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Demonstrate using PyStow for API configuration #142

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Demonstrate using PyStow for API configuration #142

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3093da6
Update apikey_manager.py
cthoyt Jun 24, 2022
4172dfc
Update apikey_manager.py
cthoyt Jun 24, 2022
25f71a1
Cleanup and add docs
cthoyt Jun 24, 2022
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Documentation
cthoyt Jun 24, 2022
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Merge branch 'main' into pystow-config
cthoyt Jul 6, 2022
338a280
Update poetry.lock
cthoyt Jul 6, 2022
e45c215
Merge branch 'main' into pystow-config
cthoyt Jul 7, 2022
ea5978f
Update poetry.lock
cthoyt Jul 7, 2022
ec248c8
Merge branch 'main' into pystow-config
cthoyt Jul 25, 2022
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sdads
cthoyt Jul 25, 2022
4ca44f9
Update apikey_manager.py
cthoyt Jul 25, 2022
b94de6d
Update ontoportal_implementation_base.py
cthoyt Jul 25, 2022
b6ae167
Pass through bioportal config
cthoyt Jul 25, 2022
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Update ontoportal_implementation_base.py
cthoyt Jul 25, 2022
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Update ontoportal_implementation_base.py
cthoyt Jul 25, 2022
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4 changes: 4 additions & 0 deletions .github/workflows/main.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,8 @@ jobs:
#----------------------------------------------
- name: Run tests
run: poetry run python -m unittest discover
env:
BIOPORTAL_API_KEY: ${{ secrets.BIOPORTAL_API_KEY }}

#----------------------------------------------
# coverage report
Expand All @@ -93,6 +95,8 @@ jobs:
poetry run coverage run -m unittest discover
poetry run coverage xml
poetry run coverage report -m
env:
BIOPORTAL_API_KEY: ${{ secrets.BIOPORTAL_API_KEY }}

#----------------------------------------------
# upload coverage results
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10 changes: 10 additions & 0 deletions README.md
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Expand Up @@ -218,6 +218,16 @@ runoak -i obolibrary:go.obo viz GO:0005773

## Configuration

Configuration for an arbitrary `key` (e.g., `bioportal_api_token`)
can be set in the following ways:

1. Set `OAKLIB_<key>` in the environment
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I'm a little confused by this because it seems like just BIOPORTAL_API_KEY is the required when using an environment variable. I.e. this works:

BIOPORTAL_API_KEY=[redacted] runoak -i bioportal: search swim

As opposed to:

OAKLIB_BIOPORTAL_API_KEY=[redacted] runoak -i bioportal: search swim

2. Create a configuration file `~/.config/oaklib.ini`
and set the `[oaklib]` section in it with the given key-value pair like
`<key> = <value>`
3. Use the CLI command `runoak set-apikey <key> <value>` to automatically create
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When I tried running this:

runoak set-apikey -e bioportal [redacted]

(also, note the -e is required) I got this error:

Traceback (most recent call last):
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/bin/runoak", line 5, in <module>
    main()
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/Users/PAKalita/Work/ontology-access-kit/src/oaklib/cli.py", line 2220, in set_apikey
    set_apikey_value(endpoint, keyval)
  File "/Users/PAKalita/Work/ontology-access-kit/src/oaklib/utilities/apikey_manager.py", line 42, in set_apikey_value
    pystow.write_config(APP_NAME, key, value)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/pystow/config_api.py", line 135, in write_config
    cfp.set(module, key, value)
  File "/Users/PAKalita/.pyenv/versions/3.9.11/lib/python3.9/configparser.py", line 1204, in set
    super().set(section, option, value)
  File "/Users/PAKalita/.pyenv/versions/3.9.11/lib/python3.9/configparser.py", line 902, in set
    raise NoSectionError(section) from None
configparser.NoSectionError: No section: 'oaklib'

and populate the appropriate configuration file.

OAK uses [`pystow`](https://github.com/cthoyt/pystow) for caching. By default,
this goes inside `~/.data/`, but can be configured following
[these instructions](https://github.com/cthoyt/pystow#%EF%B8%8F%EF%B8%8F-configuration).
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