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Launch Interactive Concept Set Load Editor

Source: R/manifest_conceptSets.R
launchConceptSetsLoadEditor.Rd

Opens an interactive Shiny application for creating, viewing and editing the concept sets load metadata file (conceptSetsLoad.csv). This allows you to add, remove, and modify concept set metadata including labels, tags, domain, and ATLAS IDs without manually editing the CSV file.

Usage

launchConceptSetsLoadEditor(
  conceptSetsFolderPath = here::here("inputs/conceptSets")
)

Arguments

conceptSetsFolderPath

Character. Path to conceptSets folder where conceptSetsLoad.csv will be saved. Defaults to "inputs/conceptSets".

Value

Invisibly launches a Shiny app. Saves conceptSetsLoad.csv when the user user clicks "Save".

Details

Features:

  • View existing concept sets in a data table

  • Edit cells directly in the table

  • Add new concept sets rows with form inputs

  • Delete selected rows

  • Save to conceptSetsLoad.csv

  • Input validation for required fields

Table Columns:

  • atlasId: ATLAS cohort definition ID (numeric)

  • label: Cohort name/label (character) - editing updates file_name automatically

  • category: Broad category (character)

  • subCategory: Sub-category (character)

  • sourceCode: Whether this concept set represents source codes (TRUE/FALSE)

  • domain: OMOP domain (drug_exposure, condition_occurrence, measurement, procedure)

  • file_name: Auto-generated as json/{label}.json (read-only)

Workflow:

  1. Call this function to launch the editor app

  2. Add/edit concept sets as needed

  3. Click "Save Concept Set Load File" to save to inputs/conceptSets/conceptSetsLoad.csv

  4. Use importAtlasConceptSets() to import conceptSets from ATLAS

  5. Use loadConceptSetManifest() to load the imported conceptSets

Examples

if (FALSE) {
  # Launch the concept set load editor
  launchConceptSetsLoadEditor()
}