Fix ref download issue. Add template checker

neurogenomics · Oct 2, 2024 · 4519395 · 4519395
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -7,6 +7,11 @@ assignees: ''
 
 ---
 
+:warning: :warning: :warning: 
+PLEASE NOTE, YOUR ISSUE WILL BE AUTOMATICALLY CLOSED IF IT DOES NOT USE AND COMPLETE THE TEMPLATE.
+These templates are designed to give us the basic information necessary to help debug your issues.  
+:warning: :warning: :warning: 
+
 ## 1. Bug description
 
 (A clear and concise description of what the bug is.)

diff --git a/.github/workflows/auto-close-issues.yml b/.github/workflows/auto-close-issues.yml
@@ -0,0 +1,16 @@
+on:
+  issues:
+    types: [opened, edited]
+
+jobs:
+  auto_close_issues:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+      - name: Automatically close issues that don't follow the issue template
+        uses: lucasbento/auto-close-issues@v1.0.2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          issue-close-message: "@${issue.user.login}: hello! :wave:\n\nThis issue is being automatically closed because it does not follow the issue template." # optional property
+          closed-issues-label: "🙁 Not following issue template" # optional property
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: 2.0.12
+Version: 2.0.13
 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: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Config/testthat/edition: 3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+# MAGMA.Celltyping 2.0.13
+
+## New features
+
+* Fully remove deprecated function `format.sumstats.for.magma`
+* Add auto-close-template: https://github.com/marketplace/actions/auto-close-issues
+
+## Bug fixes
+
+* Update URLs for getting MAGMA reference genome files (#154).
+* *test-magma_links.R*: `package_version` comparisons now only work with strings instead of numbers.
+
 # MAGMA.Celltyping 2.0.12
 
 ## Bug fixes

diff --git a/R/format_sumstats_for_magma.r b/R/format_sumstats_for_magma.r
@@ -21,7 +21,4 @@ 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_example_gwas_raw.R b/R/get_example_gwas_raw.R
@@ -2,9 +2,9 @@
 #'
 #' Write example GWAS summary statistics to disk.
 #'
-#' @param save_path Path to save sum stats.
 #' @param timeout How many seconds to wait before timeout.
 #' @param verbose Print messages. 
+#' @inheritParams get_data
 #'
 #' @return Path to sumstats
 #'

diff --git a/R/get_genome_ref.R b/R/get_genome_ref.R
@@ -32,28 +32,21 @@
 #' 
 #' @examples
 #' \dontrun{
-#' genome_ref_path <- MAGMA.Celltyping::get_genome_ref()
+#' genome_ref_path <- get_genome_ref()
 #' }
 get_genome_ref <- function(genome_ref_path = NULL,
                            storage_dir = tools::R_user_dir(
                                "MAGMA.Celltyping",
                                which="cache"),
-                           method = c("magma","piggback"),
+                           method = c("magma"),
                            population = c("eur", "afr", "amr", "eas", "sas"),
                            timeout = 60 * 5,
                            verbose = TRUE) {
     #### population ####
     dir.create(storage_dir,showWarnings = FALSE, recursive = TRUE)
     population <- tolower(population[1])
+    population <- match.arg(population)
     method <- tolower(method[1])
-    pop_opts <- c("eur", "afr", "amr", "eas", "sas")
-    if (!population %in% pop_opts) {
-        stop_msg <- paste0(
-            "population must be one of:\n",
-            paste0(" - ", pop_opts, collapse = "\n")
-        )
-        stop(stop_msg)
-    }
     #### Set up paths ####
     if (is.null(genome_ref_path)) {
         genome_ref_dir <- file.path(storage_dir, 
@@ -83,7 +76,12 @@ get_genome_ref <- function(genome_ref_path = NULL,
                 verbose = verbose
             )
         }
-
+      ### Reference file is too large to be stored in GitHub Releases now
+      #else if(method == "piggyback"){
+            # get_genome_ref_piggyback(
+            #     genome_ref_dir = genome_ref_dir, 
+            #     verbose = verbose
+            # )
     }
     #### Return the folder + the file prefix ####
     return(genome_ref_path)

diff --git a/R/get_genome_ref_magma.R b/R/get_genome_ref_magma.R
@@ -6,18 +6,22 @@
 #' 
 #' @param genome_ref_dir Folder to download reference to.
 #' @param verbose Print messages.
-#' @source \href{https://ctg.cncr.nl/software/MAGMA/ref_data/}{MAGMA archives} 
+#' @source \href{https://cncr.nl/research/magma/}{MAGMA site} 
 #' 
 #' @keywords internal
 get_genome_ref_magma <- function(genome_ref_dir, 
+                                 population = "eur",
                                  timeout = 60 * 5,
                                  verbose = TRUE) {
     #### Get link ####
-    input_url <- paste(
-        "https://ctg.cncr.nl/software/MAGMA",
-        "ref_data",paste0(basename(genome_ref_dir),".zip"), 
-        sep="/"
-        )
+    link_dict <- list(
+      "g1000_eur"="https://vu.data.surfsara.nl/index.php/s/VZNByNwpD8qqINe/download",
+      "g1000_afr"="https://vu.data.surfsara.nl/index.php/s/ePXET6IWVTwTes4/download",
+      "g1000_eas"="https://vu.data.surfsara.nl/index.php/s/dz6PYdKOi3xVqHn/download",
+      "g1000_sas"="https://vu.data.surfsara.nl/index.php/s/C6UkTV5nuFo8cJC/download",
+      "g1000_amr"="https://vu.data.surfsara.nl/index.php/s/TXDEm70eEO7AgOb/download"
+    )
+    input_url <- link_dict[[paste0("g1000_",tolower(population))]]
     ##### Link to 1000 genomes reference data. ####
     zipfile <- sprintf("%s.zip", genome_ref_dir)
     #### Download file ####

diff --git a/R/get_genome_ref_piggyback.R b/R/get_genome_ref_piggyback.R
@@ -6,24 +6,27 @@
 #' 
 #' @param genome_ref_dir Folder to download reference to.
 #' @param verbose Print messages.
+#' @inheritDotParams get_data
 #' @source 
 #' \code{
-#' genome_ref_path <- MAGMA.Celltyping::get_genome_ref(method = "magma")
+#' genome_ref_path <- get_genome_ref(method = "magma")
 #'
 #' piggyback::pb_upload(file = genome_ref_path,
 #'                      repo = "neurogenomics/MAGMA_Celltyping",
 #'                      overwrite = TRUE)
 #' }
 #' @keywords internal
 get_genome_ref_piggyback <- function(genome_ref_dir,  
-                                     verbose = TRUE) {
+                                     verbose = TRUE,
+                                     ...) {
     ##### Link to 1000 genomes reference data. ####
     zipfile <- sprintf("%s.zip", genome_ref_dir)
     #### Download file ####
     options(timeout = 60 * 5)
     get_data(paste0(basename(genome_ref_dir),".zip"),
              repo = "neurogenomics/MAGMA_Celltyping", 
-             storage_dir = genome_ref_dir)
+             storage_dir = genome_ref_dir,
+             ...)
     #### Unzip file ####
     messager("Unzipping file.", v = verbose) 
     utils::unzip(

diff --git a/README.md b/README.md
@@ -1,20 +1,20 @@
 <img src='https://github.com/neurogenomics/MAGMA_Celltyping/raw/master/inst/hex/hex.png' title='Hex sticker for MAGMA.Celltyping' height='300'><br>
 [![License:
 GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
-[![](https://img.shields.io/badge/devel%20version-2.0.9-black.svg)](https://github.com/neurogenomics/MAGMA_Celltyping)
+[![](https://img.shields.io/badge/devel%20version-2.0.13-black.svg)](https://github.com/neurogenomics/MAGMA_Celltyping)
 [![](https://img.shields.io/github/languages/code-size/neurogenomics/MAGMA_Celltyping.svg)](https://github.com/neurogenomics/MAGMA_Celltyping)
 [![](https://img.shields.io/github/last-commit/neurogenomics/MAGMA_Celltyping.svg)](https://github.com/neurogenomics/MAGMA_Celltyping/commits/master)
 <br> [![R build
 status](https://github.com/neurogenomics/MAGMA_Celltyping/workflows/rworkflows/badge.svg)](https://github.com/neurogenomics/MAGMA_Celltyping/actions)
-[![](https://codecov.io/gh/neurogenomics/MAGMA_Celltyping/branch/master/graph/badge.svg)](https://codecov.io/gh/neurogenomics/MAGMA_Celltyping)
+[![](https://codecov.io/gh/neurogenomics/MAGMA_Celltyping/branch/master/graph/badge.svg)](https://app.codecov.io/gh/neurogenomics/MAGMA_Celltyping)
 <br>
 <a href='https://app.codecov.io/gh/neurogenomics/MAGMA_Celltyping/tree/master' target='_blank'><img src='https://codecov.io/gh/neurogenomics/MAGMA_Celltyping/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>  
 <h4>  
 Authors: <i>Brian Schilder, Alan Murphy, Julien Bryois, Nathan
 Skene</i>  
 </h4>
 <h4>  
-README updated: <i>Apr-12-2023</i>  
+README updated: <i>Oct-02-2024</i>  
 </h4>
 
 ## Introduction

diff --git a/man/get_example_gwas_raw.Rd b/man/get_example_gwas_raw.Rd
diff --git a/man/get_genome_ref.Rd b/man/get_genome_ref.Rd
diff --git a/man/get_genome_ref_magma.Rd b/man/get_genome_ref_magma.Rd
diff --git a/man/get_genome_ref_piggyback.Rd b/man/get_genome_ref_piggyback.Rd
diff --git a/tests/testthat/test-magma_links.R b/tests/testthat/test-magma_links.R
@@ -11,17 +11,17 @@ test_that("magma_links works", {
         magma_mac <-MAGMA.Celltyping:::magma_links(latest_only = TRUE,
                                os = "Mac",
                                verbose = FALSE)
-        testthat::expect_true(to_version(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_true(to_version(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_true(to_version(magma_linux)>=1.1) 
+        testthat::expect_true(to_version(magma_linux)>="1.1") 
 
         #### All ####
         meta <- MAGMA.Celltyping:::magma_links(latest_only = FALSE,