Create httr2_sandfly_biological_association.R

src/R/httr2_sandfly_biological_association.R

@@ -0,0 +1,52 @@
+#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 dataframe of biological association from a taxon_name_id
+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"
+
+#find biological association data for the id
+#Define endpoints
+endpoint_bioass = "/biological_associations" #second objectives: get the biological association of a taxon_id of a taxon name
+
+#Define request
+req_bioass_sandfly = request(base_url_taxonworks_sandfly) %>% 
+  req_url_path_append(endpoint_bioass) %>%
+  req_url_query(project_token=project_token_taxonworks_sandfly) #the project_token is necessary to authorize the request
+
+#Define query
+req_bioass_sandfly_query = req_bioass_sandfly %>%
+  req_url_query(
+    "subject_taxon_name_id[]"=474243) %>%
+  req_url_query(
+    "biological_relationship_id[]"=8,
+    "biological_relationship_id[]"=12,
+    "biological_relationship_id[]"=13,
+    "biological_relationship_id[]"=14,
+    "biological_relationship_id[]"=10) %>%
+  req_url_query(
+    taxon_name_id_mode="true")
+
+#Provide access token via header
+req_bioass_sandfly_query_auth = req_bioass_sandfly_query %>%
+  req_headers(
+    'Authorization'=paste0('Token ',access_token_taxonworks_sandfly)
+  )
+
+#Perform response
+resp_perform_bioass_sandfly = req_bioass_sandfly_query_auth %>%
+  req_perform()
+resp_perform_bioass_sandfly_json = resp_perform_bioass_sandfly |> 
+  resp_body_json()
+
+resp_perform_bioass_sandfly_string = resp_perform_bioass_sandfly |> 
+  resp_body_string()
+
+#Transform to dataframe
+library(jsonlite)
+resp_perform_bioass_sandfly_dataframe = fromJSON(resp_perform_bioass_sandfly_string) %>% as.data.frame()