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rPackages.immunotation: cache external URLs

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This commit is contained in:
László Kupcsik 2024-04-13 00:07:36 +02:00
parent 7872e50e11
commit d69d444fe1
2 changed files with 84 additions and 0 deletions
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37
pkgs/development/r-modules/default.nix
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@ -1318,6 +1318,43 @@ let
buildInputs = [ cacert ] ++ attrs.buildInputs;
});
immunotation = let
MHC41alleleList = fetchurl {
url = "https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list";
hash = "sha256-CRZ+0uHzcq5zK5eONucAChXIXO8tnq5sSEAS80Z7jhg=";
};
MHCII40alleleList = fetchurl {
url = "https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list";
hash = "sha256-K4Ic2NUs3P4IkvOODwZ0c4Yh8caex5Ih0uO5jXRHp40=";
};
# List of valid countries, regions and ethnic groups
# The original page is changing a bit every day, but the relevant
# content does not. Use archive.org to get a stable snapshot.
# It can be updated from time to time, or when the package becomes
# deficient. This may be difficult to know.
# Update the snapshot date, and add id_ after it, as described here:
# https://web.archive.org/web/20130806040521/http://faq.web.archive.org/page-without-wayback-code/
validGeographics = fetchurl {
url = "https://web.archive.org/web/20240418194005id_/http://www.allelefrequencies.net/hla6006a.asp";
hash = "sha256-m7Wkmh/cPxeqn94LwoznIh+fcFXskmSGErUYj6kTqak=";
};
in old.immunotation.overrideAttrs (attrs: {
patches = [ ./patches/immunotation.patch ];
postPatch = ''
substituteInPlace "R/external_resources_input.R" --replace-fail \
"nix-NetMHCpan-4.1-allele-list" ${MHC41alleleList}
substituteInPlace "R/external_resources_input.R" --replace-fail \
"nix-NETMHCIIpan-4.0-alleles-name-list" ${MHCII40alleleList}
substituteInPlace "R/AFND_interface.R" --replace-fail \
"nix-valid-geographics" ${validGeographics}
'';
});
rstan = old.rstan.overrideAttrs (attrs: {
env = (attrs.env or { }) // {
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";

47
pkgs/development/r-modules/patches/immunotation.patch Normal file
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@ -0,0 +1,47 @@
diff --git a/R/AFND_interface.R b/R/AFND_interface.R
index b62e8e0..0f22d85 100644
--- a/R/AFND_interface.R
+++ b/R/AFND_interface.R
@@ -244,9 +244,9 @@ check_population <- function(hla_population) {
#' @return list of valid countries, regions and ethnic origin
#' @keywords internal
get_valid_geographics <- function() {
- url <- "http://www.allelefrequencies.net/hla6006a.asp?"
- html_input <- getURL(url, read_method = "html")
-
+ # http://www.allelefrequencies.net/hla6006a.asp?
+ html_input <- xml2::read_html("nix-valid-geographics")
+
rvest_tables <- rvest::html_table(html_input, fill = TRUE)
# country
diff --git a/R/external_resources_input.R b/R/external_resources_input.R
index c4b1dc1..8fc5881 100644
--- a/R/external_resources_input.R
+++ b/R/external_resources_input.R
@@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L,
# MHC I
# netmhcI_input_template is an internal variable containing list of valid
# NetMHCpan input alleles
-netmhcI_input_template <- getURL(
- URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list",
- read_method = "delim", delim = "\t",
- col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))
+netmhcI_input_template <- readr::read_delim(
+ # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list
+ "nix-NetMHCpan-4.1-allele-list",
+ delim = "\t",
+ skip = 0,
+ col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")
+ )
# MHC II
-lines <- getURL(
- URL = paste0("https://services.healthtech.dtu.dk/services/",
- "NetMHCIIpan-4.0/alleles_name.list"),
- read_method = "lines")
+# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list
+lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list")
lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t")
netmhcII_input_template <- suppressWarnings(
suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))