Added Wiki file parser

DDLGeneratr/DESCRIPTION

@@ -11,7 +11,8 @@ LazyData: true
 VignetteBuilder: knitr
 Imports: 
   SqlRender, 
-  rmarkdown
+  rmarkdown,
+  stringr
 NeedsCompilation: no
 RoxygenNote: 6.0.1
 

DDLGeneratr/NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(parseWiki)
 export(writeConstraints)
 export(writeDDL)
 export(writeIndex)
-export(writePDF)

DDLGeneratr/R/WikiParser.R

@@ -0,0 +1,69 @@
+# Copyright 2017 Observational Health Data Sciences and Informatics
+#
+# This file is part of DDLGeneratr
+#
+# 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.
+
+
+#' Parse Wiki files
+#'
+#' @description
+#' Parses all .md files in the specified location (or any subfolders), extracting definitions
+#' of the Common Data Model.
+#'
+#' @param mdFilesLocation Path to the root folder of the Wiki repository.
+#'
+#' @return
+#' A data frame with the table definitions culled from the Wiki files.
+#'
+#' @export
+parseWiki <- function(mdFilesLocation) {
+  # mdFilesLocation <- "../../CommonDataModel.wiki"
+  files <- list.files(mdFilesLocation, pattern = ".*\\.md", recursive = TRUE, full.names = TRUE)
+  file <- files[10]
+  parseTableRow <- function(row) {
+    cells <- stringr::str_trim(stringr::str_split(row, "\\|")[[1]])
+    cells <- cells[2:5]
+    return(data.frame(field = tolower(cells[1]),
+                      required = cells[2],
+                      type = toupper(cells[3]),
+                      description = cells[4]))
+  }
+
+  parseMdFile <- function(file) {
+    text <- readChar(file, file.info(file)$size)
+    lines <- stringr::str_split(text, "\n")[[1]]
+    lines <- stringr::str_trim(lines)
+    tableStart <- grep("\\s*field\\s*\\|\\s*required\\s*\\|\\s*type\\s*\\|\\s*description\\s*", tolower(lines))
+    if (length(tableStart) > 1)
+      stop("More than one table definition found in ", file)
+
+    if (length(tableStart) == 1) {
+      tableName <- basename(file)
+      tableName <- tolower(stringr::str_sub(tableName, 1, -4))
+      writeLines(paste("Parsing table", tableName))
+      tableStart <- tableStart + 2
+      tableEnd <- which(lines == "")
+      tableEnd <- min(tableEnd[tableEnd > tableStart]) - 1
+      tableDefinition <- lapply(lines[tableStart:tableEnd], parseTableRow)
+      tableDefinition <- do.call(rbind, tableDefinition)
+      tableDefinition$table <- tableName
+      return(tableDefinition)
+    } else {
+      return(NULL)
+    }
+  }
+  tableDefinitions <- lapply(files, parseMdFile)
+  tableDefinitions <- do.call(rbind, tableDefinitions)
+
+}

DDLGeneratr/man/parseWiki.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/WikiParser.R
+\name{parseWiki}
+\alias{parseWiki}
+\title{Parse Wiki files}
+\usage{
+parseWiki(mdFilesLocation)
+}
+\arguments{
+\item{mdFilesLocation}{Path to the root folder of the Wiki repository.}
+}
+\value{
+A data frame with the table definitions culled from the Wiki files.
+}
+\description{
+Parses all .md files in the specified location (or any subfolders), extracting definitions
+of the Common Data Model.
+}

DDLGeneratr/man/writePDF.Rd

@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writePDF.R
-\name{writePDF}
-\alias{writePDF}
-\title{Write PDF of CDM documentation}
-\usage{
-writePDF(mdFilesLocation, cdmVersion)
-}
-\arguments{
-\item{mdFilesLocation}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
-
-\item{cdmVersion}{The version of the OMOP Common Data Model for which the pdf document is being written. It should be written without a decimal so v5.3 becomes v5_3}
-}
-\description{
-Write PDF of CDM documentation
-}