Functions for Validating Composite Part Assemblies Plus Tests#117
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nroehner wants to merge 6 commits intoSynBioDex:developfrom
Open
Functions for Validating Composite Part Assemblies Plus Tests#117nroehner wants to merge 6 commits intoSynBioDex:developfrom
nroehner wants to merge 6 commits intoSynBioDex:developfrom
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…wo helper functions to component.by for retrieving subcomponents.
jakebeal
requested changes
Feb 23, 2022
sbol_utilities/build_planning.py
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| i = i + 1 | ||
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| return has_insert and has_backbone |
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Should also check location/constraints.
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| invalid_assemblies = [a for a in activities if is_assembly(a) and not validate_assembly(a, c)] | ||
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| return len(invalid_assemblies) == 0 |
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This can be done more efficiently by applying any to a generator.
| from sbol_utilities.workarounds import get_parent | ||
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| def get_subcomponents(c: sbol3.Component) -> List[sbol3.SubComponent]: |
| class TestBuildPlanning(unittest.TestCase): | ||
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| def test_validate_composite_part_assemblies(self): | ||
| test_doc = sbol3.Document() |
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| sbol3.set_namespace('http://testBuildPlanning.org') | ||
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| assert validate_composite_part_assemblies(assemble_BBa_K093005(test_doc)) |
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explain why these should or shouldn't work in comments
| assert not validate_composite_part_assemblies(assemble_BBa_K093005(test_doc, 'EXTRA_ASSEMBLY_COMPONENT')) | ||
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| def assemble_BBa_K093005(doc: sbol3.Document, failure_mode: Optional[str] = ''): | ||
| doc = sbol3.Document() |
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same as above; need comments to explain your testing
…plan. Also modified part in backbone validation to use is_plasmid helper function and check if component contains a single insert and a single backbone.
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Primary function validate_composite_part_assemblies returns true if the input composite part was generated only by assemblies that are valid according to SEP 055. This is a partial implementation of the best practices in SEP 055 and partially resolves #73