[R] using xpath with xml2

[Ben Tupper]

Hi,

I have mined XML extensively with R before now, but my xpath chops seem to be regressing recently. I know that I can roll up my sleeves and search through the child nodes of the root, but I can't noodle out why using the xpath description returns an empty nodeset.

Any suggestions and nudges most welcome.

### START

library(xml2)
library(httr)
library(magrittr)

daymet_uri <- "https://thredds.daac.ornl.gov/thredds/catalog/ornldaac/1328/catalog.xml"

# run the following to show the node in a browser
# httr::BROWSE(daymet_uri)

daymet <- httr::GET(daymet_uri) %>%
  httr::content(type = "text/xml", encoding = "UTF-8")

# list the children "service" and "dataset"
daymet %>% xml2::xml_children()
#{xml_nodeset (2)}
#[1] <service name="all" serviceType="Compound" base="">\n  <service name="odap" #serviceTyp ...
#[2] <dataset name="Daymet: Daily Surface Weather Data on a 1-km Grid for North America, Ve ...

# find all descendants of node name "dataset"
#
# according to this tutorial we should find 'dataset'
# https://www.w3schools.com/xml/xpath_syntax.asp
daymet %>% xml2::xml_find_all(xpath = "//dataset")
# {xml_nodeset (0)}

# I have also tried every other xpath combination I think of e.g.
#   ".//dataset", "./dataset", "/dataset" and "dataset"
# They each yield an empty nodeset

### END

> sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] magrittr_1.5 httr_1.4.1   xml2_1.2.2  

loaded via a namespace (and not attached):
[1] compiler_3.5.1 R6_2.4.0       tools_3.5.1    curl_4.2      
[5] yaml_2.2.0     Rcpp_1.0.3    


Thanks,
Ben

Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

Ecological Forecasting: https://eco.bigelow.org/