for discoverlife matcher "path.kingdom.name" is empty even though "path" and "pathIds" are populated

jhpoelen commented 5 months ago

with schema.properties being

nomer.append.schema.output=[{"column":0,"type":"path.kingdom.name"}, {"column":1,"type":"path"}, {"column": 2,"type":"pathNames"}]

and

echo -e "\tApis mellifera"\
 | nomer append\
 --include-header\
 --properties schema.properties\
 discoverlife

yielded a result with an empty kingdom name, where "Animalia" was expected.

providedExternalId	providedName	relationName	resolvedPath.kingdom.name	resolvedPath	resolvedPathNames
	Apis mellifera	HAS_ACCEPTED_NAME		Animalia \| Arthropoda \| Insecta \| Hymenoptera \| Apidae \| Apinae \| Apini \| None \| Apis \| Apis \| Apis mellifera	kingdom \| phylum \| class \| order \| family \| subfamily \| tribe \| subtribe \| genus \| subgenus \| species

whereas

echo -e "\tApis mellifera"\
 | nomer append\
 --include-header\
 --properties schema.properties\
 globalnames

produced

providedExternalId	providedName	relationName	resolvedPath.kingdom.name	resolvedPath	resolvedPathNames
	Apis mellifera	SAME_AS	Metazoa	\| Eukaryota \| Opisthokonta \| Metazoa \| Eumetazoa \| Bilateria \| Protostomia \| Ecdysozoa \| Panarthropoda \| Arthropoda \| Mandibulata \| Pancrustacea \| Hexapoda \| Insecta \| Dicondylia \| Pterygota \| Neoptera \| Endopterygota \| Hymenoptera \| Apocrita \| Aculeata \| Apoidea \| Anthophila \| Apidae \| Apinae \| Apini \| Apis \| Apis mellifera	\| superkingdom \| clade \| kingdom \| clade \| clade \| clade \| clade \| clade \| phylum \| clade \| clade \| subphylum \| class \| clade \| subclass \| infraclass \| cohort \| order \| suborder \| infraorder \| superfamily \| clade \| family \| subfamily \| tribe \| genus \| species

jhpoelen commented 5 months ago

jhpoelen commented 5 months ago

After applying a fix to nomer, the expected result was obtained via

echo -e "\tApis mellifera"\
 | nomer append\
 --include-header\
 --properties schema.properties\
 discoverlife

providedExternalId	providedName	relationName	resolvedPath.kingdom.name	resolvedPath	resolvedPathNames
	Apis mellifera	HAS_ACCEPTED_NAME	Animalia	Animalia \| Arthropoda \| Insecta \| Hymenoptera \| Apidae \| Apinae \| Apini \| None \| Apis \| Apis \| Apis mellifera	kingdom \| phylum \| class \| order \| family \| subfamily \| tribe \| subtribe \| genus \| subgenus \| species

globalbioticinteractions / nomer