Fix MAGMA executable links

neurogenomics · May 17, 2024 · 7b779c1 · 7b779c1
1 parent b4b9192
commit 7b779c1
Show file tree

Hide file tree

Showing 13 changed files with 52 additions and 23 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MAGMA.Celltyping
 Type: Package
 Title: Find Causal Cell-Types Underlying Complex Trait Genetics
-Version: 2.0.11
+Version: 2.0.12
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",
@@ -73,6 +73,6 @@ Suggests:
 SystemRequirements: A system installation of
     [MAGMA](https://ctg.cncr.nl/software/magma) is required 
     but can be installed automatically by this package.
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 Config/testthat/edition: 3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# MAGMA.Celltyping 2.0.12
+
+## Bug fixes
+
+* Update URLs for getting MAGMA executables.
+
 # MAGMA.Celltyping 2.0.11
 
 ## New features

diff --git a/R/format_sumstats_for_magma.r b/R/format_sumstats_for_magma.r
@@ -21,6 +21,7 @@ format_sumstats_for_magma <- function(path) {
     mungesumstats_deprecation_msg()
 }
 
+
 format.sumstats.for.magma <- function(path){
     format_sumstats_for_magma(path)
 }
diff --git a/R/get_genome_ref.R b/R/get_genome_ref.R
@@ -43,6 +43,7 @@ get_genome_ref <- function(genome_ref_path = NULL,
                            timeout = 60 * 5,
                            verbose = TRUE) {
     #### population ####
+    dir.create(storage_dir,showWarnings = FALSE, recursive = TRUE)
     population <- tolower(population[1])
     method <- tolower(method[1])
     pop_opts <- c("eur", "afr", "amr", "eas", "sas")

diff --git a/R/list_remote_files.R b/R/list_remote_files.R
@@ -13,7 +13,9 @@
 #' @importFrom XML htmlParse xpathSApply free
 list_remote_files <- function(URL,
                               pattern = "*.zip") {
-    # URL <- "https://ctg.cncr.nl/software/MAGMA/prog/"
+
+    # doc <- rvest::read_html("https://vu.data.surfsara.nl/index.php/s/8qDPUbOTrZ9lW2b/")
+    # rvest::html_elements(doc,"a")
     doc <- XML::htmlParse(readLines(URL), asText = TRUE)
     links <- XML::xpathSApply(doc, "//a/@href")
     XML::free(doc)

diff --git a/R/magma_download_binary.R b/R/magma_download_binary.R
@@ -9,10 +9,10 @@
 #' @keywords internal 
 magma_download_binary <- function(magma_url,
                                   dest_dir = find_install_dir(),
+                                  destfile = basename(magma_url),
                                   verbose = TRUE) {
-    #### Download the appropriate executable ####
-    destfile <- file.path(dest_dir, basename(magma_url))
-    destfile <- fix_path(destfile) 
+    #### Download the appropriate executable #### 
+    destfile <- fix_path(file.path(dest_dir,destfile)) 
     messager("Downloading MAGMA executable ==>",dest_dir, v = verbose)
     # Create the decompressed file name in advance
     destpath <- gsub("\\.zip$", "", destfile)

diff --git a/R/magma_install.R b/R/magma_install.R
@@ -19,13 +19,14 @@
 #' @export
 #' @importFrom utils unzip
 #' @examples 
-#' magma <- MAGMA.Celltyping::magma_install()
+#' magma <- magma_install()
 magma_install <- function(dest_dir = find_install_dir(),
                           desired_version = "latest",
                           upgrade = FALSE,
                           verbose = TRUE) { 
     #### Standardise desired_version ####
-    if(is.null(desired_version) || length(desired_version)==0) {
+    if(is.null(desired_version) || 
+       length(desired_version)==0) {
         desired_version <- "latest"
     }
     desired_version <- tolower(desired_version)[1]
@@ -67,6 +68,7 @@ magma_install <- function(dest_dir = find_install_dir(),
         destpath <- magma_download_binary(
             magma_url = magma_url,
             dest_dir = dest_dir,
+            destfile = paste0(names(magma_url),".zip"),
             verbose = verbose
         ) 
         dest_magma <- magma_find_executable(destpath = destpath)

diff --git a/R/magma_links.R b/R/magma_links.R
@@ -17,7 +17,7 @@ magma_links <- function(latest_only = TRUE,
                         use_local = TRUE,
                         return_table = FALSE,
                         verbose = TRUE) {
-    latest <- NULL;
+    latest <- link <- NULL;
     #### Avoid issues with subset when colnames same as variable names ####
     OS <- os;
     VERSION <- if(is.null(version)) {
@@ -34,6 +34,15 @@ magma_links <- function(latest_only = TRUE,
             magma_links_gather()
         }, error = function(e) MAGMA.Celltyping::magma_links_stored)
     }  
+    #### Fix URLs ####
+    ## Need to update this bit manually...
+    meta[version=="v1.10" & os=="Linux",link:="https://vu.data.surfsara.nl/index.php/s/zkKbNeNOZAhFXZB/download"]
+    meta[version=="v1.10" & os=="Mac",link:="https://vu.data.surfsara.nl/index.php/s/1M1d9vHtVidEwvU/download"]
+    meta[version=="v1.10" & os=="Windows",link:="https://vu.data.surfsara.nl/index.php/s/TOH4SuvczAKE29d/download"]
+    meta[version=="v1.10" & os=="source",link:="https://vu.data.surfsara.nl/index.php/s/1OOi7bxLWef0GwY/download"]
+    ## Can substitute the rest
+    meta[,link:=gsub("https://ctg.cncr.nl/software/MAGMA/prog//|https://ctg.cncr.nl/software/MAGMA/prog/archive//",
+                     "https://vu.data.surfsara.nl/index.php/s/8qDPUbOTrZ9lW2b/download?path=%2F&files=",link)]
     #### Filter by OS ####
     if (!is.null(OS)) {  
         meta <- subset(meta, os==OS)

diff --git a/R/magma_links_versions.R b/R/magma_links_versions.R
@@ -15,7 +15,13 @@ magma_links_versions <- function(links,
                                  filter_v = TRUE,
                                  verbose = TRUE){
     if(!is.character(links)) return(NULL)
-    versions <- stringr::str_split(links, "_", simplify = TRUE)[,2]
+    versions <- sapply(seq_len(length(links)),function(i){
+      if(endsWith(links[[i]],".zip")){
+        strsplit(links[[i]],"_")[[1]][2]
+      } else{
+        strsplit(names(links)[i],"_")[[1]][2] 
+      }
+    })
     versions <- gsub(".zip","",versions)
     if(unique_only){
         versions <- unique(versions)

diff --git a/man/magma_download_binary.Rd b/man/magma_download_binary.Rd
diff --git a/man/magma_install.Rd b/man/magma_install.Rd
diff --git a/tests/testthat/test-magma_links.R b/tests/testthat/test-magma_links.R
@@ -1,30 +1,27 @@
 test_that("magma_links works", {
 
     if(!is_32bit()){
-        to_numeric <- function(x){
-            as.numeric(
-                gsub(
-                    paste( c(letters,".zip"), collapse = "|" ),"",
-                    stringr::str_split(basename(x),"_")[[1]][2]
-                    )
-                )
+        to_version <- function(x){
+          package_version(
+            gsub("v","",MAGMA.Celltyping:::magma_links_versions(x))
+          )
         }
 
         #### Mac ####
-        magma_mac <- MAGMA.Celltyping:::magma_links(latest_only = TRUE,
+        magma_mac <-MAGMA.Celltyping:::magma_links(latest_only = TRUE,
                                os = "Mac",
                                verbose = FALSE)
-        testthat::expect_gte(to_numeric(magma_mac), 1.1) 
+        testthat::expect_true(to_version(magma_mac)>=1.1) 
 
         #### Windows ####
         magma_win <- MAGMA.Celltyping:::magma_links(latest_only = TRUE,
                                                     os = "Windows")
-        testthat::expect_gte(to_numeric(magma_win), 1.1) 
+        testthat::expect_true(to_version(magma_win)>=1.1) 
 
         #### Linux ####
         magma_linux <- MAGMA.Celltyping:::magma_links(latest_only = TRUE,
                                                       os = "Linux")
-        testthat::expect_gte(to_numeric(magma_linux), 1.1) 
+        testthat::expect_true(to_version(magma_linux)>=1.1) 
 
         #### All ####
         meta <- MAGMA.Celltyping:::magma_links(latest_only = FALSE,