Merge pull request #26 from nvnieuwk/add-md5-functions

Add `listToMD5`

CHANGELOG.md

@@ -4,7 +4,7 @@
 
 ### New features
 
-The first release of nft-utils
+- Added the `listToMD5` function
 
 ### Fixes
 

docs/usage.md

@@ -196,3 +196,9 @@ Without using `getRelativePath()` and by using `*.name` to capture the file name
 def stable_name       = getAllFilesFromDir(params.outdir, relative: true, ignore: ['pipeline_info/execution_*.{html,txt}'] )
 def stable_name_again = getAllFilesFromDir(params.outdir, relative: true, include: ['stable/*'] )
 ```
+
+## `listToMD5()`
+
+This function takes a list of values as input and converts the sequence to a MD5 hash. All values in the list should be of a type that can be converted to a string, otherwise the function will fail.
+
+A common use case for this function could be to read a file, remove all unstable lines from it and regerenate an MD5 hash.

pom.xml

@@ -42,6 +42,11 @@
 			<artifactId>snakeyaml</artifactId>
 			<version>2.3</version>
 		</dependency>
+		<dependency>
+			<groupId>com.joyent.util</groupId>
+			<artifactId>fast-md5</artifactId>
+			<version>2.7.1</version>
+		</dependency>
 	</dependencies>
 
 	<build>

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

@@ -4,6 +4,7 @@
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.io.UnsupportedEncodingException;
 import java.nio.file.FileSystems;
 import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
@@ -16,6 +17,8 @@
 import java.util.stream.Collectors;
 import org.yaml.snakeyaml.Yaml;
 
+import com.twmacinta.util.MD5;
+
 public class Methods {
 
   // Read a Version YAML file and return a Map of Map
@@ -184,4 +187,13 @@ public static List<String> getRelativePath(List<File> filePaths, String baseDir)
         })
         .collect(Collectors.toList());
   }
+
+  public static String listToMD5(ArrayList<Object> input) throws UnsupportedEncodingException {
+    MD5 md5 = new MD5();
+    Iterator<Object> inputIterator = input.iterator();
+    while(inputIterator.hasNext()) {
+      md5.Update(inputIterator.next().toString(), null);
+    }
+    return md5.asHex();
+  }
 }

tests/listToMD5/main.nf

@@ -0,0 +1,16 @@
+workflow TEST {
+    main:
+    def fill = "This needs to be filled in"
+    def lines = [
+        "This is a line",
+        32,
+        453.2,
+        """
+        Wow, a multiline string
+        """,
+        "${fill}"
+    ]
+
+    emit:
+    lines_out = lines
+}

tests/listToMD5/main.nf.test

@@ -0,0 +1,18 @@
+nextflow_workflow {
+
+    name "Test Workflow TEST"
+    script "./main.nf"
+    workflow "TEST"
+
+    tag "listToMD5"
+
+    test("Should run without failures") {
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out.lines_out.collect { listToMD5(it) }).match()
+        }
+
+    }
+
+}

tests/listToMD5/main.nf.test.snap

@@ -0,0 +1,14 @@
+{
+    "Should run without failures": {
+        "content": [
+            [
+                "a2112ea5e55a647ce81b27810d0d1070"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-28T14:22:04.02598768"
+    }
+}