umls 0.1.3

A library and command line tool for working with the UMLS Metathesaurus
Documentation 
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use std::path::{Path, PathBuf};

use clap::Args;
use eyre::Result;
use smol_str::SmolStr;
use umls::{
    files::Files,
    index::build::{build_index, IndexBuilderOptions},
};

#[derive(Args, Debug)]
pub struct BuildIndexArgs {
    /// The directory to write the UMLS files. Defaults to the same directory containing the UMLS data files
    #[arg(short, long, env)]
    pub output: Option<PathBuf>,

    /// If true, the index will be generated to match all strings in lowercase.
    #[arg(short = 'i', long, env)]
    pub case_insensitive: bool,

    /// The source abbreviations (SAB field) to include in the index. If empty, all sources are included.
    #[arg(short, long, env)]
    pub sources: Vec<SmolStr>,

    /// The languages (LAT field) to include in the index. If empty, all sources are included.
    #[arg(short, long, env)]
    pub languages: Vec<SmolStr>,

    /// The semantic type tree values (and their children) to include in the index. If empty, all
    /// semantic types are included.
    #[arg(short = 't', long = "types", env)]
    pub semantic_types: Vec<SmolStr>,
}

pub fn run(base_dir: &Path, files: Files, args: BuildIndexArgs) -> Result<()> {
    let output = args
        .output
        .unwrap_or_else(|| base_dir.to_path_buf())
        .join("index");

    std::fs::create_dir(&output)?;

    build_index(IndexBuilderOptions {
        output_dir: &output,
        files: &files,
        case_insensitive: args.case_insensitive,
        languages: args.languages,
        sources: args.sources,
        semantic_types: args.semantic_types,
    })?;

    Ok(())
}