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Hotfix: merge hotfix into main #13

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3e181e0
fixed issue with integer coefficient
cb-Hades Sep 15, 2025
a1ea095
fixed issue with new MNX version #12
cb-Hades Sep 15, 2025
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16 changes: 8 additions & 8 deletions MCC/DataCollection/Requests/MetaNetX.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,28 +24,28 @@ def load_metanetx_db(self):
self.depr_df = pd.DataFrame()
self.prop_df = pd.DataFrame()

# TODO: make skiprows dynamic
base_url = "http://www.metanetx.org/cgi-bin/mnxget/mnxref/{}"
# @TODO : make column names dynamic (ISSUE: header line starts with a #
base_url = "https://www.metanetx.org/ftp/latest/{}"
try:
self.xref_df = pd.read_csv(f"{self.data_path}/chem_xref.tsv", sep = "\t", skiprows = 351)
self.xref_df = pd.read_csv(f"{self.data_path}/chem_xref.tsv", sep = "\t", comment = "#", names=["#source","ID","description"])
except FileNotFoundError:
logging.warning("MetaNetX xref database not found. Downloading MetaNetX xref database, this might take a while...")
progress_download(base_url.format("chem_xref.tsv"), f"{self.data_path}/chem_xref.tsv")
self.xref_df = pd.read_csv(f"{self.data_path}/chem_xref.tsv", sep = "\t", skiprows = 351)
self.xref_df = pd.read_csv(f"{self.data_path}/chem_xref.tsv", sep = "\t", comment = "#")

try:
self.depr_df = pd.read_csv(f"{self.data_path}/chem_depr.tsv", sep = "\t", skiprows = 351)
self.depr_df = pd.read_csv(f"{self.data_path}/chem_depr.tsv", sep = "\t", comment = "#")
except FileNotFoundError:
logging.warning("MetaNetX depr database not found. Downloading MetaNetX depr database, this might take a while...")
progress_download(base_url.format("chem_depr.tsv"), f"{self.data_path}/chem_depr.tsv")
self.depr_df = pd.read_csv(f"{self.data_path}/chem_depr.tsv", sep = "\t", skiprows = 351)
self.depr_df = pd.read_csv(f"{self.data_path}/chem_depr.tsv", sep = "\t", comment = "#", names=["#deprecated_ID","ID","version"])

try:
self.prop_df = pd.read_csv(f"{self.data_path}/chem_prop.tsv", sep = "\t", skiprows = 351)
self.prop_df = pd.read_csv(f"{self.data_path}/chem_prop.tsv", sep = "\t", comment = "#")
except FileNotFoundError:
logging.warning("MetaNetX prop database not found. Downloading MetaNetX prop database, this might take a while...")
progress_download(base_url.format("chem_prop.tsv"), f"{self.data_path}/chem_prop.tsv")
self.prop_df = pd.read_csv(f"{self.data_path}/chem_prop.tsv", sep = "\t", skiprows = 351)
self.prop_df = pd.read_csv(f"{self.data_path}/chem_prop.tsv", sep = "\t", comment = "#", names=["#ID", "name", "reference", "formula", "charge", "mass", "InChI", "InChIKey", "SMILES"])

def get_assignments_by_id(self, meta_id):
result = self.prop_dict.get(meta_id, None)
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2 changes: 1 addition & 1 deletion MCC/util.py
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Expand Up @@ -155,7 +155,7 @@ def get_integer_coefficients(reaction):
non_int_found = False
for _, coeff in reaction.metabolites.items():
coeff *= factor
if not coeff.is_integer():
if not float(coeff).is_integer():
non_int_found = True
factor = 1/np.absolute(coeff)
break
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