (buildcompiler.domain.warnings.BuildWarning attribute) (buildcompiler.reporting.report.RecommendedAction attribute)

combinatorial (buildcompiler.api.options.PlanningOptions attribute) COMBINATORIAL_DERIVATION (buildcompiler.domain.design.DesignKind attribute) CombinatorialOptions (class in buildcompiler.api.options) CompatibilitySelector (class in buildcompiler.inventory.selector) COMPONENT_DEFINITION (buildcompiler.domain.design.DesignKind attribute) constraint_violations (buildcompiler.inventory.compatibility.RouteScore attribute) constraints (buildcompiler.domain.build_request.BuildRequest attribute) content (buildcompiler.adapters.protocols.ProtocolArtifact attribute) continue_on_error (buildcompiler.api.options.ExecutionOptions attribute)

D

default_ligase (buildcompiler.api.options.ReagentOptions attribute) default_restriction_enzyme (buildcompiler.api.options.ReagentOptions attribute) dependency_chain (buildcompiler.reporting.report.BuildReport attribute) DependencyChainStep (class in buildcompiler.reporting.report) DesignKind (class in buildcompiler.domain.design) display_id (buildcompiler.domain.plasmid.IndexedBackbone attribute) (buildcompiler.domain.plasmid.IndexedPlasmid attribute) (buildcompiler.domain.plasmid.IndexedStrain attribute) (buildcompiler.domain.reagent.IndexedReagent attribute) dna_componentdefinition_with_sequence() (in module buildcompiler.sbol2build) domestication (buildcompiler.api.options.BuildOptions attribute) DOMESTICATION (buildcompiler.domain.build_stage.BuildStage attribute)

domestication() (buildcompiler.buildcompiler.BuildCompiler method) (in module buildcompiler.api.compiler) domestication_artifact_to_pudu_json() (in module buildcompiler.adapters.pudu.assembly_json) domestication_artifacts_to_pudu_json() (in module buildcompiler.adapters.pudu.assembly_json) domestication_requests (buildcompiler.planning.models.BuildPlan attribute) DomesticationJob (class in buildcompiler.sbol.domestication) DomesticationOptions (class in buildcompiler.api.options) DomesticationPlan (class in buildcompiler.planning.domestication) DomesticationPlanner (class in buildcompiler.planning.domestication) DomesticationSbolResult (class in buildcompiler.sbol.domestication) DomesticationService (class in buildcompiler.sbol.domestication) DomesticationStage (class in buildcompiler.stages.domestication)

E

edges (buildcompiler.reporting.graph.BuildGraph attribute) enabled (buildcompiler.api.options.TransformationOptions attribute) enzyme_name (buildcompiler.planning.domestication.SequenceEditProposal attribute) execute() (buildcompiler.api.compiler.BuildCompiler method) (buildcompiler.execution.executor.FullBuildExecutor method)

execution (buildcompiler.api.options.BuildOptions attribute) ExecutionOptions (class in buildcompiler.api.options) executive_summary (buildcompiler.reporting.report.BuildReport attribute) executor (buildcompiler.api.compiler.BuildCompiler attribute) expand_combinatorial_derivation() (in module buildcompiler.planning.combinatorial) extract_combinatorial_design_parts() (buildcompiler.buildcompiler.BuildCompiler method)

F

FAILED (buildcompiler.domain.status.BuildStatus attribute) (buildcompiler.domain.status.StageStatus attribute) final_product_count (buildcompiler.reporting.summary.BuildSummary attribute) final_products (buildcompiler.domain.build_result.FullBuildResult attribute) find_backbone() (buildcompiler.inventory.inventory.Inventory method) find_ligase() (buildcompiler.inventory.inventory.Inventory method) find_lvl1_region_plasmids() (buildcompiler.inventory.inventory.Inventory method) find_restriction_enzyme() (buildcompiler.inventory.inventory.Inventory method) find_single_part_plasmids() (buildcompiler.inventory.inventory.Inventory method) from_dependencies() (buildcompiler.execution.executor.FullBuildExecutor class method)

from_local_documents() (buildcompiler.buildcompiler.BuildCompiler class method) from_synbiohub() (buildcompiler.api.compiler.BuildCompiler class method) full_build() (buildcompiler.api.compiler.BuildCompiler method) (buildcompiler.buildcompiler.BuildCompiler method) (in module buildcompiler.api.compiler) FullBuildExecutor (class in buildcompiler.execution.executor) FullBuildPlanner (class in buildcompiler.planning.full_build_planner) FullBuildResult (class in buildcompiler.domain.build_result) fusion_site_names (buildcompiler.sbol.domestication.DomesticationJob attribute) fusion_site_sequences (buildcompiler.sbol.domestication.DomesticationJob attribute)

G

generate_96_well_positions() (in module buildcompiler.robotutils) GENERATED (buildcompiler.domain.material_state.MaterialState attribute) generated_or_planned_materials (buildcompiler.inventory.compatibility.RouteScore attribute) get_combinatorial_derivation() (buildcompiler.sbol.resolver.SbolResolver method) get_component() (buildcompiler.sbol.resolver.SbolResolver method)

get_implementation() (buildcompiler.sbol.resolver.SbolResolver method) get_module() (buildcompiler.sbol.resolver.SbolResolver method) graph (buildcompiler.domain.build_result.FullBuildResult attribute) (buildcompiler.execution.context.BuildContext attribute) graph_summary (buildcompiler.reporting.report.BuildReport attribute)

I

id (buildcompiler.domain.build_request.BuildRequest attribute) (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.reporting.graph.BuildGraphNode attribute) identity (buildcompiler.domain.plasmid.IndexedBackbone attribute) (buildcompiler.domain.plasmid.IndexedPlasmid attribute) (buildcompiler.domain.plasmid.IndexedStrain attribute) (buildcompiler.domain.reagent.IndexedReagent attribute) identity_tiebreak (buildcompiler.inventory.compatibility.RouteScore attribute) include_detailed_report (buildcompiler.api.options.ReportingOptions attribute) include_extracted_parts (buildcompiler.sbol.assembly.AssemblyJob attribute)

include_rejected_routes (buildcompiler.api.options.ReportingOptions attribute) index_document() (buildcompiler.buildcompiler.BuildCompiler method) IndexedBackbone (class in buildcompiler.domain.plasmid) IndexedPlasmid (class in buildcompiler.domain.plasmid) IndexedReagent (class in buildcompiler.domain.reagent) IndexedStrain (class in buildcompiler.domain.plasmid) initialize_assembly_activity() (buildcompiler.sbol2build.Assembly method) inventory (buildcompiler.api.compiler.BuildCompiler attribute) (buildcompiler.execution.context.BuildContext attribute) Inventory (class in buildcompiler.inventory.inventory) is_circular() (in module buildcompiler.sbol2build)

J

json_intermediate (buildcompiler.domain.build_result.StageResult attribute)

K

kind (buildcompiler.adapters.protocols.ProtocolArtifact attribute) (buildcompiler.reporting.graph.BuildGraphNode attribute)

L

label (buildcompiler.reporting.graph.BuildGraphNode attribute) legacy_assembly_route_to_pudu_json() (in module buildcompiler.adapters.pudu.assembly_json) legacy_assembly_routes_to_pudu_json() (in module buildcompiler.adapters.pudu.assembly_json) ligase (buildcompiler.sbol.assembly.AssemblyJob attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) ligase_name (buildcompiler.planning.domestication.DomesticationPlan attribute) ligation() (in module buildcompiler.sbol2build) load_json_or_dict() (in module buildcompiler.robotutils) logger (buildcompiler.execution.context.BuildContext attribute) logs (buildcompiler.adapters.opentrons.simulation.SimulationResult attribute) (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.reporting.report.StageReportSection attribute) (buildcompiler.sbol.assembly.AssemblySbolResult attribute) (buildcompiler.sbol.domestication.DomesticationSbolResult attribute) (buildcompiler.sbol.transformation.TransformationSbolResult attribute)

lower_material_state_penalty (buildcompiler.inventory.compatibility.RouteScore attribute) lvl1_requests (buildcompiler.planning.models.BuildPlan attribute) Lvl1Route (class in buildcompiler.inventory.compatibility) lvl2_requests (buildcompiler.planning.models.BuildPlan attribute) lvl2_search (buildcompiler.api.options.PlanningOptions attribute) Lvl2Route (class in buildcompiler.inventory.compatibility) Lvl2SearchOptions (class in buildcompiler.api.options)

M

MANUAL (buildcompiler.api.options.ProtocolMode attribute) MaterialState (class in buildcompiler.domain.material_state) max_exhaustive_region_count (buildcompiler.api.options.Lvl2SearchOptions attribute) max_iterations (buildcompiler.api.options.ExecutionOptions attribute) max_rejected_routes (buildcompiler.api.options.ReportingOptions attribute) max_variants (buildcompiler.api.options.CombinatorialOptions attribute) maybe_pull() (buildcompiler.sbol.resolver.SbolResolver method) maybe_write_protocol_artifacts() (in module buildcompiler.adapters.protocols) message (buildcompiler.domain.warnings.BuildWarning attribute) (buildcompiler.reporting.report.RecommendedAction attribute) metadata (buildcompiler.adapters.opentrons.simulation.SimulationResult attribute) (buildcompiler.adapters.protocols.ProtocolArtifact attribute) (buildcompiler.domain.approvals.RequiredApproval attribute) (buildcompiler.domain.plasmid.IndexedBackbone attribute) (buildcompiler.domain.plasmid.IndexedPlasmid attribute) (buildcompiler.domain.plasmid.IndexedStrain attribute) (buildcompiler.domain.reagent.IndexedReagent attribute) (buildcompiler.domain.warnings.BuildWarning attribute) (buildcompiler.planning.models.UnsupportedPlanningRecord attribute) (buildcompiler.reporting.graph.BuildGraphEdge attribute) (buildcompiler.reporting.graph.BuildGraphNode attribute) (buildcompiler.reporting.report.DependencyChainStep attribute) (buildcompiler.reporting.report.RecommendedAction attribute) missing_display_id (buildcompiler.domain.missing_input.MissingBuildInput attribute) missing_domestications (buildcompiler.inventory.compatibility.RouteScore attribute) missing_identity (buildcompiler.domain.missing_input.MissingBuildInput attribute) missing_input_count (buildcompiler.reporting.report.StageReportSection attribute) (buildcompiler.reporting.summary.BuildSummary attribute) missing_inputs (buildcompiler.domain.build_result.FullBuildResult attribute) (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.reporting.report.BuildReport attribute) missing_kind (buildcompiler.domain.missing_input.MissingBuildInput attribute) missing_lvl1_plasmids (buildcompiler.inventory.compatibility.RouteScore attribute) MISSING_ONLY (buildcompiler.sbol.resolver.PullPolicy attribute) missing_part_identities (buildcompiler.inventory.compatibility.Lvl1Route attribute) missing_region_identities (buildcompiler.inventory.compatibility.Lvl2Route attribute) missing_required_products (buildcompiler.inventory.compatibility.RouteScore attribute) MissingBuildInput (class in buildcompiler.domain.missing_input) mode (buildcompiler.api.options.ProtocolOptions attribute) module buildcompiler.adapters.opentrons.simulation buildcompiler.adapters.protocols buildcompiler.adapters.pudu.assembly_json buildcompiler.adapters.pudu.plating_json buildcompiler.adapters.pudu.transformation_json buildcompiler.api.compiler buildcompiler.api.options buildcompiler.buildcompiler buildcompiler.constants buildcompiler.domain.approvals buildcompiler.domain.build_request buildcompiler.domain.build_result buildcompiler.domain.build_stage buildcompiler.domain.design buildcompiler.domain.material_state buildcompiler.domain.missing_input buildcompiler.domain.plasmid buildcompiler.domain.reagent buildcompiler.domain.status buildcompiler.domain.warnings buildcompiler.execution.context buildcompiler.execution.executor buildcompiler.inventory.compatibility buildcompiler.inventory.inventory buildcompiler.inventory.selector buildcompiler.planning.classifier buildcompiler.planning.combinatorial buildcompiler.planning.domestication buildcompiler.planning.full_build_planner buildcompiler.planning.models buildcompiler.planning.validation buildcompiler.plasmid buildcompiler.reporting.graph buildcompiler.reporting.report buildcompiler.reporting.summary buildcompiler.robotutils buildcompiler.sbol.assembly buildcompiler.sbol.domestication buildcompiler.sbol.resolver buildcompiler.sbol.transformation buildcompiler.sbol2build buildcompiler.stages.assembly_lvl1 buildcompiler.stages.assembly_lvl2 buildcompiler.stages.domestication buildcompiler.stages.transformation buildcompiler.transformation

MODULE_DEFINITION (buildcompiler.domain.design.DesignKind attribute)

N

name (buildcompiler.domain.plasmid.IndexedBackbone attribute) (buildcompiler.domain.plasmid.IndexedPlasmid attribute) (buildcompiler.domain.plasmid.IndexedStrain attribute) (buildcompiler.domain.reagent.IndexedReagent attribute) NEVER (buildcompiler.sbol.resolver.PullPolicy attribute)

next_actions (buildcompiler.reporting.report.BuildReport attribute) nodes (buildcompiler.reporting.graph.BuildGraph attribute) NONE (buildcompiler.api.options.ProtocolMode attribute) normalize_plating_input() (in module buildcompiler.robotutils) number_to_suffix() (in module buildcompiler.sbol2build)

O

OpentronsSimulationAdapter (class in buildcompiler.adapters.opentrons.simulation) OptionalAutomationDependencyError options (buildcompiler.api.compiler.BuildCompiler attribute) (buildcompiler.execution.context.BuildContext attribute)

ordered_lvl1_parts() (in module buildcompiler.planning.validation) original_sequence (buildcompiler.planning.domestication.SequenceEditProposal attribute)

P

parent_group (buildcompiler.domain.build_request.BuildRequest attribute) part_component (buildcompiler.sbol.domestication.DomesticationJob attribute) part_digestion() (in module buildcompiler.sbol2build) part_display_id (buildcompiler.planning.domestication.DomesticationPlan attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) part_identities (buildcompiler.inventory.compatibility.Lvl1Route attribute) part_identity (buildcompiler.planning.domestication.DomesticationPlan attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) part_in_backbone_from_sbol() (in module buildcompiler.sbol2build) part_plasmids (buildcompiler.sbol.assembly.AssemblyJob attribute) part_role (buildcompiler.planning.domestication.DomesticationPlan attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) PARTIAL_SUCCESS (buildcompiler.domain.status.BuildStatus attribute) (buildcompiler.domain.status.StageStatus attribute) path (buildcompiler.adapters.protocols.ProtocolArtifact attribute) plan (buildcompiler.domain.build_result.FullBuildResult attribute) plan() (buildcompiler.api.compiler.BuildCompiler method) (buildcompiler.planning.domestication.DomesticationPlanner method) (buildcompiler.planning.full_build_planner.FullBuildPlanner method) PLANNED (buildcompiler.domain.material_state.MaterialState attribute) planner (buildcompiler.api.compiler.BuildCompiler attribute) planning (buildcompiler.api.options.BuildOptions attribute) PlanningOptions (class in buildcompiler.api.options) plasmid (buildcompiler.sbol.transformation.TransformationJob attribute)

Plasmid (class in buildcompiler.plasmid) plasmid_locations_to_pudu_json() (in module buildcompiler.adapters.pudu.transformation_json) PLATED (buildcompiler.domain.material_state.MaterialState attribute) PLATING (buildcompiler.domain.build_stage.BuildStage attribute) plating() (buildcompiler.buildcompiler.BuildCompiler method) plating_to_pudu_json() (in module buildcompiler.adapters.pudu.plating_json) position (buildcompiler.planning.domestication.SequenceEditProposal attribute) prefer_existing_collection_material (buildcompiler.api.options.SelectionOptions attribute) prefer_higher_material_state (buildcompiler.api.options.SelectionOptions attribute) process (buildcompiler.domain.approvals.RequiredApproval attribute) product (buildcompiler.sbol.domestication.DomesticationSbolResult attribute) (buildcompiler.sbol.transformation.TransformationSbolResult attribute) product_count (buildcompiler.reporting.report.StageReportSection attribute) product_display_id (buildcompiler.sbol.assembly.AssemblyJob attribute) product_identity (buildcompiler.sbol.assembly.AssemblyJob attribute) products (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.sbol.assembly.AssemblySbolResult attribute) proposed_sequence (buildcompiler.planning.domestication.SequenceEditProposal attribute) protocol (buildcompiler.api.options.BuildOptions attribute) protocol_artifacts (buildcompiler.domain.build_result.StageResult attribute) ProtocolArtifact (class in buildcompiler.adapters.protocols) ProtocolMode (class in buildcompiler.api.options) ProtocolOptions (class in buildcompiler.api.options) PullPolicy (class in buildcompiler.sbol.resolver)

R

ran (buildcompiler.adapters.opentrons.simulation.SimulationResult attribute) reagent_type (buildcompiler.domain.reagent.IndexedReagent attribute) ReagentOptions (class in buildcompiler.api.options) reagents (buildcompiler.api.options.BuildOptions attribute) reason (buildcompiler.domain.approvals.RequiredApproval attribute) (buildcompiler.domain.missing_input.MissingBuildInput attribute) (buildcompiler.planning.domestication.SequenceEditProposal attribute) (buildcompiler.planning.models.UnsupportedPlanningRecord attribute) rebase_restriction_enzyme() (in module buildcompiler.sbol2build) RecommendedAction (class in buildcompiler.reporting.report) region_order (buildcompiler.inventory.compatibility.Lvl2Route attribute) rejected (buildcompiler.inventory.compatibility.RouteSelection attribute) rejected_alternatives (buildcompiler.reporting.report.BuildReport attribute) relationship (buildcompiler.reporting.graph.BuildGraphEdge attribute) (buildcompiler.reporting.report.DependencyChainStep attribute) report (buildcompiler.domain.build_result.FullBuildResult attribute) reporting (buildcompiler.api.options.BuildOptions attribute) ReportingOptions (class in buildcompiler.api.options) request_id (buildcompiler.inventory.compatibility.Lvl1Route attribute) (buildcompiler.inventory.compatibility.Lvl2Route attribute) request_id_for() (in module buildcompiler.planning.classifier) request_ids (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.reporting.report.StageReportSection attribute) REQUIRED (buildcompiler.domain.approvals.ApprovalStatus attribute) required_approval_count (buildcompiler.reporting.summary.BuildSummary attribute)

required_approvals (buildcompiler.domain.build_result.FullBuildResult attribute) (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.reporting.report.BuildReport attribute) required_stage (buildcompiler.domain.missing_input.MissingBuildInput attribute) RequiredApproval (class in buildcompiler.domain.approvals) restriction_enzyme (buildcompiler.sbol.assembly.AssemblyJob attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) restriction_enzyme_name (buildcompiler.planning.domestication.DomesticationPlan attribute) results_dir (buildcompiler.api.options.ProtocolOptions attribute) roles (buildcompiler.domain.plasmid.IndexedPlasmid attribute) (buildcompiler.domain.plasmid.IndexedStrain attribute) route (buildcompiler.reporting.report.RouteReport attribute) RouteReport (class in buildcompiler.reporting.report) RouteScore (class in buildcompiler.inventory.compatibility) RouteSelection (class in buildcompiler.inventory.compatibility) run() (buildcompiler.sbol.assembly.AssemblyService method) (buildcompiler.sbol.domestication.DomesticationService method) (buildcompiler.sbol.transformation.TransformationService method) (buildcompiler.sbol2build.Assembly method) (buildcompiler.stages.assembly_lvl1.AssemblyLvl1Stage method) (buildcompiler.stages.assembly_lvl2.AssemblyLvl2Stage method) (buildcompiler.stages.domestication.DomesticationStage method) (buildcompiler.stages.transformation.TransformationStage method) run_opentrons_script_to_zip() (in module buildcompiler.robotutils) run_opentrons_script_with_json_to_zip() (in module buildcompiler.robotutils)

S

sbol (buildcompiler.execution.context.BuildContext attribute) sbol_component (buildcompiler.domain.plasmid.IndexedBackbone attribute) (buildcompiler.domain.plasmid.IndexedPlasmid attribute) sbol_document (buildcompiler.api.compiler.BuildCompiler attribute) (buildcompiler.domain.build_result.StageResult attribute) sbol_module (buildcompiler.domain.plasmid.IndexedStrain attribute) SbolResolver (class in buildcompiler.sbol.resolver) scope (buildcompiler.api.options.ApprovalOptions attribute) score (buildcompiler.inventory.compatibility.Lvl1Route attribute) (buildcompiler.inventory.compatibility.Lvl2Route attribute) select_deterministic_flanking_sequence() (in module buildcompiler.planning.domestication) select_lvl1_route() (buildcompiler.inventory.selector.CompatibilitySelector method) select_lvl2_route() (buildcompiler.inventory.selector.CompatibilitySelector method) selected (buildcompiler.inventory.compatibility.RouteSelection attribute) (buildcompiler.reporting.report.RouteReport attribute) selected_lvl1_plasmids (buildcompiler.inventory.compatibility.Lvl2Route attribute) selected_part_plasmids (buildcompiler.inventory.compatibility.Lvl1Route attribute) selected_routes (buildcompiler.reporting.report.BuildReport attribute) selection (buildcompiler.api.options.BuildOptions attribute) SelectionOptions (class in buildcompiler.api.options) sequence_edit_proposals (buildcompiler.planning.domestication.DomesticationPlan attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) SequenceEditProposal (class in buildcompiler.planning.domestication) simulate (buildcompiler.api.options.ProtocolOptions attribute) simulate() (buildcompiler.adapters.opentrons.simulation.OpentronsSimulationAdapter method) SimulationResult (class in buildcompiler.adapters.opentrons.simulation) site_sequence (buildcompiler.planning.domestication.SequenceEditProposal attribute) sort_key() (buildcompiler.inventory.compatibility.RouteScore method) source (buildcompiler.reporting.graph.BuildGraphEdge attribute) (buildcompiler.reporting.report.DependencyChainStep attribute) source_design_identity (buildcompiler.domain.missing_input.MissingBuildInput attribute) source_display_id (buildcompiler.domain.build_request.BuildRequest attribute) (buildcompiler.planning.models.UnsupportedPlanningRecord attribute) source_document (buildcompiler.sbol.assembly.AssemblyJob attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) (buildcompiler.sbol.transformation.TransformationJob attribute)

source_identity (buildcompiler.domain.build_request.BuildRequest attribute) (buildcompiler.domain.warnings.BuildWarning attribute) (buildcompiler.planning.domestication.SequenceEditProposal attribute) (buildcompiler.planning.models.UnsupportedPlanningRecord attribute) source_kind (buildcompiler.domain.build_request.BuildRequest attribute) (buildcompiler.planning.models.UnsupportedPlanningRecord attribute) source_stage (buildcompiler.domain.missing_input.MissingBuildInput attribute) source_stage_result_id (buildcompiler.reporting.report.RouteReport attribute) stage (buildcompiler.domain.build_request.BuildRequest attribute) (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.domain.warnings.BuildWarning attribute) (buildcompiler.reporting.report.StageReportSection attribute) (buildcompiler.sbol.assembly.AssemblyJob attribute) stage_document (buildcompiler.sbol.assembly.AssemblySbolResult attribute) (buildcompiler.sbol.domestication.DomesticationSbolResult attribute) (buildcompiler.sbol.transformation.TransformationSbolResult attribute) stage_results (buildcompiler.domain.build_result.FullBuildResult attribute) stage_sections (buildcompiler.reporting.report.BuildReport attribute) StageReportSection (class in buildcompiler.reporting.report) StageResult (class in buildcompiler.domain.build_result) StageStatus (class in buildcompiler.domain.status) state (buildcompiler.domain.plasmid.IndexedPlasmid attribute) (buildcompiler.domain.plasmid.IndexedStrain attribute) status (buildcompiler.domain.approvals.RequiredApproval attribute) (buildcompiler.domain.build_result.FullBuildResult attribute) (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.reporting.report.BuildReport attribute) (buildcompiler.reporting.report.StageReportSection attribute) (buildcompiler.reporting.summary.BuildSummary attribute) SUCCESS (buildcompiler.domain.status.BuildStatus attribute) (buildcompiler.domain.status.StageStatus attribute) summary (buildcompiler.domain.build_result.FullBuildResult attribute) summary() (buildcompiler.reporting.graph.BuildGraph method)

T

target (buildcompiler.reporting.graph.BuildGraphEdge attribute) (buildcompiler.reporting.report.DependencyChainStep attribute) target_document (buildcompiler.sbol.assembly.AssemblyJob attribute) (buildcompiler.sbol.domestication.DomesticationJob attribute) (buildcompiler.sbol.transformation.TransformationJob attribute) to_dict() (buildcompiler.reporting.graph.BuildGraph method) (buildcompiler.reporting.report.BuildReport method) (buildcompiler.reporting.summary.BuildSummary method) to_json() (buildcompiler.reporting.report.BuildReport method) (buildcompiler.reporting.summary.BuildSummary method) to_markdown() (buildcompiler.reporting.report.BuildReport method) (buildcompiler.reporting.summary.BuildSummary method) total_assemblies (buildcompiler.inventory.compatibility.RouteScore attribute)

transformation (buildcompiler.api.options.BuildOptions attribute) TRANSFORMATION (buildcompiler.domain.build_stage.BuildStage attribute) Transformation (class in buildcompiler.sbol2build) transformation() (buildcompiler.buildcompiler.BuildCompiler method) (in module buildcompiler.api.compiler) transformation_to_pudu_json() (in module buildcompiler.adapters.pudu.transformation_json) TransformationJob (class in buildcompiler.sbol.transformation) TransformationOptions (class in buildcompiler.api.options) transformations_to_pudu_json() (in module buildcompiler.adapters.pudu.transformation_json) TransformationSbolResult (class in buildcompiler.sbol.transformation) TransformationService (class in buildcompiler.sbol.transformation) TransformationStage (class in buildcompiler.stages.transformation) TRANSFORMED (buildcompiler.domain.material_state.MaterialState attribute)

U

UNSUPPORTED (buildcompiler.domain.design.DesignKind attribute)

unsupported (buildcompiler.planning.models.BuildPlan attribute) UnsupportedPlanningRecord (class in buildcompiler.planning.models)

V

validate_lvl1_cardinality() (in module buildcompiler.planning.validation)

variant_index (buildcompiler.domain.build_request.BuildRequest attribute)

W

warning_count (buildcompiler.reporting.report.StageReportSection attribute) (buildcompiler.reporting.summary.BuildSummary attribute) warnings (buildcompiler.domain.build_result.FullBuildResult attribute) (buildcompiler.domain.build_result.StageResult attribute) (buildcompiler.planning.domestication.DomesticationPlan attribute) (buildcompiler.planning.models.BuildPlan attribute) (buildcompiler.reporting.report.BuildReport attribute)

write_assembly_pudu_input_json() (in module buildcompiler.adapters.pudu.assembly_json) write_manual_plating_protocol() (in module buildcompiler.robotutils) write_plate_map_csv() (in module buildcompiler.robotutils) write_plate_map_json() (in module buildcompiler.robotutils) write_plating_protocol_script() (in module buildcompiler.robotutils)