Merge pull request #58 from OHDSI/develop

Release 0.5.9

Author: azimov

.Rbuildignore

@@ -34,4 +34,5 @@ compare_versions
 ^Meta$
 LICENSE
 .git
-..Rcheck
+..Rcheck
+errorReportSql.txt

DESCRIPTION

@@ -1,14 +1,18 @@
 Package: ResultModelManager
 Title: Result Model Manager
-Version: 0.5.8
+Version: 0.5.9
 Authors@R:
     person("Jamie", "Gilbert", , "[email protected]", role = c("aut", "cre"))
-Description: Database data model management utilities for OHDSI packages.
+Description: Database data model management utilities for R packages in the Observational Health Data Sciences and
+    Informatics program <https://ohdsi.org>. 'ResultModelManager' provides utility functions to allow package
+    maintainers to migrate existing SQL database models, export and import results in consistent patterns.
+URL: https://github.com/OHDSI/ResultModelManager
+BugReports: https://github.com/OHDSI/ResultModelManager/issues
 License: Apache License (== 2.0)
 Encoding: UTF-8
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends:
   R (>= 4.1.0),
   R6,
@@ -25,13 +29,13 @@ Imports:
   dbplyr,
   rlang,
   lubridate,
-  fastmap
+  fastmap,
+  withr
 Suggests:
   testthat (>= 3.0.0),
   RSQLite,
   duckdb,
   RPostgres,
-  withr,
   knitr,
   rmarkdown,
   keyring,

NAMESPACE

@@ -22,9 +22,11 @@ importFrom(ParallelLogger,logError)
 importFrom(ParallelLogger,logInfo)
 importFrom(SqlRender,render)
 importFrom(SqlRender,translate)
+importFrom(dbplyr,in_schema)
 importFrom(dplyr,"%>%")
 importFrom(fastmap,fastmap)
 importFrom(pool,dbPool)
 importFrom(pool,poolClose)
 importFrom(readr,read_csv)
 importFrom(rlang,.data)
+importFrom(withr,defer)

NEWS.md

@@ -1,3 +1,12 @@
+# ResultModelManager 0.5.9
+
+Changes:
+
+1. Changes made to make package CRAN compliant
+
+2. `PooledConnectionHandler` now uses withr::defer to automatically returned pooled connections returned with 
+`getConnection`
+
 # ResultModelManager 0.5.8
 
 Bug fixes:

R/ConnectionHandler.R

@@ -28,6 +28,7 @@
 #' @import R6
 #' @importFrom DBI dbIsValid
 #' @importFrom SqlRender render translate
+#' @importFrom dbplyr in_schema
 #'
 #' @export ConnectionHandler
 ConnectionHandler <- R6::R6Class(
@@ -186,8 +187,7 @@ ConnectionHandler <- R6::R6Class(
           if (self$dbms() %in% c("postgresql", "redshift")) {
             DatabaseConnector::dbExecute(self$getConnection(), "ABORT;")
           }
-          print(sql)
-          stop(error)
+          stop(paste0(sql, "\n\n", error))
         }
       )
 
@@ -209,8 +209,7 @@ ConnectionHandler <- R6::R6Class(
           if (self$dbms() %in% c("postgresql", "redshift")) {
             self$executeFunction("ABORT;")
           }
-          print(sql)
-          stop(error)
+          stop(paste0(sql, "\n\n", error))
         }
       )
 

R/DataModel.R

@@ -39,7 +39,7 @@ checkAndFixColumnNames <-
 
     # Set all fields to requried if optional isn't specified
     if (!"optional" %in% colnames(tableSpecs)) {
-      tableSpecs$otpional <- "no"
+      tableSpecs$optional <- "no"
     }
 
     optionalNames <- tableSpecs %>%
@@ -494,7 +494,7 @@ uploadTable <- function(tableName,
 #' Upload results to the database server.
 #'
 #' @description
-#' Requires the results data model tables have been created using following the specifications, @seealso \code{\link{generateSqlSchema}} function.
+#' Requires the results data model tables have been created using following the specifications, generateSqlSchema function.
 #'
 #' Results files should be in the snake_case format for table headers and not camelCase
 #'
@@ -809,19 +809,20 @@ loadResultsDataModelSpecifications <- function(filePath) {
 #' Another assumption of this function is that we're only attempting to
 #' recast to a character data type and not try to handle different type
 #' conversions.
+#' @noRd
 formatChunk <- function(pkValuesInDb, chunk) {
   for (columnName in names(pkValuesInDb)) {
-    if (class(pkValuesInDb[[columnName]]) == "integer") {
+    if (inherits(pkValuesInDb[[columnName]], "integer")) {
       pkValuesInDb[[columnName]] <- as.numeric(pkValuesInDb[[columnName]])
     }
 
-    if (class(chunk[[columnName]]) == "integer") {
+    if (inherits(chunk[[columnName]], "integer")) {
       chunk[[columnName]] <- as.numeric(chunk[[columnName]])
     }
 
 
     if (class(pkValuesInDb[[columnName]]) != class(chunk[[columnName]])) {
-      if (class(pkValuesInDb[[columnName]]) == "character") {
+      if (inherits(pkValuesInDb[[columnName]], "character")) {
         chunk <- chunk |> dplyr::mutate_at(columnName, as.character)
       } else {
         errorMsg <- paste0(

R/PooledConnectionHandler.R

@@ -16,10 +16,15 @@
 
 
 requiredPackage <- function(packageName) {
-  packages <- utils::installed.packages()
-  packages <- as.data.frame(packages)
-  if (!packageName %in% packages$Package) {
-    utils::install.packages(packageName)
+  packageLoc <- tryCatch(
+    find.package(packageName),
+    errorr = function(...) {
+      return(NULL)
+    }
+  )
+
+  if (is.null(packageLoc)) {
+    stop(paste("Package", packageName, "is required please use install.packages to install"))
   }
 }
 
@@ -82,6 +87,7 @@ requiredPackage <- function(packageName) {
 #'
 #' @importFrom pool dbPool poolClose
 #' @importFrom DBI dbIsValid
+#' @importFrom withr defer
 #'
 #' @export PooledConnectionHandler
 PooledConnectionHandler <- R6::R6Class(
@@ -138,11 +144,21 @@ PooledConnectionHandler <- R6::R6Class(
       self$isActive <- TRUE
     },
 
+    #' Get Connection
+    #' @description
+    #' Returns a connection from the pool
+    #' When the desired frame exits, the connection will be returned to the pool
+    #' @param .deferedFrame  defaults to the parent frame of the calling block.
+    getConnection = function(.deferedFrame = parent.frame(n = 2)) {
+      conn <- pool::poolCheckout(super$getConnection())
+      withr::defer(pool::poolReturn(conn), envir = .deferedFrame)
+      return(conn)
+    },
+
     #' get dbms
     #' @description Get the dbms type of the connection
     dbms = function() {
-      conn <- pool::poolCheckout(self$getConnection())
-      on.exit(pool::poolReturn(conn))
+      conn <- self$getConnection()
       DatabaseConnector::dbms(conn)
     },
 
@@ -163,8 +179,7 @@ PooledConnectionHandler <- R6::R6Class(
     #' @param sql                                   sql query string
     #' @param snakeCaseToCamelCase                  (Optional) Boolean. return the results columns in camel case (default)
     queryFunction = function(sql, snakeCaseToCamelCase = self$snakeCaseToCamelCase) {
-      conn <- pool::poolCheckout(self$getConnection())
-      on.exit(pool::poolReturn(conn))
+      conn <- self$getConnection()
       data <- DatabaseConnector::dbGetQuery(conn, sql, translate = FALSE)
       if (snakeCaseToCamelCase) {
         colnames(data) <- SqlRender::snakeCaseToCamelCase(colnames(data))
@@ -179,8 +194,7 @@ PooledConnectionHandler <- R6::R6Class(
     #' Overrides ConnectionHandler Call. Does not translate or render sql.
     #' @param sql                                   sql query string
     executeFunction = function(sql) {
-      conn <- pool::poolCheckout(self$getConnection())
-      on.exit(pool::poolReturn(conn))
+      conn <- self$getConnection()
       DatabaseConnector::dbExecute(conn, sql, translate = FALSE)
     }
   )

R/QueryNamespace.R

@@ -20,16 +20,36 @@
 #' Given a results specification and ConnectionHandler instance - this class allow queries to be namespaced within
 #' any tables specified within a list of pre-determined tables. This allows the encapsulation of queries, using specific
 #' table names in a consistent manner that is striaghtforward to maintain over time.
-#'
+#' @importFrom fastmap fastmap
 #' @examples
-#' \dontrun{
+#'
 #' library(ResultModelManager)
-#' connectionHandler <- ConnectionHandler$new(connectionDetails = )
 #'
+#' # Create some junk test data
+#' connectionDetails <-
+#'   DatabaseConnector::createConnectionDetails(
+#'     server = "test_db.sqlite",
+#'     dbms = "sqlite"
+#'   )
+#'
+#' conn <- DatabaseConnector::connect(connectionDetails)
+#' DatabaseConnector::insertTable(
+#'   connection = conn,
+#'   tableName = "cd_cohort",
+#'   data = data.frame(
+#'     cohort_id = c(1, 2, 3),
+#'     cohort_name = c("cohort one", "cohort two", "cohort three"),
+#'     json = "{}",
+#'     sql = "SELECT 1"
+#'   )
+#' )
+#' DatabaseConnector::disconnect(conn)
+#'
+#' connectionHandler <- ConnectionHandler$new(connectionDetails = connectionDetails)
 #' tableSpecification <- data.frame(
 #'   tableName = "cohort",
 #'   columnName = c(
-#'     "cohort_definition_id",
+#'     "cohort_id",
 #'     "cohort_name",
 #'     "json",
 #'     "sql"
@@ -39,7 +59,7 @@
 #' )
 #'
 #' cohortNamespace <- QueryNamespace$new(
-#'   connnectionHandler = connnectionHandler,
+#'   connectionHandler = connectionHandler,
 #'   tableSpecification = tableSpecification,
 #'   result_schema = "main",
 #'   tablePrefix = "cd_"
@@ -48,9 +68,9 @@
 #' # Returns : "SELECT * FROM main.cd_cohort WHERE cohort_id = @cohort_id"
 #' print(cohortNamespace$render(sql))
 #' # Returns query result
-#' result <- cohortNamespace$querySql(sql, cohort_id = 1)
-#' }
-#' @importFrom fastmap fastmap
+#' result <- cohortNamespace$queryDb(sql, cohort_id = 1)
+#' # cleanup test data
+#' unlink("test_db.sqlite")
 QueryNamespace <- R6::R6Class(
   classname = "QueryNamespace",
   private = list(

R/SchemaGenerator.R

@@ -28,18 +28,16 @@
 #' Schema generator
 #' @description
 #' Take a csv schema definition and create a basic sql script with it.
-#'
+#' returns string containing the sql for the table
 #' @param csvFilepath                   Path to schema file. Csv file must have the columns:
-#'                                      "table_name", "column_name", "data_type", "is_required", "primary_key"
+#'                                      "table_name", "column_name", "data_type", "primary_key"
 #' @param schemaDefinition              A schemaDefintiion data.frame` with the columns:
 #'                                         tableName, columnName, dataType, isRequired, primaryKey
 #' @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 = NULL,
                               schemaDefinition = NULL,
                               sqlOutputPath = NULL,

README.md

@@ -1,13 +1,14 @@
 ResultModelManager
 ==================
 [![Build Status](https://github.com/OHDSI/ResultModelManager/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/ResultModelManager/actions?query=workflow%3AR-CMD-check)
-[![codecov.io](https://app.codecov.io/github/OHDSI/ResultModelManager/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/ResultModelManager?branch=main)
+[![codecov.io](https://codecov.io/github/OHDSI/ResultModelManager/coverage.svg?branch=main)](https://app.codecov.io/github/OHDSI/ResultModelManager?branch=main)
 
 ResultModelManager (RMM) [HADES](https://ohdsi.github.io/Hades/).
 
 Introduction
 ============
-RMM is an R package designed to handle common ohdsi results data management functions by providing a common API for data model migrations and definitions
+RMM is a database data model management utilities for R packages in the [Observational Health Data Sciences and Informatics program](https://ohdsi.org). RMM provides utility functions to
+allow package maintainers to migrate existing SQL database models, export and import results in consistent patterns.
 
 
 System Requirements
@@ -26,6 +27,17 @@ Installation
   remotes::install_github("OHDSI/ResultModelManager")
 ```
 
+Usage
+=====
+
+See articles:
+- [Creating migrations](https://ohdsi.github.io/ResultModelManager/articles/CreatingMigrations.html)
+- [Example Project](https://ohdsi.github.io/ResultModelManager/articles/ExampleProject.html)
+- [Upload functionality](https://ohdsi.github.io/ResultModelManager/articles/UploadFunctionality.html)
+- [Connection handler](https://ohdsi.github.io/ResultModelManager/articles/UsingConnectionHandlers.html)
+- [Using query namespaces](https://ohdsi.github.io/ResultModelManager/articles/UsingQueryNamespaces.html)
+
+
 Support
 =======
 * Developer questions/comments/feedback: <a href="http://forums.ohdsi.org/c/developers">OHDSI Forum</a>