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

use serde::{Deserialize, Serialize};
use tracing::instrument;

use htsget_config::Query;

use crate::{QueryBuilder, Result};

/// A struct to represent a POST request according to the
/// [HtsGet specification](https://samtools.github.io/hts-specs/htsget.html). It implements
/// [Deserialize] to make it more ergonomic. Each `PostRequest` can contain several regions.
#[derive(Serialize, Deserialize, Debug, Default)]
pub struct PostRequest {
  pub format: Option<String>,
  pub class: Option<String>,
  pub fields: Option<Vec<String>>,
  pub tags: Option<Vec<String>>,
  pub notags: Option<Vec<String>>,
  pub regions: Option<Vec<Region>>,
}

/// A struct that contains the data to quest for a specific region. It is only meant to be use
/// alongside a `PostRequest`
#[derive(Serialize, Deserialize, Debug)]
pub struct Region {
  #[serde(rename = "referenceName")]
  pub reference_name: String,
  pub start: Option<u32>,
  pub end: Option<u32>,
}

impl PostRequest {
  /// Converts the `PostRequest` into one or more equivalent [Queries](Query)
  #[instrument(level = "trace", skip_all, ret)]
  pub(crate) fn get_queries(self, id: impl Into<String>) -> Result<Vec<Query>> {
    if let Some(ref regions) = self.regions {
      let id = id.into();
      regions
        .iter()
        .map(|region| {
          Ok(
            self
              .get_base_query_builder(id.clone())?
              .with_reference_name(Some(region.reference_name.clone()))
              .with_range_from_u32(region.start, region.end)?
              .build(),
          )
        })
        .collect::<Result<Vec<Query>>>()
    } else {
      Ok(vec![self.get_base_query_builder(id)?.build()])
    }
  }

  fn get_base_query_builder(&self, id: impl Into<String>) -> Result<QueryBuilder> {
    QueryBuilder::new(Some(id.into()), self.format.clone())?
      .with_class(self.class.clone())?
      .with_fields_from_vec(self.fields.clone())
      .with_tags_from_vec(self.tags.clone(), self.notags.clone())
  }
}

#[cfg(test)]
mod tests {
  use htsget_config::{Class, Format};

  use super::*;

  #[test]
  fn post_request_without_regions() {
    assert_eq!(
      PostRequest {
        format: Some("VCF".to_string()),
        class: Some("header".to_string()),
        fields: None,
        tags: None,
        notags: None,
        regions: None,
      }
      .get_queries("id")
      .unwrap(),
      vec![Query::new("id", Format::Vcf).with_class(Class::Header)]
    );
  }

  #[test]
  fn post_request_with_one_region() {
    assert_eq!(
      PostRequest {
        format: Some("VCF".to_string()),
        class: Some("header".to_string()),
        fields: None,
        tags: None,
        notags: None,
        regions: Some(vec![Region {
          reference_name: "20".to_string(),
          start: Some(150),
          end: Some(153),
        }]),
      }
      .get_queries("id")
      .unwrap(),
      vec![Query::new("id", Format::Vcf)
        .with_class(Class::Header)
        .with_reference_name("20".to_string())
        .with_start(150)
        .with_end(153)]
    );
  }

  #[test]
  fn post_request_with_regions() {
    assert_eq!(
      PostRequest {
        format: Some("VCF".to_string()),
        class: Some("header".to_string()),
        fields: None,
        tags: None,
        notags: None,
        regions: Some(vec![
          Region {
            reference_name: "20".to_string(),
            start: Some(150),
            end: Some(153),
          },
          Region {
            reference_name: "11".to_string(),
            start: Some(152),
            end: Some(154),
          }
        ]),
      }
      .get_queries("id")
      .unwrap(),
      vec![
        Query::new("id", Format::Vcf)
          .with_class(Class::Header)
          .with_reference_name("20".to_string())
          .with_start(150)
          .with_end(153),
        Query::new("id", Format::Vcf)
          .with_class(Class::Header)
          .with_reference_name("11".to_string())
          .with_start(152)
          .with_end(154)
      ]
    );
  }
}