biosimulators_utils.sedml package#

Submodules#

biosimulators_utils.sedml.data_model module#

Data model for SED

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-06
Copyright:: 2020, Center for Reproducible Biomedical Modeling
License:: MIT

class biosimulators_utils.sedml.data_model.AbstractTask(id: str | None = None, name: str | None = None)[source]#

Bases: SedBase, SedIdGroupMixin

Base class for tasks

id[source]#

Type:: str

name[source]#

name

Type:: str

is_equal(other)[source]#

Determine if tasks are equal

Parameters:: other (AbstractTask) – another content item
Returns:: True, if two tasks are equal
Return type:: bool

Bases: ModelChange

An addition of an element to a model

id[source]#

Type:: str

name[source]#

name

Type:: str

target[source]#

path to the parent of the new element(s)

Type:: str

target_namespaces[source]#

map of prefixes of namespaces for the target to their URIs

Type:: dict

new_elements[source]#

new element(s)

Type:: str

is_equal(other)[source]#

Determine if model changes are equal

Parameters:: other (AddElementModelChange) – another content item
Returns:: True, if two model changes are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.Algorithm(kisao_id: str | None = None, changes: list[AlgorithmParameterChange] | None = None)[source]#

Bases: SedBase

A simulation algorithm

kisao_id[source]#

KiSAO id (e.g., KISAO_0000029)

Type:: str

changes[source]#

parameter changes

Type:: list of AlgorithmParameterChange

is_equal(other)[source]#

Determine if algorithms are equal

Parameters:: other (Algorithm) – another algorithm
Returns:: True, if two algorithms are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.AlgorithmParameterChange(kisao_id: str | None = None, new_value: str | None = None)[source]#

Bases: SedBase

A changed parameter of an algorithm

kisao_id[source]#

KiSAO id (e.g., KISAO_0000029)

Type:: str

new_value[source]#

new value

Type:: str

is_equal(other)[source]#

Determine if parameter changes are equal

Parameters:: other (AlgorithmParameterChange) – another parameter change
Returns:: True, if two parameter changes are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.AxisScale(value)[source]#

Bases: str, Enum

Scale of an axis

__format__(format_spec)[source]#: Returns format using actual value type unless __str__ has been overridden.

linear = 'linear'[source]#

log = 'log'[source]#

class biosimulators_utils.sedml.data_model.Color[source]#

Bases: str

6-character hexidecimal RGB color or 8-character hexidecimal RGBA color

Bases: ModelChange, Calculation

A replacement of an element of a model

id[source]#

Type:: str

name[source]#

name

Type:: str

target[source]#

path to the element to replace

Type:: str

target_namespaces[source]#

map of prefixes of namespaces for the target to their URIs

Type:: dict

variables[source]#

variables

Type:: list of Variable

parameters[source]#

parameters

Type:: list of Parameter

math[source]#

mathematical expression

Type:: str

is_equal(other)[source]#

Determine if model changes are equal

Parameters:: other (ComputeModelChange) – another content item
Returns:: True, if two model changes are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: SedBase, SedIdGroupMixin

A curve in a 2D plot

id[source]#

Type:: str

name[source]#

name

Type:: str

x_scale[source]#

x axis scale

Type:: AxisScale

y_scale[source]#

y axis scale

Type:: AxisScale

x_data_generator[source]#

x data generator

Type:: DataGenerator

y_data_generator[source]#

y data generator

Type:: DataGenerator

style[source]#

graphical style

Type:: Style

is_equal(other)[source]#

Determine if curves are equal

Parameters:: other (Curve) – another curve
Returns:: True, if two curves are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: Calculation, SedIdGroupMixin

A data generator

id[source]#

Type:: str

name[source]#

name

Type:: str

variables[source]#

variables

Type:: list of Variable

parameters[source]#

parameters

Type:: list of Parameter

math[source]#

mathematical expression

Type:: str

is_equal(other)[source]#

Determine if data generators: are equal

Parameters:: other (DataGenerator) – another content item
Returns:: True, if two data generators are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.DataSet(id: str | None = None, name: str | None = None, label: str | None = None, data_generator: DataGenerator | None = None)[source]#

Bases: SedBase, SedIdGroupMixin

A data set in a report

id[source]#

Type:: str

name[source]#

name

Type:: str

label[source]#

label

Type:: str

data_generator[source]#

data generator

Type:: DataGenerator

is_equal(other)[source]#

Determine if data sets are equal

Parameters:: other (DataSet) – another content item
Returns:: True, if two data sets are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.FillStyle(color: Color | None = None)[source]#

Bases: SedBase

Style of a marker

color[source]#

color

Type:: Color

is_equal(other)[source]#

Determine if fill styles are equal

Parameters:: other (FillStyle) – another fill style
Returns:: True, if two fill styles are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: Range, Calculation

A functional range

id[source]#

Type:: str

name[source]#

name

Type:: str

range[source]#

range

Type:: Range

variables[source]#

variables

Type:: list of Variable

parameters[source]#

parameters

Type:: list of Parameter

math[source]#

mathematical expression

Type:: str

is_equal(other)[source]#

Determine if ranges are equal

Parameters:: other (FunctionalRange) – another content item
Returns:: True, if two ranges are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.LineStyle(type: LineStyleType | None = None, color: Color | None = None, thickness: float | None = None)[source]#

Bases: SedBase

Style of a line

type[source]#

type

Type:: LineStyleType

color[source]#

color

Type:: Color

thickness[source]#

type

Type:: float

is_equal(other)[source]#

Determine if line styles are equal

Parameters:: other (FillStyle) – another line style
Returns:: True, if two line styles are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.LineStyleType(value)[source]#

Bases: str, Enum

Style of a line of a curve

__format__(format_spec)[source]#: Returns format using actual value type unless __str__ has been overridden.

dash = 'dash'[source]#

dashDot = 'dashDot'[source]#

dashDotDot = 'dashDotDot'[source]#

dot = 'dot'[source]#

none = 'none'[source]#

solid = 'solid'[source]#

Bases: SedBase

Style of a marker

type[source]#

type

Type:: MarkerStyleType

size[source]#

size

Type:: float

fill_color[source]#

fill color

Type:: Color

line_color[source]#

line color

Type:: Color

line_thickness[source]#

line thickness

Type:: float

is_equal(other)[source]#

Determine if marker styles are equal

Parameters:: other (FillStyle) – another marker style
Returns:: True, if two marker styles are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.MarkerStyleType(value)[source]#

Bases: str, Enum

Style of a marker of a curve

__format__(format_spec)[source]#: Returns format using actual value type unless __str__ has been overridden.

circle = 'circle'[source]#

diamond = 'diamond'[source]#

hDash = 'hDash'[source]#

none = 'none'[source]#

plus = 'plus'[source]#

square = 'square'[source]#

star = 'star'[source]#

triangleDown = 'triangleDown'[source]#

triangleLeft = 'triangleLeft'[source]#

triangleRight = 'triangleRight'[source]#

triangleUp = 'triangleUp'[source]#

vDash = 'vDash'[source]#

xCross = 'xCross'[source]#

Bases: SedBase, SedIdGroupMixin

A model

id[source]#

Type:: str

name[source]#

name

Type:: str

source[source]#

path to the model file

Type:: str

language[source]#

URN of the format of the model

Type:: str

changes[source]#

model changes

Type:: list of ModelChange

has_structural_changes()[source]#

Check if there are structural model changes present.

Add element
Replace element
Remove element

Returns:: True, if structural model changes are present
Return type:: bool

is_equal(other)[source]#

Determine if models are equal

Parameters:: other (Model) – another content item
Returns:: True, if two models are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: ModelChange

A change of an attribute of a model

id[source]#

Type:: str

name[source]#

name

Type:: str

target[source]#

path to the model element that should be changed

Type:: str

target_namespaces[source]#

map of prefixes of namespaces for the target to their URIs

Type:: dict

new_value[source]#

new value

Type:: str

is_equal(other)[source]#

Determine if model attribute changes are equal

Parameters:: other (ModelAttributeChange) – another content item
Returns:: True, if two model attribute changes are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.ModelChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None)[source]#

Bases: SedBase, SedIdGroupMixin, TargetGroupMixin

A change to a model

id[source]#

Type:: str

name[source]#

name

Type:: str

target[source]#

path to the model element that should be changed

Type:: str

target_namespaces[source]#

map of prefixes of namespaces for the target to their URIs

Type:: dict

is_equal(other)[source]#

Determine if model changes are equal

Parameters:: other (ModelChange) – another content item
Returns:: True, if two model changes are equal
Return type:: bool

class biosimulators_utils.sedml.data_model.ModelLanguage(value)[source]#

Bases: str, Enum

Model language

BNGL = 'urn:sedml:language:bngl'[source]#

CellML = 'urn:sedml:language:cellml'[source]#

CopasiML = 'urn:sedml:language:copasiml'[source]#

GINML = 'urn:sedml:language:ginml'[source]#

HOC = 'urn:sedml:language:hoc'[source]#

Kappa = 'urn:sedml:language:kappa'[source]#

LEMS = 'urn:sedml:language:lems'[source]#

MASS = 'urn:sedml:language:mass'[source]#

MorpheusML = 'urn:sedml:language:morpheusml'[source]#

NMODL = 'urn:sedml:language:nmodl'[source]#

NeuroML = 'urn:sedml:language:neuroml'[source]#

RBA = 'urn:sedml:language:rba'[source]#

SBML = 'urn:sedml:language:sbml'[source]#

SLI = 'urn:sedml:language:sli'[source]#

Smoldyn = 'urn:sedml:language:smoldyn'[source]#

VCML = 'urn:sedml:language:vcml'[source]#

XPP = 'urn:sedml:language:xpp'[source]#

ZGINML = 'urn:sedml:language:zginml'[source]#

__format__(format_spec)[source]#: Returns format using actual value type unless __str__ has been overridden.

pharmML = 'urn:sedml:language:pharmml'[source]#

class biosimulators_utils.sedml.data_model.ModelLanguageEdamId(value)[source]#

Bases: str, Enum

Model language EDAM id

BNGL = 'format_3972'[source]#

CellML = 'format_3240'[source]#

CopasiML = 'format_9003'[source]#

GENESIS = 'format_9056'[source]#

GINML = 'format_9009'[source]#

HOC = 'format_9005'[source]#

Kappa = 'format_9006'[source]#

LEMS = 'format_9004'[source]#

MASS = 'format_9011'[source]#

MorpheusML = 'format_9002'[source]#

NCS = 'format_9057'[source]#

NMODL = 'format_9052'[source]#

NeuroML = 'format_3971'[source]#

RBA = 'format_9012'[source]#

SBML = 'format_2585'[source]#

SLI = 'format_9054'[source]#

Smoldyn = 'format_9001'[source]#

VCML = 'format_9000'[source]#

XPP = 'format_9010'[source]#

ZGINML = 'format_9008'[source]#

__format__(format_spec)[source]#: Returns format using actual value type unless __str__ has been overridden.

pharmML = 'format_9007'[source]#

class biosimulators_utils.sedml.data_model.ModelLanguagePattern(value)[source]#

Bases: str, Enum

Model language

BNGL = '^urn:sedml:language:bngl(\\.|$)'[source]#

CellML = '^urn:sedml:language:cellml(\\.\\d+_\\d+)?$'[source]#

CopasiML = '^urn:sedml:language:copasiml(\\.|$)'[source]#

GENESIS = '^urn:sedml:language:genesis(\\.|$)'[source]#

GINML = '^urn:sedml:language:ginml(\\.|$)'[source]#

HOC = '^urn:sedml:language:hoc(\\.|$)'[source]#

Kappa = '^urn:sedml:language:kappa(\\.|$)'[source]#

LEMS = '^urn:sedml:language:lems(\\.|$)'[source]#

MASS = '^urn:sedml:language:mass(\\.|$)'[source]#

MorpheusML = '^urn:sedml:language:morpheusml(\\.|$)'[source]#

NCS = '^urn:sedml:language:ncs(\\.|$)'[source]#

NMODL = '^urn:sedml:language:nmodl(\\.|$)'[source]#

NeuroML = '^urn:sedml:language:neuroml(\\.version-\\d+_\\d+_\\d+\\.level\\-\\d+)?$'[source]#

RBA = '^urn:sedml:language:rba(\\.|$)'[source]#

SBML = '^urn:sedml:language:sbml(\\.level\\-\\d+\\.version\\-\\d+)?$'[source]#

SLI = '^urn:sedml:language:sli(\\.|$)'[source]#

Smoldyn = '^urn:sedml:language:smoldyn(\\.|$)'[source]#

VCML = '^urn:sedml:language:vcml(\\.|$)'[source]#

XPP = '^urn:sedml:language:xpp(\\.|$)'[source]#

ZGINML = '^urn:sedml:language:zginml(\\.|$)'[source]#

__format__(format_spec)[source]#: Returns format using actual value type unless __str__ has been overridden.

pharmML = '^urn:sedml:language:pharmml(\\.|$)'[source]#

class biosimulators_utils.sedml.data_model.OneStepSimulation(id: str | None = None, name: str | None = None, algorithm: Algorithm | None = None, step: float | None = None)[source]#

Bases: Simulation

A single simulation step

id[source]#

Type:: str

name[source]#

name

Type:: str

algorithm[source]#

algorithm

Type:: Algorithm

step[source]#

step

Type:: float

is_equal(other)[source]#

Determine if simulations are equal

Parameters:: other (OneStepSimulation) – another content item
Returns:: True, if two simulations are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.Output(id: str | None = None, name: str | None = None)[source]#

Bases: SedBase, SedIdGroupMixin

An output

id[source]#

Type:: str

name[source]#

name

Type:: str

is_equal(other)[source]#

Determine if outputs are equal

Parameters:: other (Output) – another content item
Returns:: True, if two outputs are equal
Return type:: bool

class biosimulators_utils.sedml.data_model.Parameter(id: str | None = None, name: str | None = None, value: float | None = None)[source]#

Bases: SedBase, SedIdGroupMixin

A parameter involved in a data generator

id[source]#

Type:: str

name[source]#

name

Type:: str

value[source]#

value

Type:: float

is_equal(other)[source]#

Determine if data generator parameters are equal

Parameters:: other (Parameter) – another content item
Returns:: True, if two data generator parameters are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.Plot(id: str | None = None, name: str | None = None)[source]#

Bases: Output

A 2D plot

id[source]#

Type:: str

name[source]#

name

Type:: str

class biosimulators_utils.sedml.data_model.Plot2D(id: str | None = None, name: str | None = None, curves: list[Curve] | None = None)[source]#

Bases: Plot

A 2D plot

id[source]#

Type:: str

name[source]#

name

Type:: str

curves[source]#

curves

Type:: list of Curve

is_equal(other)[source]#

Determine if plots are equal

Parameters:: other (Plot2D) – another plot
Returns:: True, if two plots are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.Plot3D(id: str | None = None, name: str | None = None, surfaces: list[Surface] | None = None)[source]#

Bases: Plot

A 3D plot

id[source]#

Type:: str

name[source]#

name

Type:: str

surfaces[source]#

surfaces

Type:: list of Surface

is_equal(other)[source]#

Determine if plots are equal

Parameters:: other (Plot3D) – another plot
Returns:: True, if two plots are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.Range(id: str | None = None, name: str | None = None)[source]#

Bases: SedBase, SedIdGroupMixin

A range

id[source]#

Type:: str

name[source]#

name

Type:: str, optional

is_equal(other)[source]#

Determine if ranges are equal

Parameters:: other (Range) – another content item
Returns:: True, if two ranges are equal
Return type:: bool

class biosimulators_utils.sedml.data_model.RemoveElementModelChange(id: str | None = None, name: str | None = None, target: str | None = None, target_namespaces: dict | None = None)[source]#

Bases: ModelChange

A removal of an element from a model

id[source]#

Type:: str

name[source]#

name

Type:: str

target[source]#

path to the element to remove

Type:: str

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: AbstractTask

A repeated task

id[source]#

Type:: str

name[source]#

name

Type:: str

range[source]#

range of the iterations of the repeated task

Type:: Range

reset_model_for_each_iteration[source]#

whether to reset the model for each iteration of the repeated task

Type:: bool

changes[source]#

set value model changes

Type:: list of SetValueComputeModelChange

sub_tasks[source]#

sub-tasks

Type:: list of SubTask

ranges[source]#

ranges

Type:: list of Range

is_equal(other)[source]#

Determine if repeated tasks are equal

Parameters:: other (RepeatedTask) – another content item
Returns:: True, if two repeated tasks are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: ModelChange

A replacement of an element of a model

id[source]#

Type:: str

name[source]#

name

Type:: str

target[source]#

path to the element to replace

Type:: str

target_namespaces[source]#

map of prefixes of namespaces for the target to their URIs

Type:: dict

new_elements[source]#

new element(s)

Type:: str

is_equal(other)[source]#

Determine if model changes are equal

Parameters:: other (ReplaceElementModelChange) – another content item
Returns:: True, if two model changes are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.Report(id: str | None = None, name: str | None = None, data_sets: list[DataSet] | None = None)[source]#

Bases: Output

A report

id[source]#

Type:: str

name[source]#

name

Type:: str

data_sets[source]#

data sets

Type:: list of DataSet

is_equal(other)[source]#

Determine if reports are equal

Parameters:: other (Report) – another content item
Returns:: True, if two reports are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.SedBase[source]#

Bases: ABC

Base class for SED classes

is_equal(other)[source]#

Determine if simulations are equal

Parameters:: other (SedBase) – another content item
Returns:: True, if two simulations are equal
Return type:: bool

abstract to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.SedDocument(level: int = 1, version: int = 3, models: list[Model] | None = None, simulations: list[Simulation] | None = None, tasks: list[AbstractTask] | None = None, data_generators: list[DataGenerator] | None = None, outputs: list[Output] | None = None, styles: list[Style] | None = None, metadata: Metadata | None = None)[source]#

Bases: SedBase

A SED-ML document

level[source]#

level

Type:: int

version[source]#

version

Type:: int

models[source]#

models

Type:: list of Model

simulations[source]#

simulations

Type:: list of Simulation

tasks[source]#

tasks

Type:: list of AbstractTask

data_generators[source]#

data generators

Type:: list of DataGenerator

outputs[source]#

outputs

Type:: list of Output

metadata[source]#

metadata

Type:: Metadata

is_equal(other)[source]#

Determine if SED-ML documents are equal

Parameters:: other (SedDocument) – another SED-ML document
Returns:: True, if two SED-ML documents are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.SedIdGroupMixin(id: str | None = None, name: str | None = None)[source]#

Bases: ABC

Object with an id and optional name

id[source]#

Type:: str

name[source]#

name

Type:: str

is_equal(other)[source]#

Determine if simulations are equal

Parameters:: other (SedIdGroupMixin) – another content item
Returns:: True, if two simulations are equal
Return type:: bool

Bases: ComputeModelChange, Calculation

A change that sets the value of an attribute of a model within an iteration of a repeated task

id[source]#

Type:: str

name[source]#

name

Type:: str

target[source]#

path to the element to replace

Type:: str

target_namespaces[source]#

map of prefixes of namespaces for the target to their URIs

Type:: dict

variables[source]#

variables

Type:: list of Variable

parameters[source]#

parameters

Type:: list of Parameter

math[source]#

mathematical expression

Type:: str

model[source]#

model

Type:: Model

range[source]#

range

Type:: Range

symbol[source]#

symbol

Type:: str

is_equal(other)[source]#

Determine if model changes are equal

Parameters:: other (SetValueComputeModelChange) – another content item
Returns:: True, if two model changes are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.Simulation(id: str | None = None, name: str | None = None, algorithm: Algorithm | None = None)[source]#

Bases: SedBase, SedIdGroupMixin

A simulation

id[source]#

Type:: str

name[source]#

name

Type:: str

algorithm[source]#

algorithm

Type:: Algorithm

is_equal(other)[source]#

Determine if simulations are equal

Parameters:: other (Simulation) – another content item
Returns:: True, if two simulations are equal
Return type:: bool

class biosimulators_utils.sedml.data_model.SteadyStateSimulation(id: str | None = None, name: str | None = None, algorithm: Algorithm | None = None)[source]#

Bases: Simulation

A steady-state simulation

id[source]#

Type:: str

name[source]#

name

Type:: str

algorithm[source]#

algorithm

Type:: Algorithm

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: SedBase, SedIdGroupMixin

A graphical style

id[source]#

Type:: str

name[source]#

name

Type:: str

base[source]#

base style

Type:: Style

line[source]#

line style

Type:: LineStyle

marker[source]#

marker style

Type:: MarkerStyle

fill[source]#

fill style

Type:: FillStyle

is_equal(other)[source]#

Determine if styles are equal

Parameters:: other (Style) – another style
Returns:: True, if two styles are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.SubTask(task: AbstractTask | None = None, order: int | None = None)[source]#

Bases: SedBase

A subtask of a repeated task

task[source]#

task

Type:: AbstractTask

order[source]#

order in which the subtask should be executed

Type:: int

is_equal(other)[source]#

Determine if repeated tasks are equal

Parameters:: other (SubTask) – another content item
Returns:: True, if two repeated tasks are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: SedBase, SedIdGroupMixin

A surface in a 3D plot

id[source]#

Type:: str

name[source]#

name

Type:: str

x_scale[source]#

x axis scale

Type:: AxisScale

y_scale[source]#

y axis scale

Type:: AxisScale

z_scale[source]#

z axis scale

Type:: AxisScale

x_data_generator[source]#

x data generator

Type:: DataGenerator

y_data_generator[source]#

y data generator

Type:: DataGenerator

z_data_generator[source]#

z data generator

Type:: DataGenerator

style[source]#

graphical style

Type:: Style

is_equal(other)[source]#

Determine if surfaces are equal

Parameters:: other (Surface) – another surface
Returns:: True, if two surfaces are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.Symbol(value)[source]#

Bases: str, Enum

Variable sumbol

__format__(format_spec)[source]#: Returns format using actual value type unless __str__ has been overridden.

time = 'urn:sedml:symbol:time'[source]#

class biosimulators_utils.sedml.data_model.TargetGroupMixin(target=None, target_namespaces=None)[source]#

Bases: ABC

Object with an id and optional name

target[source]#

Type:: str

target_namespaces[source]#

map of prefixes of namespaces for the target to their URIs

Type:: dict

is_equal(other)[source]#

Determine if simulations are equal

Parameters:: other (TargetGroupMixin) – another content item
Returns:: True, if two simulations are equal
Return type:: bool

class biosimulators_utils.sedml.data_model.Task(id: str | None = None, name: str | None = None, model: Model | None = None, simulation: Simulation | None = None)[source]#

Bases: AbstractTask

A task

id[source]#

Type:: str

name[source]#

name

Type:: str

model[source]#

model

Type:: Model

simulation[source]#

simulation

Type:: Simulation

is_equal(other)[source]#

Determine if tasks are equal

Parameters:: other (Task) – another content item
Returns:: True, if two tasks are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: Range

A uniform range

id[source]#

Type:: str

name[source]#

name

Type:: str

start[source]#

start value

Type:: float

end[source]#

end value

Type:: float

number_of_steps[source]#

number of steps

Type:: int

type[source]#

type

Type:: UniformRangeType

is_equal(other)[source]#

Determine if ranges are equal

Parameters:: other (UniformRange) – another content item
Returns:: True, if two ranges are equal
Return type:: bool

property number_of_points[source]#

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: Simulation

A uniform time course simulation

id[source]#

Type:: str

name[source]#

name

Type:: str

algorithm[source]#

algorithm

Type:: Algorithm

initial_time[source]#

initial time

Type:: float

output_start_time[source]#

output start time

Type:: float

output_end_time[source]#

output end time

Type:: float

number_of_steps[source]#

number of time steps

Type:: int

is_equal(other)[source]#

Determine if simulations are equal

Parameters:: other (UniformTimeCourseSimulation) – another content item
Returns:: True, if two simulations are equal
Return type:: bool

property number_of_points[source]#

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

Bases: SedBase, SedIdGroupMixin

A model variable

id[source]#

Type:: str

name[source]#

name

Type:: str

target[source]#

target

Type:: str

target_namespaces[source]#

map of prefixes of namespaces for the target to their URIs

Type:: dict

symbol[source]#

symbol

Type:: str

task[source]#

task

Type:: AbstractTask

model[source]#

model

Type:: Model

is_equal(other)[source]#

Determine if data generator variables are equal

Parameters:: other (Variable) – another content item
Returns:: True, if two data generator variables are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

class biosimulators_utils.sedml.data_model.VectorRange(id: str | None = None, name: str | None = None, values: list[float] | None = None)[source]#

Bases: Range

A vector range

id[source]#

Type:: str

name[source]#

name

Type:: str

values[source]#

values

Type:: list of float

is_equal(other)[source]#

Determine if ranges are equal

Parameters:: other (VectorRange) – another content item
Returns:: True, if two ranges are equal
Return type:: bool

to_tuple()[source]#

Get a tuple representation

Returns:: tuple representation
Return type:: tuple of str

biosimulators_utils.sedml.exceptions module#

Exceptions for SED-ML

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-01-12
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

exception biosimulators_utils.sedml.exceptions.SedmlExecutionError[source]#

Bases: BioSimulatorsException

Error that a SED document could not be executed

exception biosimulators_utils.sedml.exceptions.UnsupportedModelLanguageError[source]#

Bases: BioSimulatorsException, NotImplementedError

Error that a SED document could not be executed

biosimulators_utils.sedml.exec module#

Utilities for executing tasks in SED documents

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-06
Copyright:: 2020, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.sedml.exec.exec_plot_2d(plot, variable_results, base_out_path, rel_out_path, formats, task, log)[source]#

Execute a 2D plot, generating the curves which are available

Parameters:

plot (Plot2D) – plot
variable_results (VariableResults) – result of each data generator
base_out_path (str) – base path to store the plot. Complete path is {base_out_path}/{rel_out_path}/{plot.id}.csv
rel_out_path (str, optional) – path relative to base_out_path to store the plot
formats (list of VizFormat, optional) – plot format (e.g., pdf)
task (Task) – task
log (ReportLog, optional) – log of plot

Returns:

Status: status
Exception: exception for failure
bool: whether task contributes a variable to the plot

Return type:

tuple

biosimulators_utils.sedml.exec.exec_plot_3d(plot, variable_results, base_out_path, rel_out_path, formats, task, log)[source]#

Execute a 3D plot, generating the surfaces which are available

Parameters:

plot (Plot3D) – plot
variable_results (VariableResults) – result of each data generator
base_out_path (str) – base path to store the plot. Complete path is {base_out_path}/{rel_out_path}/{plot.id}.pdf
rel_out_path (str, optional) – path relative to base_out_path to store the plot
formats (list of VizFormat, optional) – plot format (e.g., pdf)
task (Task) – task
log (ReportLog, optional) – log of plot

Returns:

Status: status
Exception: exception for failure
bool: whether task contributes a variable to the plot

Return type:

tuple

biosimulators_utils.sedml.exec.exec_repeated_task(task, task_executer, task_vars, doc, apply_xml_model_changes=False, model_etrees=None, pretty_print_modified_xml_models=False, config=None, preprocessed_task=None, get_value_executer=None, set_value_executer=None, reset_executer=None)[source]#

Execute a repeated SED task

Parameters:

task (RepeatedTask) – task

task_executer (types.FunctionType) –

function to execute each task in the SED-ML file. The function must implement the following interface:

def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **simulator_config):
    ''' Execute a simulation and return its results

    Args:
       task (:obj:`Task`): task
       variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
       preprocessed_task (:obj:`object`, optional): preprocessed information about the task, including possible
            model changes and variables. This can be used to avoid repeatedly executing the same initialization
            for repeated calls to this method.
       log (:obj:`TaskLog`, optional): log for the task
       config (:obj:`Config`, optional): BioSimulators common configuration
       **simulator_config (:obj:`dict`, optional): optional simulator-specific configuration

    Returns:
       :obj:`VariableResults`: results of variables
    '''
    pass

task_vars (list of Variable) – variables that task must record
doc (SedDocument or str) – SED document or a path to SED-ML file which defines a SED document
apply_xml_model_changes (bool, optional) – if True, apply any model changes specified in the SED-ML file before calling task_executer.
model_etrees (dict of str to etree._Element)
pretty_print_modified_xml_models (bool, optional) – if True, pretty print modified XML models
config (Config, optional) – BioSimulators common configuration

Returns:

results of the variables

Return type:

VariableResults

biosimulators_utils.sedml.exec.exec_report(report, variable_results, base_out_path, rel_out_path, formats, task, log=None, type=<class 'biosimulators_utils.sedml.data_model.Report'>)[source]#

Execute a report, generating the data sets which are available

Parameters:

report (Report) – report
variable_results (VariableResults) – result of each data generator
base_out_path (str) –
path to store the outputs
- CSV: directory in which to save outputs to files {base_out_path}/{rel_out_path}/{report.id}.csv
- HDF5: directory in which to save a single HDF5 file ({base_out_path}/reports.h5), with reports at keys {rel_out_path}/{report.id} within the HDF5 file
rel_out_path (str, optional) – path relative to base_out_path to store the outputs
formats (list of ReportFormat, optional) – report format (e.g., csv or h5)
task (Task) – task
log (ReportLog, optional) – log of report
type (types.Type) – type of output (e.g., subclass of Output such as Report, Plot2D)

Returns:

DataSetResults: report
Status: status
Exception: exception for failure
bool: whether task contribute a variable to the report

Return type:

tuple

biosimulators_utils.sedml.exec.exec_sed_doc(task_executer, doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=False, log=None, indent=0, pretty_print_modified_xml_models=False, log_level=StandardOutputErrorCapturerLevel.c, config=None, get_value_executer=None, set_value_executer=None, preprocessed_task_executer=None, reset_executer=None)[source]#

Execute the tasks specified in a SED document and generate the specified outputs

Parameters:

task_executer (types.FunctionType) –

function to execute each task in the SED-ML file. The function must implement the following interface:

def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **simulator_config):
    ''' Execute a simulation and return its results

    Args:
        task (:obj:`Task`): task
        variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
        preprocessed_task (:obj:`object`, optional): preprocessed information about the task, including possible
            model changes and variables. This can be used to avoid repeatedly executing the same initialization
            for repeated calls to this method.
        log (:obj:`TaskLog`, optional): log for the task
        config (:obj:`Config`, optional): BioSimulators common configuration
        **simulator_config (:obj:`dict`, optional): optional simulator-specific configuration

    Returns:
       :obj:`VariableResults`: results of variables
    '''
    pass

doc (SedDocument or str) – SED document or a path to SED-ML file which defines a SED document
working_dir (str) – working directory of the SED document (path relative to which models are located)
base_out_path (str) –
path to store the outputs
- CSV: directory in which to save outputs to files {base_out_path}/{rel_out_path}/{report.id}.csv
- HDF5: directory in which to save a single HDF5 file ({base_out_path}/reports.h5), with reports at keys {rel_out_path}/{report.id} within the HDF5 file
rel_out_path (str, optional) – path relative to base_out_path to store the outputs
apply_xml_model_changes (bool, optional) – if True, apply any model changes specified in the SED-ML file before calling task_executer.
log (SedDocumentLog, optional) – log of the document
indent (int, optional) – degree to indent status messages
pretty_print_modified_xml_models (bool, optional) – if True, pretty print modified XML models
log_level (StandardOutputErrorCapturerLevel, optional) – level at which to log output
config (Config) – configuration

Returns:

ReportResults: results of each report
SedDocumentLog: log of the document

Return type:

tuple

biosimulators_utils.sedml.exec.exec_task(task, task_executer, task_vars, doc, log=None, config=None, preprocessed_task=None)[source]#

Execute a basic SED task

Parameters:

task (Task) – task

task_executer (types.FunctionType) –

function to execute each task in the SED-ML file. The function must implement the following interface:

def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **simulator_config):
    ''' Execute a simulation and return its results

    Args:
        task (:obj:`Task`): task
        variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
        preprocessed_task (:obj:`object`, optional): preprocessed information about the task, including possible
            model changes and variables. This can be used to avoid repeatedly executing the same initialization
            for repeated calls to this method.
        log (:obj:`TaskLog`, optional): log for the task
        config (:obj:`Config`, optional): BioSimulators common configuration
        **simulator_config (:obj:`dict`, optional): optional simulator-specific configuration

    Returns:
        :obj:`tuple`:

            * :obj:`VariableResults`: results of variables
            * :obj:`TaskLog`: log
    '''
    pass

task_vars (list of Variable) – variables that task must record
doc (SedDocument or str) – SED document or a path to SED-ML file which defines a SED document
log (TaskLog, optional) – log
config (Config, optional) – BioSimulators common configuration

Returns:

results of the variables

Return type:

VariableResults

biosimulators_utils.sedml.exec.get_report_for_plot2d(plot)[source]#

Get a report for a 2D plot with a dataset for each data generator of the curves

Parameters:: plot (Plot2D) – plot
Returns:: report with a dataset for each data generator of the curves
Return type:: Report

biosimulators_utils.sedml.exec.get_report_for_plot3d(plot)[source]#

Get a report for a 3D plot with a dataset for each data generator of the surfaces

Parameters:: plot (Plot3D) – plot
Returns:: report with a dataset for each data generator of the surfaces
Return type:: Report

biosimulators_utils.sedml.io module#

Utilities for reading and writing SED documents to SED-ML files

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-06
License:: MIT

class biosimulators_utils.sedml.io.SedmlSimulationReader[source]#

Bases: object

SED-ML reader

errors[source]#

errors

Type:: nested list of str

warnings[source]#

warnings

Type:: nested list of str

run(filename, validate_semantics=True, validate_models_with_languages=True, validate_targets_with_model_sources=True, config=None)[source]#

Base class for reading a SED document

Parameters:

filename (str) – path to SED-ML document
validate_semantics (bool, optional) – if True, check that SED-ML is semantically valid
validate_models_with_languages (bool, optional) – if True, validate models
validate_targets_with_model_sources (bool, optional) – if True, validate targets against their models
config (Config, optional) – whether to fail on missing includes

Returns:

SED document

Return type:

data_model.SedDocument

Raises:

ValueError – if any of the following conditions are met * The SED document contains changes other than instances of SedChangeAttribute * The models or simulations don’t have unique ids * A model or simulation references cannot be resolved

class biosimulators_utils.sedml.io.SedmlSimulationWriter[source]#

Bases: object

SED-ML writer

_num_meta_id[source]#

number of assigned meta ids

Type:: int

_doc_sed[source]#

SED document

Type:: libsedml.SedDocument

_obj_to_sed_obj_map[source]#

map from data model objects to their corresponding libSED-ML objects

Type:: object => object

run(doc, filename, validate_semantics=True, validate_models_with_languages=True, validate_targets_with_model_sources=True, config=None)[source]#

Save a SED document to an SED-ML XML file

Parameters:

doc (data_model.SedDocument) – SED document
filename (str) – Path to save simulation experiment in SED-ML format
validate_semantics (bool, optional) – if True, check that SED-ML is semantically valid
validate_models_with_languages (bool, optional) – if True, validate models
validate_targets_with_model_sources (bool, optional) – if True, validate targets against their models
config (Config, optional) – whether to fail on missing includes

Raises:

NotImplementedError – document uses an supported type of task or output

biosimulators_utils.sedml.math module#

Data model for SED

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-06
License:: MIT

biosimulators_utils.sedml.math.compile_math(math)[source]#

Compile a mathematical expression

Parameters:: math (str) – mathematical expression
Returns:: compiled expression
Return type:: _ast.Expression

biosimulators_utils.sedml.math.eval_math(math, compiled_math, workspace)[source]#

Compile a mathematical expression

Parameters:

math (str) – mathematical expression
compiled_math (_ast.Expression) – compiled expression
workspace (dict) – values to use for the symbols in the expression

Returns:

result of the expression

Return type:

object

Raises:

ValueError – if the expression could not be evaluated

biosimulators_utils.sedml.math.log(*args)[source]#

Evaluate a logarithm

Parameters:: *args (list of float) – value optional proceeded by a base; otherwise the logarithm is calculated in base 10
Returns:: float

biosimulators_utils.sedml.math.piecewise(*args)[source]#

Evaluate a MathML piecewise function

Parameters:: *args (list of float) – pairs of value and conditions followed by a default value
Returns:: float

biosimulators_utils.sedml.model_utils module#

Utilities for working with models referenced by SED documents

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-04-05
License:: MIT

biosimulators_utils.sedml.model_utils.build_combine_archive_for_model(model_filename, model_language, simulation_type, archive_filename, extra_contents=None, config=None, **model_language_options)[source]#

Build A COMBINE/OMEX archive with a SED-ML file for a model

Parameters:

model_filename (str) – path to model file
model_language (ModelLanguage) – model language
simulation_type (type) – subclass of Simulation
archive_filename (str) – path to save COMBINE/OMEX archive
extra_contents (dict of str -> CombineArchiveContent, optional) – dictionary that maps the local paths of additional files to include in the COMBINE/OMEX archive to their intended locations within the COMBINE/OMEX archive
config (Config, optional) – whether to fail on missing includes
**model_language_options – additional options to pass to the methods for individual model formats

biosimulators_utils.sedml.model_utils.get_parameters_variables_outputs_for_simulation(model_filename, model_language, simulation_type, algorithm_kisao_id=None, change_level=<class 'biosimulators_utils.sedml.data_model.SedDocument'>, native_ids=False, native_data_types=False, model_language_options=None)[source]#

Get the possible observables for a simulation of a model

This method supports the following formats

SBML
SBML-fbc
SBML-qual

Parameters:

model_filename (str) – path to model file
model_language (str) – model language (e.g., urn:sedml:language:sbml)
simulation_type (types.Type) – subclass of Simulation
algorithm_kisao_id (str, optional) – KiSAO id of the algorithm for simulating the model (e.g., KISAO_0000019 for CVODE)
change_level (types.Type, optional) – level at which model changes will be made (SedDocument or Task)
native_ids (bool, optional) – whether to return the raw id and name of each model component rather than the suggested name for the variable of an associated SED-ML data generator
native_data_types (bool, optional) – whether to return new_values in their native data types
model_language_options (dict, optional) – additional options to pass to the methods for individual model formats. Dictionary that maps model languages (ModelLanguage) to dictionaries of optional keyword arguments for each language

Returns:

possible attributes of a model that can be changed and their default values list of Simulation: simulation of the model list of Variable: possible observables for a simulation of the model list of Plot: possible plots of the results of a simulation of the model

Return type:

list of ModelAttributeChange

Raises:

UnsupportedModelLanguageError – if model_language is not a supported language

biosimulators_utils.sedml.utils module#

Utilities for working with SED documents

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-06
License:: MIT

biosimulators_utils.sedml.utils.add_namespaces_to_xml_node(node, namespace_prefixes, namespaces)[source]#

Add namespaces to an XML node

Parameters:

node (libsedml.XMLNode) – XML node
namespace_prefixes (set of str) – namespace prefixes used in the node which aren’t defined in the node
namespaces (libsedml.XMLNamespaces) – namespaces for the parent document

biosimulators_utils.sedml.utils.append_all_nested_children_to_doc(doc)[source]#

Append all nested children to a SED document

Parameters:: doc (SedDocument) – SED document

biosimulators_utils.sedml.utils.apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=None, variable_values=None, range_values=None, validate_unique_xml_targets=True, set_value_executer=None, preprocessed_task_sub_executer=None)[source]#

Modify an XML-encoded model according to a model change

Parameters:

model (Model) – model
model_etree (etree._ElementTree) – element tree for model
sed_doc (SedDocument, optional) – parent SED document; used to resolve sources defined by reference to other models; required for compute changes
working_dir (str, optional) – working directory of the SED document (path relative to which models are located); required for compute changes
variable_values (dict, optional) – dictionary which contains the value of each variable of each compute model change
range_values (dict, optional) – dictionary which contains the value of each range of each set value compute model change
validate_unique_xml_targets (bool, optional) – whether to validate the XML targets match uniue objects

biosimulators_utils.sedml.utils.calc_compute_model_change_new_value(change, variable_values=None, range_values=None)[source]#

Calculate the new value of a compute model change

Parameters:

change (ComputeModelChange) – change
variable_values (dict, optional) – dictionary which contains the value of each variable of each compute model change
range_values (dict, optional) – dictionary which contains the value of each range of each set value compute model change

Returns:

new value

Return type:

float

biosimulators_utils.sedml.utils.calc_data_generator_results(data_generator, variable_results)[source]#

Calculate the results of a data generator from the results of its variables

Parameters:

data_generator (DataGenerator) – data generator
variable_results (VariableResults) – results for the variables of the data generator

Returns:

result of data generator

Return type:

numpy.ndarray

biosimulators_utils.sedml.utils.calc_data_generators_results(data_generators, variable_results, output, task, make_shapes_consistent=True)[source]#

Calculator the values of a list of data generators

Parameters:

data_generators (list of DataGenerator) – SED task
variable_results (VariableResults) – results of the SED variables involved in the data generators
output (Output) – SED output
task (Task) – SED task
make_shapes_consistent (bool, optional) – where to make the shapes of the data generators consistent (e.g., for concatenation into a table for a report)

Returns:

DataGeneratorResults: values of the data generators
dict of str to Status: dictionary that maps the id of each data generator to its status
Exception: exception for failures
bool: where the task contributes to any of the data generators

Return type:

tuple

biosimulators_utils.sedml.utils.convert_xml_node_to_string(node)[source]#

Generate a string representation of an XML node

Parameters:: node (libsedml.XMLNode) – XML node
Returns:: string representation of the node
Return type:: str

biosimulators_utils.sedml.utils.does_model_language_use_xpath_variable_targets(language)[source]#

Determine if the model language uses XPaths to target variables of data generators

Parameters:: language (str) – language
Returns:: True, if the model language is encoded in XML
Return type:: bool

biosimulators_utils.sedml.utils.get_data_generators_for_output(output)[source]#

Get the data generators involved in an output

Parameters:: output (Output) – report or plot
Returns:: data generators involved in the output
Return type:: set of DataGenerator

biosimulators_utils.sedml.utils.get_first_last_models_executed_by_task(task)[source]#

Get the models executed by a task in the order they are executed

Parameters:: task (Task) – task
Returns:: models
Return type:: tuple of Model

biosimulators_utils.sedml.utils.get_model_changes_for_task(task)[source]#

Get the changes to models for a task

Parameters:: task (Task) – task
Returns:: changes to the model
Return type:: list of ModelChange

biosimulators_utils.sedml.utils.get_models_referenced_by_model_change(change)[source]#

Get the models referenced from a model change

Parameters:: change (ModelChange) – model change
Returns:: models
Return type:: set of Model

biosimulators_utils.sedml.utils.get_models_referenced_by_range(range)[source]#

Get the models referenced by a range

Parameters:: range (Range) – range
Returns:: models
Return type:: set of Model

biosimulators_utils.sedml.utils.get_models_referenced_by_task(task)[source]#

Get the models referenced from a task

Parameters:: task (Task) – task
Returns:: models
Return type:: set of Model

biosimulators_utils.sedml.utils.get_namespaces_for_sed_object(obj)[source]#

Get the namespace prefixes and URIs defined for a SED object

Parameters:: obj (libsedml.SedBase) – SED object
Returns:: dictionary that maps the prefixes of namespaces to their URIs
Return type:: dict

biosimulators_utils.sedml.utils.get_range_len(range)[source]#

Get the length of a range

Parameters:: range (Range) – range
Returns:: length of the range
Return type:: int
Raises:: NotImplementedError – if range isn’t an instance of UniformRange, VectorRange, or FunctionalRange.

biosimulators_utils.sedml.utils.get_task_results_shape(task)[source]#

Get the shape of the results of a task

Parameters:: task (Task) – task
Returns:: shape of the results of a task
Return type:: tuple of int

biosimulators_utils.sedml.utils.get_value_of_variable_model_xml_targets(variable, model_etrees)[source]#

Get the value of a variable of a model

Parameters:

variable (Variable) – variable
model_etrees (dict of str to etree._Element) – dictionary that maps the ids of models to paths to files which contain their XML definitions

Returns:

value

Return type:

float

biosimulators_utils.sedml.utils.get_values_of_variable_model_xml_targets_of_model_change(change, sed_doc, model_etrees, working_dir)[source]#

Get the values of the model variables of a compute model change

Parameters:

change (ComputeModelChange) – compute model change
sed_doc (SedDocument) – SED document
model_etrees (dict of str to etree._Element) – map from the ids of models to element trees of their sources
working_dir (str) – working directory of the SED document (path relative to which models are located)

Returns:

dictionary which contains the value of each variable of each: compute model change

Return type:

dict

biosimulators_utils.sedml.utils.get_variables_for_data_generators(data_generators)[source]#

Get the variables involved in a collection of generators

Parameters:: data_generators (list of DataGenerator) – data generators
Returns:: variables involved in the data generators
Return type:: set of Variable

biosimulators_utils.sedml.utils.get_variables_for_task(doc, task)[source]#

Get the variables that a task must record

Parameters:

doc (SedDocument) – SED document
task (Task) – task

Returns:

variables that task must record

Return type:

list of Variable

biosimulators_utils.sedml.utils.get_xml_node_namespace_tag_target(etree, target_namespaces=None)[source]#

Get the namespace, tag, and target of an XML node

Parameters:

etree (etree._Element) – element tree
target_namespaces (dict, optional) – dictionary that maps the prefixes of namespaces to their URIs

Returns:

str: namespace URI
str: namespace prefix
str: tag
str: target for use with SED target XPaths
dict: dictionary that maps the prefixes of namespaces to their URIs

Return type:

tuple

biosimulators_utils.sedml.utils.is_executable_task(doc: SedDocument, task: Task)[source]#

Check if a task actually has outputs that a simulator needs to find

Parameters:

doc (SedDocument) – sedml document
task (Task) – task

Returns:

bool value of whether the task is an “executable” one

biosimulators_utils.sedml.utils.is_model_language_encoded_in_xml(language)[source]#

Determine if the model language is encoded in XML

Parameters:: language (str) – language
Returns:: True, if the model language is encoded in XML
Return type:: bool

biosimulators_utils.sedml.utils.remove_algorithm_parameter_changes(sed_doc)[source]#

Remove algorithm parameter changes from a SED document

Parameters:: sed_doc (SedDocument) – SED document

biosimulators_utils.sedml.utils.remove_model_changes(sed_doc)[source]#

Remove model changes from a SED document

Parameters:: sed_doc (SedDocument) – SED document

biosimulators_utils.sedml.utils.remove_plots(sed_doc)[source]#

Remove plots from a SED document

Parameters:: sed_doc (SedDocument) – SED document

biosimulators_utils.sedml.utils.replace_complex_data_generators_with_generators_for_individual_variables(sed_doc)[source]#

Remove model changes from a SED document

Parameters:: sed_doc (SedDocument) – SED document

biosimulators_utils.sedml.utils.resolve_model(model, sed_doc, working_dir)[source]#

Resolve the source of a model

Parameters:

model (Model) –
model whose source is one of the following
- A path to a file
- A URL
- A MIRIAM URN for an entry in the BioModelsl database (e.g., urn:miriam:biomodels.db:BIOMD0000000012)
- A reference to another model, using the id of the other model (e.g., #other-model-id). In this case, the model also inherits changes from the parent model.
sed_doc (SedDocument) – parent SED document; used to resolve sources defined by reference to other models
working_dir (str) – working directory of the SED document (path relative to which models are located)

Returns:

temporary path to the source of the modified model, if the model needed to be resolved from

Return type:

str

biosimulators_utils.sedml.utils.resolve_model_and_apply_xml_changes(orig_model, sed_doc, working_dir, apply_xml_model_changes=True, save_to_file=True, pretty_print_modified_xml_models=False, set_value_executer=None, preprocessed_task_sub_executer=None)[source]#

Resolve the source of a model and, optionally, apply XML changes to the model.

Parameters:

model (Model) –
model whose source is one of the following
- A path to a file
- A URL
- A MIRIAM URN for an entry in the BioModelsl database (e.g., urn:miriam:biomodels.db:BIOMD0000000012)
- A reference to another model, using the id of the other model (e.g., #other-model-id). In this case, the model also inherits changes from the parent model.
sed_doc (SedDocument) – parent SED document; used to resolve sources defined by reference to other models
working_dir (str) – working directory of the SED document (path relative to which models are located)
apply_xml_model_changes (bool, optional) – if True, apply any model changes specified in the SED-ML file before calling task_executer.
save_to_file (bool) – whether to save the resolved/modified model to a file
pretty_print_modified_xml_models (bool, optional) – if True, pretty print modified XML models

Returns:

Model: modified model
str: temporary path to the source of the modified model, if the model needed to be resolved from a remote source of modified
etree._Element: element tree for the resolved/modified model

Return type:

tuple

biosimulators_utils.sedml.utils.resolve_range(range, model_etrees=None)[source]#

Resolve the values of a range

Parameters:

range (Range) – range
model_etrees (dict of str to etree._Element) – map from the ids of models to element trees of their sources; required to resolve variables of functional ranges

Returns:

values of the range

Return type:

list of float

Raises:

NotImplementedError – if range isn’t an instance of UniformRange, VectorRange, or FunctionalRange.

biosimulators_utils.sedml.validation module#

Methods for validating SED objects

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-09
License:: MIT

biosimulators_utils.sedml.validation.validate_algorithm(algorithm)[source]#

Validate an algorithm

Parameters:

algorithm (Algorithm) – algorithm

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_calculation(calculation)[source]#

Validate that all of the symbols needed for a calculation are defined

Parameters:

expression (Calculation)

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of warmings (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_data_generator(data_generator, model_etrees=None, validate_targets_with_model_sources=True)[source]#

Validate a data generator

Parameters have ids
Variables have ids
Variables have target OR symbol
Variables don’t have model references
Have math
Math is valid

Parameters:

data_generator (DataGenerator) – data generator
model_etrees (dict, optional) – dictionary that maps models to XML element trees of their sources
validate_targets_with_model_sources (bool, optional) – whether to validate the targets of the variables of the data generator

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of warnings (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_data_generator_variables(variables, model_etrees=None, validate_targets_with_model_sources=True)[source]#

Check variables have a symbol or target

Parameters:

variables (list of Variable) – variables
model_etrees (dict, optional) – dictionary that maps models to XML element trees of their sources
validate_targets_with_model_sources (bool, optional) – whether to validate the targets of the variables of the data generator

Returns:

nested list of errors (e.g., required ids missing or ids not unique)

Return type:

nested list of str

biosimulators_utils.sedml.validation.validate_doc(doc, working_dir, validate_semantics=True, validate_models_with_languages=True, validate_targets_with_model_sources=True, config=None)[source]#

Validate a SED document

Parameters:

doc (SedDocument) – SED document
working_dir (str) – working directory (e.g., for referencing model files)
validate_semantics (bool, optional) – if True, check that SED-ML is semantically valid
validate_models_with_languages (bool, optional) – if True, validate models
validate_targets_with_model_sources (bool, optional) – if True, validate targets against their models
config (Config, optional) – whether to fail on missing includes

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_model(model, model_ids, working_dir, validate_models_with_languages=True, config=None, check_in_model_source=True, model_etree=None)[source]#

Check a model

Parameters:

model (Model) – model
model_ids (list of str) – ids of models
working_dir (str) – working directory (e.g., for referencing model files)
validate_models_with_languages (bool, optional) – if True, validate models
config (Config, optional) – whether to fail on missing includes

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of warnings (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_model_change_types(changes, types=(<class 'biosimulators_utils.sedml.data_model.ModelChange'>, ))[source]#

Check that model changes are valid

Parameters:

changes (list of ModelChange) – model changes
types (type or tuple of type, optional) – valid type(s) of model changes

Returns:

nested list of errors (e.g., required ids missing or ids not unique)

Return type:

nested list of str

biosimulators_utils.sedml.validation.validate_model_changes(model, check_in_model_source=True, model_etree=None)[source]#

Check that model changes are semantically valid

Check that the variables of compute model changes are valid

Parameters:: model (Model) – model
Returns:: nested list of errors (e.g., required ids missing or ids not unique)
Return type:: nested list of str

biosimulators_utils.sedml.validation.validate_model_language(language, valid_languages)[source]#

Check that model is encoded in a specific language

Parameters:

language (str) – model language
valid_language (ModelLanguage or list of ModelLanguage) – valid language(s)

Returns:

nested list of errors (e.g., required ids missing or ids not unique)

Return type:

nested list of str

biosimulators_utils.sedml.validation.validate_model_source(model, model_ids, working_dir, validate_models_with_languages=True, config=None)[source]#

Check the source of a model

Parameters:

model (Model) – model
model_ids (list of str) – ids of models
working_dir (str) – working directory (e.g., for referencing model files)
validate_models_with_languages (bool, optional) – if True, validate models
config (Config, optional) – whether to fail on missing includes

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of warnings (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_model_with_language(source, language, name=None, config=None)[source]#

Check that a model is valid

Parameters:

source (str) – path to model
language (ModelLanguage) – language
name (str, optional) – name of model for use in error messages
config (Config, optional) – whether to fail on missing includes

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
object: model object

Return type:

tuple

biosimulators_utils.sedml.validation.validate_output(output)[source]#

Validate an output

Reports * Data sets have ids and labels * Data sets reference data generators
Plots
- Curves and surfaces have ids
- x, y, z attributes reference data generators

Parameters:

output (Output) – output

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of warnings (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_reference(obj, obj_label, attr_name, attr_label)[source]#

biosimulators_utils.sedml.validation.validate_repeated_task_has_one_model(task)[source]#

Validate a that a repeated task involves a single model

Parameters:

task (RepeatedTask) – repeated task

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of warnings (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_simulation(simulation)[source]#

Check that simulation is a valid simulation

Parameters:

simulation (Simulation) – simulation

Returns:

nested list of str: nested list of errors (e.g., required ids missing or ids not unique)
nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

Return type:

tuple

biosimulators_utils.sedml.validation.validate_simulation_type(simulation, types)[source]#

Check that simulation is a time course simulation

Parameters:

simulation (Simulation) – simulation
types (type) – valid simulation types

Returns:

nested list of errors (e.g., required ids missing or ids not unique)

Return type:

nested list of str

biosimulators_utils.sedml.validation.validate_target(target, namespaces, context, language, model_id, model_etree=None, doc=None, check_in_model_source=False, warn_xpaths_not_validated=True, model_change=False)[source]#

Validate that a target is a valid XPath and that the namespaces needed to resolve a target are defined

Parameters:

target (str) – XPath to a model element or attribute
namespaces (dict) – dictionary that maps prefixes of namespaces to their URIs
context (type)
language (str) – model language
model_id (str) – model id
model_etree (etree.Element, optional) – XML element tree for model source
doc (SedDocument, optional) – SED document
check_in_model_source (bool, optional) – whether to check that the target exists in the source
warn_xpaths_not_validated (bool, optional) – whether to warn that XPaths cannot be validated
model_changes (bool, optional) – whether the model has changes that could validate or invalidate XPaths.

Returns:

nested list of errors (e.g., required ids missing or ids not unique)

Return type:

nested list of str

biosimulators_utils.sedml.validation.validate_target_xpaths(targets, model_etree, attr='id', separator=None)[source]#

Validate that the target of each model change or variable matches one object in an XML-encoded model and, optionally, return the value of one of its attributes.

Parameters:

targets (list of TargetGroupMixin) – model changes or variables
model_source (lxml.etree._ElementTree) – element tree for the XML model document
attr (str, optional) – attribute to get values of
separator (str, optional) – string to use when combining attributes into a single id (i.e. ‘J0.n’ from ‘J0’ and ‘n’.) If None, don’t combine and just use final id.

Returns:

dictionary that maps each XPath to the: value of the attribute of the object in the XML file that matches the XPath

Return type:

dict of str to str

biosimulators_utils.sedml.validation.validate_task(task)[source]#

Validate a simulation task

Parameters:: task (Task) – task
Returns:: nested list of errors (e.g., required ids missing or ids not unique)
Return type:: nested list of str

biosimulators_utils.sedml.validation.validate_uniform_range(range)[source]#

Validate a uniform range

Parameters:: range (data_model.UniformRange) – range
Returns:: nested list of errors (e.g., required ids missing or ids not unique)
Return type:: nested list of str

biosimulators_utils.sedml.warnings module#

Warnings for misuse of SED-ML

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-06
License:: MIT

exception biosimulators_utils.sedml.warnings.IllogicalSedmlWarning[source]#

Bases: BioSimulatorsWarning

Warning that a SED document is illogical, such as when a report or plot contains no datasets, curves, or surfaces.

exception biosimulators_utils.sedml.warnings.InconsistentVariableShapesWarning[source]#

Bases: BioSimulatorsWarning

Warning that the variables of a data generator have different shapes.

exception biosimulators_utils.sedml.warnings.NoCurvesWarning[source]#

Bases: IllogicalSedmlWarning

Warning that a 2D plot does not contain any curves

exception biosimulators_utils.sedml.warnings.NoDataSetsWarning[source]#

Bases: IllogicalSedmlWarning

Warning that a report does not contain any data sets

exception biosimulators_utils.sedml.warnings.NoOutputsWarning[source]#

Bases: IllogicalSedmlWarning

Warning that a SED document does not have any outputs

exception biosimulators_utils.sedml.warnings.NoSurfacesWarning[source]#

Bases: IllogicalSedmlWarning

Warning that a 3D plot does not contain any surfaces

exception biosimulators_utils.sedml.warnings.NoTasksWarning[source]#

Bases: IllogicalSedmlWarning

Warning that a SED document does not have any tasks

exception biosimulators_utils.sedml.warnings.SedmlFeatureNotSupportedWarning[source]#

Bases: BioSimulatorsWarning

Warning that a feature of a SED document was skipped because it requires a SED feature that is not yet supported. The warning is only used when skipping a portion of a document doesn’t affect the semantic meaning of the unskipped portions of the document (e.g., skipping generating a plot doesn’t adversely affect reports).