biosimulators_utils.omex_meta package#

Submodules#

biosimulators_utils.omex_meta.data_model module#

Data model for working with OMEX Metadata

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-06-23
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

class biosimulators_utils.omex_meta.data_model.OmexMetadataInputFormat(value)[source]#

Bases: str, Enum

An format for reading an OMEX Metadata file

nquads = 'nquads'[source]#

ntriples = 'ntriples'[source]#

rdfa = 'rdfa'[source]#

rdfxml = 'rdfxml'[source]#

turtle = 'turtle'[source]#

class biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat(value)[source]#

Bases: str, Enum

An format for writing an OMEX Metadata file

dot = 'dot'[source]#

html = 'html'[source]#

json = 'json'[source]#

json_triples = 'json-triples'[source]#

nquads = 'nquads'[source]#

ntriples = 'ntriples'[source]#

rdfxml = 'rdfxml'[source]#

rdfxml_abbrev = 'rdfxml-abbrev'[source]#

rdfxml_xmp = 'rdfxml-xmp'[source]#

turtle = 'turtle'[source]#

class biosimulators_utils.omex_meta.data_model.OmexMetadataSchema(value)[source]#

Bases: str, Enum

Schema for OMEX Metadata documents

biosimulations = 'BioSimulations'[source]#

rdf_triples = 'rdf_triples'[source]#

class biosimulators_utils.omex_meta.data_model.Triple(subject, predicate, object)[source]#

Bases: object

An RDF triple

subject[source]#

subject

Type:: rdflib.term.BNode, rdflib.term.Literal, or rdflib.term.URIRef

predicate[source]#

predict

Type:: rdflib.term.BNode, rdflib.term.Literal, or rdflib.term.URIRef

object[source]#

object

Type:: rdflib.term.BNode, rdflib.term.Literal, or rdflib.term.URIRef

biosimulators_utils.omex_meta.io module#

Methods for reading and writing OMEX Metadata files

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-06-23
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

class biosimulators_utils.omex_meta.io.BiosimulationsOmexMetaReader[source]#

Bases: OmexMetaReader

Utility for reading the metadata about a COMBINE/OMEX archive in an OMEX Metadata file into a dictionary with BioSimulations schema

classmethod get_combine_archive_uri(triples)[source]#

Get the URI used to the describe the COMBINE/OMEX archive in a list of RDF triples

Parameters:: triples (list of dict) – representation of the OMEX Metadata file as list of triples
Returns:: URI used to the describe the COMBINE/OMEX archive in the list of triples
Return type:: str

classmethod parse_triples_to_schema(triples, combine_archive_uri)[source]#

Convert a graph of RDF triples into BioSimulations’ metadata schema

Parameters:

triples (list of dict) – representation of the OMEX Meta file as list of triples
combine_archive_uri (str) – URI used to the describe the COMBINE/OMEX archive in the list of triples

Returns:

representation of the triples in BioSimulations’ metadata schema

Return type:

list of object

run(filename_or_filenames, archive=None, working_dir=None, config=None)[source]#

Read the metadata about a COMBINE/OMEX archive in an OMEX Metadata file into a dictionary: with BioSimulations schema

Parameters:

filename_or_filenames (str or list of str) – path or paths to OMEX Metadata files
archive (CombineArchive, optional) – parent COMBINE archive
working_dir (str, optional) – working directory (e.g., directory of the parent COMBINE/OMEX archive)
config (Config, optional) – configuration

Returns:

dict: representation of the metadata about a COMBINE/OMEX
archive in an OMEX Metadata file as a dictionary with BioSimulations schema
nested list of str: nested list of errors with the OMEX Metadata file
nested list of str: nested list of warnings with the OMEX Metadata file

Return type:

tuple

class biosimulators_utils.omex_meta.io.BiosimulationsOmexMetaWriter[source]#

Bases: OmexMetaWriter

Utility for writing the metadata about a COMBINE/OMEX archive to an OMEX Metadata file

run(el_metadatas, filename, config=None)[source]#

Write an OMEX Metadata file

Parameters:

el_metadatas (list of dict) – representation of the metadata about the elements in a COMBINE/OMEX archive in an OMEX Metadata file
filename (str) – path to save OMEX Metadata file
config (Config, optional) – configuration

class biosimulators_utils.omex_meta.io.TriplesOmexMetaReader[source]#

Bases: OmexMetaReader

Utility for reading an OMEX Metadata file into a list of triples

run(filename_or_filenames, archive=None, working_dir=None, config=None)[source]#

Read an OMEX Metadata file into a list of triples

Parameters:

filename_or_filenames (str or list of str) – path or paths to OMEX Metadata files
archive (CombineArchive, optional) – parent COMBINE archive
working_dir (str, optional) – working directory (e.g., directory of the parent COMBINE/OMEX archive)
config (Config, optional) – configuration

Returns:

list of dict: representation of the OMEX Metadata file as list of triples
nested list of str: nested list of errors with the OMEX Metadata file
nested list of str: nested list of warnings with the OMEX Metadata file

Return type:

tuple

class biosimulators_utils.omex_meta.io.TriplesOmexMetaWriter[source]#

Bases: OmexMetaWriter

Utility for writing a list of triples to an OMEX Metadata file

run(triples, filename, namespaces=None, config=None)[source]#

Write a list of triples to an OMEX Metadata file

Parameters:

triples (list of Triple) – representation of the OMEX Metadata file as list of triples
filename (str) – path to OMEX Metadata file
config (Config, optional) – configuration

biosimulators_utils.omex_meta.io.read_omex_meta_file(filename_or_filenames, archive=None, working_dir=None, config=None)[source]#

Read an OMEX Metadata file

Parameters:

filename_or_filenames (str or list of str) – path or paths to OMEX Metadata files
archive (CombineArchive, optional) – parent COMBINE archive
working_dir (str, optional) – working directory (e.g., directory of the parent COMBINE/OMEX archive)
config (Config, optional) – configuration

Returns:

object: representation of the OMEX Metadata file in schema
nested list of str: nested list of errors with the OMEX Metadata file
nested list of str: nested list of warnings with the OMEX Metadata file

Return type:

tuple

biosimulators_utils.omex_meta.io.read_omex_meta_files_for_archive(archive, archive_dirname, config=None)[source]#

Read all of the OMEX Metadata files in an archive

Parameters:

archive (CombineArchive) – COMBINE/OMEX archive
archive_dirname (str) – directory with the content of the archive
config (Config, optional) – configuration

Returns:

object: representation of the OMEX Metadata file in schema
nested list of str: nested list of errors with the OMEX Metadata file
nested list of str: nested list of warnings with the OMEX Metadata file

Return type:

tuple

biosimulators_utils.omex_meta.io.write_omex_meta_file(content, filename, config=None)[source]#

Write an OMEX Metadata file

Parameters:

content (object) – representation of the OMEX Metadata file in schema
filename (str) – path to save OMEX Metadata file
config (Config, optional) – configuration

biosimulators_utils.omex_meta.utils module#

Methods for generating OMEX metdata files for models

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-07-19
License:: MIT

biosimulators_utils.omex_meta.utils.build_omex_meta_file_for_model(model_filename, metadata_filename, metadata_format=OmexMetadataOutputFormat.rdfxml_abbrev, encoding='utf-8', archive_uri=None)[source]#

Create an OMEX metadata file for a model encoded in CellML or SBML. Also add missing metadata ids to the model file.

Parameters:

model_filename (str) – path to model to extract metadata about
metadata_filename (str) – path to save metadata
metadata_format (OmexMetadataOutputFormat, optional) – format for metadata_filename
encoding (str, optional) – encoding (e.g., utf-8)

biosimulators_utils.omex_meta.utils.get_global_combine_archive_content_uri(content_rel_uri, archive_uri=None)[source]#

Get a global URI for a content item of a COMBINE/OMEX archive

Parameters:

content_rel_uri (str) – URI for a content item of a COMBINE/OMEX archive, relative to its parent archive
archive_uri (str, optional) – URI for the parent COMBINE/OMEX archive

Returns:

global URI for the content item

Return type:

str

biosimulators_utils.omex_meta.utils.get_local_combine_archive_content_uri(content_uri, archive_uri=None)[source]#

Get the relative URI for a content item of a COMBINE/OMEX archive

Parameters:

content_uri (str) – global URI for a content item of a COMBINE/OMEX archive
archive_uri (str, optional) – URI for the parent COMBINE/OMEX archive

Returns:

tuple:

str: global URI for the content item

str: URI for the parent COMBINE/OMEX archive

biosimulators_utils.omex_meta.validation module#

Methods for validate BioSimulations metadata

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-06-23
License:: MIT

biosimulators_utils.omex_meta.validation.validate_biosimulations_metadata(metadata, archive=None, working_dir=None)[source]#

Validate BioSimulations metadata for a COMBINE/OMEX archive

Parameters:

metadata (list of dict) – BioSimulations metadata about 1 or more URIs
archive (CombineArchive, optional) – parent COMBINE archive
working_dir (str, optional) – working directory (e.g., directory of the parent COMBINE/OMEX archive)

Returns:

nested list of str: nested list of errors with the metadata
nested list of str: nested list of warnings with the metadata

Return type:

tuple

biosimulators_utils.omex_meta.validation.validate_biosimulations_metadata_for_uri(metadata, validate_minimal_metadata=False, archive=None, working_dir=None)[source]#

Validate BioSimulations metadata for a file in a COMBINE/OMEX archive

Parameters:

metadata (dict) – BioSimulations metadata
validate_minimal_metadata (bool, optional) – whether to check that all required metadata attributes are defined
archive (CombineArchive, optional) – parent COMBINE archive
working_dir (str, optional) – working directory (e.g., directory of the parent COMBINE/OMEX archive)

Returns:

nested list of str: nested list of errors with the metadata
nested list of str: nested list of warnings with the metadata

Return type:

tuple