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Knowledge-Graph-Hub / kg-phenio

A graph for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.
BSD 3-Clause "New" or "Revised" License
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Build fails due to `ModuleNotFoundError: No module named 'biolink'` #136

Closed caufieldjh closed 8 months ago

caufieldjh commented 8 months ago

Most recent build failed with:

18:02:05  Transforming to KGX TSV with config in transform.yaml...
18:02:05  [KGX][cli_utils.py][           transform] INFO: Spawning process for 'phenio-transform'
18:09:11  2024-03-06_15:09:08 | INFO     | koza.app         | Transforming source: phenio_node_sources
18:09:11  Adding node sources using kg_phenio/transform_utils/phenio/phenio_node_sources.yaml
18:09:11  Traceback (most recent call last):
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/run.py", line 100, in <module>
18:09:11      cli()
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
18:09:11      return self.main(*args, **kwargs)
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1078, in main
18:09:11      rv = self.invoke(ctx)
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
18:09:11      return _process_result(sub_ctx.command.invoke(sub_ctx))
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
18:09:11      return ctx.invoke(self.callback, **ctx.params)
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 783, in invoke
18:09:11      return __callback(*args, **kwargs)
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/run.py", line 75, in transform
18:09:11      kg_transform(*args, **kwargs)
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/kg_phenio/transform.py", line 36, in transform
18:09:11      t.run()
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/kg_phenio/transform_utils/phenio/phenio_transform.py", line 73, in run
18:09:11      self.parse(k, data_file, k)
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/kg_phenio/transform_utils/phenio/phenio_transform.py", line 181, in parse
18:09:11      transform_source(
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/koza/cli_runner.py", line 86, in transform_source
18:09:11      koza_app.process_sources()
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/koza/app.py", line 100, in process_sources
18:09:11      transform_module = importlib.import_module(transform_code)
18:09:11    File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module
18:09:11      return _bootstrap._gcd_import(name[level:], package, level)
18:09:11    File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
18:09:11    File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
18:09:11    File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
18:09:11    File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
18:09:11    File "<frozen importlib._bootstrap_external>", line 855, in exec_module
18:09:11    File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
18:09:11    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/kg_phenio/transform_utils/phenio/phenio_node_sources.py", line 125, in <module>
18:09:11      importlib.import_module("biolink.pydanticmodel_v2"), category_name
18:09:11    File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module
18:09:11      return _bootstrap._gcd_import(name[level:], package, level)
18:09:11    File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
18:09:11    File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
18:09:11    File "<frozen importlib._bootstrap>", line 972, in _find_and_load_unlocked
18:09:11    File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
18:09:11    File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
18:09:11    File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
18:09:11    File "<frozen importlib._bootstrap>", line 984, in _find_and_load_unlocked
18:09:11  ModuleNotFoundError: No module named 'biolink'

Did biolink change its module name? On my local system, with biolink-model==4.1.5, I can still import biolink without issue. The build installed biolink_model-4.1.6.