blobtk 0.8.1

Core utilities for BlobToolKit.
Documentation 
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use std::collections::HashMap;

use crate::blobdir::parse_blobdir;
use crate::cli::{self, PlotOptions, View};
use crate::plot::{plot_blob, plot_cumulative, plot_legend, plot_snail};
use crate::python::utils::{
    extract_to_bool, extract_to_option_f64, extract_to_option_origin, extract_to_option_palette,
    extract_to_option_reducer, extract_to_option_rounding_strategy, extract_to_option_scale,
    extract_to_option_shape, extract_to_option_showlegend, extract_to_option_string,
    extract_to_option_usize, extract_to_option_vec_string, extract_to_pathbuf, extract_to_view,
};
use pyo3::prelude::*;

#[pyfunction]
pub fn plot_with_options(options: &PlotOptions) -> PyResult<()> {
    let meta = parse_blobdir(&options.blobdir).unwrap();
    let view = &options.view;
    match view {
        cli::View::Blob => plot_blob(&meta, &options).unwrap(),
        cli::View::Cumulative => plot_cumulative(&meta, &options).unwrap(),
        cli::View::Legend => plot_legend(&meta, &options).unwrap(),
        cli::View::Snail => plot_snail(&meta, &None, &options).unwrap(),
    }
    Ok(())
}

fn convert_hashmap_to_options(py: Python<'_>, map: HashMap<String, PyObject>) -> PlotOptions {
    let blobdir = extract_to_pathbuf(py, &map, "blobdir");
    let view = extract_to_view(py, &map, "view");
    let shape = extract_to_option_shape(py, &map, "shape");
    let window_size = extract_to_option_string(py, &map, "window_size");
    let output = extract_to_option_string(py, &map, "output");
    let filter = extract_to_option_vec_string(py, &map, "filter");
    let segments = extract_to_option_usize(py, &map, "segments");
    let max_span = extract_to_option_usize(py, &map, "max_span");
    let max_scaffold = extract_to_option_usize(py, &map, "max_scaffold");
    let x_field = extract_to_option_string(py, &map, "x_field");
    let y_field = extract_to_option_string(py, &map, "y_field");
    let z_field = extract_to_option_string(py, &map, "z_field");
    let cat_field = extract_to_option_string(py, &map, "cat_field");
    let synonym_field = extract_to_option_string(py, &map, "synonym_field");
    let resolution = extract_to_option_usize(py, &map, "resolution");
    let hist_height = extract_to_option_usize(py, &map, "hist_height");
    let reducer_function = extract_to_option_reducer(py, &map, "reducer_function");
    let scale_function = extract_to_option_scale(py, &map, "scale_function");
    let scale_factor = extract_to_option_f64(py, &map, "scale_factor");
    let x_limit = extract_to_option_string(py, &map, "x_limit");
    let y_limit = extract_to_option_string(py, &map, "y_limit");
    let significant_digits = extract_to_option_usize(py, &map, "significant_digits");
    let decimal_precision = extract_to_option_usize(py, &map, "decimal_precision");
    let cat_count = extract_to_option_usize(py, &map, "cat_count");
    let show_legend = extract_to_option_showlegend(py, &map, "show_legend");
    let show_numbers = extract_to_bool(py, &map, "show_numbers");
    let busco_numbers = extract_to_bool(py, &map, "busco_numbers");
    let cat_order = extract_to_option_string(py, &map, "cat_order");
    let origin = extract_to_option_origin(py, &map, "origin");
    let palette = extract_to_option_palette(py, &map, "palette");
    let color = extract_to_option_vec_string(py, &map, "color");
    let rounding = extract_to_option_rounding_strategy(py, &map, "rounding");
    let badge = extract_to_bool(py, &map, "badge");
    let show_score = extract_to_bool(py, &map, "show_score");
    PlotOptions {
        blobdir,
        view,
        shape,
        window_size,
        output: output
            .map(|s| vec![s])
            .unwrap_or_else(|| vec!["output.svg".to_string()]),
        filter: filter.unwrap_or_default(),
        segments: segments.unwrap_or(1000),
        max_span,
        max_scaffold,
        x_field,
        y_field,
        z_field,
        cat_field,
        synonym_field,
        resolution: resolution.unwrap_or(30),
        hist_height,
        reducer_function: reducer_function.unwrap_or_default(),
        scale_function,
        scale_factor: scale_factor.unwrap_or(1.0),
        x_limit,
        y_limit,
        significant_digits: significant_digits.unwrap_or(3) as u32,
        decimal_precision: decimal_precision.unwrap_or(2) as u32,
        cat_count: cat_count.unwrap_or(10),
        show_legend: show_legend.unwrap_or_default(),
        show_numbers,
        busco_numbers,
        cat_order,
        origin,
        palette,
        color,
        rounding,
        badge,
        show_score,
        reference: None,
        score_type: None,
        original_fasta: None,
        original_busco: None,
        original_blobdir: None,
        original_reference: None,
        score_only: false,
        score_json: false,
    }
}

#[pyfunction]
#[pyo3(signature = (**kwds))]
pub fn plot(py: Python<'_>, kwds: Option<HashMap<String, PyObject>>) -> PyResult<()> {
    let options = match kwds {
        Some(map) => convert_hashmap_to_options(py, map),
        None => panic!["No arguments provided"],
    };
    plot_with_options(&options)
}

#[pyfunction]
#[pyo3(signature = (**kwds))]
pub fn blob(py: Python<'_>, kwds: Option<HashMap<String, PyObject>>) -> PyResult<()> {
    let options = match kwds {
        Some(map) => convert_hashmap_to_options(py, map),
        None => panic!["No arguments provided"],
    };
    let blob_options = PlotOptions {
        view: View::Blob,
        ..options
    };
    plot_with_options(&blob_options)
}

#[pyfunction]
#[pyo3(signature = (**kwds))]
pub fn cumulative(py: Python<'_>, kwds: Option<HashMap<String, PyObject>>) -> PyResult<()> {
    let options = match kwds {
        Some(map) => convert_hashmap_to_options(py, map),
        None => panic!["No arguments provided"],
    };
    let cumulative_options = PlotOptions {
        view: View::Cumulative,
        ..options
    };
    plot_with_options(&cumulative_options)
}

#[pyfunction]
#[pyo3(signature = (**kwds))]
pub fn legend(py: Python<'_>, kwds: Option<HashMap<String, PyObject>>) -> PyResult<()> {
    let options = match kwds {
        Some(map) => convert_hashmap_to_options(py, map),
        None => panic!["No arguments provided"],
    };
    let legend_options = PlotOptions {
        view: View::Legend,
        ..options
    };
    plot_with_options(&legend_options)
}

#[pyfunction]
#[pyo3(signature = (**kwds))]
pub fn snail(py: Python<'_>, kwds: Option<HashMap<String, PyObject>>) -> PyResult<()> {
    let options = match kwds {
        Some(map) => convert_hashmap_to_options(py, map),
        None => panic!["No arguments provided"],
    };
    let snail_options = PlotOptions {
        view: View::Snail,
        ..options
    };
    plot_with_options(&snail_options)
}