Alabaster process all of annotationhub....

annotationhub_alabaster.R

library(alabaster)
library(AnnotationHub)
library(jsonlite)
ah = AnnotationHub()

STAGE_DIR = '/tmp/ah_staging'
dir.create(STAGE_DIR, showWarnings = FALSE)

write_error = function(dirname, e) {
  jsonlite::write_json(list(message=jsonlite::unbox(e$message)), file.path(dirname,'error.json'))
}


for(i in seq_along(ah)) {
  obj = ah[[i]]
  dirname = file.path(STAGE_DIR, sprintf('ah_%d', i))
  jsonfname = file.path(dirname, 'metadata.json')
  unlink(dirname, recursive = TRUE, force=TRUE)
  json = tryCatch(
    expr=alabaster.base::stageObject(obj, STAGE_DIR, sprintf('ah_%d', i)),
    error = function(e) write_error(dirname, e),
    finally=list(error=TRUE)
  )
  json[['_id']]=i
  jsonlite::write_json(json, jsonfname, auto_unbox=TRUE)
  message(i)
}