Orphanet transform fails due to missing ExternalReference

[caufieldjh]

Describe the bug

On the most recent KG build, the transform stage fails due to an issue in the Orphanet transform.

Stack trace:

[2024-01-01T18:36:11.453Z] [2024-01-01 10:36:11][INFO   ][root    ] Parsing OrphanetTransform
[2024-01-01T18:36:37.854Z] Parsing data/raw/orphanet_gene.xml to JSON...
[2024-01-01T18:36:37.854Z] Transforming using source in kg_idg/transform_utils/orphanet/orphanet_gene.yaml
[2024-01-01T18:36:37.854Z] [2024-01-01 10:36:35][INFO   ][koza.app] Transforming source: orphanet_gene
[2024-01-01T18:36:41.976Z] Traceback (most recent call last):
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/run.py", line 167, in <module>
[2024-01-01T18:36:41.976Z]     cli()
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
[2024-01-01T18:36:41.976Z]     return self.main(*args, **kwargs)
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1078, in main
[2024-01-01T18:36:41.976Z]     rv = self.invoke(ctx)
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
[2024-01-01T18:36:41.976Z]     return _process_result(sub_ctx.command.invoke(sub_ctx))
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
[2024-01-01T18:36:41.976Z]     return ctx.invoke(self.callback, **ctx.params)
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 783, in invoke
[2024-01-01T18:36:41.976Z]     return __callback(*args, **kwargs)
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/run.py", line 66, in transform
[2024-01-01T18:36:41.976Z]     kg_transform(*args, **kwargs)
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/transform.py", line 60, in transform
[2024-01-01T18:36:41.976Z]     t.run()
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/transform_utils/orphanet/orphanet.py", line 49, in run
[2024-01-01T18:36:41.976Z]     self.parse(name, entry, name)
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/transform_utils/orphanet/orphanet.py", line 68, in parse
[2024-01-01T18:36:41.976Z]     transform_source(
[2024-01-01T18:36:41.976Z]   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
[2024-01-01T18:36:41.976Z]     source_koza.process_sources()
[2024-01-01T18:36:41.976Z]   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
[2024-01-01T18:36:41.976Z]     transform_module = importlib.import_module(transform_code)
[2024-01-01T18:36:41.976Z]   File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module
[2024-01-01T18:36:41.976Z]     return _bootstrap._gcd_import(name[level:], package, level)
[2024-01-01T18:36:41.976Z]   File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
[2024-01-01T18:36:41.976Z]   File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
[2024-01-01T18:36:41.976Z]   File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
[2024-01-01T18:36:41.976Z]   File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
[2024-01-01T18:36:41.976Z]   File "<frozen importlib._bootstrap_external>", line 855, in exec_module
[2024-01-01T18:36:41.976Z]   File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
[2024-01-01T18:36:41.976Z]   File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/transform_utils/orphanet/orphanet_gene.py", line 58, in <module>
[2024-01-01T18:36:41.976Z]     all_ex_refs = gene["Gene"]["ExternalReferenceList"]["ExternalReference"]
[2024-01-01T18:36:41.976Z] KeyError: 'ExternalReference'

For reference, the last working build goes like this for this transform:

[2023-12-01T18:36:10.185Z] [2023-12-01 10:36:09][INFO   ][root    ] Parsing OrphanetTransform
[2023-12-01T18:36:36.587Z] Parsing data/raw/orphanet_gene.xml to JSON...
[2023-12-01T18:36:36.587Z] Transforming using source in kg_idg/transform_utils/orphanet/orphanet_gene.yaml
[2023-12-01T18:36:36.587Z] [2023-12-01 10:36:33][INFO   ][koza.app] Transforming source: orphanet_gene
[2023-12-01T18:36:39.815Z] [2023-12-01 10:36:39][INFO   ][koza.io.reader.json_reader] Finished processing 3945 rows for orphanet_gene from file data/raw/orphanet_gene.json