[ temp-query-deprecation-fix ⚙ .venv] ~/code/metakb % metakb update -r civic
Harvesting sources...
Harvesting CIViC...
(CIViCPy cache is also being updated)
Traceback (most recent call last):
File "/Users/jss009/code/metakb/.venv/bin/metakb", line 8, in <module>
sys.exit(cli())
^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/asyncclick/core.py", line 1205, in __call__
return anyio.run(self._main, main, args, kwargs, **opts)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/anyio/_core/_eventloop.py", line 74, in run
return async_backend.run(func, args, {}, backend_options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/anyio/_backends/_asyncio.py", line 2034, in run
return runner.run(wrapper())
^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/.pyenv/versions/3.12.2/lib/python3.12/asyncio/runners.py", line 118, in run
return self._loop.run_until_complete(task)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/.pyenv/versions/3.12.2/lib/python3.12/asyncio/base_events.py", line 685, in run_until_complete
return future.result()
^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/anyio/_backends/_asyncio.py", line 2022, in wrapper
return await func(*args)
^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/asyncclick/core.py", line 1208, in _main
return await main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/asyncclick/core.py", line 1120, in main
rv = await self.invoke(ctx)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/asyncclick/core.py", line 1739, in invoke
return await _process_result(await sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/asyncclick/core.py", line 1485, in invoke
return await ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/asyncclick/core.py", line 824, in invoke
rv = await rv
^^^^^^^^
File "/Users/jss009/code/metakb/src/metakb/cli.py", line 511, in update
_harvest_sources(sources, refresh_source_caches)
File "/Users/jss009/code/metakb/src/metakb/cli.py", line 576, in _harvest_sources
source = source_class(update_cache=True, update_from_remote=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/src/metakb/harvesters/civic.py", line 43, in __init__
civicpy.update_cache(from_remote_cache=update_from_remote)
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/civicpy/civic.py", line 269, in update_cache
genes = _get_elements_by_ids('gene', allow_cached=False, get_all=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/civicpy/civic.py", line 1203, in _get_elements_by_ids
response_elements = _request_all(element)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/jss009/code/metakb/.venv/lib/python3.12/site-packages/civicpy/civic.py", line 1300, in _request_all
response = resp.json()['data'][pluralize(element)]
~~~~~~~~~~~^^^^^^^^
KeyError: 'data'
this appears to be something about the schema that's fixed in civicpy 3.1.0, but because our dependency declaration is "civicpy~=3.0.0", we're not able to install it.
github-actions[bot]
commented
3 weeks ago
this appears to be something about the schema that's fixed in
civicpy3.1.0, but because our dependency declaration is "civicpy~=3.0.0", we're not able to install it.