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Managed Biosim pipeline

Command Overview

  1. upload OMEX files
  2. refresh status
  3. download runs
  4. compare runs
  5. publish

Setup

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>>

upload OMEX files

poetry run python main.py upload_omex --help
Usage: 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.

refresh status

poetry run python main.py refresh_status --help
Usage: 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.

download runs

poetry run python main.py download_runs --help
Usage: 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.

compare runs

poetry run python main.py compare_runs --help
Usage: 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.

publish

poetry run python main.py publish --help
Usage: 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.