Merge pull request #14 from inbo/develop

Version 0.4

Author: ThierryO

DESCRIPTION

@@ -1,11 +1,10 @@
 Package: n2khelper
 Title: Auxiliary Functions for the Analysis and Reporting of the Natura 2000
     Monitoring
-Version: 0.2
-Date: 2016-05-30
+Version: 0.4
+Date: 2017-07-28
 Authors@R: c(person("Thierry", "Onkelinx", email = "thierry.onkelinx@inbo.be", role = c("aut", "cre")))
-Description: Functions for importing the raw data, creating analysis dataset
-    and running the analysis for the Common Breeding Bird Survey in Flanders.
+Description: Auxiliary functions for analysing Natura 2000 monitoring data.
 Depends:
     R (>= 3.2.0)
 Imports:
@@ -15,6 +14,9 @@ Imports:
     lubridate,
     methods,
     assertthat,
+    DBI,
+    tidyr,
+    lazyeval,
     RODBC
 License: GPL-3
 LazyData: true
@@ -45,6 +47,7 @@ Collate:
     'git_connection.R'
     'git_recent.R'
     'git_sha.R'
+    'is_chartor.R'
     'is_git_repo.R'
     'list_files_git.R'
     'match_nbn_key.R'

NAMESPACE

@@ -13,13 +13,15 @@ export(check_single_logical)
 export(check_single_numeric)
 export(check_single_posix)
 export(check_single_probability)
+export(connect_nbn)
 export(connect_result)
 export(cut_date)
 export(get_nbn_key)
 export(get_nbn_key_multi)
 export(get_nbn_name)
 export(git_connect)
 export(git_connection)
+export(is.chartor)
 export(is_git_repo)
 export(match_nbn_key)
 export(odbc_connect)
@@ -38,26 +40,39 @@ exportMethods(write_delim_git)
 importClassesFrom(git2r,cred_ssh_key)
 importClassesFrom(git2r,cred_user_pass)
 importClassesFrom(git2r,git_repository)
+importFrom(DBI,dbExistsTable)
+importFrom(DBI,dbGetInfo)
+importFrom(DBI,dbGetQuery)
+importFrom(DBI,dbListFields)
 importFrom(RODBC,odbcClose)
 importFrom(RODBC,odbcDriverConnect)
 importFrom(RODBC,sqlClear)
 importFrom(RODBC,sqlColumns)
 importFrom(RODBC,sqlQuery)
-importFrom(RODBC,sqlTables)
+importFrom(assertthat,'on_failure<-')
 importFrom(assertthat,assert_that)
 importFrom(assertthat,has_name)
 importFrom(assertthat,is.count)
 importFrom(assertthat,is.flag)
 importFrom(assertthat,is.string)
 importFrom(assertthat,noNA)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,collect)
+importFrom(dplyr,count_)
 importFrom(dplyr,data_frame)
+importFrom(dplyr,filter_)
 importFrom(dplyr,funs)
 importFrom(dplyr,group_by_)
+importFrom(dplyr,inner_join)
 importFrom(dplyr,mutate_)
 importFrom(dplyr,mutate_each_)
 importFrom(dplyr,select_)
+importFrom(dplyr,semi_join)
+importFrom(dplyr,slice_)
+importFrom(dplyr,src_postgres)
 importFrom(dplyr,summarise_)
+importFrom(dplyr,tbl)
+importFrom(dplyr,ungroup)
 importFrom(git2r,add)
 importFrom(git2r,commit)
 importFrom(git2r,config)
@@ -67,6 +82,7 @@ importFrom(git2r,hashfile)
 importFrom(git2r,head)
 importFrom(git2r,push)
 importFrom(git2r,repository)
+importFrom(lazyeval,interp)
 importFrom(lubridate,is.Date)
 importFrom(lubridate,is.POSIXt)
 importFrom(lubridate,year)
@@ -80,6 +96,7 @@ importFrom(plyr,ddply)
 importFrom(stats,aggregate)
 importFrom(stats,as.formula)
 importFrom(stats,na.fail)
+importFrom(tidyr,spread_)
 importFrom(utils,file_test)
 importFrom(utils,read.delim)
 importFrom(utils,read.table)

R/check_dbtable.R

@@ -1,33 +1,48 @@
 #' Check if a table is available in a given ODBC connection
 #' @param error Indicates the behaviour when a table is missing. Gives an error
 #'    when error = TRUE (default). Return FALSE otherwise.
-#' @param schema The schema. Defaults to 'dbo'
+#' @param schema The schema. Defaults to 'public'
 #' @inheritParams odbc_get_id
 #' @export
-#' @importFrom RODBC sqlTables
+#' @importFrom assertthat assert_that is.string
+#' @importFrom dplyr %>%
+#' @importFrom DBI dbExistsTable dbGetInfo
 #' @importFrom stats na.fail
 #' @return TRUE when all tables are present in the ODBC connection.
-check_dbtable <- function(table, schema = "dbo", channel, error = TRUE){
+check_dbtable <- function(table, schema = "public", channel, error = TRUE){
+  # nocov start
   table <- check_character(x = table, name = "table", na.action = na.fail)
   if (length(table) == 0) {
     stop("'table' must contain at least one value")
   }
-  schema <- check_single_character(x = schema, name = "schema")
-  if (class(channel) != "RODBC") {
-    stop("channel is not an ODBC connection")
+  assert_that(is.string(schema))
+  if (has_name(channel, "con")) {
+    assert_that(inherits(channel$con, "DBIConnection"))
+    this_channel <- channel$con
+  } else {
+    assert_that(inherits(channel, "DBIConnection"))
+    this_channel <- channel
   }
-  # nocov start
 
-  available <- sqlTables(channel = channel, schema = schema)$TABLE_NAME
-  check <- table %in% available
-  if (all(check)) {
+  test <- sapply(
+    table,
+    function(x){
+      c(schema, x) %>%
+        dbExistsTable(conn = this_channel)
+    }
+  )
+  if (all(test)) {
     return(TRUE)
   }
   if (error) {
-    stop(
-      "Table(s) missing: ",
-      paste(table[!check], collapse = ", ")
-    )
+    names(test)[!test] %>%
+      paste(collapse = ", ") %>%
+      sprintf(
+        fmt = "Table(s) %s not found in schema %s on database %s",
+        schema,
+        dbGetInfo(this_channel)$dbname
+      ) %>%
+      stop(call. = FALSE)
   } else {
     return(FALSE)
   }

R/check_dbtable_variable.R

@@ -2,13 +2,13 @@
 #' @param error Indicates the behaviour when a variable is missing. Gives an error when error = TRUE (default). Return FALSE otherwise.
 #' @inheritParams odbc_get_id
 #' @export
-#' @importFrom RODBC sqlColumns
+#' @importFrom DBI dbListFields
 #' @importFrom stats na.fail
 #' @return TRUE when all variables are present in the table.
 check_dbtable_variable <- function(
   table,
   variable,
-  schema = "dbo",
+  schema = "public",
   channel,
   error = TRUE
 ){
@@ -24,12 +24,8 @@ check_dbtable_variable <- function(
   check_dbtable(table = table, schema = schema, channel = channel, error = TRUE)
   # nocov start
 
-  available <- sqlColumns(
-    channel = channel,
-    sqtable = table,
-    schema = schema
-  )$COLUMN_NAME
-  check <- variable %in% available
+  check <- variable %in%
+    dbListFields(conn = channel$con, name = c(schema, table))
   if (all(check)) {
     return(TRUE)
   }

R/check_id.R

@@ -2,31 +2,18 @@
 #' @inheritParams odbc_get_id
 #' @export
 #' @importFrom assertthat assert_that is.count
-#' @importFrom RODBC sqlQuery
+#' @importFrom DBI dbGetQuery
 check_id <- function(value, variable, table, channel){
   assert_that(is.count(value))
   variable <- check_single_character(variable, name = "variable")
   check_dbtable_variable(table = table, variable = variable, channel = channel)
 
   # nocov start
   sql <- paste("SELECT", variable, "FROM", table, "WHERE", variable, "=", value)
-  selection <- sqlQuery(
-    channel = channel,
-    query = sql,
-    stringsAsFactors = FALSE,
-    as.is = TRUE
+  selection <- dbGetQuery(
+    conn = channel$con,
+    statement = sql
   )
-  if (!inherits(selection, "data.frame")) {
-    if (length(grep("Invalid column name", selection)) > 0) {
-      stop(
-        "The variable '", variable, "' doesn't exists in table '", table, "'"
-      )
-    }
-    if (length(grep("Conversion failed", selection))) {
-      stop(paste(selection, collapse = "\n"))
-    }
-  }
-
   if (nrow(selection) == 0) {
     return(FALSE)
   } else {

R/connect_result.R

@@ -1,35 +1,36 @@
 #' Opens an ODBC connection to the 'results' database
 #' @export
-#' @importFrom RODBC odbcDriverConnect
-#' @param develop Logical value. Indicates the location ton the results database
-#' @param username the username to connect to the database. Use a trusted connection when missing
-#' @param password the password for the username. Ignored when using a trusted connection.
+#' @importFrom dplyr src_postgres
+#' @param username the username to connect to the database.
+#' @param password the password for the username.
+#' @param develop Logical value. Indicates the location of the results database
 #' @importFrom assertthat assert_that is.flag noNA is.string
-connect_result <- function(develop = TRUE, username, password){
+connect_result <- function(username, password, develop = TRUE){
   assert_that(is.flag(develop))
   assert_that(noNA(develop))
+  assert_that(is.string(username))
+  assert_that(is.string(password))
+
+  dbname <- "n2kresult"
   if (develop) {
-    server <- "INBODEV02\\development"
+  # nocov start
+    host <- "localhost"
+  # nocov end
   } else {
     stop("Production database not yet defined")
   }
-  driver <- ifelse(.Platform$OS.type == "windows", "SQL Server", "FreeTDS")
-  if (missing(username)) {
-    authentication <- "Trusted_Connection=Yes;"
-  } else {
-    assert_that(is.string(username))
-    if (username == "") {
-      authentication <- "Trusted_Connection=Yes;"
-    } else {
-      assert_that(is.string(password))
-      authentication <- sprintf("Uid=%s;Pwd=%s", username, password)
-    }
-  }
-  connection <- sprintf(
-    "Driver=%s;Server=%s;Database=D0116on00_SoortenMeetnetAnalyse;%s",
-    driver,
-    server,
-    authentication
+  # nocov start
+  src_postgres(
+    host = host,
+    dbname = dbname,
+    user = username,
+    password = password
   )
-  odbcDriverConnect(connection)
+  # nocov end
+}
+
+#' Open a trusted connection to the NBN database
+#' @export
+connect_nbn <- function(){
+  odbcDriverConnect(connection = nbn.dsn)
 }