mikeroswell
commented
2 years ago Looks like it is overspecifying st in natserv:::handle_sptax
Suggest edit from current:
if (!all(names(st) %in% c("level", "scientificTaxonomy", "informalTaxonomy")))
to
if (!all(names(st) %in% c("level", "kingdom", "scientificTaxonomy", "informalTaxonomy")))
sckott
maelle
I can download all plants:
ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Plantae", level = "kingdom"))works, but if I try to download a group of animals, I get a 505 error:ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order")) # 505 errorI wonder if this is because when
level !="kingdom"kingdommust also be supplied, based on the documentation here. This is just a guess!Thanks for your help!!!
Session Info
```r ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Plantae", level = "kingdom")) # works ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order")) # 505 error R version 4.1.2 (2021-11-01) -- "Bird Hippie" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #get bug occurrences and statuses > # update natserv from time to tim > # remotes::install_github("ropensci/natserv") > library(natserv) #this is how we get naturserve status > library(rgbif) #how we get gbif observations > library(tidyverse) ── Attaching packages ───────────────────────────────────────────────── tidyverse 1.3.1 ── ✓ ggplot2 3.3.5 ✓ purrr 0.3.4 ✓ tibble 3.1.6 ✓ dplyr 1.0.7 ✓ tidyr 1.1.4 ✓ stringr 1.4.0 ✓ readr 2.1.1 ✓ forcats 0.5.1 ── Conflicts ──────────────────────────────────────────────────── tidyverse_conflicts() ── x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag() > library(patchwork) > # when downloading data from gbif, will need to combine different record types into DF > bind.gbif<-function(gbif){bind_rows(gbif[[2]][[3]], gbif[[3]][[3]])} > #next, download status classifications from natureserve > lep_stats <- ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order") + , location = list(nation ="US", subnation ="MD") #this filters to only include species that have a MD status, but retains status for all localities + , page = 0 + , per_page = 5e3)[[1]] %>% + unnest(cols=nations) %>% + unnest (cols = "subnations", names_repair ="unique") %>% + filter(subnationCode == "MD") #here is the step where I drop other localities, but this could be dropped at some point. Error: Internal Server Error (HTTP 500) > traceback() 8: stop(sprintf("%s (HTTP %s)", x$message, x$status_code), call. = FALSE) 7: temp$raise_for_status() 6: ns_POST(url = file.path(ns_base(), "api/data/speciesSearch"), body = list(criteriaType = "species", textCriteria = list(text) %|lst|% NULL, statusCriteria = list(status) %|lst|% NULL, locationCriteria = list(location) %|lst|% NULL, speciesTaxonomyCriteria = list(species_taxonomy) %|lst|% NULL, recordSubtypeCriteria = list(record_subtype) %|lst|% NULL, pagingOptions = paging, modifiedSince = modified_since), ...) 5: ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order"), location = list(nation = "US", subnation = "MD"), page = 0, per_page = 5000) 4: unnest(., cols = nations) 3: unnest(., cols = "subnations", names_repair = "unique") 2: filter(., subnationCode == "MD") 1: ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order"), location = list(nation = "US", subnation = "MD"), page = 0, per_page = 5000)[[1]] %>% unnest(cols = nations) %>% unnest(cols = "subnations", names_repair = "unique") %>% filter(subnationCode == "MD") > #next, download status classifications from natureserve > plant_stats <- ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Plantae", level = "kingdom") + , location = list(nation ="US", subnation ="MD") #this filters to only include species that have a MD status, but retains status for all localities + , page = 0 + , per_page = 5e3)[[1]] %>% + unnest(cols=nations) %>% + unnest (cols = "subnations", names_repair ="unique") %>% + filter(subnationCode == "MD") #here is the step where I drop other localities, but this could be dropped at some point. New names: * exotic -> exotic...15 * native -> native...16 * exotic -> exotic...17 * native -> native...18 > #next, download status classifications from natureserve > lep_stats <- ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "Order") + , location = list(nation ="US", subnation ="MD") #this filters to only include species that have a MD status, but retains status for all localities + , page = 0 + , per_page = 5e3)[[1]] %>% + unnest(cols=nations) %>% + unnest (cols = "subnations", names_repair ="unique") %>% + filter(subnationCode == "MD") #here is the step where I drop other localities, but this could be dropped at some point. Error: Internal Server Error (HTTP 500) > #next, download status classifications from natureserve > lep_stats <- ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order") + , location = list(nation ="US", subnation ="MD") #this filters to only include species that have a MD status, but retains status for all localities + , page = 0 + , per_page = 5e3)[[1]] %>% + unnest(cols=nations) %>% + unnest (cols = "subnations", names_repair ="unique") %>% + filter(subnationCode == "MD") #here is the step where I drop other localities, but this could be dropped at some point. Error: Internal Server Error (HTTP 500) > ?ns_search_spp > ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order")) Error: Internal Server Error (HTTP 500) > #next, download status classifications from natureserve > lep_stats <- ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Hymenoptera", level = "order") + , location = list(nation ="US", subnation ="MD") #this filters to only include species that have a MD status, but retains status for all localities + , page = 0 + , per_page = 5e3)[[1]] %>% + unnest(cols=nations) %>% + unnest (cols = "subnations", names_repair ="unique") %>% + filter(subnationCode == "MD") #here is the step where I drop other localities, but this could be dropped at some point. Error: Internal Server Error (HTTP 500) > #next, download status classifications from natureserve > lep_stats <- ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Insecta", level = "class") + , location = list(nation ="US", subnation ="MD") #this filters to only include species that have a MD status, but retains status for all localities + , page = 0 + , per_page = 5e3)[[1]] %>% + unnest(cols=nations) %>% + unnest (cols = "subnations", names_repair ="unique") %>% + filter(subnationCode == "MD") #here is the step where I drop other localities, but this could be dropped at some point. Error: Internal Server Error (HTTP 500) > #next, download status classifications from natureserve > lep_stats <- ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Insecta", level = "class")) Error: Internal Server Error (HTTP 500) > ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Bombus", level = "genus")) Error: Internal Server Error (HTTP 500) > ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Plantae", level = "kingdom")) $results # A tibble: 20 × 15 recordType elementGlobalId uniqueId nsxUrl elcode scientificName formattedScientif… primaryCommonNa… primaryCommonNa…, lastModified, classificationStatus ,
# speciesGlobal , gRank
$resultsSummary
name value
1 page 0
2 recordsPerPage 20
3 totalPages 1662
4 totalResults 33226
5 species_total 33226
> ns_search_spp(species_taxonomy = list(scientificTaxonomy = "lepidoptera", level = "order"))
Error: Internal Server Error (HTTP 500)
> ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order"))
Error: Internal Server Error (HTTP 500)
> ns_search_spp
function (text = NULL, text_adv = NULL, status = NULL, location = NULL,
species_taxonomy = NULL, record_subtype = NULL, modified_since = NULL,
page = NULL, per_page = NULL, ...)
{
paging <- handle_paging(page, per_page)
text <- handle_text(text, text_adv)
status <- handle_status(status)
location <- handle_location(location)
species_taxonomy <- handle_sptax(species_taxonomy)
record_subtype <- handle_subtype(record_subtype)
assert(modified_since, "character")
res <- ns_POST(url = file.path(ns_base(), "api/data/speciesSearch"),
body = list(criteriaType = "species", textCriteria = list(text) %|lst|%
NULL, statusCriteria = list(status) %|lst|% NULL,
locationCriteria = list(location) %|lst|% NULL, speciesTaxonomyCriteria = list(species_taxonomy) %|lst|%
NULL, recordSubtypeCriteria = list(record_subtype) %|lst|%
NULL, pagingOptions = paging, modifiedSince = modified_since),
...)
parse_search(res)
}
> ns_base
Error: object 'ns_base' not found
> natserv:::ns_base()
[1] "https://explorer.natureserve.org"
> #next, download status classifications from natureserve
> lep_stats <- ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order", kingdom = "Animalia"))
Error: `species_taxonomy` must be a list w/ 'informalTaxonomy' or 'level' and 'scientificTaxonomy'
> devtools::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os macOS Monterey 12.1
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2022-01-18
rstudio 2021.09.0+351 Ghost Orchid (desktop)
pandoc 2.17.0.1 @ /usr/local/bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.0)
broom 0.7.11 2022-01-03 [1] CRAN (R 4.1.2)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.0)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.1.0)
cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.0)
colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.0)
conditionz 0.1.0 2019-04-24 [1] CRAN (R 4.1.0)
crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.0)
crul 1.2.0 2021-11-22 [1] CRAN (R 4.1.0)
curl 4.3.2 2021-06-23 [1] CRAN (R 4.1.0)
data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.0)
DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.0)
dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.1.0)
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.0)
devtools 2.4.3 2021-11-30 [1] CRAN (R 4.1.0)
dplyr * 1.0.7 2021-06-18 [1] CRAN (R 4.1.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
forcats * 0.5.1 2021-01-27 [1] CRAN (R 4.1.0)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0)
generics 0.1.1 2021-10-25 [1] CRAN (R 4.1.0)
ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.1.0)
glue 1.6.0 2021-12-17 [1] CRAN (R 4.1.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
haven 2.4.3 2021-08-04 [1] CRAN (R 4.1.0)
hms 1.1.1 2021-09-26 [1] CRAN (R 4.1.0)
httpcode 0.3.0 2020-04-10 [1] CRAN (R 4.1.0)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0)
jsonlite 1.7.3 2022-01-17 [1] CRAN (R 4.1.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0)
lubridate 1.8.0 2021-10-07 [1] CRAN (R 4.1.0)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.0)
modelr 0.1.8 2020-05-19 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
natserv * 1.0.0.91 2022-01-18 [1] Github (ropensci/natserv@72acf2e)
oai 0.3.2 2021-05-13 [1] CRAN (R 4.1.0)
patchwork * 1.1.1 2020-12-17 [1] CRAN (R 4.1.0)
pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.0)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2)
readr * 2.1.1 2021-11-30 [1] CRAN (R 4.1.0)
readxl 1.3.1 2019-03-13 [1] CRAN (R 4.1.0)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.0)
reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0)
rgbif * 3.6.0 2021-06-02 [1] CRAN (R 4.1.0)
rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.0)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
rvest 1.0.2 2021-10-16 [1] CRAN (R 4.1.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0)
stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.0)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
testthat 3.1.1 2021-12-03 [1] CRAN (R 4.1.0)
tibble * 3.1.6 2021-11-07 [1] CRAN (R 4.1.0)
tidyr * 1.1.4 2021-09-27 [1] CRAN (R 4.1.0)
tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0)
tidyverse * 1.3.1 2021-04-15 [1] CRAN (R 4.1.0)
triebeard 0.3.0 2016-08-04 [1] CRAN (R 4.1.0)
tzdb 0.2.0 2021-10-27 [1] CRAN (R 4.1.0)
urltools 1.7.3 2019-04-14 [1] CRAN (R 4.1.0)
usethis 2.1.5 2021-12-09 [1] CRAN (R 4.1.0)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
uuid 1.0-3 2021-11-01 [1] CRAN (R 4.1.0)
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whisker 0.4 2019-08-28 [1] CRAN (R 4.1.0)
withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.0)
wk 0.6.0 2022-01-03 [1] CRAN (R 4.1.2)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.1.0)
[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
────────────────────────────────────────────────────────────────────────────────────────────────
```