add a test for the help message

nextflow-io · Aug 5, 2024 · 2d457f8 · 2d457f8
1 parent dd24d07
commit 2d457f8
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Showing 3 changed files with 36 additions and 3 deletions.
diff --git a/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy b/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy
@@ -389,7 +389,7 @@ class SchemaValidator extends PluginExtensionPoint {
             if (paramNames.size() > 1) {
                 paramNames.remove(0)
                 paramNames.each {
-                    paramOptions = (Map) paramOptions.properties[it] ?: [:]
+                    paramOptions = (Map) paramOptions?.properties?[it] ?: [:]
                 }
             }
             if (!paramOptions) {
@@ -471,7 +471,7 @@ class SchemaValidator extends PluginExtensionPoint {
                         "      ." + it[4..it.length()-1]
                     }
                     .join("\n")
-                helpMessage += "    " + colors.dim + "options: " + colors.reset + "\n" + subParamsHelpString + "\n"
+                helpMessage += "    " + colors.dim + "options".padRight(11) + ": " + colors.reset + "\n" + subParamsHelpString + "\n"
                 continue
             }
             def String value = option.value

diff --git a/plugins/nf-schema/src/test/nextflow/validation/ParamsHelpTest.groovy b/plugins/nf-schema/src/test/nextflow/validation/ParamsHelpTest.groovy
@@ -112,7 +112,7 @@ class ParamsHelpTest extends Dsl2Spec{
                 .toString()
                 .readLines()
                 .findResults {it.contains('publish_dir_mode') && 
-                    it.contains('(accepted: symlink, rellink, link, copy, copyNoFollow') 
+                    it.contains('(accepted: symlink, rellink') 
                     ? it : null }
 
         then:
@@ -178,4 +178,33 @@ class ParamsHelpTest extends Dsl2Spec{
         error.message == "Specified param 'no_exist' does not exist in JSON schema."
         !stdout
     }
+
+    def 'should print a help message of nested parameter' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema_nested_parameters.json').toAbsolutePath().toString()
+        def SCRIPT = """
+            include { paramsHelp } from 'plugin/nf-schema'
+            params.help = 'this.is'
+
+            def command = "nextflow run <pipeline> --input samplesheet.csv --outdir <OUTDIR> -profile docker"
+            
+            def help_msg = paramsHelp(command, parameters_schema: '$schema')
+            log.info help_msg
+        """
+
+        when:
+        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.startsWith('--this.is') ||
+                    it.contains('description:') ||
+                    it.contains('options    :') ||
+                    it.contains('.so')
+                    ? it : null }
+
+        then:
+        noExceptionThrown()
+        stdout.size() == 4
+    }
 }
diff --git a/plugins/nf-schema/src/testResources/nextflow_schema_nested_parameters.json b/plugins/nf-schema/src/testResources/nextflow_schema_nested_parameters.json
@@ -9,15 +9,19 @@
             "required": ["this"],
             "properties": {
                 "this": {
+                    "description": "this is this",
                     "type": "object",
                     "properties": {
                         "is":{
+                            "description": "is this is?",
                             "type": "object",
                             "properties": {
                                 "so": {
+                                    "description": "so so so",
                                     "type": "object",
                                     "properties": {
                                         "deep": {
+                                            "description": "so deep",
                                             "type": "boolean"
                                         }
                                     }