Decode && / || boolean operators when re-emitting from BNG-XML#76
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wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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Decode && / || boolean operators when re-emitting from BNG-XML#76wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
&& / || boolean operators when re-emitting from BNG-XML#76wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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BNG2.pl's <Expression> serializer rewrites the binary operators ``&&`` and ``||`` as the function-call-shaped strings ``(L)and(R)`` and ``(L)or(R)`` (see Perl2/Expression.pm: '&&' => 'and'). Reading <Expression> verbatim and re-emitting it into a regenerated .bngl file confuses BNG2.pl's BNGL parser, which sees ``and(...)`` as a function call and aborts with "Missing end parentheses ... at and(...)". Fix: in xmlparsers, run a regex pass that maps ``)and(`` → ``) && (`` and ``)or(`` → ``) || (`` before storing the function expression. The match is anchored on the close-paren of the left operand because BNG2.pl always wraps both operands in parens for these forms — so ``)and(`` / ``)or(`` only ever appear as the boolean-operator encoding and never as the suffix of a user identifier or a literal function call.
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Summary
BNG2.pl's
<Expression>serializer rewrites the binary operators&&and||as the function-call-shaped strings(L)and(R)and(L)or(R)(seePerl2/Expression.pm:'&&' => 'and'). Whenbionetgen.modelapireads<Expression>verbatim and re-emits the function body into a regenerated.bngl, BNG2.pl's BNGL parser seesand(...)as a function call and aborts:This breaks any round-trip workflow (parse a BNGL → regenerate it → re-run with BNG2.pl) for models that use boolean operators inside function bodies. Smallest repro is a function like:
After XML round-trip this becomes
if((plusBafA1==1)and(t>=0), 0, 1)which BNG2.pl rejects.Fix
In
bionetgen/modelapi/xmlparsers.py, add a regex pass that maps)and(→) && (and)or(→) || (before storing the function expression. The match is intentionally anchored on the close-paren of the left operand because BNG2.pl always wraps both operands in parens for these forms — so)and(/)or(only ever appear as the boolean-operator encoding and never as the tail of a user-defined identifier (e.g.random(x)) or a literal function call.Test plan
&&/||in a function body: parse → write_model → BNG2.pl simulaterandom(x) + myop(y)is preserved verbatim (no spurious rewrites of)and(-shaped substrings that aren't actually boolean ops — there shouldn't be any, but worth checking)