caroott / arc-validate

Home of all the tools and libraries to create and run validation of ARCs

arc-validate

Home of all the tools and libraries to create and run validation of ARCs:

• ARCExpect (docs 📓) - easy to use and understand APIs to create and execute validation cases.
• ARCValidationPackages (docs 📓) - package for installing, updating, and executing ARC validation packages.
• arc-validate/ (docs 📓) - CLI tool that offers commands for validating ARCs and managing validation packages.

Docker container

This repository provides a docker container that has the arc-validate tool pre-installed for using it in DataHUB-CI jobs.

Use the containers tagged with main for production use.

Project aim

Validation of ARCs based on:

• ARCTokenization: Structural ontologies for file formats (for parsing/tokenizing files): INVMSO, STDMSO, ASSMSO
• OBO.NET:
  • parsing ontologies, generation of OBO graphs based on ontology term relation
  • code genearation of ontology modules with accessible terms
• ARCGraph: Graph representation of file content based on structural ontologies via OBO graph
• Graph-based completion of File content (missing cells -> empty tokens) via ARCGraph
• ARCExpect: Expecto-like API for creating validation cases
• Validation Packages: API for installing and executing additional validation packages

Project layout

flowchart TD

ControlledVocabulary("<b>ControlledVocabulary:</b><br>Data model for CVs")
ARCTokenization("<b>ARCTokenization:</b><br>Tokenization of ARCs into CVs")
OBO.NET("<b>OBO.NET:</b><br>OBO Ontology data model and parsing")
ARCGraph("<b>ARCGraph:</b><br>Graph based on structural ontologies")
ARCExpect("<b>ARCExpect:</b><br>Expecto-like API for validation")
ARCValidationPackages("<b>ARCValidationPackages:</b><br>API for additional validation packages")
arc-validate("<b>arc-validate:</b><br>validation CLI tool")

arc-validate --depends on--> ARCExpect
arc-validate --depends on--> ARCValidationPackages
ARCTokenization --depends on--> ControlledVocabulary
ARCTokenization --depends on--> OBO.NET
ARCExpect --depends on--> ARCGraph
ARCExpect --depends on--> ARCTokenization
ARCGraph --depends on--> ARCTokenization
ARCGraph --depends on--> OBO.NET

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