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https://github.com/bluebrain/bbp-atlas-pipeline-validator

Validation of Atlas pipeline configuration

https://github.com/bluebrain/bbp-atlas-pipeline-validator

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.1%) to scientific vocabulary

Keywords

atlas database
Last synced: 5 months ago · JSON representation

Repository

Validation of Atlas pipeline configuration

Basic Info
  • Host: GitHub
  • Owner: BlueBrain
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 23.4 KB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
atlas database
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License

README.md

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:

```python from pipelinevalidator.pipelinevalidator import pipeline_validator

pathtofile = "./myconfig.json" token = "THISISMYNEXUSTOKEN" whitelistedvars = ["var1", "var2"]

pipelinevalidator(pathtofile, token, whitelistedvars) ```

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:

json { "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

Owner

  • Name: The Blue Brain Project
  • Login: BlueBrain
  • Kind: organization
  • Email: bbp.opensource@epfl.ch
  • Location: Geneva, Switzerland

Open Source Software produced and used by the Blue Brain Project

GitHub Events

Total
  • Watch event: 1
  • Member event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Member event: 1
  • Fork event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 16
  • Total Committers: 3
  • Avg Commits per committer: 5.333
  • Development Distribution Score (DDS): 0.438
Past Year
  • Commits: 11
  • Committers: 2
  • Avg Commits per committer: 5.5
  • Development Distribution Score (DDS): 0.182
Top Committers
Name Email Commits
Leonardo Cristella l****a@e****h 9
Konstantinos Platis k****s@e****h 5
Konstantinos Platis 5****s 2
Committer Domains (Top 20 + Academic)
epfl.ch: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: about 15 hours
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: about 15 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • kplatis (4)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 24 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 3
pypi.org: bbp-atlas-pipeline-validator

A pipeline validator for Blue Brain Project

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 24 Last month
Rankings
Dependent packages count: 10.3%
Average: 34.0%
Dependent repos count: 57.7%
Maintainers (3)
bbp.opensource kplatis obi.maintainer
Last synced: 6 months ago

Dependencies

setup.py pypi
  • bigtree *
  • jsonschema >=4.18.4
  • pytest >=7.4.0
  • requests >=2.31.0