Fix bug in handling non-unique filenames by sorting via hash

askimed · Sep 23, 2023 · 67eadd7 · 67eadd7
1 parent b8383ac
commit 67eadd7
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Showing 5 changed files with 187 additions and 5 deletions.
diff --git a/src/main/java/com/askimed/nf/test/lang/channels/ChannelItemComparator.java b/src/main/java/com/askimed/nf/test/lang/channels/ChannelItemComparator.java
@@ -1,10 +1,11 @@
 package com.askimed.nf.test.lang.channels;
 
-import java.io.File;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Comparator;
 import java.util.Map;
 
+import com.askimed.nf.test.lang.extensions.PathExtension;
 import com.askimed.nf.test.util.AnsiColors;
 
 public class ChannelItemComparator implements Comparator<Object> {
@@ -74,14 +75,30 @@ private boolean isPath(Object a) {
 
 	@SuppressWarnings({ "rawtypes" })
 	private int compareMaps(Map a, Map b) {
-		// since we converted all nested maps to treemaps, toString returns keys sorted in deterministic order.
+		// since we converted all nested maps to treemaps, toString returns keys sorted
+		// in deterministic order.
 		return compareStrings(a.toString(), b.toString());
 	}
 
 	public int comparePaths(String a, String b) {
-		String name1 = new File(a).getName();
-		String name2 = new File(b).getName();
-		return name1.compareTo(name2);
+		// sort path by filename
+		Path path1 = Path.of(a);
+		Path path2 = Path.of(b);
+		String name1 = path1.getFileName().toString();
+		String name2 = path2.getFileName().toString();
+		int result = name1.compareTo(name2);
+		if (result != 0) {
+			return result;
+		}
+		// filenames are equal -> sort by hash to get deterministic order
+		try {
+			String hash1 = PathExtension.getMd5(path1);
+			String hash2 = PathExtension.getMd5(path2);
+			return hash1.compareTo(hash2);
+		} catch (Exception e) {
+			throw new RuntimeException(e);
+		}
+
 	}
 
 	public int compareStrings(String a, String b) {

diff --git a/src/test/java/com/askimed/nf/test/lang/WorkflowTest.java b/src/test/java/com/askimed/nf/test/lang/WorkflowTest.java
@@ -115,4 +115,13 @@ public void testHangingWorkflowIssue57() throws Exception {
 
 	}
 
+	@Test
+	public void testWorkflowNonUniqueFilenames() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/non-unique-filenames/main.nf.test"});
+		assertEquals(0, exitCode);
+
+	}
+
 }
diff --git a/test-data/workflow/non-unique-filenames/main.nf b/test-data/workflow/non-unique-filenames/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+process WRITE_VERSION {
+    input:
+        val version
+
+    output:
+        path "*.txt", emit: versions
+
+    script:
+    """
+    echo ${version} > version.txt
+    """
+}
+
+workflow DUPLICATE_FILENAMES {
+    take: things
+    main:
+        WRITE_VERSION(things)
+    emit:
+        versions = WRITE_VERSION.out.versions
+}
diff --git a/test-data/workflow/non-unique-filenames/main.nf.test b/test-data/workflow/non-unique-filenames/main.nf.test
@@ -0,0 +1,21 @@
+nextflow_workflow {
+
+    name "Test duplicate filenames in one channel"
+    script "./main.nf"
+    workflow "DUPLICATE_FILENAMES"
+
+    test("Should run without failures") {
+        when {
+            workflow {
+                """
+                input[0] = Channel.of(1..50)
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+ 			assert snapshot(workflow.out).match()
+        }
+    }
+}
diff --git a/test-data/workflow/non-unique-filenames/main.nf.test.snap b/test-data/workflow/non-unique-filenames/main.nf.test.snap
@@ -0,0 +1,113 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "version.txt:md5,08c61f3fd48f12fa7c88a7f5fd01df3d",
+                    "version.txt:md5,166d77ac1b46a1ec38aa35ab7e628ab5",
+                    "version.txt:md5,1dcca23355272056f04fe8bf20edfce0",
+                    "version.txt:md5,21fa2e849284bf7681c37a8b565bd934",
+                    "version.txt:md5,22cab69bca05d296a2d779a52cdee643",
+                    "version.txt:md5,26ab0db90d72e28ad0ba1e22ee510510",
+                    "version.txt:md5,2737b49252e2a4c0fe4c342e92b13285",
+                    "version.txt:md5,2a52a5e65fc3c43f409550dfad1f904f",
+                    "version.txt:md5,2a53da1a6fbfc0bafdd96b0a2ea29515",
+                    "version.txt:md5,2fc57d6f63a9ee7e2f21a26fa522e3b6",
+                    "version.txt:md5,31d30eea8d0968d6458e0ad0027c9f80",
+                    "version.txt:md5,367764329430db34be92fd14a7a770ee",
+                    "version.txt:md5,3bb50ff8eeb7ad116724b56a820139fa",
+                    "version.txt:md5,48a24b70a0b376535542b996af517398",
+                    "version.txt:md5,4a5c26d88c514a23bf15654abd83adb1",
+                    "version.txt:md5,4d095eeac8ed659b1ce69dcef32ed0dc",
+                    "version.txt:md5,4f89a0f6c113ae3ff279af1e6c6286bb",
+                    "version.txt:md5,4fbafd6948b6529caa2b78e476359875",
+                    "version.txt:md5,50a2fabfdd276f573ff97ace8b11c5f4",
+                    "version.txt:md5,51a6d96331d5eaa300358c7a0faf168d",
+                    "version.txt:md5,59885ebc737617addaaf0cb8090203fc",
+                    "version.txt:md5,5b6b41ed9b343fed9cd05a66d36650f0",
+                    "version.txt:md5,649ee93d50739c656e94ec88a32c7ffe",
+                    "version.txt:md5,66a7c1d5cb75ef2542524d888fd32f4a",
+                    "version.txt:md5,6d7fce9fee471194aa8b5b6e47267f03",
+                    "version.txt:md5,6eb5cefde6fcb8463cea70880a44eb98",
+                    "version.txt:md5,7c5aba41f53293b712fd86d08ed5b36e",
+                    "version.txt:md5,7c67493bd72ceff21059c3d924d17518",
+                    "version.txt:md5,84bc3da1b3e33a18e8d5e1bdd7a18d7a",
+                    "version.txt:md5,87aa60e6e440a6656bc74eb20476d662",
+                    "version.txt:md5,8c9eb686bf3eb5bd83d9373eadf6504b",
+                    "version.txt:md5,90e2a51705594d033a3abe9d77b2b7ad",
+                    "version.txt:md5,93e50d72ab294091a81d828459019eba",
+                    "version.txt:md5,9ae0ea9e3c9c6e1b9b6252c8395efdc1",
+                    "version.txt:md5,a75f5a8337c6699916182b6f7c10d7a9",
+                    "version.txt:md5,aa6ed9e0f26a6eba784aae8267df1951",
+                    "version.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1",
+                    "version.txt:md5,b0771132ab2531a40c9941375ed8e290",
+                    "version.txt:md5,bb743fc2a7213949f25593c51cbee64f",
+                    "version.txt:md5,bda81ba88c634b46394ead43aff31ad5",
+                    "version.txt:md5,c30f7472766d25af1dc80b3ffc9a58c7",
+                    "version.txt:md5,cf4278314ef8e4b996e1b798d8eb92cf",
+                    "version.txt:md5,d3a57c7e953913944c76009357469568",
+                    "version.txt:md5,d5b4c7d9b06b60a7846c4529834c9812",
+                    "version.txt:md5,dbbf8220893d497d403bb9cdf49db7a4",
+                    "version.txt:md5,e760668b6273d38c832c153fde5725da",
+                    "version.txt:md5,f0287f33eba7192e2a9c6a14f829aa1a",
+                    "version.txt:md5,fa84f696e31d07f55cd45cc3c9e52f3b",
+                    "version.txt:md5,fd1bc138d22d4f78150c6e808345c2cc",
+                    "version.txt:md5,fe9d26c3e620eeb69bd166c8be89fb8f"
+                ],
+                "versions": [
+                    "version.txt:md5,08c61f3fd48f12fa7c88a7f5fd01df3d",
+                    "version.txt:md5,166d77ac1b46a1ec38aa35ab7e628ab5",
+                    "version.txt:md5,1dcca23355272056f04fe8bf20edfce0",
+                    "version.txt:md5,21fa2e849284bf7681c37a8b565bd934",
+                    "version.txt:md5,22cab69bca05d296a2d779a52cdee643",
+                    "version.txt:md5,26ab0db90d72e28ad0ba1e22ee510510",
+                    "version.txt:md5,2737b49252e2a4c0fe4c342e92b13285",
+                    "version.txt:md5,2a52a5e65fc3c43f409550dfad1f904f",
+                    "version.txt:md5,2a53da1a6fbfc0bafdd96b0a2ea29515",
+                    "version.txt:md5,2fc57d6f63a9ee7e2f21a26fa522e3b6",
+                    "version.txt:md5,31d30eea8d0968d6458e0ad0027c9f80",
+                    "version.txt:md5,367764329430db34be92fd14a7a770ee",
+                    "version.txt:md5,3bb50ff8eeb7ad116724b56a820139fa",
+                    "version.txt:md5,48a24b70a0b376535542b996af517398",
+                    "version.txt:md5,4a5c26d88c514a23bf15654abd83adb1",
+                    "version.txt:md5,4d095eeac8ed659b1ce69dcef32ed0dc",
+                    "version.txt:md5,4f89a0f6c113ae3ff279af1e6c6286bb",
+                    "version.txt:md5,4fbafd6948b6529caa2b78e476359875",
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+                    "version.txt:md5,51a6d96331d5eaa300358c7a0faf168d",
+                    "version.txt:md5,59885ebc737617addaaf0cb8090203fc",
+                    "version.txt:md5,5b6b41ed9b343fed9cd05a66d36650f0",
+                    "version.txt:md5,649ee93d50739c656e94ec88a32c7ffe",
+                    "version.txt:md5,66a7c1d5cb75ef2542524d888fd32f4a",
+                    "version.txt:md5,6d7fce9fee471194aa8b5b6e47267f03",
+                    "version.txt:md5,6eb5cefde6fcb8463cea70880a44eb98",
+                    "version.txt:md5,7c5aba41f53293b712fd86d08ed5b36e",
+                    "version.txt:md5,7c67493bd72ceff21059c3d924d17518",
+                    "version.txt:md5,84bc3da1b3e33a18e8d5e1bdd7a18d7a",
+                    "version.txt:md5,87aa60e6e440a6656bc74eb20476d662",
+                    "version.txt:md5,8c9eb686bf3eb5bd83d9373eadf6504b",
+                    "version.txt:md5,90e2a51705594d033a3abe9d77b2b7ad",
+                    "version.txt:md5,93e50d72ab294091a81d828459019eba",
+                    "version.txt:md5,9ae0ea9e3c9c6e1b9b6252c8395efdc1",
+                    "version.txt:md5,a75f5a8337c6699916182b6f7c10d7a9",
+                    "version.txt:md5,aa6ed9e0f26a6eba784aae8267df1951",
+                    "version.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1",
+                    "version.txt:md5,b0771132ab2531a40c9941375ed8e290",
+                    "version.txt:md5,bb743fc2a7213949f25593c51cbee64f",
+                    "version.txt:md5,bda81ba88c634b46394ead43aff31ad5",
+                    "version.txt:md5,c30f7472766d25af1dc80b3ffc9a58c7",
+                    "version.txt:md5,cf4278314ef8e4b996e1b798d8eb92cf",
+                    "version.txt:md5,d3a57c7e953913944c76009357469568",
+                    "version.txt:md5,d5b4c7d9b06b60a7846c4529834c9812",
+                    "version.txt:md5,dbbf8220893d497d403bb9cdf49db7a4",
+                    "version.txt:md5,e760668b6273d38c832c153fde5725da",
+                    "version.txt:md5,f0287f33eba7192e2a9c6a14f829aa1a",
+                    "version.txt:md5,fa84f696e31d07f55cd45cc3c9e52f3b",
+                    "version.txt:md5,fd1bc138d22d4f78150c6e808345c2cc",
+                    "version.txt:md5,fe9d26c3e620eeb69bd166c8be89fb8f"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-23T09:30:55.706829"
+    }
+}