Remove inclusion rule insert function

[anthonysena]

This function is not necessary as we can extract the inclusion rules names from a cohort definition set and we do not need to push this information to the database.

CohortGenerator/R/CohortStats.R

Lines 40 to 134 in e3efad6

	insertInclusionRuleNames <- function(connectionDetails = NULL,
	connection = NULL,
	cohortDefinitionSet,
	cohortDatabaseSchema,
	cohortInclusionTable = getCohortTableNames()$cohortInclusionTable) {
	# Parameter validation
	if (is.null(connection) && is.null(connectionDetails)) {
	stop("You must provide either a database connection or the connection details.")
	}
	checkmate::assertDataFrame(cohortDefinitionSet, min.rows = 1, col.names = "named")
	checkmate::assertNames(colnames(cohortDefinitionSet),
	must.include = c(
	"cohortId",
	"cohortName",
	"json"
	)
	)
	if (is.null(connection)) {
	connection <- DatabaseConnector::connect(connectionDetails)
	on.exit(DatabaseConnector::disconnect(connection))
	}
	tableList <- DatabaseConnector::getTableNames(connection, cohortDatabaseSchema)
	if (!toupper(cohortInclusionTable) %in% toupper(tableList)) {
	stop(paste0(cohortInclusionTable, " table not found in schema: ", cohortDatabaseSchema, ". Please make sure the table is created using the createCohortTables() function before calling this function."))
	}
	# Assemble the cohort inclusion rules
	# NOTE: This data frame must match the @cohort_inclusion_table
	# structure as defined in inst/sql/sql_server/CreateCohortTables.sql
	inclusionRules <- data.frame(
	cohortDefinitionId = bit64::integer64(),
	ruleSequence = integer(),
	name = character(),
	description = character()
	)
	# Remove any cohort definitions that do not include the JSON property
	cohortDefinitionSet <- cohortDefinitionSet[!(is.null(cohortDefinitionSet$json) | is.na(cohortDefinitionSet$json)), ]
	for (i in 1:nrow(cohortDefinitionSet)) {
	cohortDefinition <- RJSONIO::fromJSON(content = cohortDefinitionSet$json[i], digits = 23)
	if (!is.null(cohortDefinition$InclusionRules)) {
	nrOfRules <- length(cohortDefinition$InclusionRules)
	if (nrOfRules > 0) {
	for (j in 1:nrOfRules) {
	ruleName <- cohortDefinition$InclusionRules[[j]]$name
	ruleDescription <- cohortDefinition$InclusionRules[[j]]$description
	if (is.na(ruleName) || ruleName == "") {
	ruleName <- paste0("Unamed rule (Sequence ", j - 1, ")")
	}
	if (is.null(ruleDescription)) {
	ruleDescription <- ""
	}
	inclusionRules <- rbind(
	inclusionRules,
	data.frame(
	cohortDefinitionId = bit64::as.integer64(cohortDefinitionSet$cohortId[i]),
	ruleSequence = as.integer(j - 1),
	name = ruleName,
	description = ruleDescription
	)
	)
	}
	}
	}
	}
	# Remove any existing data to prevent duplication
	DatabaseConnector::renderTranslateExecuteSql(
	connection = connection,
	sql = "TRUNCATE TABLE @cohort_database_schema.@table;",
	progressBar = FALSE,
	reportOverallTime = FALSE,
	cohort_database_schema = cohortDatabaseSchema,
	table = cohortInclusionTable
	)
	# Insert the inclusion rules
	if (nrow(inclusionRules) > 0) {
	ParallelLogger::logInfo("Inserting inclusion rule names")
	DatabaseConnector::insertTable(
	connection = connection,
	databaseSchema = cohortDatabaseSchema,
	tableName = cohortInclusionTable,
	data = inclusionRules,
	dropTableIfExists = FALSE,
	createTable = FALSE,
	camelCaseToSnakeCase = TRUE
	)
	} else {
	warning("No inclusion rules found in the cohortDefinitionSet")
	}
	invisible(inclusionRules)
	}