When updating graph files (here, with Bioportal OPDRE):
Found 59 unexpected identifiers.
Retrieving categories in transformed/ontologies/OPDRE/OPDRE_1_nodes.tsv...
All categories in transformed/ontologies/OPDRE/OPDRE_1_nodes.tsv are as expected.
No identifiers in transformed/ontologies/OPDRE/OPDRE_1_nodes.tsv will be normalized.
Updating graph files...
Could not remap any node IDs.
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 159, in clean_and_normalize_graph
if rem_edge_count > 0:
UnboundLocalError: local variable 'rem_edge_count' referenced before assignment
This is a case where we're trying to update the edgefile by removing edges now treated as node properties, but we haven't defined the list yet.
When updating graph files (here, with Bioportal OPDRE):
This is a case where we're trying to update the edgefile by removing edges now treated as node properties, but we haven't defined the list yet.