biosimulators_utils.biosimulations package¶
Submodules¶
biosimulators_utils.biosimulations.data_model module¶
Data model for BioSimulations metadata
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-06
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
- class biosimulators_utils.biosimulations.data_model.Citation(title=None, authors=None, journal=None, volume=None, issue=None, pages=None, year=None, identifiers=None)[source]¶
Bases:
object
A citation
- class biosimulators_utils.biosimulations.data_model.ExternalReferences(identifiers=None, citations=None)[source]¶
Bases:
object
Identifiers and citations of an object
- is_equal(other)[source]¶
Determine if collections of external references are equal
- Parameters
other (
ExternalReferences
) – another collection of external referencse- Returns
True
, if two collections of external references are equal- Return type
bool
- class biosimulators_utils.biosimulations.data_model.Metadata(description=None, tags=None, authors=None, references=None, license=None, created=None, updated=None)[source]¶
Bases:
object
Metadata about an object
biosimulators_utils.biosimulations.utils module¶
Utility methods for working with BioSimulations and runBioSimulations
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-01-30
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_utils.biosimulations.utils.submit_project_to_runbiosimulations(name, filename_or_url, simulator, simulator_version='latest', cpus=1, memory=8, max_time=20, env_vars=None, email=None, public=False, config=None)[source]¶
Submit a simulation project (COMBINE/OMEX archive) to runBioSimulations and, optionally, BioSimulations
- Parameters
name (
str
) – name for the simulation runfilename_or_url (
str
) – path or URL to COMBINE/OMEX archivesimulator (
str
) – BioSimulators id for simulatorsimulator_version (
str
, optional) – simulator versioncpus (
int
, optional) – CPUsmemory (
float
, optional) – maximum memory in GBmax_time (
float
, optional) – maximum execution time in minutesenv_vars (
list
ofdict
, optional) – environment variables to execute the COMBINE/OMEX archive. Each element should have two string-valued keyskey
andvalue
email (
str
, optional) – email to receive a notification upon completion of the simulation runpublic (
bool
, optional) – whether to publish the simulation run to BioSimulationsconfig (
Config
, optional) – configuration
- Returns
runBioSimulations id
- Return type
str
- biosimulators_utils.biosimulations.utils.validate_biosimulations_api_response(response, failure_introductory_message)[source]¶
Validate a response from one of BioSimulation’s APIs.
- Parameters
response (
requests.models.Response
) – API responsefailure_introductory_message (
str
) – introductory message for failures
- Raises
requests.RequestException –