Create httr2_sandfly_taxon_names.R

src/R/v1/httr2_sandfly_taxon_names.R

@@ -0,0 +1,53 @@
+#reference: https://httr2.r-lib.org/articles/wrapping-apis.html - https://www.tidyverse.org/blog/2023/11/httr2-1-0-0/ - https://github.com/melissavanbussel/YouTube-Tutorials/blob/main/httr2/httr2_examples.R
+#objectives: get a taxon_names_id and other attributes of a taxon name, from endpoint taxon_names in a csv file
+library(httr2)
+library(tidyverse)
+
+#Define access token
+access_token_taxonworks_sandfly = TAXONWORKS_TOKEN
+project_token_taxonworks_sandfly = TAXONWORKS_PROJECT_TOKEN
+
+#Define base urls
+base_url_taxonworks_sandfly = "https://sandfly.taxonworks.org/api/v1"
+
+#Define endpoints
+endpoint_taxonnames = "/taxon_names" #first objectives: get the taxon_id of a taxon name
+
+#Define request
+req_taxonnames_sandfly = request(base_url_taxonworks_sandfly) %>% 
+  req_url_path_append(endpoint_taxonnames) %>%
+  req_url_query(project_token=project_token_taxonworks_sandfly) #the project_token is necessary to authorize the request
+
+#Define query
+req_taxonnames_sandfly_query = req_taxonnames_sandfly %>%
+  req_url_query(
+    validity="true",
+    name_exact="true")
+
+#Provide access token via header
+req_taxonnames_sandfly_query_auth = req_taxonnames_sandfly_query %>%
+  req_headers(
+    'Authorization'=paste0('Token ',access_token_taxonworks_sandfly)
+  )
+
+library(readr)
+identificati <- read_csv("lista_identificati.csv")
+lista_identificati = as_vector(identificati$name)
+#names=lapply(lista_identificati, function(lista_identificati) paste0("name=",lista_identificati))
+
+reqs = lapply(lista_identificati, function(lista_identificati) req_url_query(req_taxonnames_sandfly_query_auth,name=lista_identificati))
+
+#Perform responses
+resps = reqs %>%
+  req_perform_sequential()
+
+resp_perform_taxonnames_sandfly_string = resps |> resps_successes() |> resps_data(\(resp) resp_body_string(resp))
+
+#Transform to dataframe
+library(jsonlite)
+resp_perform_taxonnames_sandfly_dataframe = lapply(resp_perform_taxonnames_sandfly_string, function(x) fromJSON(x))
+library(dplyr)
+dataframe_identificati = bind_rows(resp_perform_taxonnames_sandfly_dataframe)
+
+
+