Package maintenance

Author: azimov

R/DataMigrationManager.R

@@ -231,7 +231,7 @@ DataMigrationManager <- R6::R6Class(
         }
 
         for (i in 1:nrow(migrations)) {
-          migration <- migrations[i,]
+          migration <- migrations[i, ]
           if (isTRUE(migration$migrationOrder <= stopMigrationVersion)) {
             private$executeMigration(migration)
           }
@@ -261,10 +261,10 @@ DataMigrationManager <- R6::R6Class(
       # Load, render, translate and execute sql
       if (self$isPackage()) {
         sql <- SqlRender::loadRenderTranslateSql(file.path(self$migrationPath, migration$migrationFile),
-                                                 dbms = private$connectionDetails$dbms,
-                                                 database_schema = self$databaseSchema,
-                                                 table_prefix = self$tablePrefix,
-                                                 packageName = self$packageName
+          dbms = private$connectionDetails$dbms,
+          database_schema = self$databaseSchema,
+          table_prefix = self$tablePrefix,
+          packageName = self$packageName
         )
         private$connectionHandler$executeSql(sql)
       } else {
@@ -276,8 +276,8 @@ DataMigrationManager <- R6::R6Class(
           sql <- SqlRender::readSql(file.path(self$migrationPath, "sql_server", migration$migrationFile))
         }
         private$connectionHandler$executeSql(sql,
-                                             database_schema = self$databaseSchema,
-                                             table_prefix = self$tablePrefix
+          database_schema = self$databaseSchema,
+          table_prefix = self$tablePrefix
         )
       }
       private$logInfo("Saving migration: ", migration$migrationFile)
@@ -287,11 +287,11 @@ DataMigrationManager <- R6::R6Class(
         VALUES ('@migration_file', @order);
       "
       private$connectionHandler$executeSql(iSql,
-                                           database_schema = self$databaseSchema,
-                                           migration_file = migration$migrationFile,
-                                           table_prefix = self$tablePrefix,
-                                           migration = paste0(self$packageTablePrefix, "migration"),
-                                           order = migration$migrationOrder
+        database_schema = self$databaseSchema,
+        migration_file = migration$migrationFile,
+        table_prefix = self$tablePrefix,
+        migration = paste0(self$packageTablePrefix, "migration"),
+        order = migration$migrationOrder
       )
       private$logInfo("Migration complete ", migration$migrationFile)
     },
@@ -305,9 +305,9 @@ DataMigrationManager <- R6::R6Class(
       );"
 
       private$connectionHandler$executeSql(sql,
-                                           database_schema = self$databaseSchema,
-                                           table_prefix = self$tablePrefix,
-                                           migration = paste0(self$packageTablePrefix, "migration")
+        database_schema = self$databaseSchema,
+        table_prefix = self$tablePrefix,
+        migration = paste0(self$packageTablePrefix, "migration")
       )
       private$logInfo("Migrations table created")
     },
@@ -319,9 +319,9 @@ DataMigrationManager <- R6::R6Class(
       sql <- "
       SELECT migration_file, migration_order FROM @database_schema.@table_prefix@migration ORDER BY migration_order;"
       migrationsExecuted <- private$connectionHandler$queryDb(sql,
-                                                              database_schema = self$databaseSchema,
-                                                              migration = paste0(self$packageTablePrefix, "migration"),
-                                                              table_prefix = self$tablePrefix
+        database_schema = self$databaseSchema,
+        migration = paste0(self$packageTablePrefix, "migration"),
+        table_prefix = self$tablePrefix
       )
 
       return(migrationsExecuted)

R/DataModel.R

@@ -44,7 +44,7 @@ checkAndFixColumnNames <-
     expectedNames <- tableSpecs %>%
       dplyr::select("columnName") %>%
       dplyr::anti_join(dplyr::filter(optionalNames, !.data$columnName %in% observeredNames),
-                       by = "columnName"
+        by = "columnName"
       ) %>%
       dplyr::arrange("columnName") %>%
       dplyr::pull()
@@ -176,7 +176,7 @@ checkAndFixDuplicateRows <-
            specifications) {
     primaryKeys <- specifications %>%
       dplyr::filter(.data$tableName == !!tableName &
-                      tolower(.data$primaryKey) == "yes") %>%
+        tolower(.data$primaryKey) == "yes") %>%
       dplyr::select("columnName") %>%
       dplyr::pull()
     duplicatedRows <- duplicated(table[, primaryKeys])
@@ -189,7 +189,7 @@ checkAndFixDuplicateRows <-
           sum(duplicatedRows)
         )
       )
-      return(table[!duplicatedRows,])
+      return(table[!duplicatedRows, ])
     } else {
       return(table)
     }
@@ -215,7 +215,7 @@ appendNewRows <-
     if (nrow(data) > 0) {
       primaryKeys <- specifications %>%
         dplyr::filter(.data$tableName == !!tableName &
-                        tolower(.data$primaryKey) == "yes") %>%
+          tolower(.data$primaryKey) == "yes") %>%
         dplyr::select("columnName") %>%
         dplyr::pull()
       newData <- newData %>%
@@ -245,10 +245,11 @@ formatDouble <- function(x) {
 
 .truncateTable <- function(tableName, connection, schema, tablePrefix) {
   DatabaseConnector::renderTranslateExecuteSql(connection,
-                                               "TRUNCATE TABLE @schema.@table_prefix@table;",
-                                               table_prefix = tablePrefix,
-                                               schema = schema,
-                                               table = tableName)
+    "TRUNCATE TABLE @schema.@table_prefix@table;",
+    table_prefix = tablePrefix,
+    schema = schema,
+    table = tableName
+  )
   invisible(NULL)
 }
 
@@ -339,7 +340,6 @@ uploadResults <- function(connection = NULL,
   start <- Sys.time()
 
   if (purgeDataModel) {
-
     if (rlang::is_interactive()) {
       if (!.removeDataUserCheck()) {
         return(invisible(NULL))
@@ -349,10 +349,11 @@ uploadResults <- function(connection = NULL,
     ParallelLogger::logInfo("Removing all records for tables within specification")
 
     invisible(lapply(unique(specifications$tableName),
-                     .truncateTable,
-                     connection = connection,
-                     schema = schema,
-                     tablePrefix = tablePrefix))
+      .truncateTable,
+      connection = connection,
+      schema = schema,
+      tablePrefix = tablePrefix
+    ))
   }
 
   # Retrieve the databaseId from the cdmSourceFile if the file exists
@@ -388,7 +389,7 @@ uploadResults <- function(connection = NULL,
 
       primaryKey <- specifications %>%
         dplyr::filter(.data$tableName == !!tableName &
-                        tolower(.data$primaryKey) == "yes") %>%
+          tolower(.data$primaryKey) == "yes") %>%
         dplyr::select("columnName") %>%
         dplyr::pull()
 
@@ -404,7 +405,7 @@ uploadResults <- function(connection = NULL,
       if (purgeSiteDataBeforeUploading && "database_id" %in% primaryKey) {
         type <- specifications %>%
           dplyr::filter(.data$tableName == !!tableName &
-                          .data$columnName == "database_id") %>%
+            .data$columnName == "database_id") %>%
           dplyr::select("dataType") %>%
           dplyr::pull()
         # Remove the existing data for the databaseId
@@ -538,8 +539,8 @@ uploadResults <- function(connection = NULL,
           primaryKeyValuesInChunk <- unique(chunk[env$primaryKey])
           duplicates <-
             dplyr::inner_join(env$primaryKeyValuesInDb,
-                              primaryKeyValuesInChunk,
-                              by = env$primaryKey
+              primaryKeyValuesInChunk,
+              by = env$primaryKey
             )
 
           if (nrow(duplicates) != 0) {
@@ -570,7 +571,7 @@ uploadResults <- function(connection = NULL,
             # Remove duplicates we already dealt with:
             env$primaryKeyValuesInDb <-
               env$primaryKeyValuesInDb %>%
-                dplyr::anti_join(duplicates, by = env$primaryKey)
+              dplyr::anti_join(duplicates, by = env$primaryKey)
           }
         }
         if (nrow(chunk) == 0) {
@@ -626,7 +627,6 @@ uploadResults <- function(connection = NULL,
 #' @export
 deleteAllRowsForPrimaryKey <-
   function(connection, schema, tableName, keyValues) {
-
     createSqlStatement <- function(i) {
       sql <- paste0(
         "DELETE FROM ",
@@ -635,7 +635,7 @@ deleteAllRowsForPrimaryKey <-
         tableName,
         "\nWHERE ",
         paste(paste0(
-          colnames(keyValues), " = '", keyValues[i,], "'"
+          colnames(keyValues), " = '", keyValues[i, ], "'"
         ), collapse = " AND "),
         ";"
       )
@@ -676,7 +676,6 @@ deleteAllRowsForDatabaseId <-
            tableName,
            databaseId,
            idIsInt = TRUE) {
-
     sql <-
       "SELECT COUNT(*) FROM @schema.@table_name WHERE database_id IN (@database_id);"
 
@@ -711,9 +710,9 @@ deleteAllRowsForDatabaseId <-
         database_id = databaseId
       )
       DatabaseConnector::executeSql(connection,
-                                    sql,
-                                    progressBar = FALSE,
-                                    reportOverallTime = FALSE
+        sql,
+        progressBar = FALSE,
+        reportOverallTime = FALSE
       )
     }
   }