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app_logger.debug(f"No outdated temporary files to be removed.")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_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")
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")
# "SPBP 18:0;O",
# "SPBP 18:0;O3",
# "Cer 18:1;3O/20:4",
# "CoA(20:3(11Z,14Z,17Z))",
# "CoA 18:2;O",
# "FACoA 18:0",
# "Cer 24:2",
# "LMGP01010594",
# "lid",
# "PLPC",
"SM d18:1/24:0",
"DHA",
]
lv = "M1"
# test_out_rule = "COMP_DB"
test_out_rule = "LipidLynxX"
# test_out_rule = "BracketsShorthand"
lynx_converter = Converter(style=test_out_rule, logger=app_logger)
for t_in in t_in_lst:
t1_out = lynx_converter.convert(t_in, level="M1")
app_logger.info(f"Input: {t_in} -> Best Output: {t1_out}")
t2_out = lynx_converter.convert(t_in_lst)
app_logger.info(f"Input: {t_in_lst} -> Best Output: {t2_out}")
app_logger.info(t2_out)
#
# t3_out = lynx_converter.convert({"1": t_in_lst})
# logger.info(f"Input: {t_in_lst} -> Best Output: {t3_out}")
# logger.info("fin")
"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")
# "HETE",
# "TG(16:0/18:2/18:2[2xDB,1xOH])",
# "PC 16:0/18:2[9,12]",
# "DG 16:2[9,12]_O-18:2_0:0",
# "14,15-HxB3 (13R)",
# "C22:5 CE",
# "15-Keto-PGF2α",
# "PGF2α",
# "8-iso PGF2a III",
# "palmitoleic acid",
"FA 16:1(9Z)"
]
lynx_gen = Encoder(style="ShorthandNotation")
for t_in in t_in_lst:
t1_out = lynx_gen.convert(t_in)
app_logger.info(f"Input: {t_in} -> Best Output: {t1_out}")
# t_lv = "B0"
# t2_out = lynx_gen.export_level(
# t_in, level=t_lv, import_rules=default_input_rules
# )
# self.logger.info(f"Input: {t_in} -> Output @ Lv {t_lv}: {t2_out}")
# t_lv_lst = ["B0"]
# t3_out = lynx_gen.export_levels(
# t_in, levels=t_lv_lst, import_rules=default_input_rules
# )
# self.logger.info(f"Input: {t_in} -> Output @ Lv {t_lv_lst}: {t3_out}")
t4_out = lynx_gen.export_all_levels(t_in)
app_logger.info(f"Input: {t_in} -> Output @ all levels: {t4_out}")
app_logger.info("fin")
if not extracted_info_dct:
self.logger.error(f"Failed to decode Lipid: {lipid_name}")
obs_alias_lst = list(set(obs_alias_lst))
if obs_alias_lst:
self.logger.debug(f"Using alias: {lipid_name} -> {obs_alias_lst}")
return extracted_info_dct
if __name__ == "__main__":
# LIPID MAPS
# t_in = "GM3(d18:1/18:2(9Z,12Z))"
# t_in = "TG (P-18:1/18:2(9Z,12Z)/20:4(5Z,8Z,11Z,14Z)(7R-OH,12S-OH))"
# t_in = "TG (P-18:1/18:2(9Z,12Z)/20:4(5,8,11,14)(7R-OH,12S-OH))"
# t_in = "TG (P-18:1/18:2(9Z,12Z)/20:4(5,8,11,14)(7R-OH,12S-OH))"
# t_in = "TG (P-18:1/18:2(9Z,12Z)/5S,15R-DiHETE)"
# MS-DIAL
# t_in = "TG(16:0/18:2/20:4<OH>)"
# t_in = "TG(16:0/18:2/HETE)"
# RefMet
t_in = "PC(36:2e)"
extractor = Decoder(rules=default_input_rules)
t_out = extractor.extract(t_in)
app_logger.info(t_out)
app_logger.info("FIN")
# r"P-20:4<{5,9,12,15},2OH{8,11},Ke{14}>",
# r"P-20:4<{5Z,9E,12E,15E},2OH{8,11},Ke{14}>",
# r"P-20:4<2OH{8R,11S},Ke{14}>",
# r"P-20:4<{5,9,12,15},2OH{8R,11S},Ke{14}>",
# r"P-20:4<{5Z,9E,12E,15E},2OH{8R,11S},Ke{14}>",
]
pl_d_lst = []
pl_s_lst = []
for hg in hg_lst:
for sn1 in sn1_lst:
for sn2 in sn2_lst:
if "-" not in sn1 and "-" not in sn2:
pl_d_lst.append(f"{hg}({sn1}_{sn2})")
pl_s_lst.append(f"{hg}({sn1}/{sn2})")
# lipid_lst = sn1_lst + sn2_lst + pl_s_lst + pl_d_lst
lipid_lst = sn1_lst
counter = 0
for pl in lipid_lst:
counter += 1
app_logger.info(f"Test Lipid #{counter} : {pl}")
pl_obj = Lipid(lipid_code=pl)
app_logger.info(f"Export JSON \n {pl_obj.to_json()}")
app_logger.info(
"".join([f"\n {s}: {pl_obj.linked_ids[s]}" for s in pl_obj.linked_ids])
)
app_logger.info("FINISHED")