Spreadsheet to LinkML Schema

Overview

Create a yaml linkml model from set of spreadsheets. It can use either tsv files or Google Sheet as an input.

The default behavior is to run the converter starting with tsv files, specifying their paths as arguments, for example, model_spreadsheets/*tsv.

If --gsheet option is used, the converter starts from downloading spreadsheets from Google Sheets. The argument must be a YAML file that has gsheet_id and a list of sheets with gid (a unique identifier for each individual sheet) and name (optionally) that will be used as a name of the downloaded TSV file (if not available gid wil be used).

Command Line

`bkbit schema2model`

$ bkbit schema2model [OPTIONS] SPREADSHEETS

Options

-o, --output <output>
Path for the yaml output file.

-t, --template <template>
Optional template yaml file with standard classes that will be added to the model.

--gsheet, --no-gsheet
Using Google Sheet as a source. If True, the arguments MUST be a yaml file with gsheet_id and gid of all the sheets.

Default:
False

--gsheet-download-dir <gsheet_download_dir>
Path used to download Google Sheets. If not specified a default directory will be created.

--fix_tsv, --no-fix_tsv
Fixing known issues with tsv files from Google Sheets.

Default:
True

--fix_tsv_save, --no-fix_tsv_save
Keeping the fixed files, relevant only if fix_tsv is True

Default:
False

--repair, --no-repair
Standard Linkml auto-repair schema

Default:
True

--fix_bican_model, --no-fix_bican_model
Automated repair specifically for the BICAN YAML model

Default:
True

Arguments

SPREADSHEETS
Required argument

Examples

Example 1: Schema defined in tsv files

# Run schema2model command
$ bkbit schema2model -o model.yaml source_model/spreadsheets/*.tsv

Example 2: Schema defined in Google Sheets

# Run schema2model command
$ bkbit schema2model -o model.yaml  --gsheet --gsheet-download-dir source_model/spreadsheets  source_model/gsheet.yaml