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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 breaks due to HsapDv prefix not specified in source map #101

Closed caufieldjh closed 1 year ago

caufieldjh commented 1 year ago

On the most recent Jenkins build:

18:22:08  Adding edge sources using kg_phenio/transform_utils/phenio/phenio_edge_sources.yaml
18:22:08  [2023-03-09 14:22:03][INFO   ][koza.app] Transforming source: phenio_edge_sources
18:25:44  Traceback (most recent call last):
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/run.py", line 98, in <module>
18:25:44      cli()
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
18:25:44      return self.main(*args, **kwargs)
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1055, in main
18:25:44      rv = self.invoke(ctx)
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
18:25:44      return _process_result(sub_ctx.command.invoke(sub_ctx))
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
18:25:44      return ctx.invoke(self.callback, **ctx.params)
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
18:25:44      return __callback(*args, **kwargs)
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/run.py", line 73, in transform
18:25:44      kg_transform(*args, **kwargs)
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/kg_phenio/transform.py", line 35, in transform
18:25:44      t.run()
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/kg_phenio/transform_utils/phenio/phenio_transform.py", line 56, in run
18:25:44      self.parse(k, data_file, k)
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/kg_phenio/transform_utils/phenio/phenio_transform.py", line 139, in parse
18:25:44      transform_source(
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/koza/cli_runner.py", line 84, in transform_source
18:25:44      source_koza.process_sources()
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/venv/lib/python3.9/site-packages/koza/app.py", line 108, in process_sources
18:25:44      importlib.reload(transform_module)
18:25:44    File "/usr/lib/python3.9/importlib/__init__.py", line 169, in reload
18:25:44      _bootstrap._exec(spec, module)
18:25:44    File "<frozen importlib._bootstrap>", line 613, in _exec
18:25:44    File "<frozen importlib._bootstrap_external>", line 855, in exec_module
18:25:44    File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
18:25:44    File "/var/lib/jenkins/workspace/ledge-graph-hub_kg-phenio_master/gitrepo/kg_phenio/transform_utils/phenio/phenio_edge_sources.py", line 122, in <module>
18:25:44      infores = infores_sources[subj_curie_prefix]
18:25:44  KeyError: 'HsapDv'

The source map in the phenio_edge_sources doesn't contain this prefix, though it corresponds to the Human Developmental Stages ontology. Likely uncovered by removing an OBO prefix. May be others.