cual-id

#!/usr/bin/env python
import click
import sys

from cualid.label import get_barcodes
from cualid.mint import create_ids
from cualid.fix import fix_ids, format_output, parse_ids

@click.group()
def cli():
    pass

@cli.group()
def create():
    """Command to create barcode labels or sample ids."""
    pass

@create.command("labels")
@click.argument('input', type=click.File('U'), required=True)
@click.option('-o', '--output-pdf', type=click.STRING, required=True)
@click.option('--suppress-ids', is_flag=True)
@click.option('--barcode', type=click.STRING, required=False)
def barcode_generator(input, output_pdf, suppress_ids, barcode):
    """This script generates a pdf of barcodes"""
    if suppress_ids and barcode == 'none':
        click.ClickException("Please don't do that").show()
        exit()

    barcodes = get_barcodes(input, output_pdf, suppress_ids, barcode)
    barcodes.save()

@create.command("ids")
@click.argument('number-of-ids', type=int)
@click.option('-l', '--length', type=int, default=8, required=False)
@click.option('-f', '--fail-threshold', type=float, default=0.99, required=False)
@click.option('-e', '--existing-ids', type=click.File('U'), default=None, required=False)
def sample_id_generator(number_of_ids, length, fail_threshold, existing_ids):
    """This script generates a file of sample IDs"""
    if fail_threshold >= 1:
        raise ValueError("")
    collected = 0
    if existing_ids:
      existing_ids = parse_ids(existing_ids, 0)
    for hrid, uuid_ in create_ids(number_of_ids, length,
                                  failure_threshold=fail_threshold,
                                  existing_ids=existing_ids):
        collected += 1
        click.echo("%s\t%s" %(hrid, uuid_))

    if collected != number_of_ids:
        click.echo(
            "\033[1;31m"
            "Could only collect %d out of %d.\nGreater than %f%% of the"
            " generated CualIDs were not sufficiently unique."
            "\033[0;0m" % (collected, number_of_ids, fail_threshold * 100), err=True)

@cli.command("fix")
@click.argument('ids-to-be-corrected', type=click.File('U'), required=True)
@click.option('--correct-ids', type=click.File('U'), required=True)
@click.option('-s', '--show', type=click.STRING, default='DFN', required=False)
@click.option('-a', '--all', is_flag=True, default=False, required=False)
def correct_ids(correct_ids, ids_to_be_corrected, show, all):
    """Compare a set of possibly invalid IDs against a correct set of IDs
    to identify errors in the IDs"""
    if all:
        show = 'DFNV'
    for line in format_output(fix_ids(correct_ids, ids_to_be_corrected), show):
        click.echo(line)


if __name__ == '__main__':
    cli()