In make_cat_maps, parsing an edgefile containing a biolink:related_to can lead to this error (in this case, from Bioportal-to-KGX):
Normalizing graph...
Found these graph files:['transformed/ontologies/RETO/RETO_8_edges.tsv', 'transformed/ontologies/RETO/RETO_8_nodes.tsv']
Retrieving entity names in transformed/ontologies/RETO/RETO_8_nodes.tsv...
Found 133441 unexpected identifiers.
Will normalize 82399 identifiers.
Wrote IRI maps to transformed/ontologies/RETO/update_id_maps.tsv.
Retrieving categories in transformed/ontologies/RETO/RETO_8_nodes.tsv...
Traceback (most recent call last):
File "/home/harry/BioPortal-to-KGX/run.py", line 138, in <module>
run()
File "/home/harry/.cache/pypoetry/virtualenvs/bioportal-to-kgx-BG6p1jeu-py3.9/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/home/harry/.cache/pypoetry/virtualenvs/bioportal-to-kgx-BG6p1jeu-py3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/harry/.cache/pypoetry/virtualenvs/bioportal-to-kgx-BG6p1jeu-py3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/harry/.cache/pypoetry/virtualenvs/bioportal-to-kgx-BG6p1jeu-py3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/harry/BioPortal-to-KGX/run.py", line 113, in run
transform_status = do_transforms(
File "/home/harry/BioPortal-to-KGX/bioportal_to_kgx/functions.py", line 339, in do_transforms
if not clean_and_normalize_graph(filepath=outdir,
File "/home/harry/.cache/pypoetry/virtualenvs/bioportal-to-kgx-BG6p1jeu-py3.9/lib/python3.9/site-packages/universalizer/norm.py", line 90, in clean_and_normalize_graph
remap_these_categories, remove_these_edges = make_cat_maps(
File "/home/harry/.cache/pypoetry/virtualenvs/bioportal-to-kgx-BG6p1jeu-py3.9/lib/python3.9/site-packages/universalizer/norm.py", line 322, in make_cat_maps
or (obj_node_id.split("/"))[-2] == "STY"
IndexError: list index out of range
This predicate is used frequently and often with object IDs which aren't the STY IRIs being checked for here, or even IRIs at all, so they fail.
Try a try.
In
make_cat_maps
, parsing an edgefile containing abiolink:related_to
can lead to this error (in this case, from Bioportal-to-KGX):This predicate is used frequently and often with object IDs which aren't the STY IRIs being checked for here, or even IRIs at all, so they fail. Try a try.