xml2yaml2xml.R

library(xml2)
library(yaml)

# note: does not handle XML attributes or namespaces.
#    should work for simple xml structure used by PEcAn 

# Convert XML to YAML
xml2yml <- function(xml_string) {
  yaml_string <- xml_string |>
    read_xml() |>
    as_list()  |>
    as.yaml()
  return(yaml_string)
}

# Convert YAML to XML
yml2xml <- function(yaml_string) {
  xml_string <- yaml_string |>
    yaml.load() |>
    as_xml_document() |>
    as.character()
  return(xml_string)
}

# Examples

## xml2yml
xml_example <- '
<pecan>
 <outdir>/tmp/</outdir>
 <pfts>
  <pft>
   <name>biocro.salix</name>
  </pft>
 </pfts>
 <meta.analysis>
  <iter>3000</iter>
 </meta.analysis>
 <ensemble>
  <size>1</size>
  <variable>StemBiom</variable>
 </ensemble>
 <model>
  <name>BIOCRO</name>
 </model>
 <run>
  <site>
   <id>288</id>
   <name>Sapelo Island</name>
  </site>
  <start.date>2004-01-01 06:00:00</start.date>
  <end.date>2005-12-31 05:59:00</end.date>
  <host>
   <name>localhost</name>
  </host>
 </run>
</pecan>'

# Convert XML to YAML
yaml_result <- xml2yml(xml_example)
cat("YAML Output:\n", yaml_result)

## yml2xml

yaml_example <- '
pecan:
  outdir: /tmp/
  pfts:
    pft:
      name: biocro.salix
  meta.analysis:
    iter: 3000
  ensemble:
    size: 1
    variable: StemBiom
  model:
    name: BIOCRO
  run:
    site:
      id: 288
      name: Sapelo Island
    start.date: 2004-01-01 06:00:00
    end.date: 2005-12-31 05:59:00
    host:
      name: localhost'

# Convert back to XML
xml_result <- yml2xml(yaml_example)
cat("\nReconstructed XML:\n", xml_result)

# Tests
xml_result == xml_example