From a4a79738258d9ba077d0d8639b3b41fd2f40eb4a Mon Sep 17 00:00:00 2001
From: unknown <ldecicco@usgs.gov>
Date: Tue, 16 Dec 2014 14:40:33 -0600
Subject: [PATCH] Fixing WaterML2 qualifier.
---
R/importWaterML2.r | 39 +++++++++++++++++++++++++++++----------
1 file changed, 29 insertions(+), 10 deletions(-)
diff --git a/R/importWaterML2.r b/R/importWaterML2.r
index 5b955009..5d4fec0b 100644
--- a/R/importWaterML2.r
+++ b/R/importWaterML2.r
@@ -77,13 +77,22 @@ importWaterML2 <- function(obs_url, asDateTime=FALSE, tz=""){
chunk <- xmlRoot(chunk)
chunkNS <- xmlNamespaceDefinitions(chunk, simplify = TRUE)
+# xp <- xpathApply(chunk, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP",
+# xpathSApply, ".//*[not(*)]",
+# function(x) setNames(ifelse(nzchar(xmlValue(x)),
+# xmlValue(x),
+# ifelse("qualifier" == xmlName(x),
+# xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x)
+# xmlName(x)),
+# namespaces = chunkNS)
+
xp <- xpathApply(chunk, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP",
xpathSApply, ".//*[not(*)]",
function(x) setNames(ifelse(nzchar(xmlValue(x)),
- xmlValue(x),
- ifelse("qualifier" == xmlName(x),
- xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x)
- xmlName(x)),
+ xmlValue(x),
+ ifelse("qualifier" == xmlName(x),
+ xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x)
+ xmlName(x,full=TRUE)),
namespaces = chunkNS)
if(length(xpathApply(doc,
@@ -91,9 +100,12 @@ importWaterML2 <- function(obs_url, asDateTime=FALSE, tz=""){
xmlValue, namespaces = ns)) != 0){
xp <- xp[-1]
}
-
+
+
DF2 <- do.call(rbind.fill.matrix, lapply(xp, t))
DF2 <- as.data.frame(DF2,stringsAsFactors=FALSE)
+
+ names(DF2)[grep("wml2",names(DF2))] <- sub("wml2:","",names(DF2)[grep("wml2",names(DF2))])
if(asDateTime){
@@ -113,6 +125,8 @@ importWaterML2 <- function(obs_url, asDateTime=FALSE, tz=""){
}
DF2$value <- as.numeric(DF2$value)
+
+#########################################
# Very specific to USGS:
defaultQualifier <- as.character(xpathApply(chunk, "//wml2:defaultPointMetadata/wml2:DefaultTVPMeasurementMetadata/wml2:qualifier/@xlink:title",namespaces = chunkNS))
@@ -120,17 +134,22 @@ importWaterML2 <- function(obs_url, asDateTime=FALSE, tz=""){
defaultQualifier <- "NA"
}
- if("qualifier" %in% names(DF2)){
- DF2$qualifier <- ifelse(defaultQualifier != DF2$qualifier,DF2$qualifier,defaultQualifier)
+ if("swe:value" %in% names(DF2)){
+ isQual <- as.character(xpathApply(chunk,
+ "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP/wml2:metadata/wml2:TVPMeasurementMetadata/wml2:qualifier/@xlink:title",
+ namespaces = chunkNS))
+ DF2$qualifier <- ifelse(defaultQualifier != isQual,isQual,defaultQualifier)
+ DF2$`swe:value` <- NULL
} else {
DF2$qualifier <- rep(defaultQualifier,nrow(DF2))
}
- DF2$qualifier <- ifelse("Provisional data subject to revision." == DF2$qualifier, "P",
- ifelse("Approved for publication. Processing and review completed." == DF2$qualifier, "A", DF2$qualifier))
+# DF2$qualifier <- ifelse("Provisional data subject to revision." == DF2$qualifier, "P",
+# ifelse("Approved for publication. Processing and review completed." == DF2$qualifier, "A", DF2$qualifier))
-
+#########################################
+
id <- as.character(xpathApply(chunk, "//gml:identifier", xmlValue, namespaces = chunkNS))
DF2$identifier <- rep(id, nrow(DF2))
--
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