1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
//! GFF record attribute entry.

use std::{
    borrow::Cow,
    error, fmt,
    str::{self, FromStr},
};

use percent_encoding::{percent_decode_str, utf8_percent_encode, AsciiSet, CONTROLS};

const PERCENT_ENCODE_SET: &AsciiSet = &CONTROLS
    .add(b'\t')
    .add(b'\n')
    .add(b'\r')
    .add(b'%')
    .add(b';')
    .add(b'=')
    .add(b'&')
    .add(b',');

const SEPARATOR: char = '=';

/// A GFF record attribute entry.
#[derive(Clone, Debug, Eq, PartialEq)]
pub struct Entry {
    key: String,
    value: String,
}

impl Entry {
    /// Creates a GFF record attribute.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_gff::record::attributes::Entry;
    /// let entry = Entry::new("gene_name", "gene0");
    /// ```
    pub fn new<K, V>(key: K, value: V) -> Self
    where
        K: Into<String>,
        V: Into<String>,
    {
        Self {
            key: key.into(),
            value: value.into(),
        }
    }

    /// Returns the key of the entry.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_gff::record::attributes::Entry;
    /// let entry = Entry::new("gene_name", "gene0");
    /// assert_eq!(entry.key(), "gene_name");
    /// ```
    pub fn key(&self) -> &str {
        &self.key
    }

    /// Returns the value of the entry.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_gff::record::attributes::Entry;
    /// let entry = Entry::new("gene_name", "gene0");
    /// assert_eq!(entry.value(), "gene0");
    /// ```
    pub fn value(&self) -> &str {
        &self.value
    }
}

impl fmt::Display for Entry {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        write!(
            f,
            "{}{}{}",
            percent_encode(self.key()),
            SEPARATOR,
            percent_encode(self.value())
        )
    }
}

/// An error returned when a raw GFF record attribute entry fails to parse.
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
    /// The input is empty.
    Empty,
    /// The input is invalid.
    Invalid,
    /// The entry key is missing.
    MissingKey,
    /// The entry key is invalid.
    InvalidKey(str::Utf8Error),
    /// The entry value is missing.
    MissingValue,
    /// The entry value is invalid.
    InvalidValue(str::Utf8Error),
}

impl error::Error for ParseError {}

impl fmt::Display for ParseError {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        match self {
            Self::Empty => f.write_str("empty input"),
            Self::Invalid => f.write_str("invalid input"),
            Self::MissingKey => f.write_str("missing key"),
            Self::InvalidKey(e) => write!(f, "invalid key: {}", e),
            Self::MissingValue => f.write_str("missing value"),
            Self::InvalidValue(e) => write!(f, "invalid value: {}", e),
        }
    }
}

impl FromStr for Entry {
    type Err = ParseError;

    fn from_str(s: &str) -> Result<Self, Self::Err> {
        if s.is_empty() {
            return Err(ParseError::Empty);
        }

        match s.split_once(SEPARATOR) {
            Some((k, v)) => {
                let key = if k.is_empty() {
                    return Err(ParseError::MissingKey);
                } else {
                    percent_decode(k).map_err(ParseError::InvalidKey)?
                };

                let value = if v.is_empty() {
                    return Err(ParseError::MissingValue);
                } else {
                    percent_decode(v).map_err(ParseError::InvalidValue)?
                };

                Ok(Self::new(key, value))
            }
            None => Err(ParseError::Invalid),
        }
    }
}

fn percent_decode(s: &str) -> Result<Cow<'_, str>, str::Utf8Error> {
    percent_decode_str(s).decode_utf8()
}

fn percent_encode(s: &str) -> Cow<'_, str> {
    utf8_percent_encode(s, PERCENT_ENCODE_SET).into()
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_fmt() {
        let entry = Entry::new("gene_name", "gene0");
        assert_eq!(entry.to_string(), "gene_name=gene0");

        let entry = Entry::new("%s", "13,21");
        assert_eq!(entry.to_string(), "%25s=13%2C21");
    }

    #[test]
    fn test_from_str() {
        assert_eq!(
            "gene_name=gene0".parse(),
            Ok(Entry::new("gene_name", "gene0"))
        );
        assert_eq!("%25s=13%2C21".parse(), Ok(Entry::new("%s", "13,21")));

        assert_eq!("".parse::<Entry>(), Err(ParseError::Empty));
        assert_eq!("gene_name".parse::<Entry>(), Err(ParseError::Invalid));
        assert_eq!("=gene0".parse::<Entry>(), Err(ParseError::MissingKey));
        assert_eq!("gene_name=".parse::<Entry>(), Err(ParseError::MissingValue));
    }
}