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| __version__ = '0.1.17' | ||
| __version__ = '0.1.18' |
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| """ Configuration | ||
| :Author: Jonathan Karr <[email protected]> | ||
| :Date: 2021-01-30 | ||
| :Copyright: 2021, Center for Reproducible Biomedical Modeling | ||
| :License: MIT | ||
| """ | ||
|
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| import os | ||
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| class Config(object): | ||
| def __init__(self, pull_docker_image=None): | ||
| if pull_docker_image is not None: | ||
| """ Configuration | ||
| Attributes: | ||
| pull_docker_image (:obj:`bool`): whether to pull the Docker image for the simulator (default: :obj:`True`) | ||
| docker_hub_username (:obj:`str`): username for Docker Hub | ||
| docker_hub_token (:obj:`str`): Token for Docker Hub | ||
| biosimulators_auth_endpoint (:obj:`str`): Authentification endpoint for the BioSimulators API | ||
| biosimulators_audience (:obj:`str`): Open API audience for the BioSimulators API | ||
| biosimulators_api_client_id (:obj:`str`): Client id of the BioSimulators API | ||
| biosimulators_api_client_secret (:obj:`str`): Client secret of the BioSimulators API | ||
| biosimulators_api_endpoint (:obj:`str`): Base URL for the BioSimulators API | ||
| biosimulators_curator_gh_ids (:obj:`list` of :obj:`str`): GitHub user ids of the BioSimulators curators | ||
| biosimulators_default_specifications_version (:obj:`str`): Default version of the BioSimulators simulation specifications | ||
| biosimulators_default_image_version (:obj:`str`): Default version of the BioSimulators Docker image format | ||
| biosimulators_docker_registry_url (:obj:`str`): URL of the Docker registry for simulators | ||
| biosimulators_docker_registry_username (:obj:`str`): username for Docker registry for simulators | ||
| biosimulators_docker_registry_token (:obj:`str`): token for Docker registry for simulators | ||
| biosimulators_docker_image_url_pattern (:obj:`str`): URL pattern for Docker images for simulators | ||
| runbiosimulations_auth_endpoint (:obj:`str`): Authentification endpoint for the runBioSimulations API | ||
| runbiosimulations_audience (:obj:`str`): Open API audience for the runBioSimulations API | ||
| runbiosimulations_api_client_id (:obj:`str`): Client id of the runBioSimulations API | ||
| runbiosimulations_api_client_secret (:obj:`str`): Client secret of the runBioSimulations API | ||
| runbiosimulations_api_endpoint (:obj:`str`): Base URL for the runBioSimulations API | ||
| """ | ||
|
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||
| def __init__(self, | ||
| pull_docker_image=None, docker_hub_username=None, docker_hub_token=None, | ||
| biosimulators_auth_endpoint=None, biosimulators_audience=None, | ||
| biosimulators_api_client_id=None, biosimulators_api_client_secret=None, | ||
| biosimulators_api_endpoint=None, | ||
| biosimulators_curator_gh_ids=None, biosimulators_default_specifications_version=None, | ||
| biosimulators_default_image_version=None, biosimulators_docker_registry_url=None, | ||
| biosimulators_docker_registry_username=None, biosimulators_docker_registry_token=None, | ||
| biosimulators_docker_image_url_pattern=None, | ||
| runbiosimulations_auth_endpoint=None, runbiosimulations_audience=None, | ||
| runbiosimulations_api_client_id=None, runbiosimulations_api_client_secret=None, | ||
| runbiosimulations_api_endpoint=None): | ||
| """ | ||
| Args: | ||
| pull_docker_image (:obj:`bool`, optional): whether to pull the Docker image for the simulator (default: :obj:`True`) | ||
| docker_hub_username (:obj:`str`, optional): username for Docker Hub | ||
| docker_hub_token (:obj:`str`, optional): Token for Docker Hub | ||
| biosimulators_auth_endpoint (:obj:`str`, optional): Authentification endpoint for the BioSimulators API | ||
| biosimulators_audience (:obj:`str`, optional): Open API audience for the BioSimulators API | ||
| biosimulators_api_client_id (:obj:`str`, optional): Client id of the BioSimulators API | ||
| biosimulators_api_client_secret (:obj:`str`, optional): Client secret of the BioSimulators API | ||
| biosimulators_api_endpoint (:obj:`str`, optional): Base URL for the BioSimulators API | ||
| biosimulators_curator_gh_ids (:obj:`list` of :obj:`str`, optional): GitHub user ids of the BioSimulators curators | ||
| biosimulators_default_specifications_version (:obj:`str`, optional): Default version of the BioSimulators simulation specifications | ||
| biosimulators_default_image_version (:obj:`str`, optional): Default version of the BioSimulators Docker image format | ||
| biosimulators_docker_registry_url (:obj:`str`, optional): URL of the Docker registry for simulators | ||
| biosimulators_docker_registry_username (:obj:`str`, optional): username for Docker registry for simulators | ||
| biosimulators_docker_registry_token (:obj:`str`, optional): token for Docker registry for simulators | ||
| biosimulators_docker_image_url_pattern (:obj:`str`, optional): URL pattern for Docker images for simulators | ||
| runbiosimulations_auth_endpoint (:obj:`str`, optional): Authentification endpoint for the runBioSimulations API | ||
| runbiosimulations_audience (:obj:`str`, optional): Open API audience for the runBioSimulations API | ||
| runbiosimulations_api_client_id (:obj:`str`, optional): Client id of the runBioSimulations API | ||
| runbiosimulations_api_client_secret (:obj:`str`, optional): Client secret of the runBioSimulations API | ||
| runbiosimulations_api_endpoint (:obj:`str`, optional): Base URL for the runBioSimulations API | ||
| """ | ||
| # Docker registry | ||
| if pull_docker_image is None: | ||
| self.pull_docker_image = os.getenv('PULL_DOCKER_IMAGE', '1').lower() in ['1', 'true'] | ||
| else: | ||
| self.pull_docker_image = pull_docker_image | ||
|
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| # Docker Hub | ||
| if docker_hub_username is None: | ||
| self.docker_hub_username = os.getenv('DOCKER_HUB_USERNAME') | ||
| else: | ||
| self.pull_docker_image = os.getenv('PULL_DOCKER_IMAGE', '1').lower() in ['1', 'true'] | ||
| self.docker_hub_username = docker_hub_username | ||
|
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| if docker_hub_token is None: | ||
| self.docker_hub_token = os.getenv('DOCKER_HUB_TOKEN') | ||
| else: | ||
| self.docker_hub_token = docker_hub_token | ||
|
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| # BioSimulators | ||
| if biosimulators_auth_endpoint is None: | ||
| self.biosimulators_auth_endpoint = os.getenv('BIOSIMULATORS_AUTH_ENDPOINT', 'https://auth.biosimulations.org/oauth/token') | ||
| else: | ||
| self.biosimulators_auth_endpoint = biosimulators_auth_endpoint | ||
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| if biosimulators_audience is None: | ||
| self.biosimulators_audience = os.getenv('BIOSIMULATORS_AUDIENCE', 'api.biosimulators.org') | ||
| else: | ||
| self.biosimulators_audience = biosimulators_audience | ||
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| if biosimulators_api_client_id is None: | ||
| self.biosimulators_api_client_id = os.getenv('BIOSIMULATORS_API_CLIENT_ID') | ||
| else: | ||
| self.biosimulators_api_client_id = biosimulators_api_client_id | ||
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| if biosimulators_api_client_secret is None: | ||
| self.biosimulators_api_client_secret = os.getenv('BIOSIMULATORS_API_CLIENT_SECRET') | ||
| else: | ||
| self.biosimulators_api_client_secret = biosimulators_api_client_secret | ||
|
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| if biosimulators_api_endpoint is None: | ||
| self.biosimulators_api_endpoint = os.getenv('BIOSIMULATORS_API_ENDPOINT', 'https://api.biosimulators.org/') | ||
| else: | ||
| self.biosimulators_api_endpoint = biosimulators_api_endpoint | ||
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| if biosimulators_curator_gh_ids is None: | ||
| ids = os.getenv('BIOSIMULATORS_CURATOR_GH_IDS', 'jonrkarr').strip() | ||
| if ids: | ||
| self.biosimulators_curator_gh_ids = [id.strip() for id in ids.split(',')] | ||
| else: | ||
| self.biosimulators_curator_gh_ids = [] | ||
| else: | ||
| self.biosimulators_curator_gh_ids = biosimulators_curator_gh_ids | ||
|
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| if biosimulators_default_specifications_version is None: | ||
| self.biosimulators_default_specifications_version = os.getenv('BIOSIMULATORS_DEFAULT_SPECIFICATIONS_VERSION', '1.0.0') | ||
| else: | ||
| self.biosimulators_default_specifications_version = biosimulators_default_specifications_version | ||
|
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| if biosimulators_default_image_version is None: | ||
| self.biosimulators_default_image_version = os.getenv('BIOSIMULATORS_DEFAULT_IMAGE_VERSION', '1.0.0') | ||
| else: | ||
| self.biosimulators_default_image_version = biosimulators_default_image_version | ||
|
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| if biosimulators_docker_registry_url is None: | ||
| self.biosimulators_docker_registry_url = os.getenv( | ||
| 'BIOSIMULATORS_DOCKER_REGISTRY_URL', os.getenv('DOCKER_REGISTRY_URL', 'ghcr.io')) | ||
| else: | ||
| self.biosimulators_docker_registry_url = biosimulators_docker_registry_url | ||
|
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| if biosimulators_docker_registry_username is None: | ||
| self.biosimulators_docker_registry_username = os.getenv( | ||
| 'BIOSIMULATORS_DOCKER_REGISTRY_USERNAME', os.getenv('DOCKER_REGISTRY_USERNAME')) | ||
| else: | ||
| self.biosimulators_docker_registry_username = biosimulators_docker_registry_username | ||
|
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| if biosimulators_docker_registry_token is None: | ||
| self.biosimulators_docker_registry_token = os.getenv( | ||
| 'BIOSIMULATORS_DOCKER_REGISTRY_TOKEN', os.getenv('DOCKER_REGISTRY_TOKEN')) | ||
| else: | ||
| self.biosimulators_docker_registry_token = biosimulators_docker_registry_token | ||
|
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| if biosimulators_docker_image_url_pattern is None: | ||
| self.biosimulators_docker_image_url_pattern = os.getenv( | ||
| 'BIOSIMULATORS_DOCKER_REGISTRY_IMAGE_URL_PATTERN', 'ghcr.io/biosimulators/{}:{}') | ||
| else: | ||
| self.biosimulators_docker_image_url_pattern = biosimulators_docker_image_url_pattern | ||
|
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| # runBioSimulations | ||
| if runbiosimulations_auth_endpoint is None: | ||
| self.runbiosimulations_auth_endpoint = os.getenv( | ||
| 'RUNBIOSIMULATIONS_AUTH_ENDPOINT', 'https://auth.biosimulations.org/oauth/token') | ||
| else: | ||
| self.runbiosimulations_auth_endpoint = runbiosimulations_auth_endpoint | ||
|
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| if runbiosimulations_audience is None: | ||
| self.runbiosimulations_audience = os.getenv('RUNBIOSIMULATIONS_AUDIENCE', 'dispatch.biosimulations.org') | ||
| else: | ||
| self.runbiosimulations_audience = runbiosimulations_audience | ||
|
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| if runbiosimulations_api_client_id is None: | ||
| self.runbiosimulations_api_client_id = os.getenv('RUNBIOSIMULATIONS_API_CLIENT_ID') | ||
| else: | ||
| self.runbiosimulations_api_client_id = runbiosimulations_api_client_id | ||
|
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| if runbiosimulations_api_client_secret is None: | ||
| self.runbiosimulations_api_client_secret = os.getenv('RUNBIOSIMULATIONS_API_CLIENT_SECRET') | ||
| else: | ||
| self.runbiosimulations_api_client_secret = runbiosimulations_api_client_secret | ||
|
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| if runbiosimulations_api_endpoint is None: | ||
| self.runbiosimulations_api_endpoint = os.getenv('RUNBIOSIMULATIONS_API_ENDPOINT', 'https://run.api.biosimulations.org/') | ||
| else: | ||
| self.runbiosimulations_api_endpoint = runbiosimulations_api_endpoint |
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