Script that checks the status of HMDB identifiers

checkOutdated.groovy

urlPrefix = "http://www.hmdb.ca/metabolites/"

secondaries = new HashMap()
outdated = new ArrayList()

def renewFile(file) {
  if (ui.fileExists(file)) ui.remove(file)
  ui.newFile(file)
  return file
}
outdatedFile = "/HMDB/outdated-10k.txt"
renewFile(outdatedFile)
secondariesFile = "/HMDB/secondaries-10k.txt"
renewFile(secondariesFile)

for (int i=1; i<=10000; i++) {
  hmdbid = "HMDB" + String.format("%05d", i);
  println "checking $hmdbid ..."
  try {
    pageContent = bioclipse.download(urlPrefix + hmdbid)
  
    if (!secondaries.containsKey(hmdbid)) { // skip, already did this one
      contentModel = jsoup.parseString(pageContent)
      tableContent = jsoup.select(contentModel, "table.content-table th")
      if (tableContent == null) {
        // Outdated HMDB ID ?
        println "Oudated HMDB? $hmdbid"
        outdated.add(hmdbid)
      } else {
        // OK, valid HMDB ID, it seems
        for (element in tableContent) {
          if ("Secondary Accession Numbers" == element.ownText()) {
            for (sibling in element.siblingElements()) {
              for (secid in jsoup.select(sibling, "ul li")) {
                secondaries.put(secid.ownText(), hmdbid)
                println secid.ownText() + ", $hmdbid"
                ui.append(secondariesFile, secid.ownText() + ", ${hmdbid}\n")
              }
            }
          }
        }
      }
    }
  } catch (Exception exception) {
    println "Oudated HMDB? $hmdbid (${exception.message})"
    outdated.add(hmdbid)
    ui.append(outdatedFile, hmdbid + "\n")
  }  
  sleep(500)
}