CODEWITHSUNDEEP
rxml
user2807119
user2807119

Reputation: 353

Extract attributes in XML using R

Trying to extract two attributes from the XML file extract (from a large XML file) namely 'nmRegime' and 'CalendarSystemT' (this is the date). Once extract those two records need to be saved as two columns in a data frame in R along with the filename.
There are several 'event' nodes within one given XML file and there are nearly 100 individual XML files.

<Event tEV="FirA" clearEV="false" onEV="true" dateOriginEV="Calendar" nYrsFromStEV="" nDaysFromStEV="" tFaqEV="Blank" tAaqEV="Blank" aqStYrEV="0" aqEnYrEV="0" nmEV="Fire_Cool" categoryEV="CatUndef" tEvent="Doc" idSP="105" nmRegime="Wheat, Tilled, stubble cool burn" regimeInstance="1">
      <notesEV></notesEV>
      <dateEV CalendarSystemT="FixedLength">19710331</dateEV>
      <FirA fracAfctFirA="0.6" fracGbfrToAtmsFirA="0.98" fracStlkToAtmsFirA="0.98" fracLeafToAtmsFirA="0.98" fracGbfrToGlitFirA="0.02" fracStlkToSlitFirA="0.02" fracLeafToLlitFirA="0.02" fracCortToCodrFirA="1.0" fracFirtToFidrFirA="1.0" fracDGlitToAtmsFirA="0.931" fracRGlitToAtmsFirA="0.931" fracDSlitToAtmsFirA="0.931" fracRSlitToAtmsFirA="0.931" fracDLlitToAtmsFirA="0.931" fracRLlitToAtmsFirA="0.931" fracDCodrToAtmsFirA="0.0" fracRCodrToAtmsFirA="0.0" fracDFidrToAtmsFirA="0.0" fracRFidrToAtmsFirA="0.0" fracDGlitToInrtFirA="0.019" fracRGlitToInrtFirA="0.019" fracDSlitToInrtFirA="0.019" fracRSlitToInrtFirA="0.019" fracDLlitToInrtFirA="0.019" fracRLlitToInrtFirA="0.019" fracDCodrToInrtFirA="0.0" fracRCodrToInrtFirA="0.0" fracDFidrToInrtFirA="0.0" fracRFidrToInrtFirA="0.0" fracSopmToAtmsFirA="" fracLrpmToAtmsFirA="" fracMrpmToAtmsFirA="" fracSommToAtmsFirA="" fracLrmmToAtmsFirA="" fracMrmmToAtmsFirA="" fracMicrToAtmsFirA="" fracSopmToInrtFirA="" fracLrpmToInrtFirA="" fracMrpmToInrtFirA="" fracSommToInrtFirA="" fracLrmmToInrtFirA="" fracMrmmToInrtFirA="" fracMicrToInrtFirA="" fracMnamNToAtmsFirA="" fracSAmmNToAtmsFirA="" fracSNtrNToAtmsFirA="" fracDAmmNToAtmsFirA="" fracDNtrNToAtmsFirA="" fixFirA="" phaFirA="" />
    </Event>

Had some success in extracting 'nmRegime' but no success with 'CalendarSystemT'. Used below code for data extraction.
The second question, is there a way to loop the list of XML files and do this operation?

# get records
library(xml2)
recs <- xml_find_all(xml, "//Event")

#extract the names
labs <- trimws(xml_attr(recs, "nmRegime"))
names <- labs[!is.na(labs)]

# Extract the date 
recs_t <- xml_find_all(xml, "//Event/dateEV")
time <- trimws(xml_attr(recs_t, "CalendarSystemT"))

Upvotes: 0

Views: 694

Answers (1)

Dave2e
Dave2e

Reputation: 24079

The calendar time value is not an attribute but is stored as the node's element and is accessed directly.

Also note that if an Event Node is missing a "dateEV" then there will be problems aligning the "labs" with the "time". It is better to extract the time value from each parent node instead of the entire document.

library(xml2)
library(dplyr)

xml<- read_xml('<Event tEV="FirA" clearEV="false" onEV="true" dateOriginEV="Calendar" nYrsFromStEV="" nDaysFromStEV="" tFaqEV="Blank" tAaqEV="Blank" aqStYrEV="0" aqEnYrEV="0" nmEV="Fire_Cool" categoryEV="CatUndef" tEvent="Doc" idSP="105" nmRegime="Wheat, Tilled, stubble cool burn" regimeInstance="1">
      <notesEV></notesEV>
      <dateEV CalendarSystemT="FixedLength">19710331</dateEV>
      <FirA fracAfctFirA="0.6" fracGbfrToAtmsFirA="0.98" fracStlkToAtmsFirA="0.98" fracLeafToAtmsFirA="0.98" fracGbfrToGlitFirA="0.02" fracStlkToSlitFirA="0.02" fracLeafToLlitFirA="0.02" fracCortToCodrFirA="1.0" fracFirtToFidrFirA="1.0" fracDGlitToAtmsFirA="0.931" fracRGlitToAtmsFirA="0.931" fracDSlitToAtmsFirA="0.931" fracRSlitToAtmsFirA="0.931" fracDLlitToAtmsFirA="0.931" fracRLlitToAtmsFirA="0.931" fracDCodrToAtmsFirA="0.0" fracRCodrToAtmsFirA="0.0" fracDFidrToAtmsFirA="0.0" fracRFidrToAtmsFirA="0.0" fracDGlitToInrtFirA="0.019" fracRGlitToInrtFirA="0.019" fracDSlitToInrtFirA="0.019" fracRSlitToInrtFirA="0.019" fracDLlitToInrtFirA="0.019" fracRLlitToInrtFirA="0.019" fracDCodrToInrtFirA="0.0" fracRCodrToInrtFirA="0.0" fracDFidrToInrtFirA="0.0" fracRFidrToInrtFirA="0.0" fracSopmToAtmsFirA="" fracLrpmToAtmsFirA="" fracMrpmToAtmsFirA="" fracSommToAtmsFirA="" fracLrmmToAtmsFirA="" fracMrmmToAtmsFirA="" fracMicrToAtmsFirA="" fracSopmToInrtFirA="" fracLrpmToInrtFirA="" fracMrpmToInrtFirA="" fracSommToInrtFirA="" fracLrmmToInrtFirA="" fracMrmmToInrtFirA="" fracMicrToInrtFirA="" fracMnamNToAtmsFirA="" fracSAmmNToAtmsFirA="" fracSNtrNToAtmsFirA="" fracDAmmNToAtmsFirA="" fracDNtrNToAtmsFirA="" fixFirA="" phaFirA="" />
    </Event>')

recs <- xml_find_all(xml, "//Event")

#extract the names 
labs <- trimws(xml_attr(recs, "nmRegime")) names <- labs[!is.na(labs)]

# Extract the date  
time <- xml_find_first(recs, ".//dateEV") %>% xml_text() %>% trimws()

To answer your second question, yes you could can wrap the above script into a function and then use lapply to loop through your entire list of files.
See this question and answer for details: R XML - combining parent and child nodes(w same name) into data frame

Upvotes: 1

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