diff --git a/NAMESPACE b/NAMESPACE
index dc8481305363622832f63a55d36baa4c1fd24eab..35aff21d1b6fc7d5b2b39ad396078454113f1b9b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -18,7 +18,7 @@ export(readNWISsite)
export(readNWISuv)
export(readWQPdata)
export(readWQPqw)
-export(renameColumns)
+export(renameNWISColumns)
export(whatNWISdata)
export(whatNWISsites)
export(whatWQPsites)
diff --git a/R/importRDB1.r b/R/importRDB1.r
index e9c409b1cb33bcbc37c119f7729e56d25ea858f1..f5ed78d8ba3cb8443f8382fe3ef9078ea63b95d6 100644
--- a/R/importRDB1.r
+++ b/R/importRDB1.r
@@ -57,6 +57,12 @@ importRDB1 <- function(obs_url, asDateTime=FALSE, qw=FALSE, convertType = TRUE,
}
if(url.exists(obs_url)){
+
+ # 400 bad site id
+ # 404 outside date range, wrong pcode
+ # 200 cool
+
+
retval = tryCatch({
h <- basicHeaderGatherer()
doc <- getURL(obs_url, headerfunction = h$update)
diff --git a/R/importWaterML1.r b/R/importWaterML1.r
index cffff197855b0c377cc7666ffd5a0a643c6f9d05..af4227eb01d216baab8dfaf3b7cd7cf18573fc5c 100644
--- a/R/importWaterML1.r
+++ b/R/importWaterML1.r
@@ -115,130 +115,136 @@ importWaterML1 <- function(obs_url,asDateTime=FALSE, tz=""){
value <- as.numeric(xpathSApply(subChunk, "ns1:value",namespaces = chunkNS, xmlValue))
- value[value == noValue] <- NA
-
- attNames <- xpathSApply(subChunk, "ns1:value/@*",namespaces = chunkNS)
- attributeNames <- unique(names(attNames))
-
- x <- lapply(attributeNames, function(x) xpathSApply(subChunk, paste0("ns1:value/@",x),namespaces = chunkNS))
-
-
- methodDescription <- as.character(xpathApply(subChunk, "ns1:method/ns1:methodDescription", namespaces = chunkNS, xmlValue))
-
- if(length(methodDescription) > 0 & methodDescription != ""){
- valueName <- paste("X",methodDescription,pCode,statCd,sep="_")
- } else {
- valueName <- paste("X",pCode,statCd,sep="_")
- }
-
-
- assign(valueName,value)
+ if(length(value)!=0){
- df <- data.frame(agency = rep(agency,length(value)),
- site_no = rep(site,length(value)),
- stringsAsFactors=FALSE)
-
- if(length(attributeNames) > 0){
- for(k in 1:length(attributeNames)){
- attVal <- as.character(x[[k]])
- if(length(attVal) == nrow(df)){
- df$temp <- as.character(x[[k]])
+ value[value == noValue] <- NA
- } else {
- attrList <- xpathApply(subChunk, "ns1:value", namespaces = chunkNS, xmlAttrs)
- df$temp <- sapply(1:nrow(df),function(x) as.character(attrList[[x]][attributeNames[k]]))
- df$temp[is.na(df$temp)] <- ""
- }
- names(df)[which(names(df) %in% "temp")] <- attributeNames[k]
-
+ attNames <- xpathSApply(subChunk, "ns1:value/@*",namespaces = chunkNS)
+ attributeNames <- unique(names(attNames))
+
+ x <- lapply(attributeNames, function(x) xpathSApply(subChunk, paste0("ns1:value/@",x),namespaces = chunkNS))
+
+
+ methodDescription <- as.character(xpathApply(subChunk, "ns1:method/ns1:methodDescription", namespaces = chunkNS, xmlValue))
+
+ valueName <- paste("X",pCode,statCd,sep="_")
+
+ if(length(methodDescription) > 0){
+ if(methodDescription != ""){
+ valueName <- paste("X",methodDescription,pCode,statCd,sep="_")
+ }
}
- }
-
- df <- cbind(df, get(valueName))
- names(df)[length(df)] <- valueName
-
- if("qualifiers" %in% names(df)){
- qualName <- paste(valueName,"cd",sep="_")
- names(df)[which(names(df) == "qualifiers")] <- qualName
- }
-
- if("dateTime" %in% attributeNames){
- if(asDateTime){
-
- # Common options:
- # YYYY
- # YYYY-MM-DD
- # YYYY-MM-DDTHH:MM
- # YYYY-MM-DDTHH:MM:SS
- # YYYY-MM-DDTHH:MM:SSZ
- # YYYY-MM-DDTHH:MM:SS.000
- # YYYY-MM-DDTHH:MM:SS.000-XX:00
- datetime <- xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS)
-
- numChar <- nchar(datetime)
-
- if(abs(max(numChar) - min(numChar)) != 0){
- message("Mixed date types")
- } else {
- numChar <- numChar[1]
- if(numChar == 4){
- datetime <- as.POSIXct(datetime, "%Y", tz = "UTC")
- } else if(numChar == 10){
- datetime <- as.POSIXct(datetime, "%Y-%m-%d", tz = "UTC")
- } else if(numChar == 16){
- datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M", tz = "UTC")
- } else if(numChar == 19){
- datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%S", tz = "UTC")
- } else if(numChar == 20){
- datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%S", tz = "UTC")
- } else if(numChar == 23){
- datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%OS", tz = "UTC")
- } else if(numChar == 24){
- datetime <- substr(datetime,1,23)
- datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%OS", tz = "UTC")
- } else if(numChar == 29){
- tzHours <- as.numeric(substr(datetime,24,numChar-3))
-
- datetime <- substr(datetime,1,23)
- datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%OS", tz = "UTC")
- datetime <- datetime - tzHours*60*60
- df$tz_cd <- as.character(zoneAbbrievs[tzHours])
+
+
+ assign(valueName,value)
+
+ df <- data.frame(agency = rep(agency,length(value)),
+ site_no = rep(site,length(value)),
+ stringsAsFactors=FALSE)
+
+ if(length(attributeNames) > 0){
+ for(k in 1:length(attributeNames)){
+ attVal <- as.character(x[[k]])
+ if(length(attVal) == nrow(df)){
+ df$temp <- as.character(x[[k]])
+
+ } else {
+ attrList <- xpathApply(subChunk, "ns1:value", namespaces = chunkNS, xmlAttrs)
+ df$temp <- sapply(1:nrow(df),function(x) as.character(attrList[[x]][attributeNames[k]]))
+ df$temp[is.na(df$temp)] <- ""
}
+ names(df)[which(names(df) %in% "temp")] <- attributeNames[k]
+
}
-
- if(tz != ""){
- attr(datetime, "tzone") <- tz
+ }
+
+ df <- cbind(df, get(valueName))
+ names(df)[length(df)] <- valueName
+
+ if("qualifiers" %in% names(df)){
+ qualName <- paste(valueName,"cd",sep="_")
+ names(df)[which(names(df) == "qualifiers")] <- qualName
+ }
+
+ if("dateTime" %in% attributeNames){
+ if(asDateTime){
+
+ # Common options:
+ # YYYY
+ # YYYY-MM-DD
+ # YYYY-MM-DDTHH:MM
+ # YYYY-MM-DDTHH:MM:SS
+ # YYYY-MM-DDTHH:MM:SSZ
+ # YYYY-MM-DDTHH:MM:SS.000
+ # YYYY-MM-DDTHH:MM:SS.000-XX:00
+ datetime <- xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS)
+
+ numChar <- nchar(datetime)
+
+ if(abs(max(numChar) - min(numChar)) != 0){
+ message("Mixed date types")
+ } else {
+ numChar <- numChar[1]
+ if(numChar == 4){
+ datetime <- as.POSIXct(datetime, "%Y", tz = "UTC")
+ } else if(numChar == 10){
+ datetime <- as.POSIXct(datetime, "%Y-%m-%d", tz = "UTC")
+ } else if(numChar == 16){
+ datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M", tz = "UTC")
+ } else if(numChar == 19){
+ datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%S", tz = "UTC")
+ } else if(numChar == 20){
+ datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%S", tz = "UTC")
+ } else if(numChar == 23){
+ datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%OS", tz = "UTC")
+ } else if(numChar == 24){
+ datetime <- substr(datetime,1,23)
+ datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%OS", tz = "UTC")
+ } else if(numChar == 29){
+ tzOffset <- as.character(substr(datetime,24,numChar))
+
+ tzHours <- as.numeric(substr(tzOffset,1,3))
+
+ datetime <- substr(datetime,1,23)
+ datetime <- as.POSIXct(datetime, "%Y-%m-%dT%H:%M:%OS", tz = "UTC")
+ datetime <- datetime - tzHours*60*60
+ df$tz_cd <- as.character(zoneAbbrievs[tzOffset])
+ }
+ }
+
+ if(tz != ""){
+ attr(datetime, "tzone") <- tz
+ }
+
+
+ } else {
+ datetime <- as.character(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS))
}
+ df$dateTime <- datetime
+ }
+
+ colNames <- names(df)
+
+ if( exists("qualName")){
+ columnsOrdered <- c("agency","site_no","dateTime","tz_cd",attributeNames[attributeNames != "dateTime"],qualName,valueName)
} else {
- datetime <- as.character(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS))
+ columnsOrdered <- c("agency","site_no","dateTime","tz_cd",attributeNames[attributeNames != "dateTime"],valueName)
}
- df$dateTime <- datetime
+ columnsOrderd <- columnsOrdered[columnsOrdered %in% names(df)]
- }
-
- colNames <- names(df)
-
- if( exists("qualName")){
- columnsOrdered <- c("agency","site_no","dateTime","tz_cd",attributeNames[attributeNames != "dateTime"],qualName,valueName)
- } else {
- columnsOrdered <- c("agency","site_no","dateTime","tz_cd",attributeNames[attributeNames != "dateTime"],valueName)
- }
-
- columnsOrderd <- columnsOrdered[columnsOrdered %in% names(df)]
-
- df <- df[,columnsOrderd]
-
- if (1 == i & valuesIndex[1] == j){
- mergedDF <- df
- } else {
- similarNames <- intersect(names(mergedDF), names(df))
- mergedDF <- merge(mergedDF, df,by=similarNames,all=TRUE)
+ df <- df[,columnsOrderd]
+
+ if (1 == i & valuesIndex[1] == j){
+ mergedDF <- df
+ } else {
+ similarNames <- intersect(names(mergedDF), names(df))
+ mergedDF <- merge(mergedDF, df,by=similarNames,all=TRUE)
+ }
}
}
-
}
return (mergedDF)