Iterating rvest scrape function gives: "Error in open.connection(x, "rb") : Timeout was reached"

Question

I'm scraping this website using the "rvest"-package. When I iterate my function too many times I get "Error in open.connection(x, "rb") : Timeout was reached". I have searched for similar questions but the answers seems to lead to dead ends. I have a suspicion that it is server side and the website has a build-in restriction on how many times I can visit the page. How do investigate this hypothesis?

The code: I have the links to the underlying web pages and want to construct a data frame with the information extracted from the associated web pages. I have simplified my scraping function a bit as the problem is still occurring with a simpler function:

scrape_test = function(link) {

  slit <-  str_split(link, "/") %>%
    unlist()
  id <- slit[5]
  sem <- slit[6]

  name <- link %>% 
    read_html(encoding = "UTF-8") %>%
    html_nodes("h2") %>%
    html_text() %>%
    str_replace_all("\r\n", "") %>%
    str_trim()

  return(data.frame(id, sem, name))
}

I use the purrr-package map_df() to iterate the function:

test.data = links %>%
  map_df(scrape_test)

Now, if I iterate the function using only 50 links I receive no error. But when I increase the number of links I encounter the before-mentioned error. Furthermore I get the following warnings:

"In bind_rows_(x, .id) : Unequal factor levels: coercing to character"
"closing unused connection 4 (link)"

EDIT: The following code making an object of links can be used to reproduce my results:

links <- c(rep("http://karakterstatistik.stads.ku.dk/Histogram/NMAK13032E/Winter-2013/B2", 100))

I forgot a "link %>%" as I simplified my function directly in stack overflow, sorry about that. The problem lies in the multiple iterations where it suddenly gives the error when you reach too many links. — ScrapeGoat
Maybe try inserting a Sys.sleep(x) (insert your x of choice) into your function to pause in between requests? — Weihuang Wong
Yes, that would definitely be a possible solution. How do I know what "x" should be? Are there any tricks or is it trial and error? However, as I want to iterate 1000 links as a start and possible 32000 I probably need another solution since setting x=2 would take a long while to run. — ScrapeGoat

Weihuang Wong Weihuang Wong · Accepted Answer · 2016-08-20T17:57:51

With large scraping tasks I would usually do a for-loop, which helps with troubleshooting. Create an empty list for your output:

d <- vector("list", length(links))

Here I do a for-loop, with a tryCatch block so that if the output is an error, we wait a couple of seconds and try again. We also include a counter that moves on to the next link if we're still getting an error after five attempts. In addition, we have if (!(links[i] %in% names(d))) so that if we have to break the loop, we can skip the links we've already scraped when we restart the loop.

for (i in seq_along(links)) {
  if (!(links[i] %in% names(d))) {
    cat(paste("Doing", links[i], "..."))
    ok <- FALSE
    counter <- 0
    while (ok == FALSE & counter <= 5) {
      counter <- counter + 1
      out <- tryCatch({                  
                  scrape_test(links[i])
                },
                error = function(e) {
                  Sys.sleep(2)
                  e
                }
              )
      if ("error" %in% class(out)) {
        cat(".")
      } else {
        ok <- TRUE
        cat(" Done.")
      }
    }
    cat("\n")
    d[[i]] <- out
    names(d)[i] <- links[i]
  }
}

Iterating rvest scrape function gives: "Error in open.connection(x, "rb") : Timeout was reached"

1 Answers