Decode && / || boolean operators when re-emitting from BNG-XML

[wshlavacek]

Summary

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'). When bionetgen.modelapi reads <Expression> verbatim and re-emits the function body into a regenerated .bngl, BNG2.pl's BNGL parser sees and(...) as a function call and aborts:

Missing end parentheses ... at and(t>=0))

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:

toggle = if((plusBafA1==1) && (t>=0), 0, 1)

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

• Existing CI passes
• Round-trip a model with && / || in a function body: parse → write_model → BNG2.pl simulate
• Verify random(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)

[wshlavacek]

Summary

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'). When bionetgen.modelapi reads <Expression> verbatim and re-emits the function body into a regenerated .bngl, BNG2.pl's BNGL parser sees and(...) as a function call and aborts:

Missing end parentheses ... at and(t>=0))

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:

toggle = if((plusBafA1==1) && (t>=0), 0, 1)

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

• Existing CI passes
• Round-trip a model with && / || in a function body: parse → write_model → BNG2.pl simulate
• Verify random(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)

[wshlavacek]

Summary

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'). When bionetgen.modelapi reads <Expression> verbatim and re-emits the function body into a regenerated .bngl, BNG2.pl's BNGL parser sees and(...) as a function call and aborts:

Missing end parentheses ... at and(t>=0))

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:

toggle = if((plusBafA1==1) && (t>=0), 0, 1)

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

• Existing CI passes
• Round-trip a model with && / || in a function body: parse → write_model → BNG2.pl simulate
• Verify random(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)

[wshlavacek]

Summary

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'). When bionetgen.modelapi reads <Expression> verbatim and re-emits the function body into a regenerated .bngl, BNG2.pl's BNGL parser sees and(...) as a function call and aborts:

Missing end parentheses ... at and(t>=0))

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:

toggle = if((plusBafA1==1) && (t>=0), 0, 1)

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

• Existing CI passes
• Round-trip a model with && / || in a function body: parse → write_model → BNG2.pl simulate
• Verify random(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)

[wshlavacek]

Summary

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'). When bionetgen.modelapi reads <Expression> verbatim and re-emits the function body into a regenerated .bngl, BNG2.pl's BNGL parser sees and(...) as a function call and aborts:

Missing end parentheses ... at and(t>=0))

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:

toggle = if((plusBafA1==1) && (t>=0), 0, 1)

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

• Existing CI passes
• Round-trip a model with && / || in a function body: parse → write_model → BNG2.pl simulate
• Verify random(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)

[wshlavacek]

Summary

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'). When bionetgen.modelapi reads <Expression> verbatim and re-emits the function body into a regenerated .bngl, BNG2.pl's BNGL parser sees and(...) as a function call and aborts:

Missing end parentheses ... at and(t>=0))

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:

toggle = if((plusBafA1==1) && (t>=0), 0, 1)

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

• Existing CI passes
• Round-trip a model with && / || in a function body: parse → write_model → BNG2.pl simulate
• Verify random(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)

[wshlavacek]

Summary

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'). When bionetgen.modelapi reads <Expression> verbatim and re-emits the function body into a regenerated .bngl, BNG2.pl's BNGL parser sees and(...) as a function call and aborts:

Missing end parentheses ... at and(t>=0))

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:

toggle = if((plusBafA1==1) && (t>=0), 0, 1)

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

• Existing CI passes
• Round-trip a model with && / || in a function body: parse → write_model → BNG2.pl simulate
• Verify random(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)

[wshlavacek]

Summary

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'). When bionetgen.modelapi reads <Expression> verbatim and re-emits the function body into a regenerated .bngl, BNG2.pl's BNGL parser sees and(...) as a function call and aborts:

Missing end parentheses ... at and(t>=0))

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:

toggle = if((plusBafA1==1) && (t>=0), 0, 1)

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

• Existing CI passes
• Round-trip a model with && / || in a function body: parse → write_model → BNG2.pl simulate
• Verify random(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)