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Export formats

Following Heta specifications exporting to different formats can be done by #export action. The following formats are implemented in Heta compiler.

See also Features support table

The general format for all export actions is the following:

#export {
    format: JSON, // or other supported formats, required
    filepath: path/to/output, // Relative or absolute path to generated directory or file, not required
    spaceFilter: "regex-expression" // only filtered namespaces will be exported, see RegExp rules
    ... // other options
};

See also Regular expressions' syntax.

JSON

Export to JSON structure (array) storing the content of whole platform or selected namespaces (see spaceFilter option). Can work with abstract namespaces.

Properties

property type required default ref description
omit string[] Array of properties paths to exclude from output.
noUnitsExpr boolean false If false or not set all units will be written in format of UnitsExpr. If true all unit will be written in Unit array format.

Output files

[filepath]/output.json : all content created for selected space.

Example

#export {
    format: JSON,
    filepath: output, // save result in file "dist/output.json"
    omit: [aux.wiki], // omit aux.wiki properties from components
    noUnitsExpr: false, // save units in format UnitsExpr
    spaceFilter: "nameless|another"
};

YAML

Export to YAML structure (array) representing the content of namespace. Can work with abstract namespaces.

Properties

All options is the same as for JSON format.

Output files

[filepath]/output.yml : all content created for selected space.

Example

#export {
    format: YAML,
    filepath: output, // save result in file "dist/output.json"
    omit: [aux.wiki], // omit aux.wiki properties from components
    noUnitsExpr: false, // save units in format UnitsExpr
    spaceFilter: ".+" // all namespaces
};

DBSolve

Export to DBSolve format which is the model format for DBSolveOptimum.

This is the updated version of SLV export format which supports compartment volumes changed in time and initializing records by arbitrary expressions.

Properties

property type required default ref description
powTransform "keep" / "operator" / "function" "keep" This is option describing if the transformation of x^y and pow(x, y) is required.
groupConstBy string/path tags[0] How to group const in Initial Values of DBSolve file. Should be written in format of JSON path
version string 26 SLV file version: 26 (for DBSolveOptimum 2020) or 25 (for earlier versions)

Output files

[filepath]/[namespace].slv : model created based on namespace which can be opened by DBSolveOptimum.

Known restrictions

  • Infinity, -Infinity, NaN values is not supported
  • boolean operators like and, or, etc. are not supported

Example

#export {
    format: DBSolve,
    filepath: model, // save results in file "dist/model.slv"
    spaceFilter: nameless, // namespace used for model generation
    powTransform: keep // use x^y and pow(x, y) without changes
    version: "25"
};

SLV

Export to SLV format which is the model format for DBSolveOptimum.

Properties

property type required default ref description
eventsOff boolean if eventsOff = true the switchers will not be exported to DBSolve events.
powTransform "keep" / "operator" / "function" "keep" This is option describing if the transformation of x^y and pow(x, y) is required.
groupConstBy string/path tags[0] How to group const in Initial Values of DBSolve file. Should be written in format of JSON path
version string 26 SLV file version: 26 (for DBSolveOptimum 2020) or 25 (for earlier versions)

Output files

[filepath]/[namespace].slv : model created based on namespace which can be opened by DBSolveOptimum.

Known restrictions

  • Compartment which changes in time may result in wrong ODE.
  • CSwitcher and DSwitcher are not supported.
  • Initialization of Record by expression does not work: x1 .= k1 * A (not supported).
  • Infinity, -Infinity, NaN values is not supported
  • boolean operators like and, or, etc. are not supported

Example

#export {
    format: SLV,
    filepath: model, // save results in file "dist/model.slv"
    spaceFilter: "^nameless$", // namespace used for model generation
    eventsOff: false, // all switchers will be transformed to DBSolve events
    powTransform: keep, // use x^y and pow(x, y) without changes
    groupConstBy: "tags[1]" // use the second tag
};

SBML

Export to SBML format. Can work with abstract namespaces.

Properties

property type required default ref description
version string L2V4 SBML version in format: L2V4. Possible values are L2V3, L2V4, L2V5, L3V1, L3V2

Output files

[filepath]/[namespace].xml : SBML formatted model

Example:

#export {
    format: SBML,
    filepath: model, // save results in file "dist/model.xml"
    spaceFilter: nameless, // namespace used for model generation
    version: L2V4 // Level 2 Version 4
};

Simbio

Export to Simbiology/Matlab code (m files). The code can be run to create simbiology project.

Properties

Output files

[filepath]/[namespace].m : Code which can be run in Matlab environment to generate Simbio model. [filepath]/fun.m : Auxilary mathematical functions to support Simbio code. This code should be placed in the same directory as simbio project.

Example:

#export {
    format: Simbio,
    filepath: model, // save results in directory "dist/model"
    spaceFilter: nameless // namespace used for model generation
};

Mrgsolve

Export to mrgsolve model format (cpp file).

Properties

Output files

[filepath]/[namespace].cpp : Code which can be run in mrgsolve environment. [filepath]/run.cpp : Code for fast run.

Known restrictions

  • CSwitcher is not supported.
  • DSwitcher is not supported.
  • Initialization by MathExpr is not supported. Do not use S1 .= x * y.

Example:

#export {
    format: Mrgsolve,
    filepath: model, // save results in file "dist/model.cpp"
    spaceFilter: nameless // namespace used for model generation
};

Table

To export platform content in tabular format: CSV, Excel, etc. The format of tables corresponds to the tabular (xlsx) heta module. It can be loaded as a module in another projects. Can work with abstract namespaces.

This statement combines a series of formats supported by https://www.npmjs.com/package/xlsx library. For the list of supported files see the docs https://github.com/SheetJS/sheetjs#supported-output-formats.

Properties

property type required default ref description
omitRows number If set this creates empty rows in output sheets.
omit string[] Array of properties paths to exclude from output.
bookType string[] csv One of the supported file types, see xlsx docs.
splitByClass boolean If true the components will be split by class and saved as several sheets: one sheet/file per a class.

bookType

Multi-scheets formats Single-scheet format
xlsx (.xlsx), xlsm (.xlsm), xlsb (.xlsb), biff8 (.xls), wk3 (.wk3), csv (.csv), txt (.txt), sylk (.sylk),
biff5 (.xls), biff4 (.xls), biff3 (.xls), biff2 (.xls), html (.html), dif (.dif), dbf (.dbf), wk1 (.dbf),
xlml (.xls), ods (.ods), fods (.fods) rtf (.rtf), prn (.prn), eth (.eth)

Output files

[filepath]/output.[extension] : Table file. The extension depends on bookType property. or [filepath]/[Class].[extension] : If you use CSV and similar one-page file types.

Example 1:

// save a platform in CSV
#export {
    format: Table,
    filepath: platform
};

Example 2:

#export {
    format: Table,
    filepath: output, // save result in file "dist/output.xlsx"
    spaceFilter: nameless, // output everything from nameless namespace
    omitRows: 5, // include 5 empty rows between header and the first line
    omit: [aux.wiki], // omit aux.wiki properties from components
    bookType: html // save as HTML table
};

XLSX

Creation of Excel file (.xlsx). This works in the same way as the Table format with bookType: xlsx. Can work with abstract namespaces.

Properties

Output files

[filepath]/output.xlsx : File which can be opened in Excel.

Example:

#export {
    format: XLSX,
    filepath: output, // save result in file "dist/output.xlsx"
    omitRows: 3, // include 3 empty rows between header and the first line
    omit: [aux.wiki], // omit aux.wiki properties from components
    splitByClass: true // split classed to different sheets
};

Julia

Creation of Julia files (.jl).

Properties

Output files

[filepath]/model.jl : File storing model code for all namespaces. [filepath]/run.jl : Code to run model.

Example:

#export {
    format: Julia,
    filepath: julia_code, // save result in directory "dist/julia_code"
    spaceFilter: nameless // create model based on nameless namespace
};

Matlab

Creation of Matlab files (.m) which represent ODE and code to run ODE.

Properties

Output files

[filepath]/model.m : File storing model code. [filepath]/param.m : storing constants initialization [filepath]/run.m : Code to run model.

Known restrictions

  • CSwitcher is not supported.

Example:

#export {
    format: Matlab,
    filepath: matlab_code, // save result in directory "dist/matlab_code"
    spaceFilter: (nameless|another_one) // create two models based on namespaces
};

Dot

Export namespaces to the graph in format (See detaild in https://graphviz.org/). Each namespace in separate file.

Properties

Output files

[filepath]/[namespace].m : File storing model code.

Example:

#export {
    format: Dot,
    filepath: schemes, // save result in directory "dist/schemes"
};

Features support

na means "not applicable"

SLV DBSolve Julia Mrgsolve/R Matlab Simbio/Matlab SBML JSON, YAML Table Dot
@UnitDef class na na na na na + + + + na
@TimeSwitcher class + + + + + + + + + na
@TimeSwitcher {start: 6} + + + + + + + + + na
@TimeSwitcher {start: 0} + + + + + - + + + na
@TimeSwitcher {start: time_start} with ref to @Const + + + + + + + + + na
@TimeSwitcher {period: 12} infinite repeat + + + + + + + + + na
@TimeSwitcher {stop: 120} stop time for repeat + + + + + + + + + na
@CSwitcher class - + + + + + + + + na
@CSwitcher with interpolation - - + - + + na na na na
@DSwitcher class - + + + + + + + + na
@DSwitcher with interpolation - - + - + + na na na na
MathExpr: arithmetic functions + + + + + + + + + na
MathExpr: boolean operators - - + + + + + + + na
MathExpr: ternary operator + + + - + + + + + na
MathExpr: piecewise function - - + - + + + + + na
MathExpr: e, pi + + + + + + + + + na
MathExpr: Infinity, NaN - - + + + + + + + na
Const: Infinity, NaN - - + + + + + + + na
@Scenario support - - - - - - - + + na
@Record {ss: true, ...} - - + - - - - + + na
#defineFunction, (sub) means substitution +(sub) +(sub) + +(sub) + +(sub) + + + na

Math expressions conversions

Skipped cell means no conversion

SLV/DBSolve Julia Mrgsolve/R Simbio/Matlab
abs(x) fabs(x)
add(x, y) x + y +(x, y)
ceil(x)
cube(x) pow(x, 3) or x ^ 3 NaNMath.pow(x, 3)
divide(x, y) x / y /(x, y)
exp(x)
floor(x)
ln(x) NaNMath.log(x)
log(x) NaNMath.log(x) log(x)
logbase(x, base) log(x) / log(base) NaNMath.log(base, x) (log(x)/log(base))
log10(x) NaNMath.log10(x)
log2(x) log(x) / log(2) NaNMath.log2(x) (log(x)/log(2))
multiply(x, y) x * y *(x, y)
pow(x, y) pow(x, y) or x ^ y NaNMath.pow(x, y) power(x, y)
sign(x)
sqrt(x) NaNMath.sqrt(x)
nthRoot(x, n) pow(x, 1/n) or x ^ (1/n) NaNMath.pow(x, (1/n))
square(x) pow(x, 2) or x ^ 2 NaNMath.pow(x, 2)
subtract(x, y) x - y -(x, y)
max(x, y) max2(x, y) std::max(x, y) max(x, y)
max(x, y, z) max3(x, y, z) std::max(x, y, z) max([x, y, z])
min(x, y) min2(x, y) std::min(x, y) min(x, y)
min(x, y, z) min3(x, y, z) std::min(x, y, z) min([x, y, z])
factorial(n) fact(n)
ifgt(x, y, z1, z2) x > y ? z1 : z2 tern__(x>y, z1, z2)
ifge(x, y, z1, z2) x >= y ? z1 : z2 tern__(x>=y, z1, z2)
iflt(x, y, z1, z2) x < y ? z1 : z2 tern__(x<y, z1, z2)
ifle(x, y, z1, z2) x <= y ? z1 : z2 tern__(x<=y, z1, z2)
ifeq(x, y, z1, z2) x == y ? z1 : z2 tern__(x==y, z1, z2)
x ^ y x ^ y or pow(x, y) NaNMath.pow(x, y) pow(x, y)
e exp(1) exp(1.0)
pi acos(-1)
Infinity Inf
NaN NaN
t SOLVERTIME time
a and b a && b a & b
a or b a || b a | b
a xor b xor(a, b) xor(a, b)
not a !a ~a
b1 < b2 ? x : y ifgt(b1, b2, x, y) tern__(b1 < b2, x, y)
piecewise(value1, cond1, value2, cond2, ..., otherwise) not supported + not supported
acos(x), acot(x), acsc(x),asec(x), asin(x), atan(x), cos(x), cot(x), csc(x), sec(x), sin(x), tan(x)

Conversion to SBML's MathML

SBML
abs(x) <apply><abs/>(x)</apply>
add(x, y) <apply><plus/>(x) (y)</apply>
ceil(x) <apply><ceiling/>(x)</apply>
cube(x) <apply><power/>(x)<cn>3</cn></apply>
divide(x, y) <apply><divide/>(x) (y)</apply>
exp(x) <apply><exp/>(x)</apply>
floor(x) <apply><floor/>(x)</apply>
ln(x) <apply><ln/>(x)</apply>
log(x) <apply><ln/>(x)</apply>
logbase(x, base) <apply><log/><logbase>(base)</logbase>(x)</apply>
log10(x) <apply><log/>(x)</apply>
log2(x) <apply><log/><logbase><cn>2</cn></logbase>(x)</apply>
multiply(x, y) <apply><times/>(x) (y)</apply>
pow(x, y) <apply><power/>(x) (y)</apply>
sign(x) <apply><sign/>(x)</apply>
sqrt(x) <apply><root/>(x)</apply>
nthRoot(x, n) <apply><root/><degree>(n)</degree>(x)</apply>
square(x) <apply><power/>(x)<cn>2</cn></apply>
subtract(x, y) <apply><minus/>(x) (y)</apply>
max(x, y) <apply><max/>(x) (y)</apply>
max(x, y, z) <apply><max/>(x) (y) (z)</apply>
min(x, y) <apply><min/>(x) (y)</apply>
min(x, y, z) <apply><min/>(x) (y) (z)</apply>
factorial(n) <apply><factorial/>(x)</apply>
ifgt(x, y, z1, z2) not supported
ifge(x, y, z1, z2) not supported
iflt(x, y, z1, z2) not supported
ifle(x, y, z1, z2) not supported
ifeq(x, y, z1, z2) not supported
x ^ y <apply><pow/>(x) (y)</apply>
e <exponentiale/>
pi <pi/>
Infinity <infinity/>
NaN <notanumber/>
t <csymbol definitionURL="http:https://www.sbml.org/sbml/symbols/time">t</csymbol>
a and b <apply><and/>(a) (b)</apply>
a or b <apply><or/>(a) (b)</apply>
a xor b <apply><xor/>(a) (b)</apply>
not a <apply><not/>(a)</apply>
b1 < b2 ? x : y <piecewise><piece>(x)<apply><lt/>(b1) (b2)</apply></piece><otherwise>(y)</otherwise></piecewise>
piecewise(value1, cond1, value2, cond2, ..., otherwise) <piecewise><piece>(value1) (cond1)</piece><piece>(value2) (cond2)</piece><otherwise>(otherwise)</otherwise></piecewise>
acos(x), acot(x), acsc(x),asec(x), asin(x), atan(x), cos(x), cot(x), csc(x), sec(x), sin(x), tan(x) <apply><arccos/>(x)</apply>...