Mercurial > repos > iuc > ebi_search_rest_results
comparison generate_macros.py @ 0:bb7989bd88ba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
author | iuc |
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date | Thu, 01 Dec 2016 15:28:20 -0500 |
parents | |
children | b6029f2c71cb |
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-1:000000000000 | 0:bb7989bd88ba |
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1 #!/usr/bin/env python3 | |
2 | |
3 import ebeye_urllib | |
4 | |
5 | |
6 def add_option(value, name, selected=False): | |
7 to_write = '<option ' | |
8 to_write += 'value="%s"' % (value) | |
9 if selected: | |
10 to_write += ' selected="true"' | |
11 to_write += '>%s' % (name) | |
12 to_write += '</option>\n' | |
13 return to_write | |
14 | |
15 | |
16 def add_select_parameter(name, label, multiple=False): | |
17 to_write = '<param ' | |
18 to_write += 'name="%s" ' % (name) | |
19 to_write += 'type="select" ' | |
20 to_write += 'label="%s" ' % (label) | |
21 if multiple: | |
22 to_write += 'multiple=\"true\"' | |
23 to_write += '>\n' | |
24 return to_write | |
25 | |
26 | |
27 def write_macros_file(macros_filepath, domains_fields): | |
28 spaces = ' ' | |
29 to_write = '<macros>\n' | |
30 | |
31 to_write += '%s<xml name="requirements">\n' % (spaces) | |
32 to_write += '%s<requirements>\n' % (2 * spaces) | |
33 to_write += '%s<requirement type="package" version="3.1.1">xmltramp2</requirement>\n' % (3 * spaces) | |
34 to_write += '%s<requirement type="package" version="1.12">urllib3</requirement>\n' % (3 * spaces) | |
35 to_write += '%s<yield/>\n' % (3 * spaces) | |
36 to_write += '%s</requirements>\n' % (2 * spaces) | |
37 to_write += '%s</xml>\n' % (spaces) | |
38 | |
39 to_write += '%s<xml name="inputs">\n' % (spaces) | |
40 | |
41 to_write += '%s<conditional name="searched_domain">\n' % (2 * spaces) | |
42 to_write += '%s%s' % (3 * spaces, add_select_parameter( | |
43 'domain', | |
44 'Domain to query')) | |
45 | |
46 sorted_domains = [(d, domains_fields[d]['name']) for d in domains_fields.keys()] | |
47 sorted_domains = sorted(sorted_domains, key=lambda tup: tup[1]) | |
48 for domain in sorted_domains: | |
49 to_write += '%s%s' % (4 * spaces, add_option( | |
50 domain[0], | |
51 domain[1])) | |
52 | |
53 to_write += '%s</param>\n\n' % (3 * spaces) | |
54 | |
55 for d in sorted_domains: | |
56 domain = d[0] | |
57 to_write += '%s<when value="%s">\n' % (3 * spaces, domain) | |
58 | |
59 to_write += '%s%s' % (4 * spaces, add_select_parameter( | |
60 'fields', | |
61 'Fields to extract', | |
62 multiple=True)) | |
63 for field in domains_fields[domain]['retrievable_fields']: | |
64 to_write += '%s%s' % (5 * spaces, add_option( | |
65 field, | |
66 field, | |
67 selected=True)) | |
68 to_write += '%s<validator type="no_options" message="Please select at least one field" />\n' % (5 * spaces) | |
69 to_write += '%s</param>\n' % (4 * spaces) | |
70 | |
71 to_write += '%s<repeat name="queries" title="Add a query">\n' % ( | |
72 4 * spaces) | |
73 | |
74 to_write += '%s%s' % (5 * spaces, add_select_parameter( | |
75 'combination_operation', | |
76 'Combination operation')) | |
77 to_write += '%s%s' % (6 * spaces, add_option('AND', 'AND')) | |
78 to_write += '%s%s' % (6 * spaces, add_option('OR', 'OR')) | |
79 to_write += '%s%s' % (6 * spaces, add_option('NOT', 'NOT')) | |
80 to_write += '%s</param>\n' % (5 * spaces) | |
81 | |
82 to_write += '%s%s' % (5 * spaces, add_select_parameter( | |
83 'query_field', | |
84 'Fields')) | |
85 for field in domains_fields[domain]['searchable_fields']: | |
86 to_write += '%s%s' % (6 * spaces, add_option(field, field)) | |
87 to_write += '%s</param>\n' % (5 * spaces) | |
88 | |
89 to_write += '%s<conditional name="comp_operation">\n' % (5 * spaces) | |
90 to_write += '%s%s' % (6 * spaces, add_select_parameter( | |
91 'operation', | |
92 'Comparison operation')) | |
93 to_write += '%s%s' % (7 * spaces, add_option('equal', 'equal')) | |
94 to_write += '%s%s' % (7 * spaces, add_option('not', 'not')) | |
95 to_write += '%s%s' % (7 * spaces, add_option('range', 'range')) | |
96 to_write += '%s</param>\n' % (6 * spaces) | |
97 | |
98 to_write += '%s<when value="equal">\n' % (6 * spaces) | |
99 to_write += '%s<param name="query_text" type="text" label="Searched term"/>\n' % (7 * spaces) | |
100 to_write += '%s</when>\n' % (6 * spaces) | |
101 | |
102 to_write += '%s<when value="not">\n' % (6 * spaces) | |
103 to_write += '%s<param name="query_text" type="text" label="Searched term"/>\n' % (7 * spaces) | |
104 to_write += '%s<param name="not_query_text" type="text" label="Limiting term"/>\n' % (7 * spaces) | |
105 to_write += '%s</when>\n' % (6 * spaces) | |
106 | |
107 to_write += '%s<when value="range">\n' % (6 * spaces) | |
108 to_write += '%s<param name="min" type="text" label="From"/>\n' % (7 * spaces) | |
109 to_write += '%s<param name="max" type="text" label="To"/>\n' % ( | |
110 7 * spaces) | |
111 to_write += '%s</when>\n' % (6 * spaces) | |
112 | |
113 to_write += '%s</conditional>\n' % (5 * spaces) | |
114 | |
115 to_write += '%s</repeat>\n' % (4 * spaces) | |
116 | |
117 to_write += '%s</when>\n\n' % (3 * spaces) | |
118 | |
119 to_write += '%s</conditional>\n' % (2 * spaces) | |
120 to_write += '%s</xml>\n' % (spaces) | |
121 | |
122 to_write += '%s<xml name="citations">\n' % (spaces) | |
123 to_write += '%s<citations>\n' % (2 * spaces) | |
124 to_write += '%s<citation type="doi">10.1093/bib/bbp065</citation>\n' % (3 * spaces) | |
125 to_write += '%s<citation type="doi">10.1093/nar/gkv316</citation>\n' % (3 * spaces) | |
126 to_write += '%s</citations>\n' % (2 * spaces) | |
127 to_write += '%s</xml>\n' % (spaces) | |
128 | |
129 to_write += '</macros>\n' | |
130 | |
131 with open(macros_filepath, 'w') as macros_file: | |
132 macros_file.write(to_write) | |
133 | |
134 | |
135 def generate_macros(): | |
136 domains_fields = ebeye_urllib.getDomainHierarchy() | |
137 write_macros_file('macros.xml', domains_fields) | |
138 | |
139 | |
140 if __name__ == '__main__': | |
141 generate_macros() |