Mercurial > repos > iuc > ebi_search_rest_results
view generate_macros.py @ 3:42d5e40fcd0b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 31d1c92a4c12b6a78693dc5091a08536a075285e
author | iuc |
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date | Thu, 09 Feb 2017 12:02:58 -0500 |
parents | b6029f2c71cb |
children |
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#!/usr/bin/env python 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"' if multiple: to_write += ' multiple="true" optional="false"' to_write += ' label="%s"' % (label) 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="2.7.12">python</requirement>\n' % (3 * 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.sort(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</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()