From d2df0257435aec0ac60b8618010540fcbf0bb26c Mon Sep 17 00:00:00 2001
From: bipin kumar <kbipinkumar@users.noreply.github.com>
Date: Tue, 3 Oct 2023 09:09:26 +0530
Subject: [PATCH] snpeff: update to 5.2

---
 BioArchLinux/snpeff/PKGBUILD   | 27 ++++++++++++++++++++-------
 BioArchLinux/snpeff/lilac.py   | 23 +++++++++++++++++++++++
 BioArchLinux/snpeff/lilac.yaml |  2 ++
 3 files changed, 45 insertions(+), 7 deletions(-)
 create mode 100644 BioArchLinux/snpeff/lilac.py

diff --git a/BioArchLinux/snpeff/PKGBUILD b/BioArchLinux/snpeff/PKGBUILD
index 20ca51e69c..5b895d18c1 100644
--- a/BioArchLinux/snpeff/PKGBUILD
+++ b/BioArchLinux/snpeff/PKGBUILD
@@ -3,24 +3,37 @@
 pkgname=snpeff
 _pkgname=SnpEff
 _pkg2=SnpSift
-pkgver=5.1
-pkgrel=3
+pkgver=5.2
+_pkgver2=5.1
+pkgrel=1
 pkgdesc="Genetic variant annotation and effect prediction toolbox. doi:10.4161/fly.19695"
 arch=('any')
 url="https://pcingola.github.io/SnpEff/"
 provides=('SnpSift')
 license=('MIT')
 depends=('java-runtime>=12' 'python' 'perl' 'antlr4')
-makedepends=('maven' 'java-environment>=12')
+makedepends=('maven' 'java-environment>=12' 'git')
 source=("$_pkgname-$pkgver.tar.gz::https://github.com/pcingola/SnpEff/archive/refs/tags/v$pkgver.tar.gz"
-        "$_pkg2-$pkgver.tar.gz::https://github.com/pcingola/SnpSift/archive/refs/tags/v$pkgver.tar.gz"
+        "$_pkg2-${_pkgver2}.tar.gz::https://github.com/pcingola/SnpSift/archive/refs/tags/v${_pkgver2}.tar.gz"
+        "https.patch::https://patch-diff.githubusercontent.com/raw/pcingola/SnpSift/pull/84.patch"
         "snpSift.sh"
         "snpEff.sh"
        )
-sha512sums=('eb12a126f71536eb04132e40b5f3e0bea33b6512dce999a70e5c170d2839d739ea8b52e5b38822e83c544693aec7ece20f13674634ae3971a6f08659dc7b9640'
+sha512sums=('df0cdb4ddde60491789494a809e8fb28a7b6c5f1b18c1f639a76828a4d2c19d27d019cb0b2362c5fa8734c21b770377b8eec6e8beb76fda287e4eda016f380e7'
             '074139695584227d3e523962b81ed1cd1687a146b973ec761e5c42fccf865b6f01bd8fc1280a1f73e7c9ab3292bfc3358d56a572f0795bd05fa879011a4ad950'
+            'eb802167761ea7de0b7fdb60b0cc9440d40ea21fe6ed164dc900452e224d71039a8e187e1b7a6499b91338580378c33aa678a23b81f3e27f0f939a4cd3ef6a0c'
             '9819376173c372cec8ae3f28d1b3857a1b63690bf16213e6f26ebd5d29150616c8f8a3d0ecf8d9ba24c34e24f28ab56edecf8c9cee3c578ae673da7c65c48f0d'
             '0eb2339b55969cc065b8c15bee06d8728b0576689217777bf24e209409d61210f91e814bb1a5dddc651dd2a3f35d0f3911bd3161d6d3275604ea58cf83f9086a')
+prepare() {
+    # fix pom.xml of SnpSift
+    cd "${srcdir}/$_pkg2-${_pkgver2}"
+    # fix http sources for dependencies
+    patch -p1 < ${srcdir}/https.patch
+    # set correct snpeff version as dependency
+    export snpver=$(sed -n '41p' pom.xml | cut -d '>' -f 2 | cut -d '<' -f 1) 
+    sed -i "41s/${snpver}/[${pkgver},)/g" pom.xml
+}
+
 build() {
 	# Build SnpEff
     cd "${srcdir}/$_pkgname-$pkgver"
@@ -37,14 +50,14 @@ build() {
 	 --quiet
 
     # Build SnpSift
-    cd "${srcdir}/$_pkg2-$pkgver"
+    cd "${srcdir}/$_pkg2-${_pkgver2}"
     mvn -e clean compile assembly:single jar:jar
     
 }
 
 package() {
     install -Dm644 ${srcdir}/$_pkgname-$pkgver/target/SnpEff-$pkgver-jar-with-dependencies.jar  "${pkgdir}"/usr/share/java/snpEff/snpEff.jar
-    install -Dm644 ${srcdir}/$_pkg2-$pkgver/target/SnpSift-$pkgver-jar-with-dependencies.jar  "${pkgdir}"/usr/share/java/snpEff/snpSift.jar
+    install -Dm644 ${srcdir}/$_pkg2-$_siftver/target/SnpSift-${_pkgver2}-jar-with-dependencies.jar  "${pkgdir}"/usr/share/java/snpEff/snpSift.jar
     install -Dm644 ${srcdir}/$_pkgname-$pkgver/config/snpEff.config "${pkgdir}"/usr/share/java/snpEff/snpEff.config
     install -Dm644 ${srcdir}/$_pkgname-$pkgver/LICENSE.md "${pkgdir}"/usr/share/licenses/$pkgname/LICENSE
     install -Dm755 snpEff.sh "${pkgdir}"/usr/bin/snpeff
diff --git a/BioArchLinux/snpeff/lilac.py b/BioArchLinux/snpeff/lilac.py
new file mode 100644
index 0000000000..4015317b76
--- /dev/null
+++ b/BioArchLinux/snpeff/lilac.py
@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+import requests
+import fileinput
+from lilaclib import *
+
+def get_latest_tag(owner, repo):
+    url = f"https://api.github.com/repos/{owner}/{repo}/tags"
+    response = requests.get(url)
+    response.raise_for_status()
+    tags = response.json()
+    latest_tag = tags[0]["name"].lstrip("v")
+    return latest_tag
+
+def pre_build():    
+    latest_tag = get_latest_tag("pcingola", "SnpSift")
+    for line in edit_file('PKGBUILD'):
+        if line.startswith('_pkgver2='):
+            current_tag = line.split("=")[1].strip()
+            if latest_tag > current_tag:
+                line = f'_pkgver2={latest_tag}'
+        print(line)
+
+    update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
\ No newline at end of file
diff --git a/BioArchLinux/snpeff/lilac.yaml b/BioArchLinux/snpeff/lilac.yaml
index 4765e6598d..3661cfba86 100644
--- a/BioArchLinux/snpeff/lilac.yaml
+++ b/BioArchLinux/snpeff/lilac.yaml
@@ -2,6 +2,8 @@ maintainers:
   - github: kbipinkumar
     email: kbipinkumar@pm.me
 build_prefix: extra-x86_64
+pre_build_script: |
+  run_cmd(['updpkgsums'])
 post_build_script: |
   git_pkgbuild_commit()
   update_aur_repo()