<reponame>Kayvv/sparc-curation-tools<filename>src/sparc/curation/tools/plot_annotation.py<gh_stars>0
import re
import argparse
import json

VERSION = '1.2.0'
AVAILABLE_PLOT_TYPES = ['heatmap', 'timeseries']
AVAILABLE_DELIMITERS = ['tab', 'comma']


def parse_num_list(string):
    m = re.match(r'^(\d+)(?:-(\d+))?$', string)
    if not m:
        raise argparse.ArgumentTypeError("'" + string + "' is not a range of numbers. Expected forms like '0-5'.")
    start = m.group(1)
    end = m.group(2) or start
    return list(range(int(start, 10), int(end, 10) + 1))


def flatten_nested_list(nested_list):
    flat_list = []
    # Iterate over all the elements in given list
    for elem in nested_list:
        # Check if type of element is list
        if isinstance(elem, list):
            # Extend the flat list by adding contents of this element (list)
            flat_list.extend(flatten_nested_list(elem))
        else:
            # Append the element to the list
            flat_list.append(elem)
    return flat_list


def main():
    parser = argparse.ArgumentParser(description='Create an annotation for a SPARC plot. '
                                                 'The Y_AXES_COLUMNS can either be single numbers or a range in the form 5-8. '
                                                 'The start and end numbers are included in the range. '
                                                 'The -y/--y-axes-columns argument will consume the positional plot type argument. '
                                                 'That means the positional argument cannot follow the -y/--y-axes-columns.')
    parser.add_argument("plot_type", help='must define a plot type which is one of; ' + ', '.join(AVAILABLE_PLOT_TYPES) + '.',
                        choices=AVAILABLE_PLOT_TYPES)
    parser.add_argument("-x", "--x-axis-column", help="integer index for the independent column (zero based). Default is 0.",
                        type=int, default=0)
    parser.add_argument("-y", "--y-axes-columns", help="list of indices for the dependent columns (zero based). Can be used multiple times."
                                                       " Can be specified as a range e.g. 5-8. Default is [].",
                        default=[], nargs='*', action="append", type=parse_num_list)
    parser.add_argument("-n", "--no-header", help="Boolean to indicate whether a header line is missing. Default is False.",
                        action="store_true", default=False)
    parser.add_argument("-r", "--row-major", help="Boolean to indicate whether the data is row major or column major. Default is False.",
                        action="store_true", default=False)
    parser.add_argument("-d", "--delimiter", help="The type of delimiter used, must be one of; " + ", ".join(AVAILABLE_DELIMITERS) + ". Default is comma.",
                        default='comma', choices=AVAILABLE_DELIMITERS)

    args = parser.parse_args()
    attrs = {
        'style': args.plot_type,
    }
    if args.x_axis_column != 0:
        attrs['x-axis'] = args.x_axis_column

    if args.delimiter != 'comma':
        attrs['delimiter'] = args.delimiter

    if len(args.y_axes_columns):
        attrs['y-axes-columns'] = flatten_nested_list(args.y_axes_columns)

    if args.no_header:
        attrs['no-header'] = args.no_header

    if args.row_major:
        attrs['row-major'] = args.row_major

    data = {
        'version': VERSION,
        'type': 'plot',
        'attrs': attrs
    }
    print(json.dumps(data))


main()

import re
import argparse
import json

VERSION = '1.2.0'
AVAILABLE_PLOT_TYPES = ['heatmap', 'timeseries']
AVAILABLE_DELIMITERS = ['tab', 'comma']


def parse_num_list(string):
    m = re.match(r'^(\d+)(?:-(\d+))?$', string)
    if not m:
        raise argparse.ArgumentTypeError("'" + string + "' is not a range of numbers. Expected forms like '0-5'.")
    start = m.group(1)
    end = m.group(2) or start
    return list(range(int(start, 10), int(end, 10) + 1))


def flatten_nested_list(nested_list):
    flat_list = []
    # Iterate over all the elements in given list
    for elem in nested_list:
        # Check if type of element is list
        if isinstance(elem, list):
            # Extend the flat list by adding contents of this element (list)
            flat_list.extend(flatten_nested_list(elem))
        else:
            # Append the element to the list
            flat_list.append(elem)
    return flat_list


def main():
    parser = argparse.ArgumentParser(description='Create an annotation for a SPARC plot. '
                                                 'The Y_AXES_COLUMNS can either be single numbers or a range in the form 5-8. '
                                                 'The start and end numbers are included in the range. '
                                                 'The -y/--y-axes-columns argument will consume the positional plot type argument. '
                                                 'That means the positional argument cannot follow the -y/--y-axes-columns.')
    parser.add_argument("plot_type", help='must define a plot type which is one of; ' + ', '.join(AVAILABLE_PLOT_TYPES) + '.',
                        choices=AVAILABLE_PLOT_TYPES)
    parser.add_argument("-x", "--x-axis-column", help="integer index for the independent column (zero based). Default is 0.",
                        type=int, default=0)
    parser.add_argument("-y", "--y-axes-columns", help="list of indices for the dependent columns (zero based). Can be used multiple times."
                                                       " Can be specified as a range e.g. 5-8. Default is [].",
                        default=[], nargs='*', action="append", type=parse_num_list)
    parser.add_argument("-n", "--no-header", help="Boolean to indicate whether a header line is missing. Default is False.",
                        action="store_true", default=False)
    parser.add_argument("-r", "--row-major", help="Boolean to indicate whether the data is row major or column major. Default is False.",
                        action="store_true", default=False)
    parser.add_argument("-d", "--delimiter", help="The type of delimiter used, must be one of; " + ", ".join(AVAILABLE_DELIMITERS) + ". Default is comma.",
                        default='comma', choices=AVAILABLE_DELIMITERS)

    args = parser.parse_args()
    attrs = {
        'style': args.plot_type,
    }
    if args.x_axis_column != 0:
        attrs['x-axis'] = args.x_axis_column

    if args.delimiter != 'comma':
        attrs['delimiter'] = args.delimiter

    if len(args.y_axes_columns):
        attrs['y-axes-columns'] = flatten_nested_list(args.y_axes_columns)

    if args.no_header:
        attrs['no-header'] = args.no_header

    if args.row_major:
        attrs['row-major'] = args.row_major

    data = {
        'version': VERSION,
        'type': 'plot',
        'attrs': attrs
    }
    print(json.dumps(data))


main()
# Iterate over all the elements in given list # Check if type of element is list # Extend the flat list by adding contents of this element (list) # Append the element to the list