{"id":16064397,"url":"https://github.com/bluebrain/bbp-atlas-pipeline-validator","last_synced_at":"2025-04-11T01:37:36.861Z","repository":{"id":257808277,"uuid":"863947731","full_name":"BlueBrain/bbp-atlas-pipeline-validator","owner":"BlueBrain","description":"Validation of Atlas pipeline 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Pipeline Validator\n\n\n## Install\n\nYou can install the file by using `pip install bbp-atlas-pipeline-validator`\n\n\n## Examples\n\nYou can use the validator in the following way:\n\n```python\nfrom pipeline_validator.pipeline_validator import pipeline_validator\n\npath_to_file = \"./my_config.json\"\ntoken = \"THIS_IS_MY_NEXUS_TOKEN\"\nwhitelisted_vars = [\"var1\", \"var2\"]\n\npipeline_validator(path_to_file, token, whitelisted_vars)\n```\n\nwhere:\n\n- `path_to_file` is the relative path to the configuration\n- `token` is a valid nexus token\n- `whitelisted_vars` is an array of accepted variables\n\n\n## Configuration Format\n\nThe JSON configuration file should be in the following format:\n\n```json\n{\n  \"rules\":[\n    {\n      \"rule\": \"\u003cNAME_OF_RULE_1\u003e\",\n      \"execute\":\n        [\n          {\n            \"brainRegion\": \"http://api.brain-map.org/api/v2/data/Structure/\u003cBRAIN_REGION_ID_1\u003e\",\n            \"container\": \"docker://\u003cPATH_TO_DOCKER_IMAGE\u003e\",\n            \"command\": \"\u003cTHE COMMAND TO BE EXECUTED\u003e\"\n          },\n          {\n            \"brainRegion\": \"http://api.brain-map.org/api/v2/data/Structure/\u003cBRAIN_REGION_ID_2\u003e\",\n            \"container\": \"docker://\u003cPATH_TO_DOCKER_IMAGE\u003e\",\n            \"command\": \"\u003cTHE COMMAND TO BE EXECUTED\u003e\"\n          }\n        ]\n    },\n    {\n      \"rule\": \"\u003cNAME_OF_RULE_2\u003e\",\n      \"execute\":\n        [\n          {\n            \"brainRegion\": \"http://api.brain-map.org/api/v2/data/Structure/\u003cBRAIN_REGION_ID_1\u003e\",\n            \"container\": \"docker://\u003cPATH_TO_DOCKER_IMAGE\u003e\",\n            \"command\": \"\u003cTHE COMMAND TO BE EXECUTED\u003e\"\n          },\n          {\n            \"brainRegion\": \"http://api.brain-map.org/api/v2/data/Structure/\u003cBRAIN_REGION_ID_2\u003e\",\n            \"container\": \"docker://\u003cPATH_TO_DOCKER_IMAGE\u003e\",\n            \"command\": \"\u003cTHE COMMAND TO BE EXECUTED\u003e\"\n          }\n        ]\n    }\n  ]\n}\n```\n\n\n## Validation Criteria\n\nThe following criteria need to be met in order for the configuration to be validated:\n\n- The configuration need to follow the above JSON schema\n- Brain region ID should be valid (exist in brain region ontology)\n- 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\n- For each command, the variables passed need to be part of the whitelisted variables\n\n\n## Funding \u0026 Acknowledgment\n\nThe development of this software was supported by funding to the Blue Brain Project, a \nresearch center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss \ngovernment’s ETH Board of the Swiss Federal Institutes of Technology.\n\nCopyright © 2023-2024 Blue Brain Project/EPFL\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fbbp-atlas-pipeline-validator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fbbp-atlas-pipeline-validator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fbbp-atlas-pipeline-validator/lists"}