fix issues and tests

nextflow-io · Aug 13, 2024 · 273a72b · 273a72b
1 parent 78e79b6
commit 273a72b
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/plugins/nf-schema/src/main/nextflow/validation/HelpMessage.groovy b/plugins/nf-schema/src/main/nextflow/validation/HelpMessage.groovy
@@ -105,7 +105,7 @@ class HelpMessage {
                         "      --" + it[4..it.length()-1]
                     }
                     .join("\n")
-                helpMessage += "    " + colors.dim + "options".padRight(optionMaxChars) + ": " + colors.reset + "\n" + subParamsHelpString + "\n"
+                helpMessage += "    " + colors.dim + "options".padRight(optionMaxChars) + ": " + colors.reset + "\n" + subParamsHelpString + "\n\n"
                 continue
             }
             def String value = option.value

diff --git a/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy b/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy
@@ -376,9 +376,9 @@ Please contact the pipeline maintainer(s) if you see this warning as a user.
         }
 
         def Map params = session.params
-        def Map validationConfig = (Map)session.config.navigate("validation")
-        validationConfig.parametersSchema = options.containsKey('parameters_schema') ? options.parameters_schema as String : config.parametersSchema
-        validationConfig.help = (Map)validationConfig.help + [command: command, beforeText: "", afterText: ""]
+        def Map validationConfig = (Map)session.config.navigate("validation") ?: [:]
+        validationConfig.parametersSchema = options.containsKey('parameters_schema') ? options.parameters_schema as String : validationConfig.parametersSchema
+        validationConfig.help = (Map)(validationConfig.help ?: [:]) + [command: command, beforeText: "", afterText: ""]
         def ValidationConfig copyConfig = new ValidationConfig(validationConfig, params)
         def HelpMessage helpMessage = new HelpMessage(copyConfig, session)
         def String help = helpMessage.getBeforeText()

diff --git a/plugins/nf-schema/src/test/nextflow/validation/ParamsHelpTest.groovy b/plugins/nf-schema/src/test/nextflow/validation/ParamsHelpTest.groovy
@@ -136,7 +136,7 @@ class ParamsHelpTest extends Dsl2Spec{
         """
 
         when:
-        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+        def result = new MockScriptRunner([validation:[monochromeLogs:true]]).setScript(SCRIPT).execute()
         def stdout = capture
                 .toString()
                 .readLines()
@@ -177,7 +177,7 @@ class ParamsHelpTest extends Dsl2Spec{
 
         then:
         def error = thrown(Exception)
-        error.message == "Specified param 'no_exist' does not exist in JSON schema."
+        error.message == "Unable to create help message: Specified param 'no_exist' does not exist in JSON schema."
         !stdout
     }
 
@@ -195,14 +195,14 @@ class ParamsHelpTest extends Dsl2Spec{
         """
 
         when:
-        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+        def result = new MockScriptRunner([validation:[monochromeLogs:true]]).setScript(SCRIPT).execute()
         def stdout = capture
                 .toString()
                 .readLines()
                 .findResults {it.startsWith('--this.is') ||
                     it.contains('description:') ||
                     it.contains('options    :') ||
-                    it.contains('.so')
+                    it.contains('this.is.so.deep')
                     ? it : null }
 
         then: