Update documentation and remove specific software packages and internal data models (#385)

* Start removing gaiaCore and gaiaDB

* Add LOCATION_HISTORY and EXTERNAL_EXPOSURE DDLs

* Reference work products

* Remove gaiaCore R Package holdovers

* Reorganize documentation

* Incorporate Andrew edits pt 1

* Incorporate remaining Andrew edits

Fixes 377 
Fixes 378 
Fixes 379 
Fixes 380
Fixes 381 
Fixes 382 
Fixes 383

Author: kzollove

.Rbuildignore

@@ -6,4 +6,6 @@
 inst/doc
 inst/config.yml
 errorReportSql.txt
-examples/
+examples/
+env/
+scratch*

.gitignore

@@ -0,0 +1,215 @@
+# Copyright 2019 Observational Health Data Sciences and Informatics
+#
+# This file is part of CdmDdlBase
+#
+# 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.
+
+#' Create the OHDSI-SQL Common Data Model DDL code
+#'
+#' The createDdl, createForeignKeys, and createPrimaryKeys functions each return a character string
+#' containing their respective DDL SQL code in OHDSQL dialect for a specific CDM version.
+#' The SQL they generate needs to be rendered and translated before it can be executed.
+#'
+#' The DDL SQL code is created from a two csv files that detail the OMOP CDM Specifications.
+#' These files also form the basis of the CDM documentation and the Data Quality
+#' Dashboard.
+#'
+#' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
+#' @return A character string containing the OHDSQL DDL
+#' @importFrom utils read.csv
+#' @export
+#' @examples
+#'\dontrun{
+#' ddl <- createDdl("5.4")
+#' pk <- createPrimaryKeys("5.4")
+#' fk <- createForeignKeys("5.4")
+#'}
+createDdl <- function(cdmVersion){
+  # prevent check NOTE from occurring due to non-standard evaluation of variables
+  cdmTableName <- cdmFieldName <- isRequired <- cdmDatatype <- NULL
+
+  # argument checks
+  stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
+
+  # cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+  # cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+  cdmTableCsvLoc <- "./inst/csv/Gaia_Table_Level.csv"
+  cdmFieldCsvLoc <- "./inst/csv/Gaia_Field_Level.csv"
+  
+  tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)
+  cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
+
+  tableList <- tableSpecs$cdmTableName
+
+  sql_result <- c()
+  sql_result <- c(paste0("--@targetDialect CDM DDL Specification for OMOP Common Data Model ", cdmVersion))
+  for (tableName in tableList){
+    fields <- subset(cdmSpecs, cdmTableName == tableName)
+    fieldNames <- fields$cdmFieldName
+
+    if ('person_id' %in% fieldNames){
+      query <- "\n\n--HINT DISTRIBUTE ON KEY (person_id)\n"
+    } else {
+      query <- "\n\n--HINT DISTRIBUTE ON RANDOM\n"
+    }
+
+    sql_result <- c(sql_result, query, paste0("CREATE TABLE @cdmDatabaseSchema.", tableName, " ("))
+
+    n_fields <- length(fieldNames)
+    for(fieldName in fieldNames) {
+
+      if (subset(fields, cdmFieldName == fieldName, isRequired) == "Yes") {
+        nullable_sql <- (" NOT NULL")
+      } else {
+        nullable_sql <- (" NULL")
+      }
+
+      if (fieldName == fieldNames[[n_fields]]) {
+        closing_sql <- (" );")
+      } else {
+        closing_sql <- (",")
+      }
+
+      if (fieldName=="offset") {
+        field <- paste0('"',fieldName,'"')
+      } else {
+        field <- fieldName
+      }
+      fieldSql <- paste0("\n\t\t\t",
+                         field," ",
+                         subset(fields, cdmFieldName == fieldName, cdmDatatype),
+                         nullable_sql,
+                         closing_sql)
+      sql_result <- c(sql_result, fieldSql)
+    }
+    sql_result <- c(sql_result, "")
+  }
+  return(paste0(sql_result, collapse = ""))
+}
+
+
+#' @describeIn createDdl createPrimaryKeys Returns a string containing the OHDSQL for creation of primary keys in the OMOP CDM.
+#' @return A string containing the OHDSQL for creation of primary keys in the OMOP CDM.
+#' @export
+createPrimaryKeys <- function(cdmVersion){
+  # prevent check NOTE from occurring due to non-standard evaluation of variables
+  isPrimaryKey <- cdmFieldName <- NULL
+
+  # argument checks
+  stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
+
+  # cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+  cdmFieldCsvLoc <- "./inst/csv/Gaia_Field_Level.csv"
+  cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
+
+  primaryKeys <- subset(cdmSpecs, isPrimaryKey == "Yes")
+  pkFields <- primaryKeys$cdmFieldName
+
+  sql_result <- c(paste0("--@targetDialect CDM Primary Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
+  for (pkField in pkFields){
+
+    subquery <- subset(primaryKeys, cdmFieldName==pkField)
+
+    sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT xpk_", subquery$cdmTableName, " PRIMARY KEY NONCLUSTERED (", subquery$cdmFieldName , ");\n"))
+
+  }
+  return(paste0(sql_result, collapse = ""))
+}
+
+#' @describeIn createDdl createForeignKeys Returns a string containing the OHDSQL for creation of foreign keys in the OMOP CDM.
+#' @return A string containing the OHDSQL for creation of foreign keys in the OMOP CDM.
+#' @export
+createForeignKeys <- function(cdmVersion){
+  # prevent check NOTE from occurring due to non-standard evaluation of variables
+  isForeignKey <- NULL
+
+  # argument checks
+  stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
+
+  # cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+  cdmFieldCsvLoc <- "./inst/csv/Gaia_Field_Level.csv"
+  cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
+
+  foreignKeys <- subset(cdmSpecs, isForeignKey == "Yes")
+  foreignKeys$key <- paste0(foreignKeys$cdmTableName, "_", foreignKeys$cdmFieldName)
+
+  sql_result <- c(paste0("--@targetDialect CDM Foreign Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
+  for (foreignKey in foreignKeys$key){
+
+    subquery <- subset(foreignKeys, foreignKeys$key==foreignKey)
+
+    sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT fpk_", subquery$cdmTableName, "_", subquery$cdmFieldName, " FOREIGN KEY (", subquery$cdmFieldName , ") REFERENCES @cdmDatabaseSchema.", subquery$fkTableName, " (", subquery$fkFieldName, ");\n"))
+
+  }
+  return(paste0(sql_result, collapse = ""))
+}
+
+
+
+# A helper function that will return a character string with the omop ascii art given a major and minor cdm version
+# example: cat(createAsciiHeader(5, 3))
+createAsciiHeader <- function(major, minor) {
+
+  stopifnot(is.numeric(major), is.numeric(minor), length(major) == 1, length(minor) == 1)
+  stopifnot(major %in% 0:99, minor %in% 0:99)
+
+  # An inner function that returns an ascii art matrix for any number between 0 and 99
+  numberMatrix <- function(num){
+    stopifnot(is.numeric(num), num %in% 0:99)
+
+    # An inner function that returns a 7x7 matrix of number ascii art for the number 0 through 9
+    # for the number 1 a 7x5 matrix is returned because 1 is narrower than other numbers.
+    singleDigit <- function(num) {
+      nums <- c('  ###     #    #####  ##### #      ####### ##### ####### #####  #####  #   #   ##   #     ##     ##    # #      #     ##    # #     ##     ##     # # #         #      ##    # #      #          #  #     ##     ##     #   #    #####  ##### #    # ###### ######    #    #####  #######     #   #   #            ########      ##     #  #    #     #      # #   #    #   #      #     #     # #     ##     #  #    #     ##     #  ###   ##### ####### #####      #  #####  #####   #     #####  ##### ')
+      numsMatrix <- matrix(data = strsplit(nums, character(0))[[1]], nrow = 7, byrow = T)
+      cols <- seq(num*7+1, num*7+7, by = 1)
+      out <- numsMatrix[1:7, cols]
+      # the number 1 is narrower than the other numbers
+      if(num == 1) out<- out[1:7, 2:6]
+      out
+    }
+
+    if(num < 10){
+      return(singleDigit(num))
+    } else {
+      space <- matrix(rep(" ", 7), nrow = 7)
+      return(cbind(singleDigit(floor(num/10)), space, singleDigit(num %% 10)))
+    }
+  }
+
+  omop <- c('.
+  ####### #     # ####### ######      #####  ######  #     #          .
+  #     # ##   ## #     # #     #    #     # #     # ##   ##    #    #.
+  #     # # # # # #     # #     #    #       #     # # # # #    #    #.
+  #     # #  #  # #     # ######     #       #     # #  #  #    #    #.
+  #     # #     # #     # #          #       #     # #     #    #    #.
+  #     # #     # #     # #          #     # #     # #     #     #  # .
+  ####### #     # ####### #           #####  ######  #     #      ##  ')
+
+  # convert to matrix and remove first column
+  omop <- matrix(strsplit(omop, character(0))[[1]], nrow = 7, byrow = TRUE)
+  omop <- omop[,c(-1, -2)]
+
+  dot <- matrix(c(rep(" ", 3*4), rep("#", 3*3)), nrow = 7, byrow = TRUE)
+  space <- matrix(rep(" ", 7), nrow = 7)
+  newline <- matrix(rep("\n", 7, nrow = 7))
+
+
+  header <- character(0)
+  headerMatrix <- cbind(omop, space, numberMatrix(major), space, dot, space, numberMatrix(minor), newline)
+  for(i in 1:7) {
+    header <- c(header, as.character(headerMatrix[i,]))
+  }
+  header <- paste(header, collapse = "")
+  return(header)
+}