Merge changes from upstream

.Rbuildignore

@@ -1,8 +1,19 @@
+extras
+license_header_stub.txt
+pom.xml
 ^.*\.Rproj$
 ^\.Rproj\.user$
 .travis.yml
 .classpath
 .project
-build
+^cran-comments.md$
 build.xml
 deploy.sh
+extras/
+pom.xml
+bin/
+.idea/
+SqlRender.iml
+license_header_stub.txt
+target/
+docs

.classpath

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="java-src"/>
+	<classpathentry kind="src" path="java"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk6"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

.travis.yml

@@ -1,71 +1,24 @@
-# .travis.yml using container-based infrastructure
-# from: https://github.com/jtilly/R-travis-container-example/blob/master/.travis.yml
-
-language: c
-
-# use containers
+language: R
+cache: packages
 sudo: false
 
-# install R: use r-packages-precise (https://cran.r-project.org/bin/linux/ubuntu/precise/)
-# as source which is white listed (https://github.com/travis-ci/apt-source-whitelist/)
-addons:
-  apt:
-    sources:
-    - r-packages-precise
-    packages:
-    - r-base-dev
-    - r-recommended
-    - pandoc
-    - default-jdk
-    - default-jre
-
-# cache local R libraries directory:
-cache:
-  directories:
-    - ~/Rlib
-
-# install the package and dependencies:
-install:
-  - mkdir -p ~/Rlib
-  - echo 'R_LIBS=~/Rlib' > .Renviron
-  - echo 'options(repos = "http://cran.rstudio.com")' > .Rprofile
-  - mkdir -p ~/.R
-  - Rscript -e 'if(!"devtools" %in% rownames(installed.packages())) { install.packages("devtools", dependencies = TRUE) }'
-  - Rscript -e 'if (!require("covr")) devtools::install_github("jimhester/covr")'
-  - Rscript -e 'if (!require("drat")) install.packages("drat")'     
-  - Rscript -e 'if(!"rJava" %in% rownames(installed.packages())) { install.packages("rJava", dependencies = TRUE) }'
-  - Rscript -e 'if(!"testthat" %in% rownames(installed.packages())) { install.packages("testthat", dependencies = TRUE) }'
-  - Rscript -e 'if(!"knitr" %in% rownames(installed.packages())) { install.packages("knitr", dependencies = TRUE) }'
-  - Rscript -e 'if(!"rmarkdown" %in% rownames(installed.packages())) { install.packages("rmarkdown", dependencies = TRUE) }'
-  - Rscript -e 'update.packages(ask = FALSE, instlib = "~/Rlib")'
-  - Rscript -e 'devtools::install_deps(pkg = ".", dependencies = TRUE)'
-
-before_script:
-  - export PKG_NAME=$(Rscript -e 'cat(paste0(devtools::as.package(".")$package))')
-  - export PKG_TARBALL=$(Rscript -e 'pkg <- devtools::as.package("."); cat(paste0(pkg$package,"_",pkg$version,".tar.gz"))')
+r_packages:
+  - covr
+  - drat
 
-# Build and check package
-script:
-  - R CMD build . --no-build-vignettes --no-manual
-  - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-  - PKG_NAME=$(ls -1t *.tar.gz | head -n 1 | sed 's/_.*gz//')
-  - _R_CHECK_CRAN_INCOMING_=FALSE R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual
-  - cat ${PKG_NAME}.Rcheck/00install.out # Print out install / compile log
+before_install:
+  - Rscript -e 'update.packages(ask = FALSE)'
+  - export LD_LIBRARY_PATH=$JAVA_HOME:$LD_LIBRARY_PATH
 
 notifications:
   recipients:
-    - [email protected]
-    - [email protected]
+  - [email protected]
+  - [email protected]
   email:
     on_success: change
     on_failure: change
 
 after_success:
-  - Rscript -e 'library(covr);codecov()'
-  # Rebuild docker container
-  - curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/development/trigger/e51f720d-c4e7-45df-b042-5d8a362bd7e0/
+  - Rscript -e 'covr::codecov()'
+  - curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
   - test $TRAVIS_PULL_REQUEST == "false" && test $TRAVIS_BRANCH == "master" && bash deploy.sh
-
-env:
-  global:
-    secure: eUCnclALTsNc8+oOVS8qeSkD8CcYwAPfq759YG/WYXHpTgWDtjCAeHBARWmELHxkGDromzT+lNL3gnbs0WfqD+Nm0prAO7tjPIVKRe4h8zDHwLgZyPQSv17YwwNQZknEPWDrP18BpGqrKCDl8qYsL80+6QVqBs1FczZI7taSfB0=

DESCRIPTION

@@ -1,19 +1,28 @@
 Package: SqlRender
 Type: Package
 Title: Rendering Parameterized SQL and Translation to Dialects
-Version: 1.1.4
-Date: 2016-05-30
-Author: Martijn J. Schuemie and Marc A. Suchard
+Version: 1.4.3
+Date: 2017-06-09
+Authors@R: c(
+    person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre")),
+    person("Marc", "Suchard", role = c("aut"))
+    )
 Maintainer: Martijn Schuemie <[email protected]>
-Description: This is an R package for rendering parameterized SQL, and
-    translating it to different SQL dialects.
-License: Apache License
+Description: A rendering tool for parameterized SQL that also translates into
+    different SQL dialects.  These dialects include Sql Server, Oracle, 
+    PostgreSql, Amazon RedShift, Impala, IBM Netezza, Google BigQuery, and Microsoft PDW.
+License: Apache License 2.0
 VignetteBuilder: knitr
+URL: https://github.com/OHDSI/SqlRender
+BugReports: https://github.com/OHDSI/SqlRender/issues
 Imports:
     rJava
 Suggests:
     testthat,
     knitr,
-    rmarkdown
+    rmarkdown,
+    shiny,
+    shinydashboard,
+    formatR
 LazyData: false
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(camelCaseToSnakeCase)
 export(createRWrapperForSql)
+export(launchSqlRenderDeveloper)
 export(loadRenderTranslateSql)
 export(readSql)
 export(renderSql)
@@ -12,3 +13,5 @@ export(translateSql)
 export(translateSqlFile)
 export(writeSql)
 import(rJava)
+importFrom(utils,install.packages)
+importFrom(utils,menu)

NEWS

@@ -0,0 +1,52 @@
+SqlRender v1.3.7 (Release date: 2017-05-03)
+===========================================
+
+Changes: 
+
+1. Added translation rules for ISNUMERIC and LOG(@expression, @base)
+
+
+Bugfixes:
+
+1. Fixed bug when trying to split SQL where reserved word 'end' is used as a field name.
+2. Fixes for Impala translations.
+3. Fixed translation issues for Oracle involving 'FROM DUAL'.
+4. Added workaround for Oracle bug for intervals greater than 99 days.
+5. Fixed bug when trying to split SQL where last line has comment but no EOL.
+
+
+SqlRender v1.3.0 (Release date: 2017-03-24)
+===========================================
+
+Changes: 
+
+1. Added ability to use regular expression in translation patterns. This allowed SELECT TOP n to be translated.
+2. Deprecated sourceDialect argument.
+3. Added translation for CONCAT function with >2 arguments to Oracle (which only allows 2 arguments)
+4. Added hints for translation optimation to massive parallel platforms like RedShift
+5. Throw warnings when translateSql is called with variable names that are not in the SQL
+6. Throw warnings when table names are too long for Oracle
+
+
+Bugfixes:
+
+1. Fixed translation for date functions so they will now work properly with datetime fields as well.
+2. Now throwing error when boolean logic cannot be parsed (instead of assuming result is TRUE)
+
+
+SqlRender v1.2.0 (Release date: 2017-01-12)
+===========================================
+
+Changes: 
+
+1. Added support for Impala
+
+Bugfixes:
+
+1. Fixed translation for DATEFROMPARTS for RedShift
+
+
+SqlRender v1.1.7 (Release date: 2016-08-15)
+===========================================
+
+Changes: initial submission to CRAN

R/HelperFunctions.R

@@ -1,6 +1,6 @@
 # @file HelperFunctions.R
 #
-# Copyright 2016 Observational Health Data Sciences and Informatics
+# Copyright 2017 Observational Health Data Sciences and Informatics
 #
 # This file is part of SqlRender
 # 
@@ -109,7 +109,7 @@ renderSqlFile <- function(sourceFile, targetFile, ...) {
 #'
 #' @param sourceFile         The source SQL file
 #' @param targetFile         The target SQL file
-#' @param sourceDialect      The source dialect. Currently, only 'sql server' for Microsoft SQL Server
+#' @param sourceDialect      Deprecated: The source dialect. Currently, only 'sql server' for Microsoft SQL Server
 #'                           is supported
 #' @param targetDialect      The target dialect. Currently 'oracle', 'postgresql', and 'redshift' are
 #'                           supported
@@ -124,11 +124,14 @@ renderSqlFile <- function(sourceFile, targetFile, ...) {
 #' @export
 translateSqlFile <- function(sourceFile,
                              targetFile,
-                             sourceDialect = "sql server",
-                             targetDialect = "oracle",
+                             sourceDialect,
+                             targetDialect,
                              oracleTempSchema = NULL) {
+  if (!missing(sourceDialect))
+    warning("sourceDialect argument is deprecated in the translateSqlFile function in SqlRender. Please update your code")
+
   sql <- readSql(sourceFile)
-  sql <- translateSql(sql, sourceDialect, targetDialect, oracleTempSchema = oracleTempSchema)$sql
+  sql <- translateSql(sql = sql, targetDialect = targetDialect, oracleTempSchema = oracleTempSchema)$sql
   writeSql(sql, targetFile)
 }
 
@@ -179,12 +182,12 @@ loadRenderTranslateSql <- function(sqlFilename,
                              package = packageName)
   }
   parameterizedSql <- readChar(pathToSql, file.info(pathToSql)$size)
-
+  
   renderedSql <- renderSql(parameterizedSql[1], ...)$sql
-
+  
   if (mustTranslate)
-    renderedSql <- translateSql(renderedSql, "sql server", dbms, oracleTempSchema)$sql
-
+    renderedSql <- translateSql(sql = renderedSql, targetDialect = dbms, oracleTempSchema = oracleTempSchema)$sql
+  
   renderedSql
 }
 
@@ -212,7 +215,7 @@ snakeCaseToCamelCase <- function(string) {
   for (number in 0:9) {
     string <- gsub(paste("_", number, sep = ""), number, string)
   }
-
+  
   string
 }
 
@@ -273,7 +276,7 @@ createRWrapperForSql <- function(sqlFilename,
       rFilename <- paste(substr(sqlFilename, 1, periodIndex), "R", sep = "")
     }
   }
-
+  
   pathToSql <- system.file(paste("sql/", "sql_server", sep = ""),
                            sqlFilename,
                            package = packageName)
@@ -287,7 +290,7 @@ createRWrapperForSql <- function(sqlFilename,
   } else {
     stop("Could not find SQL file")
   }
-
+  
   hasTempTables <- any(gregexpr("\\#", parameterizedSql)[[1]] != -1)
   hits <- gregexpr("\\{DEFAULT @[^}]*\\}", parameterizedSql)
   hits <- cbind(hits[[1]], attr(hits[[1]], "match.length"))
@@ -315,10 +318,10 @@ createRWrapperForSql <- function(sqlFilename,
     if (any(definitions[, 1] == databaseParameter))
       databaseParameters <- rbind(databaseParameters,
                                   definitions[definitions$sqlParameter == databaseParameter,
-                                  ])
+                                              ])
   }
   functionDefinitions <- definitions[!(definitions$sqlParameter %in% databaseParameters$sqlParameter), ]
-
+  
   lines <- c()
   if (createRoxygenTemplate) {
     lines <- c(lines, "#' Todo: add title")
@@ -347,12 +350,12 @@ createRWrapperForSql <- function(sqlFilename,
   for (i in 1:nrow(functionDefinitions)) {
     if (i == nrow(functionDefinitions))
       end <- ") {" else end <- ","
-    lines <- c(lines, paste("                         ",
-                            functionDefinitions$rParameter[i],
-                            " = ",
-                            functionDefinitions$value[i],
-                            end,
-                            sep = ""))
+      lines <- c(lines, paste("                         ",
+                              functionDefinitions$rParameter[i],
+                              " = ",
+                              functionDefinitions$value[i],
+                              end,
+                              sep = ""))
   }
   for (databaseParameter in databaseParameters$rParameter) {
     lines <- c(lines, paste("  ",
@@ -364,20 +367,20 @@ createRWrapperForSql <- function(sqlFilename,
   }
   lines <- c(lines,
              paste("  renderedSql <- SqlRender::loadRenderTranslateSql(\"", sqlFilename, "\",",
-                          sep = ""))
+                   sep = ""))
   lines <- c(lines, paste("              packageName = \"", packageName, "\",", sep = ""))
   lines <- c(lines, "              dbms = connectionDetails$dbms,")
   if (hasTempTables)
     lines <- c(lines, "              oracleTempSchema = oracleTempSchema,")
   for (i in 1:nrow(definitions)) {
     if (i == nrow(definitions))
       end <- ")" else end <- ","
-    lines <- c(lines, paste("              ",
-                            definitions$sqlParameter[i],
-                            " = ",
-                            definitions$rParameter[i],
-                            end,
-                            sep = ""))
+      lines <- c(lines, paste("              ",
+                              definitions$sqlParameter[i],
+                              " = ",
+                              definitions$rParameter[i],
+                              end,
+                              sep = ""))
   }
   lines <- c(lines, "  conn <- DatabaseConnector::connect(connectionDetails)")
   lines <- c(lines, "")