fix: do not include n/a clinvar ids in mappings

[korikuzma]

close #205

[korikuzma]

@susannasiebert and @acoffman

I tried updating the test cache by using the staging API URL, but getting:

╰─$ civicpy update --hard    
WARNING:root:Getting all molecular_profiles. This may take a couple of minutes...
WARNING:root:Getting all genes. This may take a couple of minutes...
WARNING:root:Getting all factors. This may take a couple of minutes...
WARNING:root:Getting all fusions. This may take a couple of minutes...
WARNING:root:Getting all variants. This may take a couple of minutes...
Traceback (most recent call last):
  File "civicpy/.venv/bin/civicpy", line 10, in <module>
    sys.exit(cli())
             ^^^^^
  File "civicpy/.venv/lib/python3.12/site-packages/click/core.py", line 1485, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "civicpy/.venv/lib/python3.12/site-packages/click/core.py", line 1406, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "civicpy/.venv/lib/python3.12/site-packages/click/core.py", line 1873, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "civicpy/.venv/lib/python3.12/site-packages/click/core.py", line 1269, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "civicpy/.venv/lib/python3.12/site-packages/click/core.py", line 824, in invoke
    return callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "civicpy/civicpy/cli.py", line 44, in update
    civic.update_cache(from_remote_cache=soft, local_cache_path=cache_save_path)
  File "civicpy/civicpy/civic.py", line 264, in update_cache
    variants = _get_elements_by_ids("variant", allow_cached=False, get_all=True)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "civicpy/civicpy/civic.py", line 1986, in _get_elements_by_ids
    e = _postprocess_response_element(e, element)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "civicpy/civicpy/civic.py", line 2088, in _postprocess_response_element
    raise Exception("Variant type {} not supported yet".format(e["__typename"]))
Exception: Variant type RegionVariant not supported yet

I tried doing a small workaround in 008ce6b to try to ignore region variants.

[susannasiebert]

If you base your PR off of #204 it should work. However, that would then require this PR to wait to be merged until the above is merged which is currently blocked by region variants going live. We expect regions to go live later this week so maybe that short of a wait is acceptable.

[susannasiebert]

#204 also resolves the test failures you are seeing which are caused by newer versions of pandas reading in empty fields as numpy NaNs instead of None. #204 updates the dependencies to requires an older version of pandas to prevent this issue from occurring.

[korikuzma]

If you base your PR off of #204 it should work. However, that would then require this PR to wait to be merged until the above is merged which is currently blocked by region variants going live. We expect regions to go live later this week so maybe that short of a wait is acceptable.

Oh perfect! I will convert this to a draft and wait until #204 is merged (didn't think to check open PRs, duh).

[susannasiebert]

@korikuzma I merged in the regions PR and merged main into this PR. So I think it is ready to be reviewed, correct?

[susannasiebert]

+1