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allow empyt value for optional numeric inputs #19

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allow empyt value for optional numeric inputs #19

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30f525a
allow empyt value for numeric inputs
bernt-matthias Jul 6, 2019
a717e6a
validate docurl
bernt-matthias Jan 13, 2020
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12 changes: 12 additions & 0 deletions CTDopts/CTDopts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
from itertools import chain
from xml.etree.ElementTree import Element, SubElement, tostring, parse
from xml.dom.minidom import parseString
import urllib2
import warnings

# dummy classes for input-file and output-file CTD types.
Expand Down Expand Up @@ -440,6 +441,8 @@ def _validate_numerical_defaults(self, default):
else:
defaults_to_validate.append(default)
for default_to_validate in defaults_to_validate:
if default_to_validate == '':
continue
try:
if self.type is int:
int(default_to_validate)
Expand Down Expand Up @@ -665,6 +668,15 @@ def _load_from_file(self, filename):
for tool_opt_attrib in ['docurl', 'category']:
if tool_opt_attrib in root.attrib:
self.opt_attribs[tool_opt_attrib] = root.attrib[tool_opt_attrib]
# check if the URL actually exists (wrong URLs cause errors in Galaxy tests)
if self.opt_attribs.has_key('docurl'):
while self.opt_attribs['docurl'] != '':
try:
urllib2.urlopen(self.opt_attribs['docurl'])
break
except (urllib2.HTTPError, urllib2.URLError):
self.opt_attribs['docurl'] = '/'.join(self.opt_attribs['docurl'].split('/')[:-1])


for tool_element in root:
if tool_element.tag in ['manual', 'description', 'executableName', 'executablePath']:
Expand Down