sbmlutils.report.sbmlinfo

Creates dictionary of information for given model.

The model dictionary can be used for rendering the HTML report. The information can be serialized to JSON for later rendering in web app.

Module Contents

Classes

SBMLDocumentInfo

Class for collecting information in JSON on an SBMLDocument to create reports.

Functions

_get_sbase_attribute(sbase, key)	Get SBase attribute.
clean_empty(d)	Remove empty fields from JSON.

Attributes

output_dir

sbmlutils.report.sbmlinfo._get_sbase_attribute(sbase, key)

Get SBase attribute.

Parameters:

• sbase (libsbml.SBase) –

• key (str) –

Return type:

Optional[Any]

sbmlutils.report.sbmlinfo.clean_empty(d)

Remove empty fields from JSON.

Reducing to core information.

Parameters:

d (Union[Dict, List, str]) –

Return type:

Union[Dict, List, str]

class sbmlutils.report.sbmlinfo.SBMLDocumentInfo(doc)

Class for collecting information in JSON on an SBMLDocument to create reports.

A single document can contain multiple models or be a hierarchical model (comp package).

Parameters:

doc (libsbml.SBMLDocument) –

static from_sbml(source)

Read model info from SBML.

Parameters:

source (Union[pathlib.Path, str]) –

Return type:

SBMLDocumentInfo

__repr__()

Get string representation.

Return type:

str

__str__()

Get string.

Return type:

str

to_json(strip=True, indent=2)

Serialize to JSON representation.

Parameters:

• strip (bool) –

• indent (int) –

Return type:

str

create_info()

Create information dictionary for report rendering.

Return type:

Dict[str, Any]

model_dict(model)

Create information for a given model.

Parameters:

model (Union[libsbml.Model, libsbml.ModelDefinition]) –

Return type:

Dict[str, Any]

add_compartment_links(compartments, species, reactions)

Add species and reaction links to compartment.

Parameters:

• compartments (List[Dict[str, Any]]) –

• species (List[Dict[str, Any]]) –

• reactions (List[Dict[str, Any]]) –

Return type:

None

add_species_links(species, reactions)

Add reaction links to species.

Parameters:

• species (List[Dict[str, Any]]) –

• reactions (List[Dict[str, Any]]) –

Return type:

None

static _sbaseref(sbaseref)

Format the SBaseRef instance.

Used to figure out the type of the SBaseRef.

Parameters:

sbaseref (libsbml.SBaseRef) – SBaseRef instance

Returns:

Dictionary containing formatted SBaseRef instance’s data

Return type:

Optional[Dict]

_create_port_map(model)

Create dictionary of symbols:port for symbols in model.

This allows to lookup port for a given Sbase.

Returns:

port dictionary for model

Parameters:

model (libsbml.Model) –

Return type:

Dict

_create_assignment_map(model)

Create dictionary of symbols:assignment for symbols in model.

This allows to lookup assignments for a given variable.

Returns:

assignment dictionary for model

Parameters:

model (libsbml.Model) –

Return type:

Dict

static _sbml_type(sbase)

Parameters:

sbase (libsbml.SBase) –

Return type:

str

static _get_pk(sbase)

Calculate primary key.

Parameters:

sbase (libsbml.SBase) –

Return type:

str

static _uuid(xml)

Generate unique identifier.

SHA1 digest of the identifier (mostly the xml string).

Parameters:

xml (str) –

Return type:

str

classmethod sbase_dict(sbase)

Info dictionary for SBase.

Parameters:

sbase (libsbml.SBase) – SBase instance for which info dictionary is to be created

Return type:

Dict[str, Any]

:return info dictionary for item

sbaseref_dict(sbaseref)

Info dictionary for SBaseRef.

Parameters:

sbaseref (libsbml.SBaseRef) – SBaseRef instance for which information dictionary is created

Returns:

information dictionary for SBaseRef

Return type:

Dict[str, Any]

classmethod cvterms(sbase)

Parse CVTerms information.

Parameters:

sbase (libsbml.SBase) – SBase instance

Return type:

Optional[List]

classmethod model_history(sbase)

Parse model history information.

:return

Parameters:

sbase (libsbml.SBase) –

Return type:

Optional[Dict]

document(doc)

Info for SBMLDocument.

Parameters:

doc (libsbml.SBMLDocument) – SBMLDocument

Returns:

information dictionary for SBMLDocument

Return type:

Dict[str, str]

model(model)

Info for SBML Model.

Parameters:

model (libsbml.Model) – Model

Returns:

information dictionary for Model

Return type:

Dict[str, str]

function_definitions(model)

Information dictionaries for FunctionDefinitions.

Returns:

list of info dictionaries for FunctionDefinitions

Parameters:

model (libsbml.Model) –

Return type:

List

unit_definitions(model)

Information for UnitDefinitions.

Returns:

list of info dictionaries for UnitDefinitions

Parameters:

model (libsbml.Model) –

Return type:

List

compartments(model, assignments)

Information for Compartments.

Returns:

list of info dictionaries for Compartments

Parameters:

• model (libsbml.Model) –

• assignments (Dict[str, Dict[str, str]]) –

Return type:

List[Dict]

species(model, assignments)

Information for Species.

Returns:

list of info dictionaries for Species

Parameters:

• model (libsbml.Model) –

• assignments (Dict[str, Dict[str, str]]) –

Return type:

List[Dict]

parameters(model, assignments)

Information for SBML Parameters.

Returns:

list of info dictionaries for Reactions

Parameters:

• model (libsbml.Model) –

• assignments (Dict[str, Dict[str, str]]) –

Return type:

List[Dict]

initial_assignments(model)

Information for InitialAssignments.

Returns:

list of info dictionaries for InitialAssignments

Parameters:

model (libsbml.Model) –

Return type:

List

rules(model)

Information for Rules.

Returns:

list of info dictionaries for Rules

Parameters:

model (libsbml.Model) –

Return type:

Dict

static _rule_variable_to_string(rule)

Format variable for rule.

Parameters:

rule (libsbml.Rule) – SBML rule instance

Return type:

str

:return formatted string representation of the rule

constraints(model)

Information for Constraints.

Returns:

list of info dictionaries for Constraints

Parameters:

model (libsbml.Model) –

Return type:

List[Dict[str, Any]]

reactions(model)

Information dictionaries for ListOfReactions.

Returns:

list of info dictionaries for Reactions

Parameters:

model (libsbml.Model) –

Return type:

List[Dict[str, Any]]

– take a look at local parameter once

static _species_reference(species)

Resolve species reference.

Parameters:

species (libsbml.SpeciesReference) –

Return type:

Dict[str, Any]

static _bounds_dict_from_reaction(reaction, model)

Render string of bounds from the reaction.

Parameters:

• reaction (libsbml.Reaction) – SBML reaction instance

• model (libsbml.Model) – SBML model instance

Returns:

String of bounds extracted from the reaction

Return type:

Optional[Dict]

static _gene_product_association_from_reaction(reaction)

Render string representation of the GeneProductAssociation for given reaction.

Parameters:

reaction (libsbml.Reaction) – SBML reaction instance

Returns:

string representation of GeneProductAssociation

Return type:

Optional[str]

static _equation_from_reaction(reaction, sep_reversible='⇆', sep_irreversible='➞', modifiers=False)

Create equation for reaction.

Parameters:

• reaction (libsbml.Reaction) – SBML reaction instance for which equation is to be generated

• sep_reversible (str) – escape sequence for reversible equation (<=>) separator

• sep_irreversible (str) – escape sequence for irreversible equation (=>) separator

• modifiers (bool) – boolean flag to use modifiers

Return type:

str

:return equation string generated for the reaction

static _modifier_equation(modifierList)

Render string representation for list of modifiers.

Parameters:

modifierList (libsbml.ListOfSpeciesReferences) – list of modifiers

Returns:

string representation for list of modifiers

Return type:

str

static _half_equation(speciesList)

Create equation string of the half reaction of the species in the species list.

Parameters:

speciesList (libsbml.ListOfSpecies) – list of species in the half reaction

Returns:

half equation string

Return type:

str

events(model)

Information dictionaries for Events.

Returns:

list of info dictionaries for Events

Parameters:

model (libsbml.Model) –

Return type:

List[Dict[str, Any]]

model_definitions()

Information for comp:ModelDefinitions.

Returns:

list of info dictionaries for comp:ModelDefinitions

Return type:

Dict

submodels(model)

Information dictionaries for comp:Submodels.

Returns:

list of info dictionaries for comp:Submodels

Parameters:

model (libsbml.Model) –

Return type:

List[Dict[str, Any]]

ports(model)

Information for comp:Ports.

Returns:

list of info dictionaries for comp:Ports

Parameters:

model (libsbml.Model) –

Return type:

List

gene_products(model)

Information dictionaries for GeneProducts.

Returns:

list of info dictionaries for Reactions

Parameters:

model (libsbml.Model) –

Return type:

List[Dict[str, Any]]

objectives(model)

Information dictionaries for Objectives.

Returns:

list of info dictionaries for Objectives

Parameters:

model (libsbml.Model) –

Return type:

List[Dict[str, Any]]

sbmlutils.report.sbmlinfo.output_dir