From cc66ea8e99f809c53cb5a23430b814f68efdb126 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 7 Oct 2015 17:19:21 +0200
Subject: Maintenance changes for the release of 0.6.4

---
 R/checkexperiment.R | 14 +++++++++-----
 R/checksubstance.R  | 10 +++++++---
 R/drdata.R          | 16 ++++++++++------
 3 files changed, 26 insertions(+), 14 deletions(-)

(limited to 'R')

diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index 2bf0ce7..8c2f472 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -9,7 +9,11 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
 
     if (!(db %in% rownames(databases))) stop("Database is not supported")
 
-    channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+    if (requireNamespace("RODBC")) {
+      channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower")
+    } else {
+      stop("For this function, the RODBC package has to be installed and configured.")
+    }
 
 
     responsename = as.character(databases[db,1])
@@ -19,7 +23,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     exptable <- paste(exptype, "s", sep="")
     commentquery <- paste("SELECT comment FROM ", exptable ,
         " WHERE ", exptype, " = ", id)
-    commentdata <- sqlQuery(channel,commentquery)
+    commentdata <- RODBC::sqlQuery(channel,commentquery)
     comment <- as.character(commentdata[[1]])
         
     expquery <- paste("SELECT experimentator,substance, ",
@@ -32,15 +36,15 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
                 endpoint, "'", sep = "")
     }
 
-    expdata <- sqlQuery(channel,expquery)
+    expdata <- RODBC::sqlQuery(channel,expquery)
 
     if (db %in% c("cytotox","enzymes")) {
         controlquery <- paste("SELECT type,response FROM controls 
             WHERE plate=",id)
-        controldata <- sqlQuery(channel,controlquery)
+        controldata <- RODBC::sqlQuery(channel,controlquery)
     }
 
-    odbcClose(channel)
+    RODBC::odbcClose(channel)
 
     op <- par(ask=TRUE)
     on.exit(par(op))
diff --git a/R/checksubstance.R b/R/checksubstance.R
index b50c3da..3e07f92 100644
--- a/R/checksubstance.R
+++ b/R/checksubstance.R
@@ -11,7 +11,11 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%",
 
     if (!(db %in% rownames(databases))) stop("Database is not supported")
 
-    channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+    if (requireNamespace("RODBC")) {
+      channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower")
+    } else {
+      stop("For this function, the RODBC package has to be installed and configured.")
+    }
 
     responsename = as.character(databases[db,1])
     testtype = as.character(databases[db,2])
@@ -41,8 +45,8 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%",
                 endpoint, "'", sep = "")
     }
 
-    data <- sqlQuery(channel,query)
-    odbcClose(channel)
+    data <- RODBC::sqlQuery(channel,query)
+    RODBC::odbcClose(channel)
 
     if (length(data$experimentator) < 1) {
         stop(paste("\nNo response data for",substance,"in database",
diff --git a/R/drdata.R b/R/drdata.R
index 15c61ac..0bf9597 100644
--- a/R/drdata.R
+++ b/R/drdata.R
@@ -1,9 +1,10 @@
 drdata <- function(substances, experimentator = "%", db = "cytotox",
-    celltype="IPC-81",enzymetype="AChE",
-    organism="Vibrio fischeri",endpoint="Luminescence",whereClause="1",
-    ok="'ok','no fit'")
+    celltype = "IPC-81", enzymetype = "AChE",
+    organism = "Vibrio fischeri", endpoint = "Luminescence", whereClause = "1",
+    ok = "'ok','no fit'")
 {
-    channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+  if (requireNamespace("RODBC")) {
+    channel <- RODBC::odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
     slist <- paste(substances,collapse="','")
     if (db == "cytotox") {
         responsetype <- "viability"
@@ -29,10 +30,13 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
         whereClause," AND ok in (",
         ok,")",sep="")
     if (db == "ecotox") query <- paste(query," AND type LIKE '",endpoint,"'",sep="")
-    data <- sqlQuery(channel,query)
-    odbcClose(channel)
+    data <- RODBC::sqlQuery(channel,query)
+    RODBC::odbcClose(channel)
     names(data)[[1]] <- "dose"
     names(data)[[2]] <- "response"
     data$substance <- factor(data$substance,levels=substances)
     return(data)
+  } else {
+    stop("For this function, the RODBC package has to be installed and configured.")
+  }
 }
-- 
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