def test_loader_template():
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<command interpreter="python">tool_wrapper.py
#include source=$tool_params
</command>
<macros>
<template name="tool_params">-a 1 -b 2</template>
</macros>
</tool>
''')
xml = tool_dir.load()
params_dict = template_macro_params(xml.getroot())
assert params_dict['tool_params'] == "-a 1 -b 2"
def test_loader():
class TestToolDirectory:
def __init__(self):
self.temp_directory = mkdtemp()
def __enter__(self):
return self
def __exit__(self, type, value, tb):
rmtree(self.temp_directory)
def write(self, contents, name="tool.xml"):
open(os.path.join(self.temp_directory, name), "w").write(contents)
def load(self, name="tool.xml", preprocess=True):
path = os.path.join(self.temp_directory, name)
if preprocess:
return load_tool(path)
else:
return parse_xml(path)
# Test simple macro replacement.
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<expand macro="inputs" />
<macros>
<macro name="inputs">
<inputs />
</macro>
</macros>
</tool>''')
xml = tool_dir.load(preprocess=False)
assert xml.find("inputs") is None
xml = tool_dir.load(preprocess=True)
assert xml.find("inputs") is not None
# Test importing macros from external files
with TestToolDirectory() as tool_dir:
tool_dir.write(SIMPLE_TOOL_WITH_MACRO)
tool_dir.write(SIMPLE_MACRO.substitute(tool_version="2.0"),
name="external.xml")
xml = tool_dir.load(preprocess=False)
assert xml.find("inputs") is None
xml = tool_dir.load(preprocess=True)
assert xml.find("inputs") is not None
# Test macros with unnamed yield statements.
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<expand macro="inputs">
<input name="first_input" />
</expand>
<expand macro="inputs">
<input name="second_input" />
</expand>
<expand macro="inputs">
<input name="third_input" />
</expand>
<macros>
<macro name="inputs">
<expand macro="foo">
<yield />
</expand>
</macro>
<macro name="foo">
<inputs>
<yield />
</inputs>
</macro>
</macros>
</tool>''')
xml = tool_dir.load()
assert xml.findall("inputs")[0].find("input").get(
"name") == "first_input"
assert xml.findall("inputs")[1].find("input").get(
"name") == "second_input"
assert xml.findall("inputs")[2].find("input").get(
"name") == "third_input"
# Test nested macro with yield statements
with TestToolDirectory() as tool_dir:
tool_dir.write("""
<tool>
<macros>
<macro name="paired_options">
<when value="paired">
<yield />
</when>
<when value="paired_collection">
<yield />
</when>
</macro>
<macro name="single_or_paired_general">
<conditional name="library">
<expand macro="paired_options">
<yield />
</expand>
</conditional>
</macro>
</macros>
<inputs>
<expand macro="single_or_paired_general"></expand>
</inputs>
</tool>
""")
xml = tool_dir.load()
# Test recursive macro applications.
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<expand macro="inputs">
<input name="first_input" />
<expand macro="second" />
</expand>
<macros>
<macro name="inputs">
<inputs>
<yield />
<input name="third_input" />
</inputs>
</macro>
<macro name="second">
<input name="second_input" />
</macro>
</macros>
</tool>''')
xml = tool_dir.load()
assert xml.find("inputs").findall("input")[0].get(
"name") == "first_input"
assert xml.find("inputs").findall("input")[1].get(
"name") == "second_input"
assert xml.find("inputs").findall("input")[2].get(
"name") == "third_input"
# Test recursive macro applications.
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<expand macro="inputs">
<input name="first_input" />
<expand macro="second" />
</expand>
<macros>
<macro name="inputs">
<inputs>
<yield />
</inputs>
</macro>
<macro name="second">
<expand macro="second_delegate" />
<input name="third_input" />
</macro>
<macro name="second_delegate">
<input name="second_input" />
</macro>
</macros>
</tool>''')
xml = tool_dir.load()
assert xml.find("inputs").findall("input")[0].get(
"name") == "first_input"
assert xml.find("inputs").findall("input")[1].get(
"name") == "second_input"
assert xml.find("inputs").findall("input")[2].get(
"name") == "third_input"
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool id="issue_647">
<macros>
<macro name="a">
<param name="a1" type="text" value="a1" label="a1"/>
<yield />
</macro>
</macros>
<inputs>
<expand macro="a">
<param name="b" type="text" value="b" label="b" />
</expand>
</inputs>
</tool>''')
xml = tool_dir.load()
assert xml.find("inputs").findall("param")[0].get("name") == "a1"
assert xml.find("inputs").findall("param")[1].get("name") == "b"
# Test <xml> is shortcut for macro type="xml"
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<expand macro="inputs" />
<macros>
<xml name="inputs">
<inputs />
</xml>
</macros>
</tool>''')
xml = tool_dir.load()
assert xml.find("inputs") is not None
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<command interpreter="python">tool_wrapper.py
#include source=$tool_params
</command>
<macros>
<template name="tool_params">-a 1 -b 2</template>
</macros>
</tool>
''')
xml = tool_dir.load()
params_dict = template_macro_params(xml.getroot())
assert params_dict['tool_params'] == "-a 1 -b 2"
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<macros>
<token name="@CITATION@">The citation.</token>
</macros>
<help>@CITATION@</help>
<another>
<tag />
</another>
</tool>
''')
xml = tool_dir.load()
help_el = xml.find("help")
assert help_el.text == "The citation.", help_el.text
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<macros>
<token name="@TAG_VAL@">The value.</token>
</macros>
<another>
<tag value="@TAG_VAL@" />
</another>
</tool>
''')
xml = tool_dir.load()
tag_el = xml.find("another").find("tag")
value = tag_el.get('value')
assert value == "The value.", value
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<macros>
<token name="@TAG_VAL@"><![CDATA[]]></token>
</macros>
<another>
<tag value="@TAG_VAL@" />
</another>
</tool>
''')
xml = tool_dir.load()
tag_el = xml.find("another").find("tag")
value = tag_el.get('value')
assert value == "", value
# Test macros XML macros with $$ expansions in attributes
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<expand macro="inputs" bar="hello" />
<expand macro="inputs" bar="my awesome" />
<expand macro="inputs" bar="doggo" />
<macros>
<xml name="inputs" tokens="bar" token_quote="$$">
<inputs type="the type is $$BAR$$" />
</xml>
</macros>
</tool>
''')
xml = tool_dir.load()
input_els = xml.findall("inputs")
assert len(input_els) == 3
assert input_els[0].attrib["type"] == "the type is hello"
assert input_els[1].attrib["type"] == "the type is my awesome"
assert input_els[2].attrib["type"] == "the type is doggo"
# Test macros XML macros with @ expansions in text
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<expand macro="inputs" foo="hello" />
<expand macro="inputs" foo="world" />
<expand macro="inputs" />
<macros>
<xml name="inputs" token_foo="the_default">
<inputs>@FOO@</inputs>
</xml>
</macros>
</tool>
''')
xml = tool_dir.load()
input_els = xml.findall("inputs")
assert len(input_els) == 3
assert input_els[0].text == "hello"
assert input_els[1].text == "world"
assert input_els[2].text == "the_default"
# Test macros XML macros with @ expansions and recursive
with TestToolDirectory() as tool_dir:
tool_dir.write('''
<tool>
<expand macro="inputs" foo="hello" />
<expand macro="inputs" foo="world" />
<expand macro="inputs" />
<macros>
<xml name="inputs" token_foo="the_default">
<expand macro="real_inputs"><cow>@FOO@</cow></expand>
</xml>
<xml name="real_inputs">
<inputs><yield /></inputs>
</xml>
</macros>
</tool>
''')
xml = tool_dir.load()
input_els = xml.findall("inputs")
assert len(input_els) == 3
assert input_els[0].find("cow").text == "hello"
assert input_els[1].find("cow").text == "world"
assert input_els[2].find("cow").text == "the_default"