Term replacement

replace.R

library(RCurl)
library(xml2)
library(dplyr)
library(stringr)

obsolete <- readr::read_tsv('obsolete-terms.txt')


# get our ontology files
ontologies <- system2("ssh" ,paste0(ontology_server," ls ", ontology_path),stdout = TRUE)
ontologies <- ontologies[!grepl('tmp|nifstd',ontologies)]
dir.create('data-raw/ontologies',recursive = TRUE,showWarnings = FALSE)
ontologies = ontologies[ontologies %in% list.files('data-raw/ontologies/')]


ontologies %>% lapply(function(x){
  RCurl::scp(ontology_server,file.path(ontology_path,x)) %>% 
    writeBin(file.path('data-raw/ontologies',x))
})


# find listed alternatives
alternative_terms <- ontologies %>% lapply(function(x){
  print(x)
  onto <- xml2::read_xml(file.path('data-raw/ontologies/',x))
  children <- xml2::xml_children(onto)
  child_types <- xml2::xml_name(children)
  
  ontos <- children[child_types == 'Ontology']
  classes <- children[child_types == 'Class']
  
  
  term_links <- xml2::xml_attr(classes,'about')
  
  alternatives <- classes %>% lapply(function(y){
    term_children <- xml2::xml_children(y)
    term_contents <- xml2::xml_name(term_children)
    term_children[term_contents =='hasAlternativeId'] %>% xml2::xml_text()
  })
  
  names(alternatives) <- term_links
  return(alternatives)
})
names(alternative_terms) <- ontologies

alternatives <- alternative_terms %>% lapply(\(x){
  x %>% sapply(length) %>% rep(names(x),.)
}) %>% unlist
to_replace <- alternative_terms %>% lapply(\(x){
  x %>% unlist
}) %>% unlist

# find replacements
obsolete$compact_names <-  obsolete$ValueUri %>% 
  stringr::str_extract('(?<=((/obo)|(/efo)|(/ORDO))/).*') %>% 
  stringr::str_replace('_',':')

obsolete$replacements <- alternatives[match(obsolete$compact_names,to_replace)]
obsolete = obsolete %>% dplyr::select(-compact_names)

readr::write_tsv(obsolete,file = 'obsolete-term-replacements.txt')