Validate Usagi File

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

Usage

updateUsagiFile(
  pathToUsagiFile,
  connection,
  vocabularyDatabaseSchema,
  pathToUpdatedUsagiFile,
  updateLevelTibble = NULL,
  appendOrClearAutoUpdatingInfo = "append",
  skipValidation = TRUE,
  sourceConceptIdOffset = 0
)

Arguments

pathToUsagiFile

Path to the Usagi mapping file to validate

connection

A DatabaseConnector connection object

vocabularyDatabaseSchema

Schema name where the vocabulary tables are stored

pathToUpdatedUsagiFile

Path where to save the updated Usagi file

updateLevelTibble

Optional tibble defining relationship update rules. Default rules are:

• "Maps to" (level 1, no review needed)

• "Concept replaced by" (level 2, review needed)

• "Concept same_as to" (level 3, review needed)

• "Concept poss_eq to" (level 4, review needed)

appendOrClearAutoUpdatingInfo

Whether to append ("append") or clear ("clear") auto-updating info

skipValidation

Whether to skip validation checks if TRUE. Default is FALSE

sourceConceptIdOffset

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