microbiomedata / iot_to_linkml

Convert Index of Terms to LinkML YAML

Convert Index of Terms to LinkML YAML.

Here's the active Index of Terms document that Mark and Montana are collaborating within. Some minor revisions might be coming based on the experiences of running it through this application.

High level to-dos:

• convert to actual LinkML artifacts after that
  • use gen-yaml for inference and expansion
• develop a general LinkML to DataHarmonizer template converter

Development or use within the repo requires Poetry

Usage within this environment

poetry run becli

Publishing

• Don't forget to update version in the [tool.poetry] section in pyproject.toml
• Some additional one-time edits may be required since this repo was just forked out of turbomam/badexperiment

Note the use of initial whitespace for keeping the PyPI password out of the zsh history. There are similar tricks for other shells like Bash.

setopt HIST_IGNORE_SPACE
export pypi_user='mamillerpa'
 export pypi_pw='<SECRET>'
poetry build
poetry publish --username $pypi_user --password $pypi_pw

pip-based installation inside of this repo

• Excessively aggressive cleanup?

# assume we're inside a venv virtual environment
deactivate
rm -rf venv
# purge under what circumstances?
python3.9 -m pip cache purge
python3.9 -m venv venv
source venv/bin/activate
python3.9 -m pip install --upgrade pip
pip install wheel
# check status of package under development
# don't continue with installation when
pip index versions iot_to_linkml
# installation of pandas is slow
#   platform dependent? M1 MBA
pip install iot_to_linkml

Usage outside of this repo

becli --help

Concerns

How to create, modify and save a LinkML schema?

• Preferably with schemaview
• Otherwise direct linkml methods
• Otherwise dict -> yaml file

Dev ops to-dos

Poetry autocomplete

Values trying to be set on a copy of a slice from a DataFrame

These error messages show paths from a previous repository, badexperiment. They have not been edited.

/Users/mark/sandbox/venv/lib/python3.9/site-packages/pandas/core/indexing.py:1667: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy self.obj[key] = value

/Users/mark/sandbox/venv/lib/python3.9/site-packages/badexperiment/sheet2yaml.py:119: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy slot_to_pack[coalesced] = slot_to_pack[repaired_col_name]

/Users/mark/sandbox/venv/lib/python3.9/site-packages/pandas/core/indexing.py:1732: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy self._setitem_single_block(indexer, value, name)