Struct gnverify::GNVerify

pub struct GNVerify {
    pub sources: Option<Vec<i64>>,
    pub preferred_only: bool,
    pub name_field: i64,
    pub batch_size: usize,
    pub format: Format,
}

Keeps configuration parameters and organizes main functions for changing configuration and performing name-strings verification and formatting of verification output.

Fields

sources: Option<Vec<i64>>

list of IDs of Data Sources. Each Data Source is a checklist of scientific names / (e.g Encyclopedia of Life, GBIF, Catalogue of Life) and can be curated to a degree, automatically curated or not curated. If a name-string has a match to any of these sources, the matching result will always be returned in preferred_results section of the output.

preferred_only: bool

Normally output would

name_field: i64

Position of ScientificName field in the document. Default value is 1 (the first field is 1, not 0). If gnverify verifies names from a txt file, it assumes that the text has one name per line, and nothing else.

batch_size: usize

size of a bach of names sent as a unit for verification to gnindex.

format: Format

sets format of the final output. It can be CSV, JSON, or Pretty JSON.

Methods

impl GNVerify

pub fn new() -> Self

Creates a new instance of GNVerify and sets default values for all fields.

pub fn sources(&mut self, sources: Vec<i64>)

Sets sources field. Sources is a list of IDs for data sources. If a match found for these data-sources, such data will be always returned to the user even if such results are not the best-scored results.

Example

use gnverify::GNVerify;

let mut gnv = GNVerify::new();
assert!(gnv.sources.is_none());
gnv.sources(vec![1,11,169]);
assert_eq!(gnv.sources.unwrap()[1], 11_i64);

pub fn name_field(&mut self, name_field: i64)

Sets the index of name-string field. For example, if your TSV file contains "ID", "ScientificName", "Reference", use name_index 2.

Example

use gnverify::GNVerify;

let mut gnv = GNVerify::new();
assert_eq!(gnv.name_field, 1);
gnv.name_field(3);
assert_eq!(gnv.name_field, 3);

pub fn preferred_only(&mut self)

Sets preferred_only field to true

Example

use gnverify::GNVerify;

let mut gnv = GNVerify::new();
assert_eq!(gnv.preferred_only, false);
gnv.preferred_only();
assert_eq!(gnv.preferred_only, true);

pub fn format(&mut self, format: Format)

Sets output format to one of: CSV, JSON, Pretty JSON.

Example

use gnverify::{GNVerify, Format};

let mut gnv = GNVerify::new();
assert_eq!(gnv.format.to_string(), "CSV");
gnv.format(Format::Pretty);
assert_eq!(gnv.format.to_string(), "Pretty");

pub fn verify_stream(
    &self,
    in_r: Receiver<Vec<Input>>,
    out_s: Sender<Vec<Output>>
)

Takes input channel with name-strings to verify and uses output channel to send back results of verification. The input channel is then cloned for several workers, so they all send data to gnindex server in parallel. There input send name-string in batches and their size is determined by batch_size field.

Example

use gnverify::{GNVerify, Input};
use crossbeam_channel::bounded;
use std::thread;

let mut gnv = GNVerify::new();

let (in_s, in_r) = bounded(0);
let (out_s, out_r) = bounded(0);
thread::spawn(move || gnv.clone().verify_stream(in_r, out_s));
let inputs: Vec<Input> = vec![Input{id: None, name: "Homo sapiens".to_owned()}];
in_s.send(inputs).unwrap();
let o = out_r.recv().unwrap();
assert_eq!(o.iter().next().unwrap().name, "Homo sapiens");

pub fn verify(&self, inputs: &Vec<Input>) -> Vec<Output>

Takes as input a vector name-strings and returns back a vector of corresponding verification outputs for the name-strings.

Example

use gnverify::{GNVerify, Input, MatchType};

let gnv = GNVerify::new();
let inputs: Vec<Input> = vec![Input{id: None, name: "Homo sapiens".to_owned()}];
let outputs = gnv.verify(&inputs);
assert_eq!(outputs.len(), 1);
if let Some(output) = outputs.iter().next() {
    assert_eq!(output.match_type.to_string(), "Exact".to_owned());
}

pub fn verify_and_format(&self, inputs: &Vec<Input>)

Convenience function that takes as an input a vector of name-strings and prints out results in desired output format.

Example

use gnverify::{GNVerify, Input, MatchType};

let gnv = GNVerify::new();
let inputs: Vec<Input> = vec![Input{id: None, name: "Homo sapiens".to_owned()}];
gnv.verify_and_format(&inputs);

pub fn format_outputs(&self, outputs: Vec<Output>, with_headers: bool)

Takes outputs of name-verification process and prints out the outputs in a desired format. It also takes with_headers parameter. If it is true, the printed output will have corresponding headers in CSV format.

Example

use gnverify::{GNVerify, Input, MatchType};

let gnv = GNVerify::new();
let inputs: Vec<Input> = vec![Input{id: None, name: "Homo sapiens".to_owned()}];
let outputs = gnv.verify(&inputs);
assert_eq!(outputs.len(), 1);
gnv.format_outputs(outputs, true);

Trait Implementations

impl Clone for GNVerify

fn clone(&self) -> GNVerify

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for GNVerify

fn fmt(&self, f: &mut Formatter) -> Result

Formats the value using the given formatter.

impl Default for GNVerify

fn default() -> GNVerify

Returns the "default value" for a type.