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* schema gen utility * setting ConnectionHandler self$snakeCaseToCamelCase * readr dependency
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| # ResultModelManager 0.0.1 | ||
| # ResultModelManager 0.1.1 | ||
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| Changes: | ||
| 1. Added snakeCaseToCamelCase parameter to public in connectionHandlers so it can be defined once if required | ||
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| 2. Added schema generator function that creates sql from csv files with table defs | ||
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| # ResultModelManager 0.1.0 | ||
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| Initial version |
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| # Copyright 2022 Observational Health Data Sciences and Informatics | ||
| # | ||
| # This file is part of CohortDiagnostics | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
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| .writeFieldDefinition <- function(field) { | ||
| field <- as.list(field) | ||
| str <- paste("\t", field$columnName, toupper(field$dataType)) | ||
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| if (field$primaryKey == "yes") { | ||
| str <- paste(str, "NOT NULL") | ||
| } | ||
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| str | ||
| } | ||
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| #' Schema generator | ||
| #' @description | ||
| #' Take a csv schema definition and create a basic sql script with it. | ||
| #' | ||
| #' @param csvFilepath Path to schema file. Csv file must have the columns: | ||
| #' "table_name", "colum_name", "data_type", "is_required", "primary_key" | ||
| #' Note - | ||
| #' @param sqlOutputPath File to write sql to. | ||
| #' @param overwrite Boolean - overwrite existing file? | ||
| #' @export | ||
| #' | ||
| #' @importFrom readr read_csv | ||
| #' @return | ||
| #' string containing the sql for the table | ||
| generateSqlSchema <- function(csvFilepath, | ||
| sqlOutputPath = NULL, | ||
| overwrite = FALSE) { | ||
| if (!is.null(sqlOutputPath) && (file.exists(sqlOutputPath) & !overwrite)) { | ||
| stop("Output file ", sqlOutputPath, "already exists. Set overwrite = TRUE to continue") | ||
| } | ||
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| checkmate::assertFileExists(csvFilepath) | ||
| schemaDefinition <- readr::read_csv(csvFilepath, show_col_types = FALSE) | ||
| colnames(schemaDefinition) <- SqlRender::snakeCaseToCamelCase(colnames(schemaDefinition)) | ||
| requiredFields <- c("tableName", "columnName", "dataType", "isRequired", "primaryKey") | ||
| checkmate::assertNames(colnames(schemaDefinition), must.include = requiredFields) | ||
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| tableSqlStr <- " | ||
| CREATE TABLE @database_schema.@table_prefix@table_name ( | ||
| @table_fields | ||
| ); | ||
| " | ||
| fullScript <- "" | ||
| defs <- "{DEFAULT @table_prefix = ''}\n" | ||
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| for (table in unique(schemaDefinition$tableName)) { | ||
| tableFields <- schemaDefinition[schemaDefinition$tableName == table, ] | ||
| fieldDefinitions <- apply(tableFields, 1, .writeFieldDefinition) | ||
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| primaryKeyFields <- tableFields[tableFields$primaryKey == "yes", ] | ||
| if (nrow(primaryKeyFields)) { | ||
| pkeyField <- paste0("\tPRIMARY KEY(", paste(primaryKeyFields$columnName, collapse = ","), ")") | ||
| fieldDefinitions <- c(fieldDefinitions, pkeyField) | ||
| } | ||
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| fieldDefinitions <- paste(fieldDefinitions, collapse = ",\n") | ||
| tableString <- SqlRender::render(tableSqlStr, | ||
| table_name = paste0("@", table), | ||
| table_fields = fieldDefinitions | ||
| ) | ||
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| tableDefStr <- paste0("{DEFAULT @", table, " = ", table, "}\n") | ||
| defs <- paste0(defs, tableDefStr) | ||
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| fullScript <- paste(fullScript, tableString) | ||
| } | ||
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| # Get fields for each table | ||
| lines <- paste(defs, fullScript) | ||
| if (!is.null(sqlOutputPath)) { | ||
| writeLines(lines, sqlOutputPath) | ||
| } | ||
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| lines | ||
| } |
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