[R] using xpath with xml2

[Ben Tupper]

Forehead smack!  Of course!

Thank you, Bill!

> On Nov 12, 2019, at 2:50 PM, William Dunlap <wdunlap using tibco.com> wrote:
> 
> > xml_ns(daymet)
> d1    <-> http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0 <http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0>
> xlink <-> http://www.w3.org/1999/xlink <http://www.w3.org/1999/xlink>
> > daymet %>% xml2::xml_find_all(xpath = "d1:dataset")
> {xml_nodeset (1)}
> [1] <dataset name="Daymet: Daily Surface Weather Data on a 1-km Grid for Nort ...
> 
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com <http://tibco.com/>
> 
> On Tue, Nov 12, 2019 at 11:35 AM Ben Tupper <btupper using bigelow.org <mailto:btupper using bigelow.org>> wrote:
> 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 <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 <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 <http://www.bigelow.org/>
> 
> Ecological Forecasting: https://eco.bigelow.org/ <https://eco.bigelow.org/>
> 
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.

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/






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