Serialize null values in channel outputs (#232)

askimed · Jul 13, 2024 · 04fa9a8 · 04fa9a8
1 parent 7b11c33
commit 04fa9a8
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Showing 6 changed files with 49 additions and 6 deletions.
diff --git a/src/main/resources/com/askimed/nf/test/lang/function/WorkflowMock.nf b/src/main/resources/com/askimed/nf/test/lang/function/WorkflowMock.nf
@@ -20,10 +20,11 @@ include { ${include} } from '${script}'
 // define custom rules for JSON that will be generated.
 def jsonOutput =
     new JsonGenerator.Options()
-        .excludeNulls()  // Do not include fields with value null..
         .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
         .build()
 
+def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
+
 
 workflow {
 
@@ -43,6 +44,6 @@ workflow.onComplete {
 		errorMessage: workflow.errorMessage,
 		errorReport: workflow.errorReport
 	]
-    new File("\${params.nf_test_output}/workflow.json").text = jsonOutput.toJson(result)
+    new File("\${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
 
 }
diff --git a/src/main/resources/com/askimed/nf/test/lang/process/WorkflowMock.nf b/src/main/resources/com/askimed/nf/test/lang/process/WorkflowMock.nf
@@ -17,10 +17,11 @@ include { ${process} } from '${script}'
 // define custom rules for JSON that will be generated.
 def jsonOutput =
     new JsonGenerator.Options()
-        .excludeNulls()  // Do not include fields with value null..
         .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
         .build()
 
+def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
+
 
 workflow {
 
@@ -83,6 +84,6 @@ workflow.onComplete {
         errorMessage: workflow.errorMessage,
         errorReport: workflow.errorReport
     ]
-    new File("\${params.nf_test_output}/workflow.json").text = jsonOutput.toJson(result)
+    new File("\${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
 
 }
diff --git a/src/main/resources/com/askimed/nf/test/lang/workflow/WorkflowMock.nf b/src/main/resources/com/askimed/nf/test/lang/workflow/WorkflowMock.nf
@@ -17,10 +17,10 @@ include { ${workflow} } from '${script}'
 // define custom rules for JSON that will be generated.
 def jsonOutput =
     new JsonGenerator.Options()
-        .excludeNulls()  // Do not include fields with value null..
         .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
         .build()
 
+def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
 
 workflow {
 
@@ -83,6 +83,6 @@ workflow.onComplete {
         errorMessage: workflow.errorMessage,
         errorReport: workflow.errorReport
     ]
-    new File("\${params.nf_test_output}/workflow.json").text = jsonOutput.toJson(result)
+    new File("\${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
 
 }
diff --git a/src/test/java/com/askimed/nf/test/lang/ProcessTest.java b/src/test/java/com/askimed/nf/test/lang/ProcessTest.java
@@ -80,6 +80,15 @@ public void testDisableAutoSortTestSuiteAndOverwrite() throws Exception {
 
 	}
 
+	@Test
+	public void testNullValuesInChannels() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/channels/null-values/return_null.nf.test" });
+		assertEquals(0, exitCode);
+
+	}
+
 	@Test
 	public void testWithNoOutputs() throws Exception {
 

diff --git a/test-data/channels/null-values/return_null.nf b/test-data/channels/null-values/return_null.nf
@@ -0,0 +1,8 @@
+process return_null {
+
+    output:
+    val null_list, emit: null_list
+
+    exec:
+    null_list = ["0", "1", "", null, "4"]
+}
diff --git a/test-data/channels/null-values/return_null.nf.test b/test-data/channels/null-values/return_null.nf.test
@@ -0,0 +1,24 @@
+nextflow_process {
+
+    name "Test Process return_null"
+    script "./return_null.nf"
+    process "return_null"
+
+    test("Should run without failures") {
+
+        when {
+            params {}
+            process {}
+        }
+
+        then {
+            assert process.success
+
+            with(process.out) {
+                assert null_list == [["0", "1", "", null, "4"]]
+            }
+        }
+
+    }
+
+}