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Test fixes...
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@jmchilton
jmchilton committed Nov 8, 2024
1 parent ffb4030 commit 2507b03
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Showing 3 changed files with 18 additions and 18 deletions.
30 changes: 15 additions & 15 deletions lib/galaxy/tools/parameters/basic.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ class ToolParameter(UsesDictVisibleKeys):
>>> trans = Bunch(app=None)
>>> p = ToolParameter(None, XML('<param argument="--parameter-name" type="text" value="default" />'))
>>> assert p.name == 'parameter_name'
>>> assert sorted(p.to_dict(trans).items()) == [('argument', '--parameter-name'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', None)]
>>> assert sorted(p.to_dict(trans).items()) == [('argument', '--parameter-name'), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', None)]
"""

name: str
Expand Down Expand Up @@ -389,7 +389,7 @@ class TextToolParameter(SimpleTextToolParameter):
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
[('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
"""

def __init__(self, tool, input_source):
Expand Down Expand Up @@ -446,9 +446,9 @@ class IntegerToolParameter(TextToolParameter):
>>> p = IntegerToolParameter(None, XML('<param name="_name" type="integer" value="10" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
>>> assert type(p.from_json("10", trans)) == int
>>> with assert_throws_param_value_error("parameter '_name': an integer or workflow parameter is required"):
>>> with assert_throws_param_value_error("Parameter '_name': an integer or workflow parameter is required"):
... p.from_json("_string", trans)
"""

Expand Down Expand Up @@ -519,9 +519,9 @@ class FloatToolParameter(TextToolParameter):
>>> p = FloatToolParameter(None, XML('<param name="_name" type="float" value="3.141592" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
>>> assert type(p.from_json("36.1", trans)) == float
>>> with assert_throws_param_value_error("parameter '_name': an integer or workflow parameter is required"):
>>> with assert_throws_param_value_error("Parameter '_name': an integer or workflow parameter is required"):
... p.from_json("_string", trans)
"""

Expand Down Expand Up @@ -594,7 +594,7 @@ class BooleanToolParameter(ToolParameter):
>>> p = BooleanToolParameter(None, XML('<param name="_name" type="boolean" checked="yes" truevalue="_truevalue" falsevalue="_falsevalue" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', True)]
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', True)]
>>> print(p.from_json('true', trans))
True
>>> print(p.to_param_dict_string(True))
Expand Down Expand Up @@ -668,7 +668,7 @@ class FileToolParameter(ToolParameter):
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]
[('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]
"""

def __init__(self, tool, input_source):
Expand Down Expand Up @@ -742,7 +742,7 @@ class FTPFileToolParameter(ToolParameter):
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]
[('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]
"""

def __init__(self, tool, input_source):
Expand Down Expand Up @@ -815,7 +815,7 @@ class HiddenToolParameter(ToolParameter):
>>> p = HiddenToolParameter(None, XML('<param name="_name" type="hidden" value="_value"/>'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
"""

def __init__(self, tool, input_source):
Expand All @@ -842,14 +842,14 @@ class ColorToolParameter(ToolParameter):
_name
>>> print(p.to_param_dict_string("#ffffff"))
#ffffff
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
>>> p = ColorToolParameter(None, XML('<param name="_name" type="color"/>'))
>>> print(p.get_initial_value(trans, {}))
#000000
>>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff" rgb="True"/>'))
>>> print(p.to_param_dict_string("#ffffff"))
(255, 255, 255)
>>> with assert_throws_param_value_error("parameter '_name': Failed to convert 'None' to RGB."):
>>> with assert_throws_param_value_error("Parameter '_name': Failed to convert 'None' to RGB."):
... p.to_param_dict_string(None)
"""

Expand Down Expand Up @@ -883,7 +883,7 @@ class BaseURLToolParameter(HiddenToolParameter):
>>> p = BaseURLToolParameter(None, XML('<param name="_name" type="base_url" value="_value"/>'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
"""

def __init__(self, tool, input_source):
Expand Down Expand Up @@ -933,7 +933,7 @@ class SelectToolParameter(ToolParameter):
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
[('argument', None), ('display', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
>>> p = SelectToolParameter(None, XML(
... '''
... <param name="_name" type="select" multiple="true">
Expand All @@ -945,7 +945,7 @@ class SelectToolParameter(ToolParameter):
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
[('argument', None), ('display', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
>>> print(p.to_param_dict_string(["y", "z"]))
y,z
"""
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy_test/api/test_jobs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -634,7 +634,7 @@ def test_submission_on_collection_with_deleted_element(self, history_id):
assert response.status_code == 400
assert (
response.json()["err_msg"]
== "parameter 'collection': the previously selected dataset collection has elements that are deleted."
== "Parameter 'collection': the previously selected dataset collection has elements that are deleted."
)

@pytest.mark.require_new_history
Expand Down
4 changes: 2 additions & 2 deletions lib/galaxy_test/api/test_tools.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -934,7 +934,7 @@ def test_data_column_defaults(self):
with self.dataset_populator.test_history(require_new=False) as history_id:
response = self._run("gx_data_column_multiple", history_id, inputs, assert_ok=False).json()
assert "err_msg" in response, str(response)
assert "parameter 'parameter': an invalid option" in response["err_msg"]
assert "Parameter 'parameter': an invalid option" in response["err_msg"]

with self.dataset_populator.test_history(require_new=True) as history_id:
response = self._run("gx_data_column_optional", history_id, inputs, assert_ok=True)
Expand Down Expand Up @@ -2217,7 +2217,7 @@ def test_implicit_conversion_and_reduce_invalid_param(self):
self._run_implicit_collection_and_reduce(history_id=history_id, param="X")
details = self.dataset_populator.get_history_dataset_details(history_id=history_id, hid=3, assert_ok=False)
assert details["state"] == "error"
assert "parameter 'col': an invalid option" in details["misc_info"]
assert "Parameter 'col': an invalid option" in details["misc_info"]

def _run_implicit_collection_and_reduce(self, history_id, param):
fasta_path = self.test_data_resolver.get_filename("1.fasta")
Expand Down

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