Add validation with nested schemas

plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

@@ -51,7 +51,6 @@ class SchemaValidator extends PluginExtensionPoint {
             'quiet',
             'syslog',
             'v',
-            'version',
 
             // Options for `nextflow run` command
             'ansi',
@@ -183,6 +182,9 @@ class SchemaValidator extends PluginExtensionPoint {
         expectedParams.push('fail_unrecognised_params')
         expectedParams.push('lenient_mode')
 
+        def Boolean lenient_mode = params.lenient_mode ? params.lenient_mode : false
+        def Boolean fail_unrecognised_params = params.fail_unrecognised_params ? params.fail_unrecognised_params : false
+
         for (String specifiedParam in specifiedParamKeys) {
             // nextflow params
             if (NF_OPTIONS.contains(specifiedParam)) {
@@ -198,7 +200,7 @@ class SchemaValidator extends PluginExtensionPoint {
             def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
             def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
             if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
-                if (params.fail_unrecognised_params) {
+                if (fail_unrecognised_params) {
                     errors << "* --${specifiedParam}: ${paramsJSON[specifiedParam]}".toString()
                 } else {
                     warnings << "* --${specifiedParam}: ${paramsJSON[specifiedParam]}".toString()
@@ -224,7 +226,7 @@ class SchemaValidator extends PluginExtensionPoint {
 
         // Validate
         try {
-            if (params.lenient_mode) {
+            if (lenient_mode) {
                 // Create new validator with LENIENT mode 
                 Validator validator = Validator.builder()
                     .primitiveValidationStrategy(PrimitiveValidationStrategy.LENIENT)
@@ -248,7 +250,7 @@ class SchemaValidator extends PluginExtensionPoint {
         }
 
         //=====================================================================//
-        // Look for other schemas to validate
+        // Look for other schemas or nested params to validate
         for (group in schemaParams) {
             def Map properties = (Map) group.value['properties']
             for (p in properties) {
@@ -269,7 +271,9 @@ class SchemaValidator extends PluginExtensionPoint {
                     if (validateFile(params, key, fileContent, schema_name, baseDir)) {
                         log.debug "Validation passed: '$key': '$file_path' with '$schema_name'"
                     }
-                }
+                }/* else if (property.containesKey('properties')) {
+                    validateNestedSchema(params, properties)
+                }*/
             }
         }
     }
@@ -300,10 +304,13 @@ class SchemaValidator extends PluginExtensionPoint {
         def List expectedParams = (List) enumsTuple[0]
         def Map enums = (Map) enumsTuple[1]
 
+        // Declare variables
+        def Boolean lenient_mode = params.lenient_mode ? params.lenient_mode : false
+
         //=====================================================================//
         // Validate
         try {
-            if (params.lenient_mode) {
+            if (lenient_mode) {
                 // Create new validator with LENIENT mode 
                 Validator validator = Validator.builder()
                     .primitiveValidationStrategy(PrimitiveValidationStrategy.LENIENT)
@@ -327,6 +334,106 @@ class SchemaValidator extends PluginExtensionPoint {
         return true
     }
 
+    //
+    // Function to validate a nested schema
+    //
+    /*void validateNestedSchema(Map params, Map schema) {
+
+        def String baseDir = session.baseDir
+
+        // Clean the parameters
+        def cleanedParams = cleanParameters(params)
+        // Convert to JSONObject
+        def paramsJSON = new JSONObject(new JsonBuilder(cleanedParams).toString())
+
+        // Collect expected parameters from the schema
+        def enumsTuple = collectEnums(schemaParams) //TODO: run this function without groups for loop
+        def List expectedParams = (List) enumsTuple[0]
+        def Map enums = (Map) enumsTuple[1]
+
+        def Boolean lenient_mode = params.lenient_mode ? params.lenient_mode : false
+        def Boolean fail_unrecognised_params = params.fail_unrecognised_params ? params.fail_unrecognised_params : false
+
+        def specifiedParamKeys = params.keySet()
+
+        for (String specifiedParam in specifiedParamKeys) {
+            // unexpected params
+            def String schema_ignore_params = params.schema_ignore_params
+            def List params_ignore = schema_ignore_params ? schema_ignore_params.split(',') + 'schema_ignore_params' as List : []
+            def expectedParamsLowerCase = expectedParams.collect{ it -> 
+                def String p = it
+                p.replace("-", "").toLowerCase() 
+            }
+            def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
+            def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
+            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
+                if (fail_unrecognised_params) {
+                    errors << "* --${specifiedParam}: ${paramsJSON[specifiedParam]}".toString()
+                } else {
+                    warnings << "* --${specifiedParam}: ${paramsJSON[specifiedParam]}".toString()
+                }
+            }
+        }
+
+        // check for warnings
+        if( this.hasWarnings() ) {
+            def msg = "The following invalid input values have been detected:\n\n" + this.getWarnings().join('\n').trim() + "\n\n"
+            log.warn(msg)
+        }
+
+        // Colors
+        def Boolean monochrome_logs = params.monochrome_logs
+        def colors = logColours(monochrome_logs)
+
+        // Validate
+        try {
+            if (lenient_mode) {
+                // Create new validator with LENIENT mode 
+                Validator validator = Validator.builder()
+                    .primitiveValidationStrategy(PrimitiveValidationStrategy.LENIENT)
+                    .build();
+                validator.performValidation(schema, paramsJSON);
+            } else {
+                schema.validate(paramsJSON)
+            }
+            if (this.hasErrors()) {
+                // Needed when fail_unrecognised_params is true
+                def msg = "${colors.red}The following invalid input values have been detected:\n\n" + this.getErrors().join('\n').trim() + "\n${colors.reset}\n"
+                log.error("ERROR: Validation of pipeline parameters failed!")
+                throw new SchemaValidationException(msg, this.getErrors())
+            }
+        } catch (ValidationException e) {
+            JSONObject exceptionJSON = (JSONObject) e.toJSON()
+            collectErrors(exceptionJSON, paramsJSON, enums)
+            def msg = "${colors.red}The following invalid input values have been detected:\n\n" + this.getErrors().join('\n').trim() + "\n${colors.reset}\n"
+            log.error("ERROR: Validation of pipeline parameters failed!")
+            throw new SchemaValidationException(msg, this.getErrors())
+        }
+
+        //=====================================================================//
+        // Look for other schemas or nested parameters to validate
+            for (p in schema) {
+                def String key = (String) p.key
+                def Map property = properties[key] as Map
+                if (property.containsKey('schema')) {
+                    def String schema_name = property['schema']
+                    def Path file_path = Nextflow.file(params[key]) as Path
+                    def String fileType = SamplesheetConverter.getFileType(file_path)
+                    def String delimiter = fileType == "csv" ? "," : fileType == "tsv" ? "\t" : null
+                    def List<Map<String,String>> fileContent
+                    if(fileType == "yaml"){
+                        fileContent = new Yaml().load((file_path.text))
+                    }
+                    else {
+                        fileContent = file_path.splitCsv(header:true, strip:true, sep:delimiter)
+                    }
+                    if (validateFile(params, key, fileContent, schema_name, baseDir)) {
+                        log.debug "Validation passed: '$key': '$file_path' with '$schema_name'"
+                    }
+                }
+            }
+
+    }*/
 
     //
     // Function to collect enums (options) of a parameter and expected parameters (present in the schema)

plugins/nf-validation/src/test/nextflow/validation/PluginExtensionMethodsTest.groovy

@@ -11,6 +11,13 @@ import org.pf4j.PluginDescriptorFinder
 import spock.lang.Shared
 import test.Dsl2Spec
 import test.OutputCapture
+
+import nextflow.cli.CmdRun
+import java.nio.file.Files
+import nextflow.Session
+import nextflow.Global
+
+
 /**
  * @author : jorge <jorge.aguilera@seqera.io>
  *
@@ -20,6 +27,9 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
     @Rule
     OutputCapture capture = new OutputCapture()
 
+    Session getSession(){
+        Global.getSession() as Session
+    }
 
     @Shared String pluginsMode
 
@@ -374,6 +384,75 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
         !stdout
     }
 
+    //
+    // Nested parameters tests
+    //
+
+    def 'should validate a schema with nested params' () {
+        given:
+        def schema = Path.of('src/testResources/nested_parameters_schema.json').toAbsolutePath().toString()
+        def  SCRIPT_TEXT = """
+            include { validateParameters } from 'plugin/nf-validation'
+
+            validateParameters('$schema')
+        """
+        and:
+        def ENV = [
+                NXF_PARAMS_FILE:'src/testResources/nested_paramteres.yml',
+        ]
+
+        when:
+        dsl_eval(SCRIPT_TEXT)
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+        then:
+        noExceptionThrown()
+        !stdout
+    }
+
+    def 'should find validation errors in nested param' () {
+        given:
+        def schema = Path.of('src/testResources/nexted_parameters_fail_schema.json').toAbsolutePath().toString()
+        def folder = Files.createTempDirectory('test')
+        def YAML = '''
+            foo: bar
+            baz:
+                qux: corge
+                grault: garply
+            '''.stripIndent()
+        def  SCRIPT_TEXT = """
+            include { validateParameters } from 'plugin/nf-validation'
+
+            validateParameters('$schema')
+
+            println(params.baz)
+            println(params.foo)
+        """
+
+        when:
+        def file = folder.resolve('params.yaml')
+        file.text = YAML
+        and:
+        def cmd = new CmdRun(sysEnv: [NXF_PARAMS_FILE: file.toString()])
+        def params = cmd.parsedParams()
+        session.params = params
+        and:
+        dsl_eval(SCRIPT_TEXT)
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+        then:
+        //params.foo == "bar"
+        def error = thrown(SchemaValidationException)
+        //error.message == "The following invalid input values have been detected:\n\n* --publish_dir_mode: 'incorrect' is not a valid choice (Available choices (5 of 6): symlink, rellink, link, copy, copyNoFollow, ... )\n\n"
+        //!stdout
+    }
+
     //
     // --help argument tests
     //

plugins/nf-validation/src/testResources/nested_parameters.yml

@@ -0,0 +1,4 @@
+foo: bar
+baz:
+    qux: corge
+    grault: garply

plugins/nf-validation/src/testResources/nested_parameters_schema.json

@@ -0,0 +1,31 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$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",
+    "definitions": {
+        "nested parameters": {
+            "title": "Some nested parameters",
+            "type": "object",
+            "properties": {
+                "foo": { 
+                    "type": "string", 
+                    "default": "bar" },
+                "baz": {
+                    "type": "object",
+                    "properties": {
+                        "qux": { 
+                            "type": "string", 
+                            "default": "corge" 
+                        },
+                        "grault": { 
+                            "type": "string", 
+                            "default": "garply" 
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

plugins/nf-validation/src/testResources/nexted_parameters_fail_schema.json

@@ -0,0 +1,32 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$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",
+    "definitions": {
+        "nested parameters": {
+            "title": "Some nested parameters",
+            "type": "object",
+            "properties": {
+                "foo": { 
+                    "type": "integer", 
+                    "default": 2 
+                },
+                "baz": {
+                    "type": "object",
+                    "properties": {
+                        "qux": { 
+                            "type": "integer", 
+                            "default": 1 
+                        },
+                        "grault": { 
+                            "type": "string", 
+                            "default": "garply" 
+                        }
+                    }
+                }
+            }
+        }
+    }
+}