Pipeline Validator

Install

You can install the file by using pip install bbp-atlas-pipeline-validator

Examples

You can use the validator in the following way:

from pipeline_validator.pipeline_validator import pipeline_validator

path_to_file = "./my_config.json"
token = "THIS_IS_MY_NEXUS_TOKEN"
whitelisted_vars = ["var1", "var2"]

pipeline_validator(path_to_file, token, whitelisted_vars)

where:

• path_to_file is the relative path to the configuration
• token is a valid nexus token
• whitelisted_vars is an array of accepted variables

Configuration Format

The JSON configuration file should be in the following format:

{
  "rules":[
    {
      "rule": "<NAME_OF_RULE_1>",
      "execute":
        [
          {
            "brainRegion": "http://api.brain-map.org/api/v2/data/Structure/<BRAIN_REGION_ID_1>",
            "container": "docker://<PATH_TO_DOCKER_IMAGE>",
            "command": "<THE COMMAND TO BE EXECUTED>"
          },
          {
            "brainRegion": "http://api.brain-map.org/api/v2/data/Structure/<BRAIN_REGION_ID_2>",
            "container": "docker://<PATH_TO_DOCKER_IMAGE>",
            "command": "<THE COMMAND TO BE EXECUTED>"
          }
        ]
    },
    {
      "rule": "<NAME_OF_RULE_2>",
      "execute":
        [
          {
            "brainRegion": "http://api.brain-map.org/api/v2/data/Structure/<BRAIN_REGION_ID_1>",
            "container": "docker://<PATH_TO_DOCKER_IMAGE>",
            "command": "<THE COMMAND TO BE EXECUTED>"
          },
          {
            "brainRegion": "http://api.brain-map.org/api/v2/data/Structure/<BRAIN_REGION_ID_2>",
            "container": "docker://<PATH_TO_DOCKER_IMAGE>",
            "command": "<THE COMMAND TO BE EXECUTED>"
          }
        ]
    }
  ]
}

Validation Criteria

The following criteria need to be met in order for the configuration to be validated:

• The configuration need to follow the above JSON schema
• Brain region ID should be valid (exist in brain region ontology)
• Within each rule, each brain region need to be followed by brain region that are not related or that they are descendants in the ontology
• For each command, the variables passed need to be part of the whitelisted variables

Funding & Acknowledgment

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

Copyright © 2023-2024 Blue Brain Project/EPFL