Merge pull request #18 from lukfor/main

Add wrapper functions for `getAllFilesFromDir` with named parameters

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,

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()
+ }
+ }
 }

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": [
  [