annotate generate_macros.py @ 1:a2c83f79f253 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 6847e1202f570ae466cf98affe54a7016fa98cd8

#!/usr/bin/env python3

import ebeye_urllib


def add_option(value, name, selected=False):
    to_write = '<option '
    to_write += 'value="%s"' % (value)
    if selected:
        to_write += ' selected="true"'
    to_write += '>%s' % (name)
    to_write += '</option>\n'
    return to_write


def add_select_parameter(name, label, multiple=False):
    to_write = '<param '
    to_write += 'name="%s" ' % (name)
    to_write += 'type="select" '
    to_write += 'label="%s" ' % (label)
    if multiple:
        to_write += 'multiple=\"true\"'
    to_write += '>\n'
    return to_write


def write_macros_file(macros_filepath, domains_fields):
    spaces = '    '
    to_write = '<macros>\n'

    to_write += '%s<xml name="requirements">\n' % (spaces)
    to_write += '%s<requirements>\n' % (2 * spaces)
    to_write += '%s<requirement type="package" version="3.1.1">xmltramp2</requirement>\n' % (3 * spaces)
    to_write += '%s<requirement type="package" version="1.12">urllib3</requirement>\n' % (3 * spaces)
    to_write += '%s<yield/>\n' % (3 * spaces)
    to_write += '%s</requirements>\n' % (2 * spaces)
    to_write += '%s</xml>\n' % (spaces)

    to_write += '%s<xml name="inputs">\n' % (spaces)

    to_write += '%s<conditional name="searched_domain">\n' % (2 * spaces)
    to_write += '%s%s' % (3 * spaces, add_select_parameter(
        'domain',
        'Domain to query'))

    sorted_domains = [(d, domains_fields[d]['name']) for d in domains_fields.keys()]
    sorted_domains = sorted(sorted_domains, key=lambda tup: tup[1])
    for domain in sorted_domains:
        to_write += '%s%s' % (4 * spaces, add_option(
            domain[0],
            domain[1]))

    to_write += '%s</param>\n\n' % (3 * spaces)

    for d in sorted_domains:
        domain = d[0]
        to_write += '%s<when value="%s">\n' % (3 * spaces, domain)

        to_write += '%s%s' % (4 * spaces, add_select_parameter(
            'fields',
            'Fields to extract',
            multiple=True))
        for field in domains_fields[domain]['retrievable_fields']:
            to_write += '%s%s' % (5 * spaces, add_option(
                field,
                field,
                selected=True))
        to_write += '%s<validator type="no_options" message="Please select at least one field" />\n' % (5 * spaces)
        to_write += '%s</param>\n' % (4 * spaces)

        to_write += '%s<repeat name="queries" title="Add a query">\n' % (
            4 * spaces)

        to_write += '%s%s' % (5 * spaces, add_select_parameter(
            'combination_operation',
            'Combination operation'))
        to_write += '%s%s' % (6 * spaces, add_option('AND', 'AND'))
        to_write += '%s%s' % (6 * spaces, add_option('OR', 'OR'))
        to_write += '%s%s' % (6 * spaces, add_option('NOT', 'NOT'))
        to_write += '%s</param>\n' % (5 * spaces)

        to_write += '%s%s' % (5 * spaces, add_select_parameter(
            'query_field',
            'Fields'))
        for field in domains_fields[domain]['searchable_fields']:
            to_write += '%s%s' % (6 * spaces, add_option(field, field))
        to_write += '%s</param>\n' % (5 * spaces)

        to_write += '%s<conditional name="comp_operation">\n' % (5 * spaces)
        to_write += '%s%s' % (6 * spaces, add_select_parameter(
            'operation',
            'Comparison operation'))
        to_write += '%s%s' % (7 * spaces, add_option('equal', 'equal'))
        to_write += '%s%s' % (7 * spaces, add_option('not', 'not'))
        to_write += '%s%s' % (7 * spaces, add_option('range', 'range'))
        to_write += '%s</param>\n' % (6 * spaces)

        to_write += '%s<when value="equal">\n' % (6 * spaces)
        to_write += '%s<param name="query_text" type="text" label="Searched term"/>\n' % (7 * spaces)
        to_write += '%s</when>\n' % (6 * spaces)

        to_write += '%s<when value="not">\n' % (6 * spaces)
        to_write += '%s<param name="query_text" type="text" label="Searched term"/>\n' % (7 * spaces)
        to_write += '%s<param name="not_query_text" type="text" label="Limiting term"/>\n' % (7 * spaces)
        to_write += '%s</when>\n' % (6 * spaces)

        to_write += '%s<when value="range">\n' % (6 * spaces)
        to_write += '%s<param name="min" type="text" label="From"/>\n' % (7 * spaces)
        to_write += '%s<param name="max" type="text" label="To"/>\n' % (
            7 * spaces)
        to_write += '%s</when>\n' % (6 * spaces)

        to_write += '%s</conditional>\n' % (5 * spaces)

        to_write += '%s</repeat>\n' % (4 * spaces)

        to_write += '%s</when>\n\n' % (3 * spaces)

    to_write += '%s</conditional>\n' % (2 * spaces)
    to_write += '%s</xml>\n' % (spaces)

    to_write += '%s<xml name="citations">\n' % (spaces)
    to_write += '%s<citations>\n' % (2 * spaces)
    to_write += '%s<citation type="doi">10.1093/bib/bbp065</citation>\n' % (3 * spaces)
    to_write += '%s<citation type="doi">10.1093/nar/gkv316</citation>\n' % (3 * spaces)
    to_write += '%s</citations>\n' % (2 * spaces)
    to_write += '%s</xml>\n' % (spaces)

    to_write += '</macros>\n'

    with open(macros_filepath, 'w') as macros_file:
        macros_file.write(to_write)


def generate_macros():
    domains_fields = ebeye_urllib.getDomainHierarchy()
    write_macros_file('macros.xml', domains_fields)


if __name__ == '__main__':
    generate_macros()