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Website update tests failing with missing sssom module #71

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bgyori opened this issue Oct 20, 2021 · 1 comment · Fixed by #70
Closed

Website update tests failing with missing sssom module #71

bgyori opened this issue Oct 20, 2021 · 1 comment · Fixed by #70

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@bgyori
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bgyori commented Oct 20, 2021

See e.g., https://github.com/biopragmatics/biomappings/runs/3954820246?check_suite_focus=true

Building SSSOM export
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.9.7/x64/bin/biomappings", line 33, in <module>
    sys.exit(load_entry_point('biomappings', 'console_scripts', 'biomappings')())
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/runner/work/biomappings/biomappings/src/biomappings/cli.py", line 46, in update
    ctx.invoke(sssom)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/home/runner/work/biomappings/biomappings/src/biomappings/export_sssom.py", line 96, in sssom
    from sssom.parsers import from_sssom_dataframe
ModuleNotFoundError: No module named 'sssom'
@bgyori
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bgyori commented Oct 20, 2021

I added sssom as an extra dependency on #70 but now I get

Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.9.7/x64/bin/biomappings", line 33, in <module>
    sys.exit(load_entry_point('biomappings', 'console_scripts', 'biomappings')())
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/decorators.py", line 21, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/runner/work/biomappings/biomappings/src/biomappings/cli.py", line 46, in update
    ctx.invoke(sssom)
  File "/opt/hostedtoolcache/Python/3.9.7/x64/lib/python3.9/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/runner/work/biomappings/biomappings/src/biomappings/export_sssom.py", line 99, in sssom
    msdf = from_sssom_dataframe(df, prefix_map=prefix_map, meta=META)
TypeError: from_sssom_dataframe() got an unexpected keyword argument 'prefix_map'

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