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Append Usagi File to Source to Concept Map Table

appendUsagiFileToSTCMtable.Rd

Reads a Usagi mapping file and appends its contents to a Source to Concept Map table. The function supports both default and extended formats for both Usagi files and STCM tables.

Usage

appendUsagiFileToSTCMtable(
  vocabularyId,
  pathToUsagiFile,
  connection,
  vocabularyDatabaseSchema,
  sourceToConceptMapTable,
  includeConcepts = c("APPROVED", "UNCHECKED", "INVALID_TARGET"),
  includeMappings = c("APPROVED"),
  skipValidation = TRUE,
  sourceConceptIdOffset = 0
)

Arguments

vocabularyId

String with the vocabulary ID

pathToUsagiFile

Path to the Usagi file

connection

Database connection object

vocabularyDatabaseSchema

Schema name containing vocabulary tables

sourceToConceptMapTable

Name of source to concept map table

includeConcepts

Vector of mapping statuses to include. Must be subset of: "APPROVED", "UNCHECKED", "FLAGGED", "INEXACT", "INVALID_TARGET"

includeMappings

Vector of mapping statuses to include. Must be subset of: "APPROVED", "UNCHECKED", "FLAGGED", "INVALID_TARGET"

skipValidation

Whether to skip validation of the Usagi file (default: TRUE)

sourceConceptIdOffset

Offset to add to source concept IDs (default: 0)

Value

NULL invisibly. The function modifies the database table directly.

Details

Default STCM columns:

  • source_code, source_concept_id, source_vocabulary_id, source_code_description

  • target_concept_id, target_vocabulary_id, valid_start_date, valid_end_date

  • invalid_reason

Extended STCM columns (includes all default columns plus):

  • source_concept_class

  • source_domain

  • source_parents_concept_ids

Extended Usagi columns:

  • ADD_INFO:sourceConceptId

  • ADD_INFO:sourceConceptClass

  • ADD_INFO:sourceDomain

If formats don't match (e.g., extended Usagi with default STCM), the extended information will be ignored with a warning.