`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)[source]¶

Get SBase attribute.

Parameters

sbase (libsbml.SBase) –
key (str) –

Return type

Optional[Any]

sbmlutils.report.sbmlinfo.clean_empty(d)[source]¶

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)[source]¶

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)[source]¶

Read model info from SBML.

Parameters: source (Union[pathlib.Path, str]) –
Return type: SBMLDocumentInfo

__repr__()[source]¶

Get string representation.

Return type: str

__str__()[source]¶

Get string.

Return type: str

to_json(strip=True, indent=2)[source]¶

Serialize to JSON representation.

Parameters

strip (bool) –
indent (int) –

Return type

str

create_info()[source]¶

Create information dictionary for report rendering.

Return type: Dict[str, Any]

model_dict(model)[source]¶

Create information for a given model.

Parameters: model (Union[libsbml.Model, libsbml.ModelDefinition]) –
Return type: Dict[str, Any]

add_compartment_links(compartments, species, reactions)[source]¶

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)[source]¶

Add reaction links to species.

Parameters

species (List[Dict[str, Any]]) –
reactions (List[Dict[str, Any]]) –

Return type

None

static _sbaseref(sbaseref)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

Parameters: sbase (libsbml.SBase) –
Return type: str

static _get_pk(sbase)[source]¶

Calculate primary key.

Parameters: sbase (libsbml.SBase) –
Return type: str

static _uuid(xml)[source]¶

Generate unique identifier.

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

Parameters: xml (str) –
Return type: str

classmethod sbase_dict(sbase)[source]¶

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)[source]¶

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)[source]¶

Parse CVTerms information.

Parameters: sbase (libsbml.SBase) – SBase instance
Return type: Optional[List]

classmethod model_history(sbase)[source]¶

Parse model history information.

:return

Parameters: sbase (libsbml.SBase) –
Return type: Optional[Dict]

document(doc)[source]¶

Info for SBMLDocument.

Parameters: doc (libsbml.SBMLDocument) – SBMLDocument
Returns: information dictionary for SBMLDocument
Return type: Dict[str, str]

model(model)[source]¶

Info for SBML Model.

Parameters: model (libsbml.Model) – Model
Returns: information dictionary for Model
Return type: Dict[str, str]

function_definitions(model)[source]¶

Information dictionaries for FunctionDefinitions.

Returns: list of info dictionaries for FunctionDefinitions
Parameters: model (libsbml.Model) –
Return type: List

unit_definitions(model)[source]¶

Information for UnitDefinitions.

Returns: list of info dictionaries for UnitDefinitions
Parameters: model (libsbml.Model) –
Return type: List

compartments(model, assignments)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

Information for InitialAssignments.

Returns: list of info dictionaries for InitialAssignments
Parameters: model (libsbml.Model) –
Return type: List

rules(model)[source]¶

Information for Rules.

Returns: list of info dictionaries for Rules
Parameters: model (libsbml.Model) –
Return type: Dict

static _rule_variable_to_string(rule)[source]¶

Format variable for rule.

Parameters: rule (libsbml.Rule) – SBML rule instance
Return type: str

:return formatted string representation of the rule

constraints(model)[source]¶

Information for Constraints.

Returns: list of info dictionaries for Constraints
Parameters: model (libsbml.Model) –
Return type: List[Dict[str, Any]]

reactions(model)[source]¶

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)[source]¶

Resolve species reference.

Parameters: species (libsbml.SpeciesReference) –
Return type: Dict[str, Any]

static _bounds_dict_from_reaction(reaction, model)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

Information dictionaries for Events.

Returns: list of info dictionaries for Events
Parameters: model (libsbml.Model) –
Return type: List[Dict[str, Any]]

model_definitions()[source]¶

Information for comp:ModelDefinitions.

Returns: list of info dictionaries for comp:ModelDefinitions
Return type: Dict

submodels(model)[source]¶

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)[source]¶

Information for comp:Ports.

Returns: list of info dictionaries for comp:Ports
Parameters: model (libsbml.Model) –
Return type: List

gene_products(model)[source]¶

Information dictionaries for GeneProducts.

Returns: list of info dictionaries for Reactions
Parameters: model (libsbml.Model) –
Return type: List[Dict[str, Any]]

objectives(model)[source]¶

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[source]¶

sbmlutils.report.sbmlinfo¶

Module Contents¶

Classes¶

Functions¶

Attributes¶

`sbmlutils.report.sbmlinfo`¶