Error in check_number() when using Req_retry()

[nclsbarreto]

Hello,

I am trying to connect to a website to do some scraping. I am trying to learn how to slow down the requests because if I request to many times in a minute, I get a AWS challenge from the website that httr2 cant push past. If i wait the change goes away and it works just fine (which is annoying because it means the full pull I have to do will take a while, but whatever. Below is only going to one URL, but I have a couple hundred I want to pull (that are different URLs in the same website).

Any clarification, or advice, would be super helpful.

Thank you for rvest, httr, and httr2 in general, I have taught myself how to use them with the good good documentation and it has helped streamline a lot of my work!

Here is the normal code working just fine (i.e. i have not tried to call it quickly)

> table_url[1] %>%
+   request() %>% 
+   req_headers(
+     authority = "www.hospitalsafetygrade.org",
+     accept = "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7",
+     `accept-language` = "en-US,en;q=0.9",
+     `cache-control` = "no-cache",
+   ) %>% 
+   req_retry(max_seconds = 15,
+             is_transient = ~resp_status(.x) %in% c(429, 500, 503, 202),
+             after = ~.x) %>%
+   req_perform(verbosity = 1) 
-> GET /table-details/the-queens-medical-center HTTP/1.1
-> Host: www.hospitalsafetygrade.org
-> User-Agent: httr2/0.2.3 r-curl/4.3.2 libcurl/7.64.1
-> Accept-Encoding: deflate, gzip
-> authority: www.hospitalsafetygrade.org
-> accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7
-> accept-language: en-US,en;q=0.9
-> cache-control: no-cache
-> 
<- HTTP/1.1 200 OK
<- Date: Sat, 11 Nov 2023 01:02:28 GMT
<- Content-Type: text/html; charset=utf-8
<- Transfer-Encoding: chunked
<- Connection: keep-alive
<- Server: Apache/2.2.34 (Amazon)
<- X-AWC-Cache: partial
<- Set-Cookie: sid=6b3aad3f8ec0fd5382d3bde1d0dbc2d0; path=/; HttpOnly
<- 
<httr2_response>
GET https://www.hospitalsafetygrade.org/table-details/the-queens-medical-center
Status: 200 OK
Content-Type: text/html
Body: In memory (80435 bytes)

Here is the code that causes the errors - at the bottom it says "Error in check_number():! seconds must be a number" but I don't understand the error...I have been working on this a bit (took me a while to realize the status 202 meant it was giving me a redirect to a challenge)

> table_url[1] %>%
+   request() %>% 
+   req_headers(
+     authority = "www.hospitalsafetygrade.org",
+     accept = "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7",
+     `accept-language` = "en-US,en;q=0.9",
+     `cache-control` = "no-cache",
+   ) %>% 
+   req_retry(max_seconds = 15,
+             is_transient = ~resp_status(.x) %in% c(429, 500, 503, 202),
+             after = ~.x) %>%
+   req_perform(verbosity = 1) 
-> GET /table-details/the-queens-medical-center HTTP/1.1
-> Host: www.hospitalsafetygrade.org
-> User-Agent: httr2/0.2.3 r-curl/4.3.2 libcurl/7.64.1
-> Accept-Encoding: deflate, gzip
-> authority: www.hospitalsafetygrade.org
-> accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7
-> accept-language: en-US,en;q=0.9
-> cache-control: no-cache
-> 
<- HTTP/1.1 202 Accepted
<- Server: awselb/2.0
<- Date: Sat, 11 Nov 2023 00:50:46 GMT
<- Content-Length: 2411
<- Connection: keep-alive
<- x-amzn-waf-action: challenge
<- Cache-Control: no-store, max-age=0
<- Content-Type: text/html; charset=UTF-8
<- 
Error in `check_number()`:
! `seconds` must be a number
Run `rlang::last_trace()` to see where the error occurred.
Warning message:
In if (is.na(after)) { :
  the condition has length > 1 and only the first element will be used
> rlang::last_trace()
<error/rlang_error>
Error in `check_number()`:
! `seconds` must be a number
---
Backtrace:
    x
 1. +-... %>% req_perform(verbosity = 1)
 2. \-httr2::req_perform(., verbosity = 1)
 3.   \-httr2:::sys_sleep(delay)
 4.     \-httr2:::check_number(seconds, "`seconds`")
Run rlang::last_trace(drop = FALSE) to see 1 hidden frame.
> ?httr2::check_number()
Error in .helpForCall(topicExpr, parent.frame()) : 
  no methods for ‘check_number’ and no documentation for it as a function
> ?check_number()
Error in .helpForCall(topicExpr, parent.frame()) : 
  no methods for ‘check_number’ and no documentation for it as a function

here is my system information

R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RPostgreSQL_0.7-4 tmap_3.3-3        odbc_1.3.4        logger_0.2.2      DBI_1.1.3         glue_1.6.2        httr2_0.2.3       chromote_0.1.2   
 [9] magrittr_2.0.3    jsonlite_1.8.4    xml2_1.3.3        openxlsx_4.2.5    dbplyr_2.3.2      rvest_1.0.3       lubridate_1.9.2   forcats_1.0.0    
[17] stringr_1.5.0     dplyr_1.1.1       purrr_1.0.1       readr_2.1.4       tidyr_1.3.0       tibble_3.2.1      ggplot2_3.4.2     tidyverse_2.0.0  
[25] pacman_0.5.1     

loaded via a namespace (and not attached):
 [1] sf_1.0-12           bit64_4.0.5         RColorBrewer_1.1-3  httr_1.4.4          tools_4.1.1         utf8_1.2.2          R6_2.5.1           
 [8] KernSmooth_2.23-20  colorspace_2.0-3    raster_3.6-20       sp_1.5-0            withr_2.5.0         tidyselect_1.2.0    tictoc_1.2         
[15] processx_3.7.0      leaflet_2.1.2       curl_4.3.2          bit_4.0.4           compiler_4.1.1      leafem_0.2.0        cli_3.6.1          
[22] scales_1.2.1        classInt_0.4-7      proxy_0.4-27        rappdirs_0.3.3      digest_0.6.29       base64enc_0.1-3     dichromat_2.0-0.1  
[29] pkgconfig_2.0.3     htmltools_0.5.3     sessioninfo_1.2.2   fastmap_1.1.0       htmlwidgets_1.5.4   rlang_1.1.0         readxl_1.4.2       
[36] Microsoft365R_2.4.0 rstudioapi_0.14     generics_0.1.3      crosstalk_1.2.0     zip_2.2.1           AzureGraph_1.3.2    Rcpp_1.0.10        
[43] munsell_0.5.0       fansi_1.0.3         abind_1.4-5         terra_1.7-23        lifecycle_1.0.3     stringi_1.7.6       leafsync_0.1.0     
[50] snakecase_0.11.0    tmaptools_3.1-1     grid_4.1.1          blob_1.2.3          parallel_4.1.1      promises_1.2.0.1    lattice_0.20-45    
[57] stars_0.6-1         hms_1.1.2           ps_1.7.1            pillar_1.8.1        codetools_0.2-18    XML_3.99-0.10       selectr_0.4-2      
[64] png_0.1-7           vctrs_0.6.1         tzdb_0.3.0          cellranger_1.1.0    gtable_0.3.1        AzureAuth_1.3.3     janitor_2.1.0      
[71] lwgeom_0.2-11       e1071_1.7-11        later_1.3.0         viridisLite_0.4.1   class_7.3-20        websocket_1.4.1     units_0.8-0  

[hadley]

Could you please rework your reproducible example to use the reprex package ? That makes it easier to see both the input and the output, formatted in such a way that I can easily re-run in a local session.

[nclsbarreto]

Of course, sorry about that. I have cleaned it up a bit (in the hopes of making it more clear). The the error "Caused by error in read_xml.raw(): ! Failed to parse text" is what happens when it runs into the challenge (i.e. when I don't try to avoid it with headers)

library(pacman)
#> Warning: package 'pacman' was built under R version 4.1.3
p_load(tidyverse,
       rvest,
       dbplyr,
       openxlsx,
       xml2, 
       jsonlite,
       magrittr,
       chromote, 
       httr2, 
       reprex)

url <- "https://www.hospitalsafetygrade.org/search?findBy=state&state_prov=&rPos=0&rSort=grade"

lf_url <- "https://www.hospitalsafetygrade.org"

date.code <- url %>% 
  request() %>%
  req_perform() %>%
  resp_body_html() %>%
  html_elements('#HeaderSearch') %>%
  html_text2() %>%
  str_extract("_LEAP_DB_VERSION.*;") %>%
  str_extract("\\d+")

get_lf_data_url <- function(state) {
  table_data_url <- glue::glue("https://blink.atlasworks.com/api/v01/searchResult/HospitalLocations{date.code}/SearchResults?apiKey=4Gp6IU1Y0xVQ1uJodq1MDvdl1bXxY0&f.state={state}") %>%
    request() %>%
    req_perform() %>%
    resp_body_json() %$%
    response %$%
    html %>%
    read_html() %>% 
    html_nodes('.itemWrapper') %>%
    html_node("a") %>%
    html_attr('href') %>%
    paste0(lf_url, .) %>%
    gsub("/h/", "/table-details/", .)
  
  return(table_data_url)
} 

# state.abb[state.abb %in% c("HI",  # not using every state while testing
#                            "WA",
#                            "OR",
#                            "CA",
#                            "CO",
#                            "GA",
#                            "VA",
#                            "DC",
#                            "MD")]

lf_data_url <- map(state.abb[state.abb %in% c("HI",
                                              "WA",
                                              "OR",
                                              "CA",
                                              "CO",
                                              "GA",
                                              "VA",
                                              "DC",
                                              "MD")],
                   get_lf_data_url,
                   .progress = list(format = "{cli::pb_bar} {cli::pb_percent} | ETA: {cli::pb_eta} | total: [{cli::pb_elapsed}]")) %>%
  unlist()
#> ========>---------------------- 25% | ETA: 3s | total: [1.1s]
#> ===========>------------------- 38% | ETA: 2s | total: [1.3s]
#> ===============>--------------- 50% | ETA: 2s | total: [1.6s]
#> ==========================>---- 88% | ETA: 0s | total: [2s]

lf_data_list <- tibble(hospital_name = "", 
                       hospital_address = "", 
                       overall_grade = "",
                       grade_date = "", 
                       data = list())  

get_lf_data <- function(table.path) {
  det.req <- table.path %>%
    request() %>%
    req_perform() 
  
  lf_data_detail <- lf_data_list %>%
    add_row(hospital_name = det.req %>%
              resp_body_html() %>%
              html_elements(".detailWrapper h1") %>%
              html_text2(), 
            hospital_address = det.req %>%
              resp_body_html() %>%
              html_elements('.detailWrapper div[class="address"]') %>%
              html_text2(), 
            overall_grade = det.req %>%
              resp_body_html() %>%
              html_elements(".gradeWrapper") %>%
              html_attrs() %>%
              pluck(1) %>%
              str_extract(., ".$") %>%
              toupper(), 
            grade_date = det.req %>%
              resp_body_html() %>%
              html_elements(".gradeWrapper") %>%
              html_text2(),
            nest(det.req %>%
                   resp_body_html() %>%
                   html_table(., convert = FALSE) %>%
                   bind_rows(.id = "measure_type")))
  
  return(lf_data_detail)
}

map(lf_data_url[1:6],
    get_lf_data,
    .progress = list(format = "{cli::pb_bar} {cli::pb_percent} | ETA: {cli::pb_eta} | total: [{cli::pb_elapsed}]")) %>%
  bind_rows()
#> Error in `map()`:
#> i In index: 1.
#> Caused by error in `read_xml.raw()`:
#> ! Failed to parse text
#> Backtrace:
#>      x
#>   1. +-... %>% bind_rows()
#>   2. +-dplyr::bind_rows(.)
#>   3. | \-rlang::list2(...)
#>   4. +-purrr::map(lf_data_url[1:6], get_lf_data, .progress = list(format = "{cli::pb_bar} {cli::pb_percent} | ETA: {cli::pb_eta} | total: [{cli::pb_elapsed}]"))
#>   5. | \-purrr:::map_("list", .x, .f, ..., .progress = .progress)
#>   6. |   +-purrr:::with_indexed_errors(...)
#>   7. |   | \-base::withCallingHandlers(...)
#>   8. |   +-purrr:::call_with_cleanup(...)
#>   9. |   \-global .f(.x[[i]], ...)
#>  10. |     \-lf_data_list %>% ...
#>  11. +-tibble::add_row(...)
#>  12. | \-tibble::tibble(...)
#>  13. |   \-tibble:::tibble_quos(xs, .rows, .name_repair)
#>  14. |     \-rlang::eval_tidy(xs[[j]], mask)
#>  15. +-... %>% html_text2()
#>  16. +-rvest::html_text2(.)
#>  17. +-rvest::html_elements(., ".detailWrapper h1")
#>  18. +-httr2::resp_body_html(.)
#>  19. | +-xml2::read_html(resp$body, ...)
#>  20. | \-xml2:::read_html.default(resp$body, ...)
#>  21. |   +-base::suppressWarnings(...)
#>  22. |   | \-base::withCallingHandlers(...)
#>  23. |   +-xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
#>  24. |   \-xml2:::read_xml.raw(...)
#>  25. \-base::.handleSimpleError(...)
#>  26.   \-purrr (local) h(simpleError(msg, call))
#>  27.     \-cli::cli_abort(...)
#>  28.       \-rlang::abort(...)

get_lf_data_slow <- slowly(get_lf_data, rate = rate_delay(10), quiet = FALSE)

lf_data_raw <- map(lf_data_url[1:5],
                   get_lf_data_slow,
                   .progress = list(format = "{cli::pb_bar} {cli::pb_percent} | ETA: {cli::pb_eta} | total: [{cli::pb_elapsed}]")) %>%
  bind_rows()
#> Error in `map()`:
#> i In index: 1.
#> Caused by error in `read_xml.raw()`:
#> ! Failed to parse text
#> Backtrace:
#>      x
#>   1. +-... %>% bind_rows()
#>   2. +-dplyr::bind_rows(.)
#>   3. | \-rlang::list2(...)
#>   4. +-purrr::map(lf_data_url[1:5], get_lf_data_slow, .progress = list(format = "{cli::pb_bar} {cli::pb_percent} | ETA: {cli::pb_eta} | total: [{cli::pb_elapsed}]"))
#>   5. | \-purrr:::map_("list", .x, .f, ..., .progress = .progress)
#>   6. |   +-purrr:::with_indexed_errors(...)
#>   7. |   | \-base::withCallingHandlers(...)
#>   8. |   +-purrr:::call_with_cleanup(...)
#>   9. |   \-purrr (local) .f(.x[[i]], ...)
#>  10. |     \-global f(...)
#>  11. |       \-lf_data_list %>% ...
#>  12. +-tibble::add_row(...)
#>  13. | \-tibble::tibble(...)
#>  14. |   \-tibble:::tibble_quos(xs, .rows, .name_repair)
#>  15. |     \-rlang::eval_tidy(xs[[j]], mask)
#>  16. +-... %>% html_text2()
#>  17. +-rvest::html_text2(.)
#>  18. +-rvest::html_elements(., ".detailWrapper h1")
#>  19. +-httr2::resp_body_html(.)
#>  20. | +-xml2::read_html(resp$body, ...)
#>  21. | \-xml2:::read_html.default(resp$body, ...)
#>  22. |   +-base::suppressWarnings(...)
#>  23. |   | \-base::withCallingHandlers(...)
#>  24. |   +-xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
#>  25. |   \-xml2:::read_xml.raw(...)
#>  26. \-base::.handleSimpleError(...)
#>  27.   \-purrr (local) h(simpleError(msg, call))
#>  28.     \-cli::cli_abort(...)
#>  29.       \-rlang::abort(...)

get_lf_data.retry <- function(table.path) {
  det.req <- table.path %>%
    request() %>%
    req_headers(
      authority = "www.hospitalsafetygrade.org",
      accept = "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7",
      `accept-language` = "en-US,en;q=0.9",
      `cache-control` = "no-cache",
    ) %>% 
    req_retry(max_seconds = 15,
              is_transient = ~resp_status(.x) %in% c(429, 500, 503, 202),
              after = ~.x) %>%
    req_perform() 
  
  lf_data_detail <- lf_data_list %>%
    add_row(hospital_name = det.req %>%
              resp_body_html() %>%
              html_elements(".detailWrapper h1") %>%
              html_text2(), 
            hospital_address = det.req %>%
              resp_body_html() %>%
              html_elements('.detailWrapper div[class="address"]') %>%
              html_text2(), 
            overall_grade = det.req %>%
              resp_body_html() %>%
              html_elements(".gradeWrapper") %>%
              html_attrs() %>%
              pluck(1) %>%
              str_extract(., ".$") %>%
              toupper(), 
            grade_date = det.req %>%
              resp_body_html() %>%
              html_elements(".gradeWrapper") %>%
              html_text2(),
            nest(det.req %>%
                   resp_body_html() %>%
                   html_table(., convert = FALSE) %>%
                   bind_rows(.id = "measure_type")))
  
  return(lf_data_detail)
}

map(lf_data_url[1:6],
    get_lf_data.retry,
    .progress = list(format = "{cli::pb_bar} {cli::pb_percent} | ETA: {cli::pb_eta} | total: [{cli::pb_elapsed}]")) %>%
  bind_rows()
#> Warning in if (is.na(after)) {: the condition has length > 1 and only the first
#> element will be used
#> Error in `map()`:
#> i In index: 1.
#> Caused by error in `check_number()`:
#> ! `seconds` must be a number
#> Backtrace:
#>      x
#>   1. +-... %>% bind_rows()
#>   2. +-dplyr::bind_rows(.)
#>   3. | \-rlang::list2(...)
#>   4. +-purrr::map(lf_data_url[1:6], get_lf_data.retry, .progress = list(format = "{cli::pb_bar} {cli::pb_percent} | ETA: {cli::pb_eta} | total: [{cli::pb_elapsed}]"))
#>   5. | \-purrr:::map_("list", .x, .f, ..., .progress = .progress)
#>   6. |   +-purrr:::with_indexed_errors(...)
#>   7. |   | \-base::withCallingHandlers(...)
#>   8. |   +-purrr:::call_with_cleanup(...)
#>   9. |   \-global .f(.x[[i]], ...)
#>  10. |     \-... %>% req_perform()
#>  11. \-httr2::req_perform(.)
#>  12.   \-httr2:::sys_sleep(delay)
#>  13.     \-httr2:::check_number(seconds, "`seconds`")
#>  14.       \-rlang::abort(glue("{name} must be a number"))

^{Created on 2023-11-13 with reprex v2.0.2}

Session info

sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value
#>  version  R version 4.1.1 (2021-08-10)
#>  os       Windows 10 x64 (build 19045)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United States.1252
#>  ctype    English_United States.1252
#>  tz       America/Los_Angeles
#>  date     2023-11-13
#>  pandoc   2.14.0.3 @ C:/Program Files/RStudio/bin/pandoc/ (via rmarkdown)
#> 
#> - Packages -------------------------------------------------------------------
#>  package     * version date (UTC) lib source
#>  chromote    * 0.1.2   2023-08-11 [1] CRAN (R 4.1.1)
#>  cli           3.6.1   2023-03-23 [1] CRAN (R 4.1.3)
#>  colorspace    2.0-3   2022-02-21 [1] CRAN (R 4.1.3)
#>  curl          4.3.2   2021-06-23 [1] CRAN (R 4.1.3)
#>  DBI           1.1.3   2022-06-18 [1] CRAN (R 4.1.3)
#>  dbplyr      * 2.3.2   2023-03-21 [1] CRAN (R 4.1.3)
#>  digest        0.6.29  2021-12-01 [1] CRAN (R 4.1.3)
#>  dplyr       * 1.1.1   2023-03-22 [1] CRAN (R 4.1.3)
#>  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.3)
#>  evaluate      0.16    2022-08-09 [1] CRAN (R 4.1.3)
#>  fansi         1.0.3   2022-03-24 [1] CRAN (R 4.1.3)
#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.3)
#>  forcats     * 1.0.0   2023-01-29 [1] CRAN (R 4.1.3)
#>  fs            1.5.2   2021-12-08 [1] CRAN (R 4.1.3)
#>  generics      0.1.3   2022-07-05 [1] CRAN (R 4.1.3)
#>  ggplot2     * 3.4.2   2023-04-03 [1] CRAN (R 4.1.3)
#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.1.3)
#>  gtable        0.3.1   2022-09-01 [1] CRAN (R 4.1.3)
#>  highr         0.9     2021-04-16 [1] CRAN (R 4.1.3)
#>  hms           1.1.2   2022-08-19 [1] CRAN (R 4.1.3)
#>  htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.1.3)
#>  httr          1.4.4   2022-08-17 [1] CRAN (R 4.1.3)
#>  httr2       * 0.2.3   2023-05-08 [1] CRAN (R 4.1.1)
#>  jsonlite    * 1.8.4   2022-12-06 [1] CRAN (R 4.1.3)
#>  knitr         1.40    2022-08-24 [1] CRAN (R 4.1.3)
#>  later         1.3.0   2021-08-18 [1] CRAN (R 4.1.3)
#>  lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.1.3)
#>  lubridate   * 1.9.2   2023-02-10 [1] CRAN (R 4.1.3)
#>  magrittr    * 2.0.3   2022-03-30 [1] CRAN (R 4.1.3)
#>  munsell       0.5.0   2018-06-12 [1] CRAN (R 4.1.3)
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[hadley]

This problem is this code:

 req_retry(max_seconds = 15,
              is_transient = ~resp_status(.x) %in% c(429, 500, 503, 202),
              after = ~.x)

after is a callback function that takes a response and is supposed to return a number, but you're returning a response. I'll see if I can make the error message more clear.

[hadley]

Note to self: implementation saved in stash "a31a6943a9d7abfaa85f55ad5bea369f876e3b3b".

[nclsbarreto]

Ahhh got it. Takes a number...hence check_number() that makes sense. Thank you for your response. the documentation for how backoff and after should be used for testing a request() was confusing me a bit.