Skip to content

fix: improve netzschleuder internals #40

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

Merged
schochastics merged 9 commits into from
Jun 2, 2025
Merged

fix: improve netzschleuder internals #40

Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
3e670bf
replaced [x] with [[x]]
schochastics Apr 29, 2025
ab13e18
properly close unz connections
schochastics Apr 29, 2025
47fc1cf
named return of resolve_names
schochastics Apr 29, 2025
0f9dcc4
refer to named resolved names
schochastics Apr 29, 2025
51c0808
Apply suggestions from code review
schochastics May 24, 2025
dd8bd49
review changes
schochastics May 31, 2025
229c756
use path argument of req_perform
schochastics Jun 1, 2025
485eb7f
moved on.exit comands
schochastics Jun 1, 2025
f0e6378
removed unnecessary resp
schochastics Jun 1, 2025
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
92 changes: 56 additions & 36 deletions R/netzschleuder.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ get_base_req <- function() {
.pkg_env$base_req
}

make_request <- function(path, token = NULL, method = "GET") {
make_request <- function(path, token = NULL, method = "GET", file = NULL) {
rlang::check_installed("httr2")
req <- httr2::req_url_path(get_base_req(), path)
req <- httr2::req_method(req, method)
Expand All @@ -24,7 +24,7 @@ make_request <- function(path, token = NULL, method = "GET") {
req <- httr2::req_headers(req, `WWW-Authenticate` = token)
}

resp <- httr2::req_perform(req)
resp <- httr2::req_perform(req, path = file)

if (httr2::resp_status(resp) != 200) {
stop("Failed to download file. Status: ", httr2::resp_status(resp))
Expand All @@ -40,16 +40,17 @@ resolve_name <- function(x) {
x <- sub("//", "/", x)

if (grepl("/", x)) {
x_split <- strsplit(x, "/", fixed = TRUE)[[1]]
if (length(x_split) > 2) {
res_names <- strsplit(x, "/", fixed = TRUE)[[1]]
bad_names_format <- (length(res_names) > 2)
if (bad_names_format) {
cli::cli_abort(
"{.arg name} has {length(x_split)} components instead of 2."
"{.arg name} is not correctly formatted."
)
}
return(x_split)
} else {
c(x, x)
res_names <- c(x, x)
}
rlang::set_names(res_names, c("collection", "network"))
}

download_file <- function(zip_url, token = NULL, file, size_limit) {
Expand All @@ -62,8 +63,7 @@ download_file <- function(zip_url, token = NULL, file, size_limit) {
"i" = "To download the file, set {.arg size_limit} to a value greater than {gb_size}"
))
}
resp <- make_request(zip_url, token, method = "GET")
writeBin(httr2::resp_body_raw(resp), file)
make_request(zip_url, token, method = "GET", file = file)
invisible(NULL)
}

Expand Down Expand Up @@ -109,17 +109,23 @@ download_file <- function(zip_url, token = NULL, file, size_limit) {
ns_metadata <- function(name, collection = FALSE) {
rlang::check_installed("cli")
net_ident <- resolve_name(name)
path <- sprintf("api/net/%s", net_ident[[1]])
collection_url <- sprintf("https://networks.skewed.de/net/%s", net_ident[[1]])
path <- sprintf("api/net/%s", net_ident[["collection"]])
collection_url <- sprintf(
"https://networks.skewed.de/net/%s",
net_ident[["collection"]]
)
resp <- make_request(path)
raw <- httr2::resp_body_json(resp)
class(raw) <- c("ns_meta", class(raw))
raw[["is_collection"]] <- collection
raw[["collection_name"]] <- net_ident[[1]]
raw[["collection_name"]] <- net_ident[["collection"]]
if (collection) {
return(raw)
} else if (
net_ident[[1]] == net_ident[[2]] &&
}

# Check if collection equals network and multiple nets exist
if (
net_ident[["collection"]] == net_ident[["network"]] &&
length(unlist(raw$nets)) > 1 &&
!collection
) {
Expand All @@ -129,22 +135,27 @@ ns_metadata <- function(name, collection = FALSE) {
"i" = "see {.url {collection_url}}"
)
)
} else if (net_ident[[1]] == net_ident[[2]]) {
}

# If collection equals network
if (net_ident[["collection"]] == net_ident[["network"]]) {
return(raw)
} else {
idx <- which(unlist(raw[["nets"]]) == net_ident[[2]])
if (length(idx) == 0) {
cli::cli_abort(
c(
"{net_ident[[2]]} is not part of the collection {net_ident[[1]]}.",
"i" = "see {.url {collection_url}}"
)
}

# Find matching network
idx <- which(unlist(raw[["nets"]]) == net_ident[["network"]])
if (length(idx) == 0) {
cli::cli_abort(
c(
"{net_ident[[2]]} is not part of the collection {net_ident[[1]]}.",
"i" = "see {.url {collection_url}}"
)
}
raw[["analyses"]] <- raw[["analyses"]][[net_ident[[2]]]]
raw[["nets"]] <- raw[["nets"]][idx]
raw
)
}

raw[["analyses"]] <- raw[["analyses"]][[net_ident[["network"]]]]
raw[["nets"]] <- raw[["nets"]][idx]
raw
}

#' @rdname netzschleuder
Expand All @@ -162,18 +173,22 @@ ns_df <- function(name, token = NULL, size_limit = 1) {
))
}
meta <- name
net_ident <- c(meta[["collection_name"]], meta[["nets"]])
net_ident <- c(
collection = meta[["collection_name"]],
network = meta[["nets"]]
)
} else {
cli::cli_abort("{.arg name} must be a string or a `ns_meta` object.")
}

zip_url <- sprintf(
"net/%s/files/%s.csv.zip",
net_ident[[1]],
net_ident[[2]]
net_ident[["collection"]],
net_ident[["network"]]
)

temp <- tempfile(fileext = "zip")
on.exit(unlink(temp))
download_file(zip_url, token = token, file = temp, size_limit = size_limit)

zip_contents <- utils::unzip(temp, list = TRUE)
Expand All @@ -182,7 +197,9 @@ ns_df <- function(name, token = NULL, size_limit = 1) {
node_file_name <- grep("node", zip_contents$Name, value = TRUE)
gprops_file_name <- grep("gprops", zip_contents$Name, value = TRUE)

edges_df_raw <- utils::read.csv(unz(temp, edge_file_name))
con_edge <- unz(temp, edge_file_name)
on.exit(close(con_edge))
edges_df_raw <- utils::read.csv(con_edge)
edges_df <- suppressWarnings(minty::type_convert(edges_df_raw))
source_loc <- grep("source", names(edges_df))
target_loc <- grep("target", names(edges_df))
Expand All @@ -192,10 +209,13 @@ ns_df <- function(name, token = NULL, size_limit = 1) {
edges_df[["from"]] <- edges_df[["from"]] + 1L
edges_df[["to"]] <- edges_df[["to"]] + 1L

nodes_df_raw <- utils::read.csv(unz(temp, node_file_name))
con_nodes <- unz(temp, node_file_name)
on.exit(close(con_nodes))
nodes_df_raw <- utils::read.csv(con_nodes)

#suppress warning if no character columns found
nodes_df <- suppressWarnings(minty::type_convert(nodes_df_raw))
names(nodes_df)[1] <- "id"
names(nodes_df)[[1]] <- "id"

# netzschleuder uses 0-indexing, igraph uses 1-indexing
nodes_df[["id"]] <- nodes_df[["id"]] + 1L
Expand All @@ -210,9 +230,9 @@ ns_df <- function(name, token = NULL, size_limit = 1) {
nodes_df[["y"]] <- mat[2, ]
}

gprops_df <- readLines(unz(temp, gprops_file_name))

on.exit(unlink(temp))
con_gprops <- unz(temp, gprops_file_name)
on.exit(close(con_gprops))
gprops_df <- readLines(con_gprops)

list(nodes = nodes_df, edges = edges_df, gprops = gprops_df, meta = meta)
}
Expand Down