def remove_temp_file():
removed_files = clean_temp_folder(default_temp_folder,
default_temp_max_days,
default_temp_max_files)
if removed_files:
app_logger.info(
f"Remove temporary output files older than {default_temp_max_days} days..."
)
for removed_file in removed_files:
app_logger.info(f"File removed: {removed_file}")
else:
app_logger.debug(f"No outdated temporary files to be removed.")
def test_input_rule(test_file):
app_logger.debug("SETUP TESTS...")
app_logger.info(test_file)
in_file = None
if test_file:
in_file = get_abs_path(test_file)
if not in_file:
in_file = get_abs_path(
r"lynx/configurations/rules/input/LipidLynxX.json")
app_logger.info(f"Test file {in_file}")
rule = InputRules(test_file)
app_logger.debug(f"Got infile {in_file}")
app_logger.debug(f"test input rule {rule.sources}")
if rule.is_validated is False:
raise Exception(f"FAILED: test input rule {rule.sources}")
else:
app_logger.info(f"PASSED: test input rule {rule.sources}")
app_logger.info(f"test PASSED")
def test_output_rule(test_file):
app_logger.debug("SETUP TESTS...")
app_logger.info(test_file)
in_file = None
if test_file:
in_file = get_abs_path(test_file)
if not in_file:
in_file = get_abs_path(
r"lynx/configurations/rules/output/LipidLynxX.json")
app_logger.info(f"Test file {in_file}")
rule = OutputRules(test_file)
app_logger.debug(f"Got Output infile {in_file}")
app_logger.debug(f"test Output rule {rule.nomenclature}")
if rule.is_structure_valid is False:
raise Exception(f"FAILED: test Rule {rule.nomenclature}")
else:
app_logger.info(f"PASSED: test Rule {rule.nomenclature}")
app_logger.info(
f"Supported LMSD classes: {rule.supported_lmsd_classes}")
app_logger.info(f"test PASSED")
"MOD_ELEMENTS": {
"H": -2
},
"MOD_MASS_SHIFT": 0,
},
"5.01_OH": {
"MOD_CV": "OH",
"MOD_LEVEL": 5,
"MOD_COUNT": 1,
"MOD_SITE": ["12"],
"MOD_SITE_INFO": ["R"],
"MOD_ORDER": 5.01,
"MOD_ELEMENTS": {
"O": 1
},
"MOD_MASS_SHIFT": 16,
},
},
}
usr_mod_obj = Modifications(usr_mod_info)
app_logger.debug(usr_mod_obj)
mod_json = usr_mod_obj.to_json()
usr_sum_mods_obj = merge_mods([usr_mod_obj, usr_mod_obj])
app_logger.debug(usr_sum_mods_obj)
sum_mod_json = usr_sum_mods_obj.to_json()
app_logger.info("FINISHED")
"MOD_MASS_SHIFT": 0,
},
"5.01_OH": {
"MOD_CV": "OH",
"MOD_LEVEL": 4,
"MOD_COUNT": 1,
"MOD_SITE": ["12"],
"MOD_SITE_INFO": [""],
"MOD_ORDER": 5.01,
"MOD_ELEMENTS": {
"O": 1
},
"MOD_MASS_SHIFT": 16,
},
},
},
"NUM_C": 18,
"NUM_DB": 2,
"NUM_O": 0,
},
}
# for r in usr_res_info:
# usr_res_obj = Residue(usr_res_info[r])
# logger.debug(usr_res_obj.linked_ids)
# # usr_res_json = res_obj.to_json()
usr_res_obj = merge_residues(usr_res_info)
app_logger.debug(usr_res_obj.linked_ids)
# usr_res_json = res_obj.to_json()
app_logger.info("FINISHED")