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Knowledge-Graph-Hub / kg-microbe

https://knowledge-graph-hub.github.io/kg-microbe/index.html
BSD 3-Clause "New" or "Revised" License
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Build fails due to chebi.owl not found #50

Closed caufieldjh closed 1 year ago

caufieldjh commented 1 year ago

Build currently fails at the transform step as follows:

13:20:08  + python3.8 run.py transform
13:20:11  org.semanticweb.owlapi.io.OWLOntologyInputSourceException: java.io.FileNotFoundException: data/raw/chebi.owl (No such file or directory)
13:20:11  Use the -vvv option to show the stack trace.
13:20:11  Use the --help option to see usage information.
13:20:14  Traceback (most recent call last):
13:20:14    File "run.py", line 121, in <module>
13:20:14      cli()
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
13:20:14      return self.main(*args, **kwargs)
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/click/core.py", line 1055, in main
13:20:14      rv = self.invoke(ctx)
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
13:20:14      return _process_result(sub_ctx.command.invoke(sub_ctx))
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
13:20:14      return ctx.invoke(self.callback, **ctx.params)
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/click/core.py", line 760, in invoke
13:20:14      return __callback(*args, **kwargs)
13:20:14    File "run.py", line 69, in transform
13:20:14      kg_transform(*args, **kwargs)
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/kg_microbe/transform.py", line 43, in transform
13:20:14      t.run()
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/kg_microbe/transform_utils/traits/traits.py", line 131, in run
13:20:14      create_termlist(self.input_base_dir, "chebi")
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/kg_microbe/utils/nlp_utils.py", line 109, in create_termlist
13:20:14      transform(
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/kgx/cli/cli_utils.py", line 560, in transform
13:20:14      transform_source(
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/kgx/cli/cli_utils.py", line 869, in transform_source
13:20:14      transformer.transform(input_args, output_args)
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/kgx/transformer.py", line 236, in transform
13:20:14      self.process(source_generator, intermediate_sink)
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/kgx/transformer.py", line 332, in process
13:20:14      for rec in source:
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/kgx/source/obograph_source.py", line 62, in parse
13:20:14      yield from chain(n, e)
13:20:14    File "/var/lib/jenkins/workspace/edge-graph-hub_kg-microbe_master/gitrepo/venv/lib/python3.8/site-packages/kgx/source/obograph_source.py", line 84, in read_nodes
13:20:14      FH = open(filename, "rb")
13:20:14  FileNotFoundError: [Errno 2] No such file or directory: 'data/raw/chebi.json'

chebi.json is missing because ROBOT doesn't complete its conversion, and it doesn't do that because it can't find chebi.owl. chebi.owl.gz is successfully downloaded, but the issue here is likely with the TraitsTransform - the CHEBI transform knows it has to work with a compressed version but the TraitsTransform expects to have chebi.json ready to use.