hpo 0.12.0

Human Phenotype Ontology Similarity
Documentation 
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

//! The binary parser handles the parsing and generation of the Ontology in
//! binary format.
//! The idea is to always support old binary formats as input but only
//! generate the newest binary format.
//! That way we maintain backwards compatibility and allow clients
//! to update their versions to the newest one.
pub(crate) mod ontology;
pub(crate) mod term;
use std::{cmp::Ordering, fmt::Display};

use crate::{term::internal::HpoTermInternal, HpoError};

#[derive(Debug, Clone, Copy, Eq, PartialEq)]
pub(crate) enum BinaryVersion {
    V1,
    V2,
    V3,
}

impl TryFrom<u8> for BinaryVersion {
    type Error = HpoError;
    fn try_from(value: u8) -> Result<Self, Self::Error> {
        match value {
            1u8 => Ok(BinaryVersion::V1),
            2u8 => Ok(BinaryVersion::V2),
            3u8 => Ok(BinaryVersion::V3),
            _ => Err(HpoError::NotImplemented),
        }
    }
}

impl Display for BinaryVersion {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
        write!(
            f,
            "{}",
            match self {
                BinaryVersion::V1 => "1",
                BinaryVersion::V2 => "2",
                BinaryVersion::V3 => "3",
            }
        )
    }
}

impl From<&BinaryVersion> for u8 {
    fn from(value: &BinaryVersion) -> Self {
        match *value {
            BinaryVersion::V1 => 1,
            BinaryVersion::V2 => 2,
            BinaryVersion::V3 => 3,
        }
    }
}

impl PartialOrd for BinaryVersion {
    fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
        Some(self.cmp(other))
    }
}

impl Ord for BinaryVersion {
    fn cmp(&self, other: &Self) -> Ordering {
        u8::from(self).cmp(&u8::from(other))
    }
}

#[derive(Debug, Clone, Copy)]
pub(crate) struct Bytes<'a> {
    data: &'a [u8],
    version: BinaryVersion,
}

impl<'a> Bytes<'a> {
    pub fn new(data: &'a [u8], version: BinaryVersion) -> Self {
        Self { data, version }
    }

    pub fn len(&self) -> usize {
        self.data.len()
    }

    pub fn is_empty(&self) -> bool {
        self.data.is_empty()
    }

    pub fn subset<T>(&self, idx: T) -> Bytes<'_>
    where
        T: std::slice::SliceIndex<[u8], Output = [u8]>,
    {
        Bytes::new(&self.data[idx], self.version)
    }

    pub fn version(&self) -> BinaryVersion {
        self.version
    }

    pub fn u32_prefix(&self) -> u32 {
        assert!(self.len() > 4, "4 bytes are required to extract u32");
        u32::from_be_bytes([self[0], self[1], self[2], self[3]])
    }
}

impl<Idx> std::ops::Index<Idx> for Bytes<'_>
where
    Idx: std::slice::SliceIndex<[u8]>,
{
    type Output = Idx::Output;

    fn index(&self, idx: Idx) -> &Self::Output {
        &self.data[idx]
    }
}

/// Builder to crate multiple [`HpoTermInternal`] from raw bytes
pub(crate) struct BinaryTermBuilder<'a>(Bytes<'a>, usize);

impl<'a> BinaryTermBuilder<'a> {
    /// Crates a new [`BinaryTermBuilder`]
    pub fn new(bytes: Bytes<'a>) -> Self {
        Self(bytes, 0)
    }
}

impl Iterator for BinaryTermBuilder<'_> {
    type Item = HpoTermInternal;
    fn next(&mut self) -> Option<Self::Item> {
        let bytes = self.0.subset(self.1..);

        if bytes.is_empty() {
            return None;
        }

        let term_len = bytes.u32_prefix() as usize;

        assert!(
            (bytes.len() >= term_len),
            "Invalid bytes left over in BinaryTermBuilder"
        );

        self.1 += term_len;
        Some(HpoTermInternal::try_from(bytes).expect("Invalid byte input"))
    }
}