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fix: improve netzschleuder internals #40

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fix: improve netzschleuder internals #40

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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
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48 changes: 30 additions & 18 deletions R/netzschleuder.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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 Down Expand Up @@ -109,17 +110,20 @@ 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]] &&
net_ident[["collection"]] == net_ident[["network"]] &&
length(unlist(raw$nets)) > 1 &&
!collection
) {
Expand All @@ -129,10 +133,10 @@ ns_metadata <- function(name, collection = FALSE) {
"i" = "see {.url {collection_url}}"
)
)
} else if (net_ident[[1]] == net_ident[[2]]) {
} else if (net_ident[["collection"]] == net_ident[["network"]]) {
return(raw)
} else {
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Couldn't some of the else if in this file be removed to instead just have if's?

if bla
return thing
if blop
return thing

idx <- which(unlist(raw[["nets"]]) == net_ident[[2]])
idx <- which(unlist(raw[["nets"]]) == net_ident[["network"]])
if (length(idx) == 0) {
cli::cli_abort(
c(
Expand All @@ -141,7 +145,7 @@ ns_metadata <- function(name, collection = FALSE) {
)
)
}
raw[["analyses"]] <- raw[["analyses"]][[net_ident[[2]]]]
raw[["analyses"]] <- raw[["analyses"]][[net_ident[["network"]]]]
raw[["nets"]] <- raw[["nets"]][idx]
raw
}
Expand All @@ -163,14 +167,15 @@ ns_df <- function(name, token = NULL, size_limit = 1) {
}
meta <- name
net_ident <- c(meta[["collection_name"]], meta[["nets"]])
names(net_ident) <- c("collection", "network")
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could the names be added in the previous call?

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")
Expand All @@ -182,7 +187,8 @@ 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)
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 +198,12 @@ 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)
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 @@ -210,8 +218,12 @@ ns_df <- function(name, token = NULL, size_limit = 1) {
nodes_df[["y"]] <- mat[2, ]
}

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

on.exit(close(con_edge))
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would it make sense to take a dependency on withr and use withr::local_connection()? Or to define a helper since we'd call it at least four times?

on.exit(close(con_nodes))
on.exit(close(con_gprops))
on.exit(unlink(temp))

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