zenleaf / entrez-rs

A Rust wrapper around the Entrez API. Helps you access the Entrez API using idiomatic Rust. It also provides tools to parse the XML results from Entrez.

entrez-rs

A Rust wrapper for the Entrez API

release:

master:

This library helps you access the Entrez API using idiomatic Rust. It also provides tools to parse the XML results from Entrez.

Installation

Add the following to your Cargo.toml:

   [dependencies]
   entrez-rs = "0.1.4"

Usage

use entrez_rs::eutils::{Eutils, ESearch, EFetch, DB};
use entrez_rs::parser::esearch::{ESearchResult};
use entrez_rs::parser::pubmed::{PubmedArticleSet};
use entrez_rs::errors::Error;

fn main() -> Result<(), Error>  {
        let xml = ESearch::new(
            DB::Pubmed, 
            "eclampsia")
            .run()?;

        let parsed = ESearchResult::read(&xml);

        println!("{:#?}", &parsed?
                          .id_list
                          .ids);
        
        let pm_xml = EFetch::new(
              DB::Pubmed,
              vec!["33246200", "33243171"])
              .run()?;
        
        let pm_parsed = PubmedArticleSet::read(&pm_xml);

        println!("{}", pm_parsed?.articles);

        Ok(())
}

Will add a walkthrough and tutorial of the API as soon as it reaches beta level.

Inspired by Entrez Direct, Entrezpy and BioPython.

entrez-rs's Issues

Why is only Pubmed implemented as a database?

You can access more than just one database via the NCBI. In my opinion, the following query cannot be mapped with this library:

#!/bin/sh
esearch -db nuccore -query "Sclerotinia sclerotiorum 1980 [TITLE]"  | efilter -molecule mrna | efetch -format fasta > s_sclerot.fa

Need DTD parsers instead of manual methods.

There are various, large DTDs with contents that may change overtime. The current method of using handwritten structs for parsing may not be maintainable. Instead, need to implement a DTD parser which can be used with the XML parser.