koza

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Closes #132 and #134 This is a fairly large one. Several updates and changes, some needed in general, some to make it play more nicely with [cookiecutter for ingests](https://github.com/monarch-initiative/cookiecutter-monarch-ingest) -...

glass-ships

We could use `duckdb` for this. An example, as used in the cookiecutter-monarch-ingest: ```python from pathlib import Path import duckdb nodes_file = "output/{{ cookiecutter.__ingest_name }}_nodes.tsv" edges_file = "output/{{ cookiecutter.__ingest_name }}_edges.tsv"...

glass-ships

glass-ships

Source Config: Metadata - Revisit `DatasetDescription` fields

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Currently, the `metadata.yaml` file (properties defined in `koza/model/config/source_config.py`) is not being used in any way other than documentation, and has fields with misleading names relative to how they're being used:...

glass-ships

RE: https://github.com/monarch-initiative/monarch-ingest/issues/585 Koza will likely need some changes in preparation for being used in standalone ingests for the Monarch KG.

glass-ships

CSV Reader: Handle varying line lengths

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Currently varying line lengths will raise an exception and hard fail. We should probably make these warnings and report out which lines vary. Could also create a custom exception and...

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Curie Cleaner: Mappings should be in a yaml somewhere?

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https://github.com/monarch-initiative/koza/blob/c08b69bce43b339002e19b13ee7e987a1d715faf/src/koza/model/curie_cleaner.py#L6 @kevinschaper may have more insight

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Source: log filtered rows during _get_row()

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https://github.com/monarch-initiative/koza/blob/c08b69bce43b339002e19b13ee7e987a1d715faf/src/koza/model/source.py#L89

glass-ships

process maps in json or yaml as is; sane defaults for tsv maps

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Koza should be able to take a yaml or json file as a map and just make it available as a dictionary without any special configuration.

kshefchek

New command: Create a koza project?

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This may still be of use. Or could be made redundant by the current planned work on creating the monarch-ingest cookiecutter template.

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