Merge branch '2.4.0dev' into add/debug-messages

Author: nvnieuwk

CHANGELOG.md

@@ -12,6 +12,7 @@
 1. Move the unpinned version check to an observer. This makes sure the warning is always shown and not only when importing a function.
 2. Added a missing inherited method to the observer to fix issues with workflow output publishing
 3. Fixed unexpected failures with samplesheet schemas using `anyOf`, `allOf` and `oneOf`
+4. Fixed an error with help messages when the `type` keyword was missing
 
 ## Improvements
 

plugins/nf-schema/src/main/nextflow/validation/help/HelpMessageCreator.groovy

@@ -172,10 +172,14 @@ class HelpMessageCreator {
     //
     private List<String> getHelpListParams(Map<String,Map> params, Integer maxChars, String parentParameter = "") {
         def List helpMessage = []
-        def Integer typeMaxChars = longestStringLength(params.collect { key, value -> value.type instanceof String ? "[${value.type}]" : value.type as String})
+        def Integer typeMaxChars = longestStringLength(params.collect { key, value -> 
+            def Object type = value.get("type", "")
+            return type instanceof String && type.length() > 0 ? "[${type}]" : type as String}
+        )
         for (String paramName in params.keySet()) {
-            def Map paramOptions = params.get(paramName) as Map 
-            def String type = paramOptions.type instanceof String ? '[' + paramOptions.type + ']' : paramOptions.type as String
+            def Map paramOptions = params.get(paramName) as Map
+            def Object paramType = paramOptions.get("type", "")
+            def String type = paramType instanceof String && paramType.length() > 0 ? '[' + paramType + ']' : paramType as String
             def String enumsString = ""
             if (paramOptions.enum != null) {
                 def List enums = (List) paramOptions.enum

plugins/nf-schema/src/test/nextflow/validation/HelpMessageCreatorTest.groovy

@@ -494,4 +494,39 @@ Reference genome options
         assert resultHelp.size() == 0, "Found extra unexpected lines: ${resultHelp}"
     }
 
+    def 'should get a help message when missing the type keyword' () {
+        given:
+        def validationConfig = [
+            monochromeLogs: true,
+            parametersSchema: 'src/testResources/nextflow_schema_no_type.json',
+            help: [
+                enabled: true
+            ]
+        ]
+        def params = [:]
+        def config = new ValidationConfig(validationConfig, params)
+        def helpCreator = new HelpMessageCreator(config, session)
+
+        when:
+        def help = helpCreator.getShortMessage("") + helpCreator.getAfterText()
+
+        then:
+        noExceptionThrown()
+        def expectedHelp = """--input        [string]          Path to comma-separated file containing information about the samples in the experiment. 
+--help         [boolean, string] Show the help message for all top level parameters. When a parameter is given to `--help`, the full 
+help message of that parameter will be printed. 
+--helpFull     [boolean]         Show the help message for all non-hidden parameters. 
+--showHidden   [boolean]         Show all hidden parameters in the help message. This needs to be used in combination with `--help` 
+or `--helpFull`. 
+ 
+------------------------------------------------------
+
+"""
+        def resultHelp = help.readLines()
+        expectedHelp.readLines().each {
+            assert help.contains(it)
+            resultHelp.removeElement(it)
+        }
+        assert resultHelp.size() == 0, "Found extra unexpected lines: ${resultHelp}"
+    }
 }

plugins/nf-schema/src/testResources/nextflow_schema_no_type.json

@@ -0,0 +1,18 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/testpipeline/master/nextflow_schema.json",
+    "title": "nf-core/testpipeline pipeline parameters",
+    "description": "this is a test",
+    "type": "object",
+    "properties": {
+        "input": {
+            "type": "string",
+            "format": "file-path",
+            "mimetype": "text/csv",
+            "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
+            "description": "Path to comma-separated file containing information about the samples in the experiment.",
+            "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/testpipeline/usage#samplesheet-input).",
+            "fa_icon": "fas fa-file-csv"
+        }
+    }
+}