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Commit 67a23d71 authored by Kevin M. Smith's avatar Kevin M. Smith
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Catch <values> without <value> error. 

This catches responses that return <values> without associated <value>.

Example Below: 
  
  url = "http://waterservices.usgs.gov/nwis/iv/?format=waterml,1.1&huc=02&startDT=2014-10-11T00:00:00.000&endDT=2014-10-11T00:30:00.000&parameterCd=00060,00065"
  data <- getWaterML1Data(url)

WaterML Response (chunk)
  <ns1:timeSeries xmlns:ns1="http://www.cuahsi.org/waterML/1.1/" name="USGS:01350080:00065:00011">
  <ns1:sourceInfo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ns1:SiteInfoType">
  <ns1:siteName>MANOR KILL AT WEST CONESVILLE NEAR GILBOA NY</ns1:siteName>
  <ns1:siteCode network="NWIS" agencyCode="USGS">01350080</ns1:siteCode>
  <ns1:timeZoneInfo siteUsesDaylightSavingsTime="false">
  <ns1:defaultTimeZone zoneOffset="-05:00" zoneAbbreviation="EST"/>
  <ns1:daylightSavingsTimeZone zoneOffset="-04:00" zoneAbbreviation="EDT"/>
  </ns1:timeZoneInfo>
  <ns1:geoLocation>
  <ns1:geogLocation xsi:type="ns1:LatLonPointType" srs="EPSG:4326">
  <ns1:latitude>42.37694444</ns1:latitude>
  <ns1:longitude>-74.4130556</ns1:longitude>
  </ns1:geogLocation>
  </ns1:geoLocation>
  <ns1:siteProperty name="siteTypeCd">ST</ns1:siteProperty>
  <ns1:siteProperty name="hucCd">02020005</ns1:siteProperty>
  <ns1:siteProperty name="stateCd">36</ns1:siteProperty>
  <ns1:siteProperty name="countyCd">36095</ns1:siteProperty>
  </ns1:sourceInfo>
  <ns1:variable ns1:oid="45807202">
  <ns1:variableCode network="NWIS" vocabulary="NWIS:UnitValues" default="true" variableID="45807202">00065</ns1:variableCode>
  <ns1:variableName>Gage height, ft</ns1:variableName>
  <ns1:variableDescription>Gage height, feet</ns1:variableDescription>
  <ns1:valueType>Derived Value</ns1:valueType>
  <ns1:unit>
  <ns1:unitCode>ft</ns1:unitCode>
  </ns1:unit>
  <ns1:options>
  <ns1:option name="Statistic" optionCode="00011"/>
  </ns1:options>
  <ns1:noDataValue>-999999.0</ns1:noDataValue>
  </ns1:variable>
  <ns1:values>
  <ns1:method methodID="1">
  <ns1:methodDescription>[backup from well]</ns1:methodDescription>
  </ns1:method>
  </ns1:values>
  <ns1:values>
  <ns1:value qualifiers="P" dateTime="2014-10-11T00:00:00.000-05:00">0.85</ns1:value>
  <ns1:value qualifiers="P" dateTime="2014-10-11T00:15:00.000-05:00">0.85</ns1:value>
  <ns1:value qualifiers="P" dateTime="2014-10-11T00:30:00.000-05:00">0.85</ns1:value>
  <ns1:qualifier qualifierID="0" ns1:network="NWIS" ns1:vocabulary="uv_rmk_cd">
  <ns1:qualifierCode>P</ns1:qualifierCode>
  <ns1:qualifierDescription>Provisional data subject to revision.</ns1:qualifierDescription>
  </ns1:qualifier>
  <ns1:method methodID="12">
  <ns1:methodDescription/>
  </ns1:method>
  </ns1:values>
  </ns1:timeSeries>
parent 1e1c5804
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1 merge request!38Catch <values> without <value> error.
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R/getWaterML1Data.r
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...@@ -60,20 +60,20 @@ getWaterML1Data <- function(obs_url){ ...@@ -60,20 +60,20 @@ getWaterML1Data <- function(obs_url){
chunk <- xmlDoc(timeSeries[[i]]) chunk <- xmlDoc(timeSeries[[i]])
chunk <- xmlRoot(chunk) chunk <- xmlRoot(chunk)
chunkNS <- xmlNamespaceDefinitions(chunk, simplify = TRUE) chunkNS <- xmlNamespaceDefinitions(chunk, simplify = TRUE)
# site <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteProperty[@name='hucCd']", namespaces = chunkNS, xmlValue)) # site <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteProperty[@name='hucCd']", namespaces = chunkNS, xmlValue))
site <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteCode", namespaces = chunkNS, xmlValue)) site <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteCode", namespaces = chunkNS, xmlValue))
agency <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteCode/@agencyCode", namespaces = chunkNS)) agency <- as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:siteCode/@agencyCode", namespaces = chunkNS))
pCode <-as.character(xpathApply(chunk, "ns1:variable/ns1:variableCode", namespaces = chunkNS, xmlValue)) pCode <-as.character(xpathApply(chunk, "ns1:variable/ns1:variableCode", namespaces = chunkNS, xmlValue))
statCd <- as.character(xpathApply(chunk, "ns1:variable/ns1:options/ns1:option/@optionCode", namespaces = chunkNS)) statCd <- as.character(xpathApply(chunk, "ns1:variable/ns1:options/ns1:option/@optionCode", namespaces = chunkNS))
valuesIndex <- as.numeric(which("values" == names(chunk))) valuesIndex <- as.numeric(which("values" == names(chunk)))
zoneAbbrievs <- c(as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:timeZoneInfo/ns1:defaultTimeZone/@zoneAbbreviation", namespaces = chunkNS)), zoneAbbrievs <- c(as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:timeZoneInfo/ns1:defaultTimeZone/@zoneAbbreviation", namespaces = chunkNS)),
as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:timeZoneInfo/ns1:daylightSavingsTimeZone/@zoneAbbreviation", namespaces = chunkNS))) as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:timeZoneInfo/ns1:daylightSavingsTimeZone/@zoneAbbreviation", namespaces = chunkNS)))
names(zoneAbbrievs) <- c(as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:timeZoneInfo/ns1:defaultTimeZone/@zoneOffset", namespaces = chunkNS)), names(zoneAbbrievs) <- c(as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:timeZoneInfo/ns1:defaultTimeZone/@zoneOffset", namespaces = chunkNS)),
as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:timeZoneInfo/ns1:daylightSavingsTimeZone/@zoneOffset", namespaces = chunkNS))) as.character(xpathApply(chunk, "ns1:sourceInfo/ns1:timeZoneInfo/ns1:daylightSavingsTimeZone/@zoneOffset", namespaces = chunkNS)))
for (j in valuesIndex){ for (j in valuesIndex){
subChunk <- xmlRoot(xmlDoc(chunk[[j]])) subChunk <- xmlRoot(xmlDoc(chunk[[j]]))
...@@ -82,67 +82,69 @@ getWaterML1Data <- function(obs_url){ ...@@ -82,67 +82,69 @@ getWaterML1Data <- function(obs_url){
methodID <- padVariable(methodID,2) methodID <- padVariable(methodID,2)
value <- as.numeric(xpathSApply(subChunk, "ns1:value",namespaces = chunkNS, xmlValue)) value <- as.numeric(xpathSApply(subChunk, "ns1:value",namespaces = chunkNS, xmlValue))
datetime <- as.POSIXct(strptime(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS),"%Y-%m-%dT%H:%M:%S")) if(length(value)!=0){
tzHours <- substr(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS), datetime <- as.POSIXct(strptime(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS),"%Y-%m-%dT%H:%M:%S"))
24, tzHours <- substr(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS),
nchar(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS))) 24,
if(mean(nchar(tzHours),rm.na=TRUE) == 6){ nchar(xpathSApply(subChunk, "ns1:value/@dateTime",namespaces = chunkNS)))
tzAbbriev <- zoneAbbrievs[tzHours] if(mean(nchar(tzHours),rm.na=TRUE) == 6){
} else { tzAbbriev <- zoneAbbrievs[tzHours]
tzAbbriev <- rep(as.character(zoneAbbrievs[1]),length(datetime)) } else {
} tzAbbriev <- rep(as.character(zoneAbbrievs[1]),length(datetime))
timeZoneLibrary <- setNames(c("America/New_York","America/New_York","America/Chicago","America/Chicago",
"America/Denver","America/Denver","America/Los_Angeles","America/Los_Angeles",
"America/Anchorage","America/Anchorage","America/Honolulu","America/Honolulu"),
c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
timeZone <- as.character(timeZoneLibrary[tzAbbriev])
if(length(unique(timeZone)) == 1){
datetime <- as.POSIXct(as.character(datetime), tz = unique(timeZone))
} else {
warning("Mixed time zone information")
for(i in seq_along(datetime)){
datetime[i] <- as.POSIXct(as.character(datetime[i]), tz = timeZone[i])
} }
}
qualifier <- as.character(xpathSApply(subChunk, "ns1:value/@qualifiers",namespaces = chunkNS))
valueName <- paste(methodID,pCode,statCd,sep="_")
qualName <- paste(methodID,pCode,statCd,"cd",sep="_")
valueName <- paste("X",valueName,sep="")
qualName <- paste("X",qualName,sep="")
assign(valueName,value)
assign(qualName,qualifier)
if(length(get(qualName))!=0){
df <- data.frame(rep(agency,length(datetime)),
rep(site,length(datetime)),
datetime,
tzAbbriev,
get(valueName),
get(qualName),
stringsAsFactors=FALSE)
names(df) <- c("agency_cd","site_no","datetime","tz_cd",valueName,qualName) timeZoneLibrary <- setNames(c("America/New_York","America/New_York","America/Chicago","America/Chicago",
} else { "America/Denver","America/Denver","America/Los_Angeles","America/Los_Angeles",
df <- data.frame(rep(agency,length(datetime)), "America/Anchorage","America/Anchorage","America/Honolulu","America/Honolulu"),
rep(site,length(datetime)), c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
datetime, timeZone <- as.character(timeZoneLibrary[tzAbbriev])
tzAbbriev, if(length(unique(timeZone)) == 1){
get(valueName),stringsAsFactors=FALSE) datetime <- as.POSIXct(as.character(datetime), tz = unique(timeZone))
} else {
warning("Mixed time zone information")
for(i in seq_along(datetime)){
datetime[i] <- as.POSIXct(as.character(datetime[i]), tz = timeZone[i])
}
}
names(df) <- c("agency_cd","site_no","datetime","tz_cd",valueName) qualifier <- as.character(xpathSApply(subChunk, "ns1:value/@qualifiers",namespaces = chunkNS))
}
valueName <- paste(methodID,pCode,statCd,sep="_")
if (1 == i & valuesIndex[1] == j){ qualName <- paste(methodID,pCode,statCd,"cd",sep="_")
mergedDF <- df valueName <- paste("X",valueName,sep="")
} else { qualName <- paste("X",qualName,sep="")
similarNames <- intersect(names(mergedDF), names(df))
mergedDF <- merge(mergedDF, df,by=similarNames,all=TRUE) assign(valueName,value)
# mergedDF <- merge(mergedDF, df,by=c("agency_cd","site_no","datetime","tz_cd"),all=TRUE) assign(qualName,qualifier)
if(length(get(qualName))!=0){
df <- data.frame(rep(agency,length(datetime)),
rep(site,length(datetime)),
datetime,
tzAbbriev,
get(valueName),
get(qualName),
stringsAsFactors=FALSE)
names(df) <- c("agency_cd","site_no","datetime","tz_cd",valueName,qualName)
} else {
df <- data.frame(rep(agency,length(datetime)),
rep(site,length(datetime)),
datetime,
tzAbbriev,
get(valueName),stringsAsFactors=FALSE)
names(df) <- c("agency_cd","site_no","datetime","tz_cd",valueName)
}
if (1 == i & valuesIndex[1] == j){
mergedDF <- df
} else {
similarNames <- intersect(names(mergedDF), names(df))
mergedDF <- merge(mergedDF, df,by=similarNames,all=TRUE)
# mergedDF <- merge(mergedDF, df,by=c("agency_cd","site_no","datetime","tz_cd"),all=TRUE)
}
} }
} }
} }
......
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