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

__format__(format_spec)[source]#

Returns format using actual value type unless __str__ has been overridden.

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

__format__(format_spec)[source]#

Returns format using actual value type unless __str__ has been overridden.

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

__format__(format_spec)[source]#

Returns format using actual value type unless __str__ has been overridden.

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

Copyright:

2021, Center for Reproducible Biomedical Modeling

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

Copyright:

2021, Center for Reproducible Biomedical Modeling

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

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