Merge pull request #85 from gladkia/84-fix-bioc-errors-amazon-s3-url-…

…unreachable 84 fix bioc errors amazon s3 url unreachable
gladkia · Aug 25, 2024 · 425cda0 · 425cda0
2 parents c26ffa2 + 6a5b028
commit 425cda0
Show file tree

Hide file tree

Showing 6 changed files with 9 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: igvShiny
 Title: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive
     tool for visualization and exploration integrated genomic data)
-Version: 1.0.2
-Date: 2024-08-16
+Version: 1.0.3
+Date: 2024-08-25
 Authors@R: c(
     person("Paul","Shannon", role = c("aut"), 
     email = "[email protected]"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+## igvShiny 1.0.3 - 2024-08-25
+* stop using Amazon S3 URLs by default
+
 ## igvShiny 1.0.2 - 2024-08-16
 * fix issue with VCF files
 

diff --git a/R/GWASTrack.R b/R/GWASTrack.R
@@ -79,7 +79,7 @@ setGeneric("getUrl",
 #'   )
 #' getUrl(track)
 #' 
-#' url <- "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz"
+#' url <- "https://gladki.pl/igvShiny/gwas_sample.tsv.gz"
 #' track <- GWASTrack(
 #'   "remote url gwas",
 #'   url,

diff --git a/R/genomeSpec.R b/R/genomeSpec.R
@@ -59,8 +59,7 @@ get_css_genomes <- function(test = FALSE) {
   if (test)
     return(get_basic_genomes())
 
-  current.genomes.file <-
-    "https://s3.amazonaws.com/igv.org.genomes/genomes.json"
+  current.genomes.file <- "https://igv.org/genomes/genomes.json"
 
   if (!RCurl::url.exists(current.genomes.file))
     return(get_basic_genomes())

diff --git a/inst/unitTests/test_GWASTrack.R b/inst/unitTests/test_GWASTrack.R
@@ -31,7 +31,7 @@ test_urlConstructor <- function()
 {
     message(sprintf("--- test_urlConstructor"))
 
-    url <- "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz"
+    url <- "https://gladki.pl/igvShiny/gwas_sample.tsv.gz"
     gwasTrack <- GWASTrack("remote url gwas",
                            url,
                            chrom.col=3,

diff --git a/man/GWASTrack-class.Rd b/man/GWASTrack-class.Rd