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ropensci / ritis

Integrated Taxonomic Information Service (ITIS) R client
https://docs.ropensci.org/ritis
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`parse_raw()` errors on empty input when tibble >= 3.0.0 #26

Open rix133 opened 11 months ago

rix133 commented 11 months ago

The call to ritis::terms gives an error

ritis::terms("Boleophthalmus dussumieri", what = "scientific")

Error:
! The `x` argument of `as_tibble()` can't be missing as of tibble
  3.0.0.
Session Info ```r > sessionInfo() R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=Estonian_Estonia.utf8 LC_CTYPE=Estonian_Estonia.utf8 [3] LC_MONETARY=Estonian_Estonia.utf8 LC_NUMERIC=C [5] LC_TIME=Estonian_Estonia.utf8 time zone: Europe/Tallinn tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] taxize_0.9.100 loaded via a namespace (and not attached): [1] gridExtra_2.3 remotes_2.4.2.1 inline_0.3.19 sandwich_3.0-2 [5] readxl_1.4.3 rlang_1.1.2 magrittr_2.0.3 multcomp_1.4-25 [9] matrixStats_1.1.0 compiler_4.3.2 loo_2.6.0 callr_3.7.3 [13] vctrs_0.6.4 reshape2_1.4.4 httpcode_0.3.0 stringr_1.5.1 [17] pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.1.1 backports_1.4.1 [21] ellipsis_0.3.2 pander_0.6.5 utf8_1.2.4 threejs_0.3.3 [25] promises_1.2.1 markdown_1.11 ps_1.7.5 xfun_0.41 [29] jsonlite_1.8.7 later_1.3.1 parallel_4.3.2 prettyunits_1.2.0 [33] R6_2.5.1 dygraphs_1.1.1.6 stringi_1.8.1 StanHeaders_2.26.28 [37] cellranger_1.1.0 estimability_1.4.1 knitr_1.45 iterators_1.0.14 [41] Rcpp_1.0.11 rstan_2.32.3 triebeard_0.4.1 zoo_1.8-12 [45] base64enc_0.1-3 bayesplot_1.10.0 httpuv_1.6.12 Matrix_1.6-3 [49] splines_4.3.2 igraph_1.5.1 tidyselect_1.2.0 rstudioapi_0.15.0 [53] abind_1.4-5 codetools_0.2-19 miniUI_0.1.1.1 curl_5.1.0 [57] processx_3.8.2 pkgbuild_1.4.2 lattice_0.22-5 tibble_3.2.1 [61] plyr_1.8.9 shiny_1.8.0 bridgesampling_1.1-2 posterior_1.5.0 [65] coda_0.19-4 survival_3.5-7 RcppParallel_5.1.7 xml2_1.3.5 [69] xts_0.13.1 pillar_1.9.0 ritis_1.0.0 tensorA_0.36.2 [73] foreach_1.5.2 checkmate_2.3.0 DT_0.30 stats4_4.3.2 [77] shinyjs_2.1.0 distributional_0.3.2 generics_0.1.3 ggplot2_3.4.4 [81] rstantools_2.3.1.1 munsell_0.5.0 scales_1.2.1 gtools_3.9.4 [85] xtable_1.8-4 glue_1.6.2 emmeans_1.8.9 tools_4.3.2 [89] shinystan_2.6.0 data.table_1.14.8 colourpicker_1.3.0 mvtnorm_1.2-3 [93] grid_4.3.2 bold_1.3.0 ape_5.7-1 urltools_1.7.3 [97] QuickJSR_1.0.7 crosstalk_1.2.0 colorspace_2.1-0 nlme_3.1-163 [101] cli_3.6.1 fansi_1.0.5 solrium_1.2.0 Brobdingnag_1.2-9 [105] dplyr_1.1.4 V8_4.4.0 gtable_0.3.4 digest_0.6.33 [109] crul_1.4.0 TH.data_1.1-2 brms_2.20.4 htmlwidgets_1.6.3 [113] farver_2.1.1 htmltools_0.5.7 lifecycle_1.0.4 mime_0.12 [117] shinythemes_1.2.0 MASS_7.3-60 ```
carolinetang77 commented 11 months ago

The same error occurs in ritis::full_record() and ritis::hierarchy_full():

ritis::full_record("175299")
Error:
! The `x` argument of `as_tibble()` can't be missing as of tibble 3.0.0.
ritis::hierarchy_full("175299")
Error:
! The `x` argument of `as_tibble()` can't be missing as of tibble 3.0.0.
rix133 commented 11 months ago

ok anyhow seems that the whole ITIS service is down right now and it does not handle this well

rix133 commented 11 months ago

so the input that the parse raw gets from ITIS json request is "" (empty string) and the tibble wants some input in here https://github.com/ropensci/ritis/blob/95f190cd328c80e75aa9619f04db7cd1016f7e9c/R/zzz.R#L62

jcblum commented 11 months ago

Thanks for noting the ITIS outage, @rix133, and for tracing this issue to the root cause. By the time I could investigate, I could no longer reproduce the error (since ITIS was responding again), so your follow-up was a big help!

tibble::tibble() returns an empty tibble, so I think that's the immediate fix here. However, I also think it would be nice if there was more user feedback that the ITIS request came back empty. I'm opening a separate feature issue for that.