Closed justaddcoffee closed 3 years ago
Still failing, but a little further into the transform step (during the go-json transform):
12:50:01 Parsing data/raw/go-plus.json
12:50:01 [KGX][json_transformer.py][ parse] INFO: Parsing data/raw/go-plus.json
12:50:01 [KGX][json_transformer.py][ load_nodes] INFO: Loading 81389 nodes into networkx.MultiDiGraph
12:50:13 [KGX][json_transformer.py][ load_edges] INFO: Loading 170422 edges into networkx.MultiDiGraph
12:50:13 Traceback (most recent call last):
12:50:13 File "run.py", line 165, in <module>
12:50:13 cli()
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/click/core.py", line 829, in __call__
12:50:13 return self.main(*args, **kwargs)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/click/core.py", line 782, in main
12:50:13 rv = self.invoke(ctx)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
12:50:13 return _process_result(sub_ctx.command.invoke(sub_ctx))
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
12:50:13 return ctx.invoke(self.callback, **ctx.params)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/click/core.py", line 610, in invoke
12:50:13 return callback(*args, **kwargs)
12:50:13 File "run.py", line 64, in transform
12:50:13 kg_transform(*args, **kwargs)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/kg_covid_19/transform.py", line 62, in transform
12:50:13 t.run(ONTOLOGIES[source])
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/kg_covid_19/transform_utils/ontology/ontology_transform.py", line 36, in run
12:50:13 self.parse(k, data_file, k)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/kg_covid_19/transform_utils/ontology/ontology_transform.py", line 59, in parse
12:50:13 transformer.parse(data_file, compression=compression, provided_by=source)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/kgx/transformers/json_transformer.py", line 228, in parse
12:50:13 self.load(obj['graphs'][0])
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/kgx/transformers/json_transformer.py", line 80, in load
12:50:13 self.load_edges(obj['edges'])
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/kgx/transformers/json_transformer.py", line 108, in load_edges
12:50:13 self.load_edge(edge)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/kgx/transformers/json_transformer.py", line 296, in load_edge
12:50:13 element = self.toolkit.get_element(mapping)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/bmt/toolkit.py", line 369, in get_element
12:50:13 parsed_name = parse_name(name)
12:50:13 File "/var/lib/jenkins/workspace/_19_fix_pyshex_issue_run_jenkins/gitrepo/venv/lib/python3.7/site-packages/bmt/utils.py", line 123, in parse_name
12:50:13 if name.startswith("biolink"):
12:50:13 AttributeError: 'NoneType' object has no attribute 'startswith
@deepakunni3 thoughts?
This bug was fixed in KGX 0.2.4 but since KG-COVID-19 is relying on a fork of KGX, those changes never made it there. I'll patch the fork for now
Thanks @deepakunni3!
@deepakunni3 could you ping me after you've updated the forked KGX? (No rush on this though)
I updated the fork to use an earlier version of bmt which doesn't manifest that same issue.
At some point next week, lets ditch the fork completely and use a stable KGX version (this will require some rewrites to our merge YAML).
At some point next week, lets ditch the fork completely and use a stable KGX version (this will require some rewrites to our merge YAML).
Thanks @deepakunni3! Glad to help us move to the stable KGX version too
Fixes a build issue seemingly caused by problematic pyshex version 0.7.15 - I'm pinning this to 0.7.14 for now