From 7694758ad6dd6467ebd53b5e87bcbd5a3a370e08 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Wed, 2 Oct 2024 10:23:07 +0200
Subject: [PATCH] Add wrapper functions for `getAllFilesFromDir` with named
 parameters

---
 .../java/nf_core/nf/test/utils/Methods.java   | 32 ++++++++++++++++---
 tests/getAllFilesFromDir/main.nf.test         | 24 ++++++++++++++
 tests/getAllFilesFromDir/main.nf.test.snap    | 18 +++++++++++
 3 files changed, 70 insertions(+), 4 deletions(-)

diff --git a/src/main/java/nf_core/nf/test/utils/Methods.java b/src/main/java/nf_core/nf/test/utils/Methods.java
index d5de51d..80f6c99 100644
--- a/src/main/java/nf_core/nf/test/utils/Methods.java
+++ b/src/main/java/nf_core/nf/test/utils/Methods.java
@@ -12,10 +12,7 @@
 import java.nio.file.Paths;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.stream.Collectors;
 import org.yaml.snakeyaml.Yaml;
 
@@ -48,6 +45,33 @@ public static Map<String, Map<String, Object>> removeNextflowVersion(CharSequenc
     return yamlData;
   }
 
+  //wrapper functions for getAllFilesFromDir with default options
+  public static List getAllFilesFromDir(String path) throws IOException {
+    return getAllFilesFromDir(new LinkedHashMap<String, Object>(), path);
+  }
+
+  //wrapper functions for getAllFilesFromDir with named options
+  public static List getAllFilesFromDir(LinkedHashMap<String, Object> options, String path) throws IOException {
+    if (path == null || path.isEmpty()) {
+      throw new IllegalArgumentException("The 'path' parameter is required.");
+    }
+    //TODO: check if path exists
+
+    // Extract optional parameters from the map (use defaults if not provided)
+    Boolean includeDir = (Boolean) options.getOrDefault("includeDir", true);
+    List<String> ignoreGlobs = (List<String>) options.getOrDefault("ignore", new ArrayList<String>());
+    String ignoreFilePath = (String) options.get("ignoreFile");
+    Boolean relative = (Boolean) options.getOrDefault("relative", false);
+
+    List<File> files = getAllFilesFromDir(path, includeDir, ignoreGlobs, ignoreFilePath);
+
+    if (relative) {
+      return getRelativePath(files, path);
+    } else {
+      return files;
+    }
+  }
+
   // Return all files in a directory and its sub-directories
   // matching or not matching supplied glob
   public static List<File> getAllFilesFromDir(String outdir, boolean includeDir, List<String> ignoreGlobs,
diff --git a/tests/getAllFilesFromDir/main.nf.test b/tests/getAllFilesFromDir/main.nf.test
index cb435af..5712e76 100644
--- a/tests/getAllFilesFromDir/main.nf.test
+++ b/tests/getAllFilesFromDir/main.nf.test
@@ -24,4 +24,28 @@ nextflow_pipeline {
           ).match()
         }
     }
+
+    test("getAllFilesFromDir with named params") {
+            when {
+                params {
+                    outdir = "$outputDir"
+                }
+            }
+
+            then {
+              //with default params and relative
+              println(getAllFilesFromDir(params.outdir))
+              println(getAllFilesFromDir(params.outdir, relative: true))
+              // Use getAllFilesFromDir() to get a list of all files and folders from the output directory, minus the timestamped files
+              def stable_name  = getAllFilesFromDir(params.outdir, ignore: ['pipeline_info/execution_*.{html,txt}'])
+              // works also with spaces.
+              def stable_content = getAllFilesFromDir params.outdir, includeDir: false, ignore: ['pipeline_info/execution_*.{html,txt}'], ignoreFile: 'tests/getAllFilesFromDir/.nftignore'
+              assert snapshot(
+                // Only snapshot name
+                stable_name*.name,
+                // Snapshot content
+                stable_content
+              ).match()
+            }
+        }
 }
diff --git a/tests/getAllFilesFromDir/main.nf.test.snap b/tests/getAllFilesFromDir/main.nf.test.snap
index 446cf60..d5b0414 100644
--- a/tests/getAllFilesFromDir/main.nf.test.snap
+++ b/tests/getAllFilesFromDir/main.nf.test.snap
@@ -1,4 +1,22 @@
 {
+    "getAllFilesFromDir with named params": {
+        "content": [
+            [
+                "pipeline_info",
+                "stable",
+                "stable_content.txt",
+                "stable_name.txt"
+            ],
+            [
+                "stable_content.txt:md5,f6d73f703cda1c725ea78369a6c3a48d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.07.0"
+        },
+        "timestamp": "2024-10-02T10:15:47.491035"
+    },
     "getAllFilesFromDir": {
         "content": [
             [