def test_ToolInput_get_lower_param_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_lower_param_desc`."""
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[1],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
sub_param_desc = tool_input.get_lower_param_desc()
assert '> - {% icon param-collection %}' in sub_param_desc
def test_ToolInput_get_formatted_inputs():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_inputs`."""
# test no input
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[1]["inputs"][0],
wf_param_values={},
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
inputlist = tool_input.get_formatted_inputs()
assert inputlist == ''
# test collection
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[1]["inputs"][0],
wf_param_values=wf_param_values["add_to_database"],
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
inputlist = tool_input.get_formatted_inputs()
assert 'param-collection' in inputlist
assert '(Input dataset collection)' in inputlist
# test single input
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[2]["inputs"][0],
wf_param_values=wf_param_values["tables"][0],
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
inputlist = tool_input.get_formatted_inputs()
assert 'param-file' in inputlist
assert '(Input dataset)' in inputlist
def test_ToolInput_get_formatted_section_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_section_desc`."""
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[1],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
section_paramlist = tool_input.get_formatted_section_desc()
assert '> - In *"' in section_paramlist
assert '> - {%' in section_paramlist
def test_ToolInput_get_lower_param_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_lower_param_desc`."""
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[1],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
sub_param_desc = tool_input.get_lower_param_desc()
assert '> - {% icon param-collection %}' in sub_param_desc
def test_ToolInput_get_formatted_conditional_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_conditional_desc`."""
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[5],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
conditional_paramlist = tool_input.get_formatted_conditional_desc()
assert '> - *"' in conditional_paramlist
assert '"*: `Yes`' in conditional_paramlist
assert '> - *"' in conditional_paramlist
def test_ToolInput_get_formatted_section_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_section_desc`."""
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[1],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
section_paramlist = tool_input.get_formatted_section_desc()
assert '> - In *"' in section_paramlist
assert '> - {%' in section_paramlist
def test_ToolInput_get_formatted_repeat_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_repeat_desc`."""
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[2],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
repeat_desc = tool_input.get_formatted_repeat_desc()
assert '> - In *"' in repeat_desc
assert '> - {% icon param-repeat %} *"Insert' in repeat_desc
assert '> -' in repeat_desc
def test_ToolInput_get_formatted_conditional_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_conditional_desc`."""
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[5],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
conditional_paramlist = tool_input.get_formatted_conditional_desc()
assert '> - *"' in conditional_paramlist
assert '"*: `Yes`' in conditional_paramlist
assert '> - *"' in conditional_paramlist
def test_ToolInput_get_formatted_repeat_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_repeat_desc`."""
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[2],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
repeat_desc = tool_input.get_formatted_repeat_desc()
assert '> - In *"' in repeat_desc
assert '> - Click on' in repeat_desc
assert '> - In *"1:' in repeat_desc
assert '> -' in repeat_desc
assert '> - In *"2:' in repeat_desc
def test_ToolInput_init():
"""Test :func:`planemo.training.tool_input.ToolInput.init`."""
# test type exception
exp_exception = "No type for the parameter t"
with assert_raises_regexp(Exception, exp_exception):
ToolInput(tool_inp_desc={'name': 't'},
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
# test with param not in workflow and exception
exp_exception = "t not in workflow"
with assert_raises_regexp(Exception, exp_exception):
ToolInput(tool_inp_desc={
'name': 't',
'type': ''
},
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
# test with param not in workflow but no exception
tool_input = ToolInput(tool_inp_desc={
'name': 't',
'type': ''
},
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
assert "save_db" in tool_input.wf_param_values
# test with param in workflow
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[0],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
assert "save_db" not in tool_input.wf_param_values
assert tool_input.wf_param_values == "workdb.sqlite"
def test_ToolInput_get_formatted_inputs():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_inputs`."""
# test no input
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[1]["inputs"][0],
wf_param_values={},
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
inputlist = tool_input.get_formatted_inputs()
assert inputlist == ''
# test collection
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[1]["inputs"][0],
wf_param_values=wf_param_values["add_to_database"],
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
inputlist = tool_input.get_formatted_inputs()
assert 'param-collection' in inputlist
assert '(Input dataset collection)' in inputlist
# test single input
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[2]["inputs"][0],
wf_param_values=wf_param_values["tables"][0],
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
inputlist = tool_input.get_formatted_inputs()
assert 'param-file' in inputlist
assert '(Input dataset)' in inputlist
def test_ToolInput_get_formatted_other_param_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_other_param_desc`."""
# test default value of the tool
tool_input = ToolInput(
tool_inp_desc={'value': 10, 'name': 't', 'type': ''},
wf_param_values={'t': 10},
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
assert tool_input.get_formatted_other_param_desc() == ''
# test boolean parameter
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[3],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
assert tool_input.get_formatted_other_param_desc() == ''
tool_input.wf_param_values = 'true'
assert '*: `Yes`' in tool_input.get_formatted_other_param_desc()
# test select parameter
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[5]['cases'][0]['inputs'][0],
wf_param_values=wf_param_values['query_result'],
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
assert '*: `&`' in tool_input.get_formatted_other_param_desc()
# test other parameter
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[4],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=True)
assert '*: ``' in tool_input.get_formatted_other_param_desc()
def test_ToolInput_get_formatted_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_desc`."""
# test no param values
tool_input = ToolInput(tool_inp_desc={
'value': 10,
'name': 't',
'type': ''
},
wf_param_values={},
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
assert tool_input.get_formatted_desc() == ''
# test data
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[2]["inputs"][0],
wf_param_values=wf_param_values["tables"][0],
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
inputlist = tool_input.get_formatted_inputs()
formatted_desc = tool_input.get_formatted_desc()
assert inputlist == formatted_desc
# test section
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[1],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
section_paramlist = tool_input.get_formatted_section_desc()
formatted_desc = tool_input.get_formatted_desc()
assert section_paramlist == formatted_desc
# test conditional
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[5],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
conditional_paramlist = tool_input.get_formatted_conditional_desc()
formatted_desc = tool_input.get_formatted_desc()
assert conditional_paramlist == formatted_desc
# test repeat
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[2],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
repeat_desc = tool_input.get_formatted_repeat_desc()
formatted_desc = tool_input.get_formatted_desc()
assert repeat_desc == formatted_desc
# test other
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[3],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
param_desc = tool_input.get_formatted_other_param_desc()
formatted_desc = tool_input.get_formatted_desc()
assert param_desc == formatted_desc
def test_ToolInput_get_formatted_other_param_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_other_param_desc`."""
# test default value of the tool
tool_input = ToolInput(tool_inp_desc={
'value': 10,
'name': 't',
'type': ''
},
wf_param_values={'t': 10},
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
assert tool_input.get_formatted_other_param_desc() == ''
# test boolean parameter
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[3],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
assert tool_input.get_formatted_other_param_desc() == ''
tool_input.wf_param_values = 'true'
assert '*: `Yes`' in tool_input.get_formatted_other_param_desc()
# test select parameter
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[5]['cases'][0]['inputs'][0],
wf_param_values=wf_param_values['query_result'],
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
assert '*: `&`' in tool_input.get_formatted_other_param_desc()
# test other parameter
tool_input = ToolInput(tool_inp_desc=tool_inp_desc[4],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=True)
assert '*: ``' in tool_input.get_formatted_other_param_desc()
def test_ToolInput_get_formatted_desc():
"""Test :func:`planemo.training.tool_input.ToolInput.get_formatted_desc`."""
# test no param values
tool_input = ToolInput(
tool_inp_desc={'value': 10, 'name': 't', 'type': ''},
wf_param_values={},
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
assert tool_input.get_formatted_desc() == ''
# test data
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[2]["inputs"][0],
wf_param_values=wf_param_values["tables"][0],
wf_steps=wf_steps,
level=1,
should_be_there=False,
force_default=False)
inputlist = tool_input.get_formatted_inputs()
formatted_desc = tool_input.get_formatted_desc()
assert inputlist == formatted_desc
# test section
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[1],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
section_paramlist = tool_input.get_formatted_section_desc()
formatted_desc = tool_input.get_formatted_desc()
assert section_paramlist == formatted_desc
# test conditional
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[5],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
conditional_paramlist = tool_input.get_formatted_conditional_desc()
formatted_desc = tool_input.get_formatted_desc()
assert conditional_paramlist == formatted_desc
# test repeat
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[2],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
repeat_desc = tool_input.get_formatted_repeat_desc()
formatted_desc = tool_input.get_formatted_desc()
assert repeat_desc == formatted_desc
# test other
tool_input = ToolInput(
tool_inp_desc=tool_inp_desc[3],
wf_param_values=wf_param_values,
wf_steps=wf_steps,
level=1,
should_be_there=True,
force_default=False)
param_desc = tool_input.get_formatted_other_param_desc()
formatted_desc = tool_input.get_formatted_desc()
assert param_desc == formatted_desc