cycle20 / EZCancerTarget

Collect drug compound data based on editable target table and scan various sources to augment dataset
https://cycle20.github.io/EZCancerTarget/
GNU General Public License v3.0
1 stars 1 forks source link

fdaLabel service access issues #50

Closed cycle20 closed 3 years ago

cycle20 commented 3 years ago

Failed workflow https://github.com/cycle20/scancer/runs/3382057150?check_suite_focus=true clue_76_logs_322.zip

2021-08-20 12:56:33 :: from cache: https://nctr-crs.fda.gov/fdalabel/services/spl/summaries?pert=trometamol&ingr=FALSE
fdaLabel :: trometamol :: results not found
# sleeping 30 secs
Error: Problem with `mutate()` column `fdaSearchResults`.
ℹ `fdaSearchResults = list(getFDALabelResults(pert_iname))`.
✖ Timeout was reached: [nctr-crs.fda.gov] Connection timed out after 10001 milliseconds
ℹ The error occurred in row 3536.
Backtrace:
     █
  1. ├─global::main()
  2. │ └─global::patch(clueTable)
  3. │   └─global::fdaLabel(clueTable)
  4. │     └─clueTable %>% mutate(fdaSearchResults = list(getFDALabelResults(pert_iname)))
  5. ├─dplyr::mutate(., fdaSearchResults = list(getFDALabelResults(pert_iname)))
  6. ├─dplyr:::mutate.data.frame(., fdaSearchResults = list(getFDALabelResults(pert_iname)))
  7. │ └─dplyr:::mutate_cols(.data, ..., caller_env = caller_env())
  8. │   ├─base::withCallingHandlers(...)
  9. │   └─mask$eval_all_mutate(quo)
 10. ├─getFDALabelResults(pert_iname)
 11. │ └─global::getPageCached(...)
 12. │   └─downloadFunc(url)
 13. │     └─httr::POST(...)
 14. │       └─httr:::request_perform(req, hu$handle$handle)
 15. │         ├─httr:::request_fetch(req$output, req$url, handle)
 16. │         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 17. │           └─curl::curl_fetch_memory(url, handle = handle)
 18. └─base::.handleSimpleError(...)
 19.   └─dplyr:::h(simpleError(msg, call))
There were 29 warnings (use warnings() to see them)
Execution halted
Error: Process completed with exit code 1.

https://github.com/cycle20/scancer/runs/3382210926?check_suite_focus=true clue_77_logs_323.zip

cycle20 commented 3 years ago

I couldn't reproduce the Connection timed out after 10001 milliseconds issue, however another issue encountered and fixed during local testing of getFDALabelResult