Upload Vocabulary Folder to CDM Tables

Uploads all vocabulary files from a folder to the CDM tables. This includes:

• Adding vocabularies to the VOCABULARY table

• Adding concept classes to the CONCEPT_CLASS table

• Adding mappings to the Source to Concept Map table

• Creating corresponding CONCEPT entries

Usage

vocabularyFolderToSTCMVocabularyConcepClassTables(
  pathToVocabularyFolder,
  connection,
  vocabularyDatabaseSchema,
  sourceToConceptMapTable,
  skipValidation = TRUE,
  pathToValidatedUsagiFolder = NULL
)

Arguments

pathToVocabularyFolder

Path to folder containing vocabulary files

connection

A DatabaseConnector connection object

vocabularyDatabaseSchema

Schema name where the vocabulary tables are stored

sourceToConceptMapTable

Name of the source to concept map table

skipValidation

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

pathToValidatedUsagiFolder

Path where validated Usagi files will be saved if validation is performed

Value

NULL invisibly. The function modifies the database tables directly.

Details

The vocabulary folder must contain:

• vocabularies.csv: A file describing the vocabularies with columns:

  • source_vocabulary_id

  • source_vocabulary_name

  • source_concept_id_offset

  • path_to_usagi_file

  • path_to_news_file

  • ignore

• Usagi mapping files as referenced in vocabularies.csv

• NEWS files containing version information as referenced in vocabularies.csv