sssom-py

sssom-py copied to clipboard

Create tool eco-system for validating SSSOM files

3

SSSOM files are beginning to be produced, but few are correctly formatted. We need to: 1. Roll out a simple UI on top fastapi app for validating sssom files 2....

matentzn

Relevant conversation: https://github.com/mapping-commons/sssom-py/pull/324#discussion_r1030443563 Reason for pinning: When updating linkml from v1.3.13 to v1.3.14, it gave an error which is being worked on as this issue is being created.

hrshdhgd

Warning: ``` sssom/util.py:895: DtypeWarning: Columns (5) have mixed types. Specify dtype option on import or set low_memory=False. ``` Solution: set `low_memory=False`

hrshdhgd

Simple OMOP concept relationship importer of mappings.

matentzn

Delete all validation files since they may be old

3

Fixes #317

hrshdhgd

Clean up tests/data/validation_data

1

There are quite a few JSON files in there which were from an ancient SSSOM version. We should 1. regenerate all the data in the tests/data/validation_data using the up-to-date sssom-py...

matentzn

New method: flip

2

@kevinscharper noted in https://github.com/monarch-initiative/monarch-ingest/issues/326 that if you are not careful and "blindly apply" a mapping file to a dataset, you may end up applying it the wrong way. For example,...

matentzn

Add GitHub action that refreshes external context

1

You can sync the bioregistry context like this: ``` make sssom/external_context.py -B ``` We should add a github action that does this and creates a pull request so we can...

matentzn

Lessons learnt from @cthoyt so far: - [ ] Ensured docstrings of all functions I touched are up to date - [ ] Checked that my coding aligns with the...

matentzn

Short parameters for SSSOM

1

This is the `short: long` list of CLI params - -c: --config - -C: --prefix-map-mode - -d: --output-directory - -D: --predicates - -e: --url - -E: --embedded-mode - -f: --fields...

hrshdhgd