Lossless BNG-XML \xe2\x86\x92 BNGL round-trip for tfun, rule modifiers, selectors#87
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wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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Lossless BNG-XML \xe2\x86\x92 BNGL round-trip for tfun, rule modifiers, selectors#87wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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Three related fidelity fixes when reading BNG2.pl-emitted BNG-XML and
re-emitting BNGL:
1. tfun placeholder reconstruction. BNG2.pl serializes ``tfun(...)``
calls (both the inline-array form ``tfun([xs],[ys],ctr)`` and the
file-based ``TFUN(ctr,"file")`` form) by replacing the function body
with a ``__TFUN_VAL__`` / ``__TFUN__VAL__`` placeholder and stashing
the real arguments on attributes of the <Function> element
(``@ctrName``, ``@xData``, ``@yData``, ``@method``, ``@file``).
``FunctionBlockXML`` was reading the placeholder verbatim into the
regenerated BNGL, which BNG2.pl can't re-parse. Reconstruct the call
from the attributes via a new ``_resolve_expression`` helper.
2. ``RuleMod`` now supports multiple modifiers per rule. A rule can
legitimately carry, say, ``DeleteMolecules`` together with
``include_reactants(...)``. ``RuleMod.modifiers: list[str]`` stores
the BNGL serialization of each modifier in insertion order;
``__str__`` prefers the list when non-empty, falling back to the
single ``self.type`` for backwards compatibility.
3. ``include_reactants`` / ``exclude_reactants`` /
``include_products`` / ``exclude_products`` are now emitted as rule
modifiers instead of being dropped with a stderr warning. BNG2.pl
serializes these as ``ListOfInclude{Reactants,Products}`` /
``ListOfExclude{Reactants,Products}`` children on the rule, each
carrying a pattern-index suffix (``_RP<n>`` / ``_PP<n>``) on the
selector id and one or more ``<Pattern>`` entries. New helpers
``_build_selector_modifier`` and ``_format_selector_pattern`` on
``RuleBlockXML`` mirror those back as e.g.
``include_reactants(1, MyMol)`` so the rule round-trips through
BNG2.pl's BNGL parser.
The ``get_rule_mod`` body is also tightened: it now tolerates rules
that have no ``ListOfOperations`` at all (previously: ``KeyError``)
and returns ``None`` only when there is genuinely no modifier to
report, rather than dropping a real modifier on the floor when the
``ListOfOperations`` happens to be empty.
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Summary
Three related fidelity fixes when reading BNG2.pl-emitted BNG-XML and re-emitting BNGL. Each fixes a specific shape that the parser currently drops, mangles, or warns about and ignores.
1. `tfun` placeholder reconstruction
BNG2.pl serializes `tfun(...)` calls — both the inline-array form `tfun([xs],[ys],ctr)` and the file-based `TFUN(ctr,"file")` form — by replacing the function body with a `TFUN_VAL` / `TFUN__VAL` placeholder and stashing the real arguments on attributes of the `` element (`@ctrName`, `@xData`, `@yData`, `@method`, `@file`).
`FunctionBlockXML.parse_xml` was reading the placeholder verbatim into the regenerated BNGL, which BNG2.pl can't re-parse. New `_resolve_expression` helper reconstructs the call from the attributes.
2. `RuleMod` supports multiple modifiers per rule
A single rule can legitimately carry, say, `DeleteMolecules` together with `include_reactants(...)`. `RuleMod.modifiers: list[str]` stores the BNGL serialization of each modifier in insertion order. `str` prefers the list when non-empty, falling back to the single `self.type` so existing callers that read `rule_mod.type` keep working.
3. `include` / `exclude` reactants / products as rule modifiers
These are now emitted as rule modifiers instead of being dropped with a stderr warning. BNG2.pl serializes them as `ListOfInclude{Reactants,Products}` / `ListOfExclude{Reactants,Products}` children on the rule, each carrying a pattern-index suffix (`_RP` / `_PP`) on the selector id and one or more `` entries. New helpers `_build_selector_modifier` and `_format_selector_pattern` mirror those back as e.g. `include_reactants(1, MyMol)`.
The `get_rule_mod` body is also tightened: it now tolerates rules that have no `ListOfOperations` at all (previously `KeyError`) and returns `None` only when there's genuinely no modifier to report, instead of dropping a real one when `ListOfOperations` happens to be missing.
Note on conflict with #76
This PR and #76 both modify the import block of `xmlparsers.py` to add `import re`, and both modify `FunctionBlockXML.parse_xml` to wrap the `Expression` read. The two rewrites compose — `_decode_xml_boolean_ops(_resolve_expression(...))` is the combined call — but I've kept them as separate PRs since the audit's table 0.4 split them. Whichever lands first, the other rebases trivially.
Test plan