Fixes for R check

.Rbuildignore

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

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(

R/PooledConnectionHandler.R

@@ -16,9 +16,13 @@
 
 
 requiredPackage <- function(packageName) {
-  packageLoc <- tryCatch(find.package("foo"), errorr = function(...) {
-    return(NULL)
-  })
+  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"))
   }
@@ -83,6 +87,7 @@ requiredPackage <- function(packageName) {
 #'
 #' @importFrom pool dbPool poolClose
 #' @importFrom DBI dbIsValid
+#' @importFrom withr defer
 #'
 #' @export PooledConnectionHandler
 PooledConnectionHandler <- R6::R6Class(

R/QueryNamespace.R

@@ -20,15 +20,21 @@
 #' 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
 #'
 #' library(ResultModelManager)
 #'
 #' # Create some junk test data
-#' connectionDetails <- DatabaseConnector::createConnectionDetails(server = ":memory:", dbms = "sqlite")
+#' 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),
@@ -53,7 +59,7 @@
 #' )
 #'
 #' cohortNamespace <- QueryNamespace$new(
-#'   connnectionHandler = connnectionHandler,
+#'   connectionHandler = connectionHandler,
 #'   tableSpecification = tableSpecification,
 #'   result_schema = "main",
 #'   tablePrefix = "cd_"
@@ -62,8 +68,9 @@
 #' # Returns : "SELECT * FROM main.cd_cohort WHERE cohort_id = @cohort_id"
 #' print(cohortNamespace$render(sql))
 #' # Returns query result
-#' result <- cohortNamespace$querySql(sql, cohort_id = 1)
-#'
+#' result <- cohortNamespace$queryDb(sql, cohort_id = 1)
+#' # cleanup test data
+#' unlink("test_db.sqlite")
 QueryNamespace <- R6::R6Class(
   classname = "QueryNamespace",
   private = list(

R/SchemaGenerator.R

@@ -30,7 +30,7 @@
 #' 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.

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://app.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>