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Knowledge-Graph-Hub / kg-idg

A Knowledge Graph to Illuminate the Druggable Genome
https://knowledge-graph-hub.github.io/kg-idg/
BSD 3-Clause "New" or "Revised" License
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Transforms fail due to `ImportError: cannot import name 'InformationResource' from 'biolink.model'` #129

Closed caufieldjh closed 1 year ago

caufieldjh commented 1 year ago

Describe the bug

During the drugcentral-reference transform:

[2023-05-30T18:44:50.728Z] [2023-05-30 11:44:46][INFO   ][koza.app] Transforming source: drugcentral-reference
[2023-05-30T18:44:50.728Z] Traceback (most recent call last):
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/run.py", line 167, in <module>
[2023-05-30T18:44:50.728Z]     cli()
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
[2023-05-30T18:44:50.728Z]     return self.main(*args, **kwargs)
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1055, in main
[2023-05-30T18:44:50.728Z]     rv = self.invoke(ctx)
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
[2023-05-30T18:44:50.728Z]     return _process_result(sub_ctx.command.invoke(sub_ctx))
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
[2023-05-30T18:44:50.728Z]     return ctx.invoke(self.callback, **ctx.params)
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
[2023-05-30T18:44:50.728Z]     return __callback(*args, **kwargs)
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/run.py", line 66, in transform
[2023-05-30T18:44:50.728Z]     kg_transform(*args, **kwargs)
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/transform.py", line 60, in transform
[2023-05-30T18:44:50.728Z]     t.run()
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/transform_utils/drug_central/drug_central.py", line 67, in run
[2023-05-30T18:44:50.728Z]     self.parse(name, data_file, k)
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/transform_utils/drug_central/drug_central.py", line 179, in parse
[2023-05-30T18:44:50.728Z]     transform_source(
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/koza/cli_runner.py", line 84, in transform_source
[2023-05-30T18:44:50.728Z]     source_koza.process_sources()
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/koza/app.py", line 105, in process_sources
[2023-05-30T18:44:50.728Z]     transform_module = importlib.import_module(transform_code)
[2023-05-30T18:44:50.728Z]   File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module
[2023-05-30T18:44:50.728Z]     return _bootstrap._gcd_import(name[level:], package, level)
[2023-05-30T18:44:50.728Z]   File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
[2023-05-30T18:44:50.728Z]   File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
[2023-05-30T18:44:50.728Z]   File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
[2023-05-30T18:44:50.728Z]   File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
[2023-05-30T18:44:50.728Z]   File "<frozen importlib._bootstrap_external>", line 855, in exec_module
[2023-05-30T18:44:50.728Z]   File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
[2023-05-30T18:44:50.728Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/transform_utils/drug_central/drugcentral-reference.py", line 4, in <module>
[2023-05-30T18:44:50.728Z]     from biolink.model import (  # type: ignore
[2023-05-30T18:44:50.728Z] ImportError: cannot import name 'InformationResource' from 'biolink.model' (/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/biolink/model.py)

This is with biolink-model 3.4.2. Sure enough, InformationResource is no longer a class in Biolink, but InformationContentEntity still is. Not sure why this just popped up today, though the last build used biolink-model 3.3.1.