uniprot 0.7.0

Rust data structures and parser for the Uniprot database(s).
Documentation 
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//! Data types for the UniParc database.

use std::io::BufRead;

mod model;

#[doc(inline)]
pub use self::model::*;

/// The sequential parser type for UniParc entries.
pub type SequentialParser<B> = super::parser::SequentialParser<B, UniParc>;

#[cfg(feature = "threading")]
/// The threaded parser type for UniParc entries.
pub type ThreadedParser<B> = super::parser::ThreadedParser<B, UniParc>;

/// The parser type for UniParc entries.
pub type Parser<B> = super::parser::Parser<B, UniParc>;

/// Parse a UniParc database XML file.
///
/// # Example:
/// ```rust,no_run
/// let mut client = ftp::FtpStream::connect("ftp.uniprot.org:21").unwrap();
/// client.login("anonymous", "anonymous").unwrap();
///
/// let f = client.get("/pub/databases/uniprot/current_release/uniparc/uniparc_all.xml.gz").unwrap();
/// let dec = libflate::gzip::Decoder::new(f).unwrap();
/// let mut parser = uniprot::uniparc::parse(std::io::BufReader::new(dec));
///
/// println!("{:#?}", parser.next())
/// ```
pub fn parse<B: BufRead + Send + 'static>(reader: B) -> Parser<B> {
    Parser::new(reader)
}

/// Parse a single UniParc entry.
///
/// This method is compatible with responses from the
/// [EBI Proteins API](https://www.ebi.ac.uk/proteins/api/).
///
/// # Example
/// ```rust
/// let api_url = "https://www.ebi.ac.uk/proteins/api/uniparc/upi/UPI0000000001";
///
/// let req = ureq::get(&api_url).set("Accept", "application/xml");
/// let reader = std::io::BufReader::new(req.call().unwrap().into_reader());
/// let entry = uniprot::uniparc::parse_entry(reader).unwrap();
///
/// println!("{:?}", entry);
/// ```
pub fn parse_entry<B: BufRead>(reader: B) -> <SequentialParser<B> as Iterator>::Item {
    SequentialParser::parse_entry(reader)
}

#[cfg(test)]
mod tests {

    use super::*;
    use crate::error::Error;
    use quick_xml::Error as XmlError;

    #[test]
    fn parse_uniparc() {
        let f = std::fs::File::open("tests/uniparc.xml").unwrap();
        let entries = super::parse(std::io::BufReader::new(f))
            .collect::<Result<Vec<_>, _>>()
            .expect("entries should parse successfully");
        assert_eq!(entries.len(), 64);
    }

    mod sequential {
        use super::*;

        #[test]
        fn parse_single_entry() {
            let f = std::fs::File::open("tests/uniparc.xml").unwrap();
            SequentialParser::new(std::io::BufReader::new(f))
                .next()
                .expect("an entry should be parsed")
                .expect("the entry should be parsed successfully");
        }

        #[test]
        fn fail_unexpected_eof() {
            let txt = &b"<uniparc><entry dataset=\"uniparc\">"[..];
            let err = SequentialParser::new(std::io::Cursor::new(txt))
                .next()
                .expect("should raise an error")
                .unwrap_err();
            match err {
                Error::Xml(XmlError::UnexpectedEof(_)) => (),
                other => panic!("unexpected error: {:?}", other),
            }
        }

        #[test]
        fn fail_unexpected_root() {
            let txt = &b"<something><entry>"[..];
            let err = SequentialParser::new(std::io::Cursor::new(txt))
                .next()
                .expect("should raise an error")
                .unwrap_err();
            match err {
                Error::UnexpectedRoot(r) => assert_eq!(r, "something"),
                other => panic!("unexpected error: {:?}", other),
            }
        }
    }

    #[cfg(feature = "threading")]
    mod threaded {
        use super::*;

        #[test]
        fn parse_single_entry() {
            let f = std::fs::File::open("tests/uniparc.xml").unwrap();
            ThreadedParser::new(std::io::BufReader::new(f))
                .next()
                .expect("an entry should be parsed")
                .expect("the entry should be parsed successfully");
        }

        #[test]
        fn fail_unexpected_eof() {
            let txt = &b"<uniparc><entry dataset=\"uniparc\">"[..];
            let err = ThreadedParser::new(std::io::Cursor::new(txt))
                .next()
                .expect("should raise an error")
                .unwrap_err();
            match err {
                Error::Xml(XmlError::UnexpectedEof(_)) => (),
                other => panic!("unexpected error: {:?}", other),
            }
        }

        #[test]
        fn fail_unexpected_root() {
            let txt = &b"<something><entry>"[..];
            let err = ThreadedParser::new(std::io::Cursor::new(txt))
                .next()
                .expect("should raise an error")
                .unwrap_err();
            match err {
                Error::UnexpectedRoot(r) => assert_eq!(r, "something"),
                other => panic!("unexpected error: {:?}", other),
            }
        }
    }
}