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edirect 22.4 #1824

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merged 2 commits into from
Aug 13, 2024
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edirect 22.4 #1824

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ca03806
edirect 22.4
YoshitakaMo Aug 13, 2024
7741faa
edirect 22.4
YoshitakaMo Aug 13, 2024
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61 changes: 14 additions & 47 deletions Formula/edirect.rb
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
class Edirect < Formula
desc "Access NCBI databases via the command-line"
homepage "https://www.ncbi.nlm.nih.gov/books/NBK179288/"
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/edirect.tar.gz"
version "22.1"
sha256 "28d9cc2d353323375a2102e9031e229943d1f1f975f140d0815db3e5a111f235"
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.4.20240812/edirect-22.4.20240812.tar.gz"
version "22.4"
sha256 "3320e0b0859b85ecd21248323c792d671bfed8c9c60b1f414a3e0e3c648d8681"

bottle do
root_url "https://ghcr.io/v2/brewsci/bio"
Expand All @@ -13,51 +13,13 @@ class Edirect < Formula
end

depends_on "cpanminus" => :build
depends_on "openssl"
depends_on "go" => :build
depends_on "openssl@3"

uses_from_macos "expat"
uses_from_macos "perl"
uses_from_macos "zlib"

# macOS CIRCLE-CI often fails on https accesses. Use ftp accesses.
resource "xtract" do
if OS.mac? && Hardware::CPU.arm?
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/xtract.Silicon.gz"
sha256 "7c841d4e2aeaf4e095ca721d2a6266422580c8fdfc5f9f33b5c55d3c8d9ca543"
elsif OS.mac?
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/xtract.Darwin.gz"
sha256 "394d2af9fe4b5595907b7cce70dd2f2f0a92a6975bb8b1502a7cdeeecbb1cfa2"
else
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/xtract.Linux.gz"
sha256 "1e97ecfda18e45311c14b1628a097443a0079013ab16da47548d4da696063152"
end
end

resource "rchive" do
if OS.mac? && Hardware::CPU.arm?
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/rchive.Silicon.gz"
sha256 "b1035e3ebf0e123303ce58f98ec17395348a3e000844a01223b3734a157ac372"
elsif OS.mac?
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/rchive.Darwin.gz"
sha256 "8fd39230d9c9dcd5c3d263201b04b065fbacf09e77e2e75000aaed38ce8f88f5"
else
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/rchive.Linux.gz"
sha256 "4a0af7405d6fc1da52ec554f4906ad6004d9662316852dd0e5816b3c0f519d5b"
end
end

resource "transmute" do
if OS.mac? && Hardware::CPU.arm?
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/transmute.Silicon.gz"
sha256 "031822fede0e89beed8f7041c973ce4af1232e377341697bb6a6501c2dbca779"
elsif OS.mac?
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/transmute.Darwin.gz"
sha256 "3dd7724b97a69f12205cbe3b09358d57f3224aadf789251f50b60ed8f3c964df"
else
url "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.1.20240517/transmute.Linux.gz"
sha256 "295e369d2ab42c62ea289e698513a468a456a67ea6360bb9d7474aa6e1f006c8"
end
end

def install
rm %w[Mozilla-CA.tar.gz]
rm Dir["*.go"]
Expand All @@ -83,12 +45,17 @@ def install
name = File.basename script
(bin/name).write_env_script(script, PERL5LIB: ENV["PERL5LIB"])
end
bin.install resource("xtract")
bin.install resource("rchive")

cd "#{libexec}/cmd" do
system "./build.sh", bin
end
cd "#{libexec}/extern" do
system "./build.sh", bin
end
end

test do
%w[efetch esearch einfo efilter epost elink].each do |exe|
%w[efetch esearch einfo efilter epost elink xtract transmute rchive].each do |exe|
assert_match version.to_s, shell_output("#{bin}/#{exe} -version")
end
# CIRCLE-CI MacOS often fails on https accesses
Expand Down