diff generate_macros.py @ 0:bb7989bd88ba draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_macros.py	Thu Dec 01 15:28:20 2016 -0500
@@ -0,0 +1,141 @@
+#!/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()