From 3e670bfbb3806090234f10afb3c92dd6c5dec835 Mon Sep 17 00:00:00 2001 From: schochastics Date: Tue, 29 Apr 2025 16:49:39 +0200 Subject: [PATCH 1/5] replaced [x] with [[x]] --- R/netzschleuder.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/netzschleuder.R b/R/netzschleuder.R index 2033701..38a08fe 100644 --- a/R/netzschleuder.R +++ b/R/netzschleuder.R @@ -195,7 +195,7 @@ ns_df <- function(name, token = NULL, size_limit = 1) { nodes_df_raw <- utils::read.csv(unz(temp, node_file_name)) #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 From ab13e18e596f08cbc095e0b38b5aafaccda5284a Mon Sep 17 00:00:00 2001 From: schochastics Date: Tue, 29 Apr 2025 17:30:05 +0200 Subject: [PATCH 2/5] properly close unz connections --- R/netzschleuder.R | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/R/netzschleuder.R b/R/netzschleuder.R index 38a08fe..2022f8a 100644 --- a/R/netzschleuder.R +++ b/R/netzschleuder.R @@ -182,7 +182,8 @@ 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)) @@ -192,7 +193,9 @@ 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" @@ -210,8 +213,12 @@ 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)) + 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) From 47fc1cf21183f06a835b510e58af257f364a327d Mon Sep 17 00:00:00 2001 From: schochastics Date: Tue, 29 Apr 2025 17:31:57 +0200 Subject: [PATCH 3/5] named return of resolve_names --- R/netzschleuder.R | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/R/netzschleuder.R b/R/netzschleuder.R index 2022f8a..5447be2 100644 --- a/R/netzschleuder.R +++ b/R/netzschleuder.R @@ -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]] + if (length(res_names) > 2) { cli::cli_abort( - "{.arg name} has {length(x_split)} components instead of 2." + "{.arg name} has {length(res_names)} components instead of 2." ) } - return(x_split) } else { - c(x, x) + res_names <- c(x, x) } + names(res_names) <- c("collection", "network") + res_names } download_file <- function(zip_url, token = NULL, file, size_limit) { From 0f9dcc43f0c9e62d95071bed45627742f73da4eb Mon Sep 17 00:00:00 2001 From: schochastics Date: Tue, 29 Apr 2025 18:33:35 +0200 Subject: [PATCH 4/5] refer to named resolved names --- R/netzschleuder.R | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/R/netzschleuder.R b/R/netzschleuder.R index 5447be2..8017090 100644 --- a/R/netzschleuder.R +++ b/R/netzschleuder.R @@ -43,7 +43,7 @@ resolve_name <- function(x) { res_names <- strsplit(x, "/", fixed = TRUE)[[1]] if (length(res_names) > 2) { cli::cli_abort( - "{.arg name} has {length(res_names)} components instead of 2." + "{.arg name} is not correctly formatted." ) } } else { @@ -110,17 +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 ) { @@ -130,10 +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 { - idx <- which(unlist(raw[["nets"]]) == net_ident[[2]]) + idx <- which(unlist(raw[["nets"]]) == net_ident[["network"]]) if (length(idx) == 0) { cli::cli_abort( c( @@ -142,7 +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 } @@ -164,14 +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") } 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") From 51c08086ab5e0c624dd5d703497a515ae66c0e0b Mon Sep 17 00:00:00 2001 From: David Schoch Date: Sat, 24 May 2025 20:54:54 +0200 Subject: [PATCH 5/5] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Maëlle Salmon --- R/netzschleuder.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/netzschleuder.R b/R/netzschleuder.R index 8017090..0a3dd8f 100644 --- a/R/netzschleuder.R +++ b/R/netzschleuder.R @@ -41,7 +41,8 @@ resolve_name <- function(x) { if (grepl("/", x)) { res_names <- strsplit(x, "/", fixed = TRUE)[[1]] - if (length(res_names) > 2) { + bad_names_format <- (length(res_names) > 2) + if (bad_names_format) { cli::cli_abort( "{.arg name} is not correctly formatted." ) @@ -49,8 +50,7 @@ resolve_name <- function(x) { } else { res_names <- c(x, x) } - names(res_names) <- c("collection", "network") - res_names + rlang::set_names(res_names, c("collection", "network")) } download_file <- function(zip_url, token = NULL, file, size_limit) {