install.packages("rgbif")

# fill in your gbif.org credentials 
user <- "" # your gbif.org username 
pwd <- "" # your gbif.org password
email <- "" # your email 

library(dplyr)
library(readr)  
library(rgbif) # for occ_download

# The 60,000 tree names file I downloaded from BGCI
file_url <- "https://data-blog.gbif.org/post/2019-07-11-downloading-long-species-lists-on-gbif_files/global_tree_search_trees_1_3.csv"

# match the names 
gbif_taxon_keys <- 
readr::read_csv(file_url) %>%
head(1000) %>% # use only first 1000 names for testing
pull("Taxon name") %>% # use fewer names if you want to just test 
name_backbone_checklist()  %>% # match to backbone
filter(!matchType == "NONE") %>% # get matched names
pull(usageKey) # get the gbif taxonkeys

# gbif_taxon_keys should be a long vector like this c(2977832,2977901,2977966,2977835,2977863)

# !!very important here to use pred_in!!
occ_download(
pred_in("taxonKey", gbif_taxon_keys),
format = "SIMPLE_CSV",
user=user,pwd=pwd,email=email
)

user <- "" # your gbif.org username 
pwd <- "" # your gbif.org password
email <- "" # your email 

library(taxize)
library(purrr)
library(tibble)
library(dplyr)
library(magrittr) # fot the %T>% pipe
library(roperators) # for %+% string operator

# pipeline for processing sci names -> downloads 

# The 60,000 tree names file I downloaded from BGCI
file_url <- "https://data-blog.gbif.org/post/2019-07-11-downloading-long-species-lists-on-gbif_files/global_tree_search_trees_1_3.csv"

# match the names 
readr::read_csv(file_url) %>% 
pull("Taxon name") %>% # use fewer names if you want to just test 
taxize::get_gbifid_(method="backbone") %>% # match names to the GBIF backbone to get taxonkeys
imap(~ .x %>% mutate(original_sciname = .y)) %>% # add original name back into data.frame
bind_rows() %T>% # combine all data.frames into one
readr::write_tsv(path = "all_matches.tsv") %>% # save as side effect for you to inspect if you want
filter(matchtype == "EXACT" & status == "ACCEPTED") %>% # get only accepted and matched names
filter(kingdom == "Plantae") %>% # remove anything that might have matched to a non-plant
pull(usagekey) %>% # get the gbif taxonkeys
paste(collapse=",") %>% 
paste('{
"creator": "' %+% user %+%'",
"notification_address": [
"' %+% email %+% '"
],
"sendNotification": true,
"format": "SIMPLE_CSV",
"predicate": {
"type": "and",
"predicates": [
{
"type": "in",
"key": "COUNTRY",
"values": ["CL"]
},
{
"type": "in",
"key": "TAXON_KEY",
"values": [',.,']
}
]}}',collapse="") %>% # create json sring 
writeLines(file("request.json")) # save the json request to use in httr::POST

{
"creator": "jwaller",
"notification_address": [
"jwaller@gbif.org"
],
"sendNotification": true,
"format": "SIMPLE_CSV",
"predicate": {
"type": "and",
"predicates": [
{
"type": "in",
"key": "COUNTRY",
"values": ["CL"]
},
{
"type": "in",
"key": "TAXON_KEY",
"values": [ 2977832,2977901,2977966,2977835,2977863,2977814,8322626 ]
}
]}}

url = "http://api.gbif.org/v1/occurrence/download/request"

library(httr)

POST(url = url, 
config = authenticate(user, pwd), 
add_headers("Content-Type: application/json"),
body = upload_file("request.json"), # path to your local file
encode = 'json') %>% 
content(as = "text")

import pandas as pd
import requests
import json
import io
from functions_query_from_species_list import *

login = ""
password = ""
URL_species_file = "https://data-blog.gbif.org/post/2019-07-11-downloading-long-species-lists-on-gbif_files/global_tree_search_trees_1_3.csv"

# Get Taxon Keys
species_list = pd.read_csv(URL_species_file, encoding='latin-1')
taxon_keys = match_species(species_list, "Taxon name")

# filter keys however you see fit
key_list = taxon_keys.loc[(taxon_keys["matchType"]=="EXACT") & (taxon_keys["status"]=="ACCEPTED")].usageKey.tolist()

# Make download query
download_query = {}
download_query["creator"] = ""
download_query["notificationAddresses"] = [""]
download_query["sendNotification"] = False # if set to be True, don't forget to add a notificationAddresses above
download_query["format"] = "SIMPLE_CSV"
download_query["predicate"] = {
    "type": "in",
    "key": "TAXON_KEY",
    "values": key_list
}

# Generate download
create_download_given_query(login, password, download_query)