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Validate Usagi File

validateUsagiFile.Rd

Reads a usagi file given in 'pathToUsagiFile' and performs the following checks: Default Usagi columns:

  • Check if all default Usagi columns are present:

  • Check if sourceCode and conceptId are unique

  • Check if sourceCode is not empty

  • Check if sourceName is not empty

  • Check if sourceName is less than 255 characters If usagi file has C&CR columns:

  • Check if concept_id is not 0 for APPROVED mappingStatus

  • Check codes with mapping to more than one domain are mapped to compatible domains

  • Check if sourceValidStartDate is before sourceValidEndDate

  • Check if ADD_INFO:sourceParents is a valid concept code in the ADD_INFO:sourceParentVocabulary If usagi file has the ADD_INFO:sourceName_fi column:

  • Check if sourceName_fi is less than 1000 characters

  • Check if sourceName_fi is the same for all the rows of a sourceConceptId

Usage

validateUsagiFile(
  pathToUsagiFile,
  connection,
  vocabularyDatabaseSchema,
  pathToValidatedUsagiFile,
  sourceConceptIdOffset
)

Arguments

pathToUsagiFile

Path to the Usagi mapping file to validate

connection

A DatabaseConnector connection object

vocabularyDatabaseSchema

Schema name where the vocabulary tables are stored

pathToValidatedUsagiFile

Path where to save the validated Usagi file

sourceConceptIdOffset

Integer offset to add to source concept IDs. Default is 0