mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
332 lines
9.5 KiB
Python
332 lines
9.5 KiB
Python
import os
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from shutil import rmtree
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from tempfile import mkdtemp
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from galaxy.tool_util.loader import load_tool, template_macro_params
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from galaxy.util import parse_xml
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from .sample_data import SIMPLE_MACRO, SIMPLE_TOOL_WITH_MACRO
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def test_loader():
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class TestToolDirectory:
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def __init__(self):
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self.temp_directory = mkdtemp()
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def __enter__(self):
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return self
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def __exit__(self, type, value, tb):
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rmtree(self.temp_directory)
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def write(self, contents, name="tool.xml"):
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open(os.path.join(self.temp_directory, name), "w").write(contents)
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def load(self, name="tool.xml", preprocess=True):
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path = os.path.join(self.temp_directory, name)
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if preprocess:
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return load_tool(path)
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else:
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return parse_xml(path)
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# Test simple macro replacement.
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<expand macro="inputs" />
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<macros>
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<macro name="inputs">
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<inputs />
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</macro>
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</macros>
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</tool>''')
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xml = tool_dir.load(preprocess=False)
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assert xml.find("inputs") is None
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xml = tool_dir.load(preprocess=True)
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assert xml.find("inputs") is not None
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# Test importing macros from external files
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with TestToolDirectory() as tool_dir:
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tool_dir.write(SIMPLE_TOOL_WITH_MACRO)
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tool_dir.write(SIMPLE_MACRO.substitute(tool_version="2.0"), name="external.xml")
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xml = tool_dir.load(preprocess=False)
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assert xml.find("inputs") is None
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xml = tool_dir.load(preprocess=True)
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assert xml.find("inputs") is not None
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# Test macros with unnamed yield statements.
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<expand macro="inputs">
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<input name="first_input" />
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</expand>
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<expand macro="inputs">
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<input name="second_input" />
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</expand>
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<expand macro="inputs">
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<input name="third_input" />
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</expand>
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<macros>
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<macro name="inputs">
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<expand macro="foo">
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<yield />
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</expand>
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</macro>
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<macro name="foo">
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<inputs>
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<yield />
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</inputs>
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</macro>
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</macros>
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</tool>''')
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xml = tool_dir.load()
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assert xml.findall("inputs")[0].find("input").get("name") == "first_input"
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assert xml.findall("inputs")[1].find("input").get("name") == "second_input"
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assert xml.findall("inputs")[2].find("input").get("name") == "third_input"
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# Test nested macro with yield statements
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with TestToolDirectory() as tool_dir:
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tool_dir.write("""
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<tool>
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<macros>
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<macro name="paired_options">
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<when value="paired">
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<yield />
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</when>
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<when value="paired_collection">
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<yield />
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</when>
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</macro>
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<macro name="single_or_paired_general">
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<conditional name="library">
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<expand macro="paired_options">
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<yield />
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</expand>
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</conditional>
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</macro>
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</macros>
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<inputs>
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<expand macro="single_or_paired_general"></expand>
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</inputs>
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</tool>
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""")
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xml = tool_dir.load()
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# Test recursive macro applications.
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<expand macro="inputs">
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<input name="first_input" />
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<expand macro="second" />
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</expand>
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<macros>
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<macro name="inputs">
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<inputs>
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<yield />
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<input name="third_input" />
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</inputs>
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</macro>
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<macro name="second">
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<input name="second_input" />
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</macro>
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</macros>
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</tool>''')
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xml = tool_dir.load()
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assert xml.find("inputs").findall("input")[0].get("name") == "first_input"
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assert xml.find("inputs").findall("input")[1].get("name") == "second_input"
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assert xml.find("inputs").findall("input")[2].get("name") == "third_input"
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# Test recursive macro applications.
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<expand macro="inputs">
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<input name="first_input" />
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<expand macro="second" />
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</expand>
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<macros>
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<macro name="inputs">
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<inputs>
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<yield />
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</inputs>
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</macro>
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<macro name="second">
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<expand macro="second_delegate" />
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<input name="third_input" />
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</macro>
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<macro name="second_delegate">
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<input name="second_input" />
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</macro>
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</macros>
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</tool>''')
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xml = tool_dir.load()
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assert xml.find("inputs").findall("input")[0].get("name") == "first_input"
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assert xml.find("inputs").findall("input")[1].get("name") == "second_input"
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assert xml.find("inputs").findall("input")[2].get("name") == "third_input"
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool id="issue_647">
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<macros>
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<macro name="a">
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<param name="a1" type="text" value="a1" label="a1"/>
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<yield />
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</macro>
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</macros>
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<inputs>
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<expand macro="a">
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<param name="b" type="text" value="b" label="b" />
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</expand>
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</inputs>
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</tool>''')
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xml = tool_dir.load()
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assert xml.find("inputs").findall("param")[0].get("name") == "a1"
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assert xml.find("inputs").findall("param")[1].get("name") == "b"
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# Test <xml> is shortcut for macro type="xml"
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<expand macro="inputs" />
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<macros>
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<xml name="inputs">
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<inputs />
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</xml>
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</macros>
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</tool>''')
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xml = tool_dir.load()
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assert xml.find("inputs") is not None
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<command interpreter="python">tool_wrapper.py
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#include source=$tool_params
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</command>
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<macros>
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<template name="tool_params">-a 1 -b 2</template>
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</macros>
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</tool>
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''')
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xml = tool_dir.load()
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params_dict = template_macro_params(xml.getroot())
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assert params_dict['tool_params'] == "-a 1 -b 2"
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<macros>
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<token name="@CITATION@">The citation.</token>
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</macros>
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<help>@CITATION@</help>
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<another>
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<tag />
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</another>
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</tool>
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''')
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xml = tool_dir.load()
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help_el = xml.find("help")
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assert help_el.text == "The citation.", help_el.text
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<macros>
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<token name="@TAG_VAL@">The value.</token>
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</macros>
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<another>
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<tag value="@TAG_VAL@" />
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</another>
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</tool>
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''')
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xml = tool_dir.load()
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tag_el = xml.find("another").find("tag")
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value = tag_el.get('value')
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assert value == "The value.", value
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<macros>
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<token name="@TAG_VAL@"><![CDATA[]]></token>
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</macros>
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<another>
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<tag value="@TAG_VAL@" />
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</another>
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</tool>
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''')
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xml = tool_dir.load()
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tag_el = xml.find("another").find("tag")
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value = tag_el.get('value')
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assert value == "", value
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# Test macros XML macros with $$ expansions in attributes
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<expand macro="inputs" bar="hello" />
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<expand macro="inputs" bar="my awesome" />
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<expand macro="inputs" bar="doggo" />
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<macros>
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<xml name="inputs" tokens="bar" token_quote="$$">
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<inputs type="the type is $$BAR$$" />
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</xml>
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</macros>
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</tool>
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''')
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xml = tool_dir.load()
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input_els = xml.findall("inputs")
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assert len(input_els) == 3
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assert input_els[0].attrib["type"] == "the type is hello"
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assert input_els[1].attrib["type"] == "the type is my awesome"
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assert input_els[2].attrib["type"] == "the type is doggo"
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# Test macros XML macros with @ expansions in text
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<expand macro="inputs" foo="hello" />
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<expand macro="inputs" foo="world" />
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<expand macro="inputs" />
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<macros>
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<xml name="inputs" token_foo="the_default">
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<inputs>@FOO@</inputs>
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</xml>
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</macros>
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</tool>
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''')
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xml = tool_dir.load()
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input_els = xml.findall("inputs")
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assert len(input_els) == 3
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assert input_els[0].text == "hello"
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assert input_els[1].text == "world"
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assert input_els[2].text == "the_default"
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# Test macros XML macros with @ expansions and recursive
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with TestToolDirectory() as tool_dir:
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tool_dir.write('''
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<tool>
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<expand macro="inputs" foo="hello" />
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<expand macro="inputs" foo="world" />
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<expand macro="inputs" />
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<macros>
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<xml name="inputs" token_foo="the_default">
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<expand macro="real_inputs"><cow>@FOO@</cow></expand>
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</xml>
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<xml name="real_inputs">
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<inputs><yield /></inputs>
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</xml>
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</macros>
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</tool>
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''')
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xml = tool_dir.load()
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input_els = xml.findall("inputs")
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assert len(input_els) == 3
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assert input_els[0].find("cow").text == "hello"
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assert input_els[1].find("cow").text == "world"
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assert input_els[2].find("cow").text == "the_default"
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