Add getAllFilesFromDir function

src/main/java/nf_core/nf/test/utils/Methods.java

@@ -1,15 +1,21 @@
 package nf_core.nf.test.utils;
 
 import org.yaml.snakeyaml.Yaml;
+
+import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 import java.util.Map;
+import java.util.regex.Pattern;
 
 public class Methods {
-  public static Map<String, Map<String, Object>> readYamlFile(String filePath) {
-    Yaml yaml = new Yaml();
-
 
+  // Read a Version YAML file and return a Map of Map
+  public static Map<String, Map<String, Object>> readVersionYamlFile(String filePath) {
+    Yaml yaml = new Yaml();
     try (FileReader reader = new FileReader(filePath)) {
       Map<String, Map<String, Object>> data = yaml.load(reader);
       return data;
@@ -19,9 +25,11 @@ public static Map<String, Map<String, Object>> readYamlFile(String filePath) {
     }
   }
 
+  // Removed the Nextflow entry from the Workflow entry
+  // within the input Version YAML file
   public static Map<String, Map<String, Object>> removeNextflowVersion(CharSequence versionFile) {
     String yamlFilePath = versionFile.toString();
-    Map<String, Map<String, Object>> yamlData = readYamlFile(yamlFilePath);
+    Map<String, Map<String, Object>> yamlData = readVersionYamlFile(yamlFilePath);
 
     if (yamlData != null) {
       // Access and use the YAML data
@@ -31,4 +39,46 @@ public static Map<String, Map<String, Object>> removeNextflowVersion(CharSequenc
     }
     return yamlData;
   }
+
+  // Return all files in a directory and its sub-directories
+  // matching or not matching supplied regexes
+  public static List<File> getAllFilesFromDir(String outdir, boolean includeDir, List<String> excludeRegexes) {
+    List<File> output = new ArrayList<>();
+    File directory = new File(outdir);
+
+    getAllFilesRecursively(directory, includeDir, excludeRegexes, output);
+
+    Collections.sort(output);
+    return output;
+  }
+
+  // Recursively list all files in a directory and its sub-directories
+  // matching or not matching supplied regexes
+  private static void getAllFilesRecursively(File directory, boolean includeDir, List<String> excludeRegexes,
+      List<File> output) {
+    File[] files = directory.listFiles();
+    if (files != null) {
+      for (File file : files) {
+        boolean matchesInclusion = includeDir || file.isFile();
+        boolean matchesExclusion = false;
+
+        if (excludeRegexes != null) {
+          for (String regex : excludeRegexes) {
+            if (Pattern.matches(regex, file.getName())) {
+              matchesExclusion = true;
+              break;
+            }
+          }
+        }
+
+        if (matchesInclusion && !matchesExclusion) {
+          output.add(file);
+        }
+
+        if (file.isDirectory()) {
+          getAllFilesRecursively(file, includeDir, excludeRegexes, output);
+        }
+      }
+    }
+  }
 }

tests/getAllFilesFromDir/main.nf

@@ -0,0 +1,23 @@
+workflow {
+
+    def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+
+    ch_stable_content = Channel.of(
+    """
+    I HAVE STABLE CONTENT
+    """.stripIndent().trim())
+    .collectFile(storeDir: "${params.outdir}/stable", name: 'stable_content.txt', sort: true, newLine: true)
+
+    ch_stable_name = Channel.of(
+    """
+    I DO NOT HAVE STABLE CONTENT
+    ${trace_timestamp}
+    """.stripIndent().trim())
+    .collectFile(storeDir: "${params.outdir}/stable", name: 'stable_name.txt', sort: true, newLine: true)
+
+    ch_unstable_name = Channel.of(
+    """
+    I DO NOT HAVE STABLE NAME
+    """.stripIndent().trim())
+    .collectFile(storeDir: "${params.outdir}/not_stable", name: "${trace_timestamp}.txt", sort: true, newLine: true)
+}

tests/getAllFilesFromDir/main.nf.test

@@ -0,0 +1,24 @@
+nextflow_pipeline {
+
+    name "Test getAllFilesFromDir"
+    script "./main.nf"
+    tag "getAllFilesFromDir"
+
+    test("getAllFilesFromDir") {
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+          def timestamp      = [/.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/]
+          def stable_name    = getAllFilesFromDir(params.outdir, false, timestamp)
+          def stable_content = getAllFilesFromDir(params.outdir, false, timestamp + [/stable_name\.txt/] )
+          assert snapshot(
+            stable_name*.name,
+            stable_content
+          ).match()
+        }
+    }
+}

tests/getAllFilesFromDir/main.nf.test.snap

@@ -0,0 +1,18 @@
+{
+    "getAllFilesFromDir": {
+        "content": [
+            [
+                "stable_content.txt",
+                "stable_name.txt"
+            ],
+            [
+                "stable_content.txt:md5,f6d73f703cda1c725ea78369a6c3a48d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-30T10:55:42.424751"
+    }
+}

tests/removeNextflowVersion/main.nf.test.snap

@@ -0,0 +1,16 @@
+{
+    "removeNextflowVersion": {
+        "content": [
+            {
+                "Workflow": {
+                    "Pipeline": "1.0.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-27T19:17:42.066036"
+    }
+}