poetry run ingest closure
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/workspace/all-ingests/.cache/pypoetry/virtualenvs/monarch-ingest-kct3006u-py3.8/lib/python3.8/site-packages/typer/main.py", line 214, in __call__
return get_command(self)(*args, **kwargs)
File "/tmp/workspace/all-ingests/.cache/pypoetry/virtualenvs/monarch-ingest-kct3006u-py3.8/lib/python3.8/site-packages/click/core.py", line 1128, in __call__
return self.main(*args, **kwargs)
File "/tmp/workspace/all-ingests/.cache/pypoetry/virtualenvs/monarch-ingest-kct3006u-py3.8/lib/python3.8/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/tmp/workspace/all-ingests/.cache/pypoetry/virtualenvs/monarch-ingest-kct3006u-py3.8/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/tmp/workspace/all-ingests/.cache/pypoetry/virtualenvs/monarch-ingest-kct3006u-py3.8/lib/python3.8/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/tmp/workspace/all-ingests/.cache/pypoetry/virtualenvs/monarch-ingest-kct3006u-py3.8/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/tmp/workspace/all-ingests/.cache/pypoetry/virtualenvs/monarch-ingest-kct3006u-py3.8/lib/python3.8/site-packages/typer/main.py", line 500, in wrapper
return callback(**use_params) # type: ignore
File "/tmp/workspace/all-ingests/monarch_ingest/main.py", line 102, in closure
apply_closure()
File "/tmp/workspace/all-ingests/monarch_ingest/cli_utils.py", line 214, in apply_closure
add_closure(node_file=f"{name}_nodes.tsv",
File "/tmp/workspace/all-ingests/.cache/pypoetry/virtualenvs/monarch-ingest-kct3006u-py3.8/lib/python3.8/site-packages/closurizer/closurizer.py", line 83, in add_closure
cur.execute(f"""
sqlite3.OperationalError: near "from": syntax error
Generating closure KG...
node_file: monarch-kg_nodes.tsv
edge_file: monarch-kg_edges.tsv
kg_archive: monarch-kg.tar.gz
closure_file: data/phenio/phenio-relations-non-redundant.tsv
fields: subject,object
output_file: monarch-kg-with-closure_edges.tsv
This looks like an sqlite error, but it's likely about files not being unpacked from the tar.gz into the right place. We should review from the top level how we handle the tarball that comes out of cat merge vs the individual node and edge files that we need in the steps that happen after - then we can make the tar archive just before releasing
Closurizer is currently failing in Jenkins with
This looks like an sqlite error, but it's likely about files not being unpacked from the tar.gz into the right place. We should review from the top level how we handle the tarball that comes out of cat merge vs the individual node and edge files that we need in the steps that happen after - then we can make the tar archive just before releasing