In `ns_search_spp` need to provide `kingdom` as well as `level`?
Closed this issue · 3 comments
mikeroswell commented
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 error
I wonder if this is because when level !="kingdom" kingdom must also be supplied, based on the documentation here. This is just a guess!
Thanks for your help!!!
Session Info
ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Plantae", level = "kingdom")) # works
ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Lepidoptera", level = "order")) # 505 error
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> #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…
<chr> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 SPECIES 137101 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes acadie… <i>Isoetes acadie… Acadian Quillwo… EN
2 SPECIES 159182 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes appala… <i>Isoetes appala… Appalachian Qui… EN
3 SPECIES 141815 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes boland… <i>Isoetes boland… Bolander's Quil… EN
4 SPECIES 138575 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes boomii <i>Isoetes boomii… Boom's Quillwort EN
5 SPECIES 135589 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes butleri <i>Isoetes butler… Butler's Quillw… EN
6 SPECIES 136878 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes echino… <i>Isoetes echino… Spiny-spore Qui… EN
7 SPECIES 151042 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes engelm… <i>Isoetes engelm… Engelmann's Qui… EN
8 SPECIES 150693 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes flacci… <i>Isoetes flacci… Southern Quillw… EN
9 SPECIES 152181 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes flacci… <i>Isoetes flacci… Southern Quillw… EN
10 SPECIES 128727 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes flacci… <i>Isoetes flacci… Southern Quillw… EN
11 SPECIES 145484 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes flacci… <i>Isoetes flacci… Southern Quillw… EN
12 SPECIES 147368 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes georgi… <i>Isoetes georgi… Georgia Quillwo… EN
13 SPECIES 1216603 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes granit… <i>Isoetes granit… Flat Rock Quill… EN
14 SPECIES 144776 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes hawaii… <i>Isoetes hawaii… Hawai`i Quillwo… EN
15 SPECIES 1216105 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes howell… <i>Isoetes howell… Howell's Quillw… EN
16 SPECIES 147799 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes hyemal… <i>Isoetes hyemal… Winter Quillwort EN
17 SPECIES 160975 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes juncif… <i>Isoetes juncif… Rush Quillwort EN
18 SPECIES 738978 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes lacust… <i>Isoetes lacust… Western Lake Qu… EN
19 SPECIES 1131640 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes lauren… <i>Isoetes lauren… NA EN
20 SPECIES 147798 ELEMENT_G… /Taxon/ELE… PPISO0… Isoetes lithop… <i>Isoetes lithop… Rock Quillwort EN
# … with 6 more variables: roundedGRank <chr>, nations <list>, lastModified <chr>, classificationStatus <chr>,
# speciesGlobal <df[,15]>, gRank <chr>
$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)
}
<bytecode: 0x7f827635ef40>
<environment: namespace:natserv>
> 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
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backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.0)
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lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0)
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[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
────────────────────────────────────────────────────────────────────────────────────────────────mikeroswell commented
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 commented
hi @mikeroswell - this pkg is looking for a new maintainer - are you interested?
maelle commented
This repository is about to be archived.