70 lines
2.7 KiB
R
70 lines
2.7 KiB
R
# Copyright 2017 Observational Health Data Sciences and Informatics
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#
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# This file is part of DDLGeneratr
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#' Parse Wiki files
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#'
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#' @description
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#' Parses all .md files in the specified location (or any subfolders), extracting definitions
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#' of the Common Data Model.
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#'
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#' @param mdFilesLocation Path to the root folder of the Wiki repository.
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#' @param output_file Path to where the output CSV file should be written.
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#' @importFrom utils write.csv
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#' @export
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parseWiki <- function(mdFilesLocation, output_file) {
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# mdFilesLocation <- "../CommonDataModel.wiki"
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files <- list.files(mdFilesLocation, pattern = ".*\\.md", recursive = TRUE, full.names = TRUE)
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file <- files[18]
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parseTableRow <- function(row) {
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cells <- stringr::str_trim(stringr::str_split(row, "\\|")[[1]])
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if (substr(row, 1, 1) == "|") {
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cells <- cells[2:5]
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}
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return(data.frame(field = tolower(cells[1]),
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required = cells[2],
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type = toupper(cells[3]),
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description = cells[4]))
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}
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parseMdFile <- function(file) {
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text <- readChar(file, file.info(file)$size)
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lines <- stringr::str_split(text, "\n")[[1]]
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lines <- stringr::str_trim(lines)
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tableStart <- grep("\\s*field\\s*\\|\\s*required\\s*\\|\\s*type\\s*\\|\\s*description\\s*", tolower(lines))
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if (length(tableStart) > 1)
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stop("More than one table definition found in ", file)
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if (length(tableStart) == 1) {
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tableName <- basename(file)
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tableName <- tolower(stringr::str_sub(tableName, 1, -4))
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writeLines(paste("Parsing table", tableName))
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tableStart <- tableStart + 2
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tableEnd <- c(which(lines == ""), length(lines) + 1)
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tableEnd <- min(tableEnd[tableEnd > tableStart]) - 1
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tableDefinition <- lapply(lines[tableStart:tableEnd], parseTableRow)
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tableDefinition <- do.call(rbind, tableDefinition)
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tableDefinition$table <- tableName
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return(tableDefinition)
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} else {
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return(NULL)
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}
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}
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tableDefinitions <- lapply(files, parseMdFile)
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tableDefinitions <- do.call(rbind, tableDefinitions)
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write.csv(tableDefinitions, output_file, row.names = FALSE)
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}
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