From 06551e73da8dcc181d7cf88fad02755d8f4d4919 Mon Sep 17 00:00:00 2001
From: Bond_009 <bond.009@outlook.com>
Date: Thu, 17 Oct 2024 12:12:18 +0200
Subject: [PATCH] Add nextflow linter to Nix flake

---
 flake.nix                           | 26 +++++++++++++++++++++++++-
 tested/languages/nextflow/linter.py | 13 +------------
 2 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/flake.nix b/flake.nix
index 27eb5ecc..38328811 100644
--- a/flake.nix
+++ b/flake.nix
@@ -70,6 +70,30 @@
           };
         };
 
+        nextflow-linter = let
+          codenarc = pkgs.fetchurl {
+            url = "https://repo1.maven.org/maven2/org/codenarc/CodeNarc/3.5.0/CodeNarc-3.5.0-all.jar";
+            hash = "sha256-wTGPxP5sjMPPake3WM6Fcz551WIe8C+c6AtCtjBa3jI=";
+          };
+          linter-rules = pkgs.fetchurl {
+            url = "https://github.com/awslabs/linter-rules-for-nextflow/releases/download/v0.1.0/linter-rules-0.1.jar";
+            hash = "sha256-IHl2jAtZyloZLXybLNBELnTyld+ZA9q5Srta7LeUeHs=";
+          };
+          slf4j-api = pkgs.fetchurl {
+            url = "https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar";
+            hash = "sha256-0+9XXj5JeWeNwBvx3M5RAhSTtNEft/G+itmCh3wWocA=";
+          };
+          slf4j-simple = pkgs.fetchurl {
+            url = "https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/1.7.36/slf4j-simple-1.7.36.jar";
+            hash = "sha256-Lzm+2UPWJN+o9BAtBXEoOhCHC2qjbxl6ilBvFHAQwQ8=";
+          };
+        in pkgs.writeScriptBin "nextflow-linter" ''
+            ${pkgs.jre_minimal}/bin/java \
+              -Dorg.slf4j.simpleLogger.defaultLogLevel=error \
+              -classpath "${linter-rules}/linter-rules-0.1.jar:${codenarc}/CodeNarc-3.5.0-all.jar:${slf4j-api}/slf4j-api-1.7.36.jar:${slf4j-simple}/slf4j-simple-1.7.36.jar" \
+              "org.codenarc.CodeNarc"
+        '';
+
         # General dependencies for other languages
         haskell-deps = [
           (pkgs.haskell.packages.ghc96.ghcWithPackages (p: [ p.aeson ]))
@@ -81,7 +105,7 @@
         java-deps = [ pkgs.openjdk21 pkgs.checkstyle ];
         kotlin-deps = [ pkgs.kotlin pkgs.ktlint ];
         csharp-deps = [ pkgs.dotnetCorePackages.sdk_8_0 ];
-        nextflow-deps = [ pkgs.groovy ];
+        nextflow-deps = [ pkgs.groovy nextflow-linter ];
 
         all-other-dependencies = haskell-deps ++ node-deps ++ bash-deps
           ++ c-deps ++ java-deps ++ kotlin-deps ++ csharp-deps ++ nextflow-deps
diff --git a/tested/languages/nextflow/linter.py b/tested/languages/nextflow/linter.py
index 4d120d20..d4e3c88e 100644
--- a/tested/languages/nextflow/linter.py
+++ b/tested/languages/nextflow/linter.py
@@ -24,24 +24,13 @@ def run_codenarc(
     submission = config.source
     language_options = config.config_for()
 
-    # TODO: find a better solution
-    if path := language_options.get("codenarc_path", None):
-        assert isinstance(path, str)
-        codenarc_path = config.resources / path
-    else:
-        return [], []
-    codenarc_path = str(codenarc_path.absolute())
     report_file = str((config.workdir / "report.json").absolute())
 
     execution_results = run_command(
         directory=submission.parent,
         timeout=remaining,
         command=[
-            "java",
-            "-Dorg.slf4j.simpleLogger.defaultLogLevel=error",
-            "-classpath",
-            f"{codenarc_path}/linter-rules-0.1.jar:{codenarc_path}/CodeNarc-3.5.0-all.jar:{codenarc_path}/slf4j-api-1.7.36.jar:{codenarc_path}/slf4j-simple-1.7.36.jar",
-            "org.codenarc.CodeNarc",
+            "nextflow-linter",
             f"-report=json:{report_file}",
             "-rulesetfiles=rulesets/general.xml",
             "-includes=**/*.nf",