curie-clean (1.0.2)

Skye Goetz (ISB) 03/26/2025

A Clojure utility for analyzing and resolving duplicate nodes in knowledge graph exchange (KGX) formatted knowledge graphs, with Tablassert integration and Biolink Model compliance. It updates Tablassert-integreated "table_configs" through a CLI.

Features

• Duplicate Detection: Identifies duplicate entries in TSV files
• Interactive Resolution: CLI prompts for handling conflicts
• YAML Configuration: Generates config files to prevent future duplicates

Requirements

• Clojure 1.10+
• Java JDK 8+
• Leiningen

Usage

For arguments...

# With Leiningen
lein run -h

To resolve duplicates...

# With Leiningen
lein run -n nodes.tsv -e edges.tsv

To test the application...

# With Leiningen
lein test

Directory Structure

curie-clean/
├── src/
│   └── duplicate_utility/
│       ├── io/
│       │   ├── tsv.clj
│       │   └── yaml.clj
│       ├── processing/
│       │   ├── duplicates.clj
│       │   └── resolution.clj
│       ├── core.clj
│       └── validation.clj
└── test/
    └── duplicate_utility/
        ├── io/
        │   ├── tsv_test.clj
        │   └── yaml_test.clj
        ├── processing/
        │   ├── duplicates_test.clj
        │   └── resolution_test.clj
        ├── core_test.clj
        ├── test_utils.clj
        └── validation_test.clj