piecewise handling fails

[paulflang]

case 000190 gives me the following error:

ERROR: LoadError: TypeError: non-boolean (Sym{Real, Nothing}) used in boolean context
Stacktrace:
  [1] (::SBML.var"#conv#31"{Dict{String, Any}, SBML.var"#27#32", SBML.var"#28#33"})(x::SBML.MathApply)
    @ SBML C:\Users\wolf5212\.julia\packages\SBML\ISPz3\src\symbolics.jl:106
  [2] convert(::Type{Num}, x::SBML.MathApply; mapping::Dict{String, Any}, convert_time::SBML.var"#27#32", convert_const::SBML.var"#28#33")
    @ SBML C:\Users\wolf5212\.julia\packages\SBML\ISPz3\src\symbolics.jl:112
  [3] convert(::Type{Num}, x::SBML.MathApply)
    @ SBML C:\Users\wolf5212\.julia\packages\SBML\ISPz3\src\symbolics.jl:106
  [4] mtk_reactions(model::SBML.Model)
    @ SBMLToolkit c:\Users\wolf5212\OneDrive - Nexus365\DPhil Project\Programmes\juliadev\dev\SBMLToolkit\src\reactionsystem.jl:97

In #40 we used

function parse_piecewise(val, cond, other)
    IfElse.ifelse(cond, val, other)
end

But could also have to do with handling of Booleans.
cc @anandijain

[exaexa]

is there a way to reproduce this? (preferably code)

[paulflang]

sbml_fn = "00190-sbml-l3v2.xml"

ml = readSBML(sbml_fn, doc -> begin
            set_level_and_version(3, 2)(doc)
            convert_simplify_math(doc)
        end)
        
convert(Num, ml.reactions["reaction1"].kinetic_math)

[exaexa]

that works for me. What precise model is that?

[exaexa]

aaaaaah I didn't see the link. Better always supply the download code or something. :D

[exaexa]

So it looks that piecewise can actually accept 1+2k arguments for any int k, and the even ones are the actual boolean conditions. Does that sound right?

[exaexa]

ref
https://www.w3.org/TR/2010/REC-MathML3-20101021/chapter4.html#contm.piecewise

[exaexa]

OK I fixed the piecewise argument order, now there's a bit more general problem:

using Symbolics
@variables a b
Core.ifelse(a < b, 2, 1)

...gives

ERROR: TypeError: non-boolean (Num) used in boolean context
Stacktrace:
 [1] top-level scope
   @ REPL[3]:1

what's the correct ifelse to use with symbolics that handles this well?

cc @ChrisRackauckas

[ChrisRackauckas]

IfElse.ifelse.

[paulflang]

also, you should return the function without evaluating it. it should only be evaluated when the simulator calls it. in your example neither a nor b has a numerical value, so the first argument to Ifelse.ifelse is of type Num or whatever, but definitely not a boolean.

[exaexa]

the eval there is evaluating the function "name", not the actual function!

I see ifelse.ifelse is correctly overloaded, good, I totally missed that fact the last time.

[paulflang]

there was no eval in you code example above.😉

[exaexa]

ok then I have no idea what eval you are talking about

[paulflang]

I was not talking about eval. I was just trying to reason why you got

ERROR: TypeError: non-boolean (Num) used in boolean context
Stacktrace:
 [1] top-level scope
   @ REPL[3]:1

[exaexa]

anyway I guess this is it? (pls ack in the PR)

julia> convert(Num, SBML.MathApply("piecewise", SBML.Math[SBML.MathIdent("p1"), SBML.MathApply("lt", SBML.Math[SBML.MathIdent("p1"), SBML.MathIdent("p2")]), SBML.MathIdent("p2")]))
IfElse.ifelse(p1 < p2, p1, p2)

Yeah the problem with Num is obvious, I was stuffing Num into the bad ifelse that can't support it. Evaluation order doesn't have much to do with that (it's just extra confusing).

[paulflang]

I don't see where the "lt" comes from. In case 00190 we just have:

        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <piecewise>
              <piece>
                <ci> p1 </ci>
                <false/>
              </piece>
              <otherwise>
                <ci> p2 </ci>
              </otherwise>
            </piecewise>
          </math>
        </kineticLaw>

[exaexa]

nah that was my testcase. 00190 produces p2 for me, which sounds okay (the ifelse gets const-folded down)

[paulflang]

Unfortunately, I found a case where piecewise still fails:

using SBML
using Symbolics

url = "https://raw.githubusercontent.com/sbmlteam/sbml-test-suite/master/cases/semantic/00191/00191-sbml-l3v2.xml"
tmpfile = download(url)
try
    ml = readSBML(tmpfile)
    convert(Num, ml.reactions["reaction1"].kinetic_math)  # works
    convert(Num, ml.reactions["reaction2"].kinetic_math)  # fails
finally
    rm(tmpfile)
end

ERROR: DomainError with �:
Unknown SBML function
Stacktrace:
  [1] allowed_sym
    @ C:\Users\wolf5212\.julia\packages\SBML\XMU1n\src\symbolics.jl:76 [inlined]
  [2] (::SBML.var"#conv#31"{Dict{String, Any}, SBML.var"#27#32", SBML.var"#28#33"})(x::SBML.MathApply)
    @ SBML C:\Users\wolf5212\.julia\packages\SBML\XMU1n\src\symbolics.jl:117
  [3] _broadcast_getindex_evalf
    @ .\broadcast.jl:648 [inlined]
  [4] _broadcast_getindex
    @ .\broadcast.jl:621 [inlined]
  [5] getindex
    @ .\broadcast.jl:575 [inlined]
  [6] copyto_nonleaf!(dest::Vector{SymbolicUtils.Sym{Real, Nothing}}, bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Tuple{Base.OneTo{Int64}}, SBML.var"#conv#31"{Dict{String, Any}, SBML.var"#27#32", SBML.var"#28#33"}, Tuple{Base.Broadcast.Extruded{Vector{SBML.Math}, Tuple{Bool}, Tuple{Int64}}}}, 
iter::Base.OneTo{Int64}, state::Int64, count::Int64)
    @ Base.Broadcast .\broadcast.jl:1078
  [7] copy
    @ .\broadcast.jl:930 [inlined]
  [8] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, SBML.var"#conv#31"{Dict{String, Any}, SBML.var"#27#32", SBML.var"#28#33"}, Tuple{Vector{SBML.Math}}})
    @ Base.Broadcast .\broadcast.jl:883
  [9] (::SBML.var"#conv#31"{Dict{String, Any}, SBML.var"#27#32", SBML.var"#28#33"})(x::SBML.MathApply)
    @ SBML C:\Users\wolf5212\.julia\packages\SBML\XMU1n\src\symbolics.jl:117
 [10] convert(::Type{Num}, x::SBML.MathApply; mapping::Dict{String, Any}, convert_time::SBML.var"#27#32", convert_const::SBML.var"#28#33")
    @ SBML C:\Users\wolf5212\.julia\packages\SBML\XMU1n\src\symbolics.jl:123
 [11] convert(::Type{Num}, x::SBML.MathApply)
    @ SBML C:\Users\wolf5212\.julia\packages\SBML\XMU1n\src\symbolics.jl:117
 [12] top-level scope
    @ REPL[46]:4

[exaexa]

@paulflang please open new issues for newly found failing test cases.

This doesn't look like piecewise problem, it says "unknown SBML function". The only actual function I see in test 191 is geq aka ≥, is that it? (pls answer in a new issue, we can't keep track of the problems this way)