create a .env file with the following. CLIENT_ID and CLIENT_SECRET are only needed for publishing which is currently performed by site administrators.
# for publication authentication
CLIENT_ID=<<auth-provider-client-id>>
CLIENT_SECRET=<<auth-provider-client-secret>>
AUTH_HOST=auth.biosimulations.org
AUTH_AUDIENCE=api.biosimulations.org
API_BASE_URL=https://api.biosimulations.org|dev
RUN_APP_BASE_URL=https://run.biosimulations.org|dev
# for pipeline
OMEX_SOURCE_DIR=<<path-to-source-omex-files>>
OMEX_OUTPUT_DIR=<<path-to-output-artifacts>>poetry run python main.py upload_omex --helpUsage: main.py upload_omex [OPTIONS]
upload and run OMEX files at BioSimulations
Options:
--simulator [tellurium|copasi|amici|vcell|pysces|libsbmlsim]
simulator to run [default: Simulator.vcell]
--project-id TEXT filter by project_id
--omex-src-dir PATH defaults env.OMEX_SOURCE_DIR
--out-dir PATH defaults to env.OMEX_OUTPUT_DIR
--help Show this message and exit.
poetry run python main.py refresh_status --helpUsage: main.py refresh_status [OPTIONS]
fetch status of runs and update biosimulations_runs.ndjson
Options:
--out-dir PATH defaults to env.OMEX_OUTPUT_DIR
--help Show this message and exit.
poetry run python main.py download_runs --helpUsage: main.py download_runs [OPTIONS]
download runs (results.zip) from BioSimulations
Options:
--omex-src-dir PATH defaults env.OMEX_SOURCE_DIR
--out-dir PATH defaults to env.OMEX_OUTPUT_DIR
--project-id TEXT filter by project_id
--simulator [tellurium|copasi|amici|vcell|pysces|libsbmlsim]
filter by simulator
--help Show this message and exit.
poetry run python main.py compare_runs --helpUsage: main.py compare_runs [OPTIONS]
compare downloaded runs
Options:
--omex-src-dir PATH defaults env.OMEX_SOURCE_DIR
--out-dir PATH defaults to env.OMEX_OUTPUT_DIR
--project-id TEXT filter by project_id
--help Show this message and exit.
poetry run python main.py publish --helpUsage: main.py publish [OPTIONS]
publish validated projects to BioSimulations
Options:
--omex-src-dir PATH defaults env.OMEX_SOURCE_DIR
--out-dir PATH defaults to env.OMEX_OUTPUT_DIR
--project-id TEXT filter by project_id
--help Show this message and exit.