Overview
Hey! It seems that cross-references to EC, rhea and other external ids are missing from the API results. I think it's an API problem rather than of the Python client because my implementation in R is also returning empty lists for EC etc.
Minimal example
from pprint import pprint
from enviPath_python import enviPath
eP = enviPath("https://envipath.org/api/legacy/", new_api=True)
eP.login("username", "password")
bbd = eP.get_package('https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1')
External references for compounds are missing
compounds = bbd.get_compounds()
for c in compounds[:5]:
print(c.get_name(), c.get_external_references())
# 2-Naphthoate {}
# trans-4-Amino-6-carboxy-2-oxo-hexa-3,5-dienoate {}
# 2-Protocatechoylphloroglucinolcarboxylate {}
# 7-Oxoheptanoate {}
# 3,7-Dimethyl-5-oxo-octyl-CoA {}
EC numbers for reactions/rules/edges are missing
reactions = bbd.get_reactions()
for r in reactions[:5]:
print(r.get_name(), r.get_ec_numbers())
# Eawag BBD reaction r1236 []
# Eawag BBD reaction r1276 []
# Eawag BBD reaction r1584 []
# Eawag BBD reaction r0028 []
# Eawag BBD reaction r0091 []
Error when getting rhea references for reactions
for r in reactions[:5]:
print(r.get_name(), r.get_rhea_references())
# ValueError: Reaction has no property rheaReferences
Overview
Hey! It seems that cross-references to EC, rhea and other external ids are missing from the API results. I think it's an API problem rather than of the Python client because my implementation in R is also returning empty lists for EC etc.
Minimal example
External references for compounds are missing
EC numbers for reactions/rules/edges are missing
Error when getting rhea references for reactions