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Convert unittesting #50

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Convert unittesting #50

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120c3e1
Added unit test for convert functionality
GregJohnsonJr Aug 22, 2023
6c9fc43
Added more test cases
GregJohnsonJr Aug 24, 2023
565835a
Slight changes
GregJohnsonJr Aug 24, 2023
0c3dc08
Update to the convert_key_translation_test
GregJohnsonJr Aug 24, 2023
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181 changes: 181 additions & 0 deletions tests/test_convert_key_translations.py
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Original file line number Diff line number Diff line change
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import uparma
import pytest
import pprint
import json
import os
from pathlib import Path

test_input_dict = {
"allow_multiple_variable_mods_on_residue": True,
"mass_diff_to_variable_mod": True,
"localize_delta_mass": False
}

test_parameter_list = [
{
"input": {
("general", "parameters"): [
{
"default_value": False,
"description": " Put mass difference as a variable modification.",
"key_translations": {
"msfragger_style_3": "mass_diff_to_variable_mod",
"ursgal_style_1": "mass_diff_to_variable_mod"
},
"name": "write_mass_diff_to_variable_mod",
"tag": [],
"triggers_rerun": True,
"value_translations": {
"msfragger_style_3": [
[
False,
0
],
[
True,
1
]
]
},
"value_type": "bool"
},
{
"default_value": False,
"description": " Static mods are not considered ",
"key_translations": {
"mascot_style_1": "MULTI_SITE_MODS",
"msfragger_style_1": "allow_multiple_variable_mods_on_residue",
"msfragger_style_2": "allow_multiple_variable_mods_on_residue",
"msfragger_style_3": "allow_multiple_variable_mods_on_residue",
"ursgal_style_1": "allow_multiple_variable_mods_on_residue"
},
"name": "allow_multiple_variable_mods_on_residue",
"tag": [
"modifications"
],
"triggers_rerun": True,
"value_translations": {
"mascot_style_1": [
[
False,
0
],
[
True,
1
]
],
"msfragger_style_1": [
[
False,
0
],
[
True,
1
]
],
"msfragger_style_2": [
[
False,
0
],
[
True,
1
]
],
"msfragger_style_3": [
[
False,
0
],
[
True,
1
]
],
"ursgal_style_1": [
[
False,
False
],
[
True,
True
]
]
},
"value_type": "bool"
},
{
"default_value": True,
"description": " Generate and use mass difference fragment index in addition to the regular fragment index for search. This allows shifted fragment ions - fragment ions with mass increased by the calculated mass difference, to be included in scoring. ",
"key_translations": {
"msfragger_style_1": "localize_delta_mass",
"msfragger_style_2": "localize_delta_mass",
"msfragger_style_3": "localize_delta_mass",
"ursgal_style_1": "localize_delta_mass"
},
"name": "localize_delta_mass",
"tag": [
"scoring",
"spectrum"
],
"triggers_rerun": True,
"value_translations": {
"msfragger_style_1": [
[
False,
0
],
[
True,
1
]
],
"msfragger_style_2": [
[
False,
0
],
[
True,
1
]
],
"msfragger_style_3": [
[
False,
0
],
[
True,
1
]
],
"ursgal_style_1": [
[
False,
False
],
[
True,
True
]
]
},
"value_type": "bool"
}
]
}
}
]
@pytest.mark.parametrize("test_parameters", test_parameter_list)
def test_load_data(test_parameters):
up = uparma.UParma(refresh_jsons=False, parameter_data=test_parameter_list[0]["input"])
translation = up.convert(param_dict=test_input_dict, translated_style="msfragger_style_3")
assert translation["allow_multiple_variable_mods_on_residue"]["translated_value"] == 1
assert translation["allow_multiple_variable_mods_on_residue"]["was_translated"]
assert translation["write_mass_diff_to_variable_mod"]["translated_value"] == 1
assert translation["write_mass_diff_to_variable_mod"]["was_translated"]