Merge pull request #613 from Devlin-Moyer/fix/FAD_ubiquinone_duplicates

Fix FAD/Ubiquinone Duplicates

code/test/sanityCheck.py

@@ -93,7 +93,7 @@ def checkUnusedEntities(model, entity_type):
 
     # collect unused entites
     unused_entities = find_unused_entities(model, entity_type)
-    assert len(unused_entities) == 0, f"Found unused {{entity_type}}!"
+    assert len(unused_entities) == 0, f"Found unused {entity_type}: {unused_entities}"
 
 
 if __name__ == "__main__":

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -103,11 +103,26 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04411"	""	"PIt8"	""	""	""	"PIt8"	"MNXR102875"	"HMR_4911"	"RCR40976"	""	0	""	""	"PIt8"
 "MAR08749"	""	"H2CO3D2"	""	""	""	"HMR_8749"	"MNXR100483"	"HMR_8749"	"RCR14128"	""	1	""	""	"HMR_8749"
 "MAR08750"	""	"H2CO3D2m"	""	""	""	"HMR_8750"	"MNXR100483"	"HMR_8750"	"RCR14129"	""	1	""	""	"HMR_8750"
+"MAR02035"	""	"r0310"	""	""	""	"r0310"	""	""	""	""	0	""	""	"r0310"
+"MAR03211"	"R00924"	""	""	"r0683"	""	"r0683"	"MNXR103101"	"HMR_3211"	"RCR14348"	""	0	""	""	"HMR_3211"
+"MAR03751"	"R02660"	""	"R02660M"	"r0560"	""	"r0560"	""	"HMR_3751"	"RCR14421"	""	0	""	""	"HMR_3751"
+"MAR03783"	"R03172"	""	"R03172M"	"r0603"	""	"r0603"	"MNXR108000"	"HMR_3783"	"RCR14424"	""	0	""	""	"HMR_3783"
+"MAR04242"	"R02487"	""	"R02487M"	"r0541"	""	"r0541"	"MNXR100293"	"HMR_4242"	"RCR14356"	""	0	""	"RHEA:30847"	"HMR_4242"
+"MAR03769"	"R04095"	""	"R04095M"	"r0655"	""	"r0655"	"MNXR95318"	"HMR_3769"	"RCR14423"	""	0	""	""	"HMR_3769"
+"MAR03838"	""	""	""	"r1453"	""	""	""	"HMR_3838"	"RCR14286"	""	0	""	""	"HMR_3838"
+"MAR02366"	""	"r1446"	""	""	""	"r1446"	""	""	""	""	0	""	""	"r1446"
+"MAR02367"	""	"r1447"	""	""	""	"r1447"	""	""	""	""	0	""	""	"r1447"
+"MAR02370"	""	"r1449"	""	""	""	"r1449"	""	""	""	""	0	""	""	"r1449"
+"MAR02372"	""	"r1450"	""	""	""	"r1450"	""	""	""	""	0	""	""	"r1450"
+"MAR02373"	""	"r1451"	""	""	""	"r1451"	""	""	""	""	0	""	""	"r1451"
+"MAR00483"	"R00849"	""	""	"r0205"	""	"r0205"	"MNXR106713"	"HMR_0483"	"RCR21050"	""	0	""	"RHEA:18977"	"HMR_0483"
+"MAR08743"	"R00408"	"SUCD1m"	""	""	""	"SUCD1m"	"MNXR99636"	"HMR_8743"	"RCR11674"	""	0	""	"RHEA:30343"	"HMR_8743"
 "MAR05294"	"R00362"	""	"R00362C"	"r1109"	""	"r1109"	"MNXR96731"	"HMR_5294"	"RCR11670"	""	0	"RHEA:10761"	"RHEA:10760"	"HMR_5294"
 "MAR11421"	""	"CITL"	""	""	""	"CITL"	"MNXR96731"	""	""	""	0	"RHEA:10761"	"RHEA:10760"	"CITL"
 "MAR00562"	""	"ETF"	""	""	""	"ETF"	"MNXR97965"	""	""	""	0	""	""	"ETF"
 "MAR00563"	""	"ETFQO"	""	""	""	"ETFQO"	"MNXR97966"	""	""	""	0	""	""	"ETFQO"
 "MAR05434"	""	"FAOXC3DC"	""	""	""	"FAOXC3DC"	""	""	""	""	0	""	""	"FAOXC3DC"
+"MAR02369"	""	"r1448"	""	""	""	"r1448"	""	""	""	""	0	""	""	"r1448"
 "MAR02185"	""	""	""	""	""	"r0701"	""	""	""	""	0	""	""	"r0701"
 "MAR11649"	""	""	""	""	""	"PAIL_hs_t1e"	""	""	""	""	0	""	""	"PAIL_hs_t1e"
 "MAR11729"	""	""	""	""	""	"2HXIC_Lt2e"	""	""	""	""	0	""	""	"2HXIC_Lt2e"