Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update to work with latest zenodo API #81

Merged
merged 2 commits into from
Oct 16, 2023
Merged

Update to work with latest zenodo API #81

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
8f46845
Update to work with latest zenodo API
dfalster Oct 16, 2023
179072a
Merge branch 'develop' into bugfix-zenodo-api-change
fontikar Oct 16, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 25 additions & 13 deletions R/load_austraits.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,12 @@ load_austraits <- function(doi = NULL, version = NULL, path = "data/austraits",
if(rlang::is_missing(path)){
stop("File path must be supplied!")
}


#remove v from version
if (!is.null(version)) {
version <- stringr::str_remove_all(version, "v")
}

# Does the path exist?
if(! file.exists(path)) {
dir.create(path, recursive=TRUE, showWarnings=FALSE) #Create folder
Expand All @@ -34,7 +39,7 @@ load_austraits <- function(doi = NULL, version = NULL, path = "data/austraits",
res <- load_json(path = path, update = update)

# Name the response list
names(res$hits$hits$files) <- res$hits$hits$metadata$version
names(res$files) <- res$metadata$version

# Create metadata table
ret <- create_metadata(res)
Expand All @@ -56,13 +61,16 @@ load_austraits <- function(doi = NULL, version = NULL, path = "data/austraits",
# Add in prefix of v
version_name <- paste0("v", version)

# Getting specific version
target <- res$hits$hits$files[[version_name]]
# Getting specific file
id <- ret[which(ret$version == version), "id"] |> as.character()

target <- res$files[[version_name]]$filename
target <- target[grep(".rds", target, fixed = TRUE)]

# Setting up the pars
url <- target$links$self[1]
file_path <- file.path(path, target$key[1])
url <- sprintf("https://zenodo.org/records/%s/files/%s", id, target)

file_path <- file.path(path, target)

#Check if version/doi is download, if not download
if(! file.exists(file_path)){
# Downloading file
Expand Down Expand Up @@ -91,7 +99,7 @@ load_json <- function(path, update){
# Does the .json exist?
if(! file.exists(file_json) | update == TRUE){
# Retrieve the .json
res <- jsonlite::read_json("https://zenodo.org/api/records/?q=conceptrecid:3568417&all_versions=true",
res <- jsonlite::read_json("https://zenodo.org/api/records/3568418/versions",
simplifyVector = T)
# Save it
jsonlite::write_json(res, file_json)
Expand All @@ -108,11 +116,15 @@ load_json <- function(path, update){

create_metadata <- function(res){
# Version table
ret <- dplyr::tibble(date = res$hits$hits$metadata$publication_date,
version = stringr::str_extract(res$hits$hits$metadata$version, "[0-9]+\\.[0-9]+\\.[0-9]"),
doi = res$hits$hits$metadata$doi) %>%
ret <-
dplyr::tibble(
date = res$metadata$publication_date,
version = stringr::str_extract(res$metadata$version, "[0-9]+\\.[0-9]+\\.[0-9]"),
doi = res$metadata$doi,
id = stringr::str_remove_all(res$metadata$doi, stringr::fixed("10.5281/zenodo.")
)) %>%
dplyr::filter(! version < 1) %>% # Exclude any versions prior to 1.0.0
as.data.frame()
dplyr::as_tibble()

# Order by numeric version
ret[order(dplyr::desc(numeric_version(ret$version))),]
Expand Down Expand Up @@ -208,7 +220,7 @@ get_version_latest <- function(path = "data/austraits", update = TRUE){
res <- load_json(path = path, update = update)

# Get all versions and remove the 'v'
version_numbers <- stringr::str_extract(res$hits$hits$metadata$version, "[0-9]+\\.[0-9]+\\.[0-9]")
version_numbers <- stringr::str_extract(res$metadata$version, "[0-9]+\\.[0-9]+\\.[0-9]")

# Order by numeric version
version_numbers <- version_numbers[order(dplyr::desc(numeric_version(version_numbers)))]
Expand Down
Loading