feat: add error if 'arrays' used in samplesheet schema but a csv/tsv …

…samplesheet is passed. Add tests for this behaviour
nextflow-io · Jan 4, 2024 · 8bc3d3a · 8bc3d3a
1 parent 69f6c8f
commit 8bc3d3a
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Showing 3 changed files with 90 additions and 3 deletions.
diff --git a/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy b/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy
@@ -187,6 +187,11 @@ class SchemaValidator extends PluginExtensionPoint {
         def List<Map<String,String>> fileContentCasted
         def Boolean s3PathCheck = params.validationS3PathCheck ? params.validationS3PathCheck : false
         def Map types = variableTypes(schemaFile.toString(), baseDir)
+        if (types.find{ it.value == "array" } as Boolean && fileType in ["csv", "tsv"]){
+            def msg = "Using \"type\": \"array\" in schema with a \".$fileType\" samplesheet is not supported\n"
+            log.error("ERROR: Validation of pipeline parameters failed!")
+            throw new SchemaValidationException(msg, [])
+        }
         def Boolean containsHeader = !(types.keySet().size() == 1 && types.keySet()[0] == "")
 
         if(!containsHeader){
@@ -433,6 +438,11 @@ class SchemaValidator extends PluginExtensionPoint {
                     def List<Map<String,String>> fileContent
                     def List<Map<String,String>> fileContentCasted
                     def Map types = variableTypes(schema_name, baseDir)
+                    if (types.find{ it.value == "array" } as Boolean && fileType in ["csv", "tsv"]){
+                        def msg = "${colors.red}Using {\"type\": \"array\"} in schema with a \".$fileType\" samplesheet is not supported${colors.reset}\n"
+                        log.error("ERROR: Validation of pipeline parameters failed!")
+                        throw new SchemaValidationException(msg, [])
+                    }
                     def Boolean containsHeader = !(types.keySet().size() == 1 && types.keySet()[0] == "")
 
                     if(!containsHeader){
@@ -556,6 +566,8 @@ class SchemaValidator extends PluginExtensionPoint {
         Boolean monochrome_logs, String paramName, Object fileContent, String schemaFilename, String baseDir, Boolean s3PathCheck = false
 
     ) {
+        // declare this once for the method
+        def colors = logColours(monochrome_logs)
 
         // Load the schema
         def String schema_string = Files.readString( Path.of(getSchemaPath(baseDir, schemaFilename)) )
@@ -612,13 +624,11 @@ class SchemaValidator extends PluginExtensionPoint {
             validator.performValidation(schema, arrayJSON);
             if (this.hasErrors()) {
                 // Needed for custom errors such as pathExists() errors
-                def colors = logColours(monochrome_logs)
                 def msg = "${colors.red}The following errors have been detected:\n\n" + this.getErrors().join('\n').trim() + "\n${colors.reset}\n"
                 log.error("ERROR: Validation of '$paramName' file failed!")
                 throw new SchemaValidationException(msg, this.getErrors())
             }
         } catch (ValidationException e) {
-            def colors = logColours(monochrome_logs)
             JSONObject exceptionJSON = (JSONObject) e.toJSON()
             JSONObject objectJSON = new JSONObject();
             objectJSON.put("objects",arrayJSON);            

diff --git a/plugins/nf-validation/src/test/nextflow/validation/PluginExtensionMethodsTest.groovy b/plugins/nf-validation/src/test/nextflow/validation/PluginExtensionMethodsTest.groovy
@@ -867,4 +867,28 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
         error.message == '''The following errors have been detected:\n\n* -- Entry 1: Missing required value: sample\n* -- Entry 2: Missing required value: sample\n\n'''
         !stdout
     }
-}
+
+    def 'should fail because of arrays with csv' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema_with_samplesheet_converter_arrays.json').toAbsolutePath().toString()
+        def  SCRIPT_TEXT = """
+            params.monochrome_logs = true
+            params.input = 'src/testResources/correct.csv'
+            include { validateParameters } from 'plugin/nf-validation'
+            
+            validateParameters(parameters_schema: '$schema', monochrome_logs: params.monochrome_logs)
+        """
+
+        when:
+        dsl_eval(SCRIPT_TEXT)
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+        then:
+        def error = thrown(SchemaValidationException)
+        error.message == '''Using {"type": "array"} in schema with a ".csv" samplesheet is not supported\n'''
+        !stdout
+    }
+}
diff --git a/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy b/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy
@@ -281,6 +281,59 @@ class SamplesheetConverterTest extends Dsl2Spec{
         !stdout
     }
 
+    def 'array errors samplesheet format - CSV' () {
+        given:
+        def SCRIPT_TEXT = '''
+            include { fromSamplesheet } from 'plugin/nf-validation'
+
+            params.input = 'src/testResources/correct.csv'
+
+            workflow {
+                Channel.fromSamplesheet("input", parameters_schema:"src/testResources/nextflow_schema_with_samplesheet_converter_arrays.json").view()
+            }
+        '''
+
+        when:
+        dsl_eval(SCRIPT_TEXT)
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.startsWith('[[') ? it : null }
+
+        then:
+        def error = thrown(SchemaValidationException)
+        def errorMessages = error.message.readLines()
+        errorMessages[0] == 'Using "type": "array" in schema with a ".csv" samplesheet is not supported'
+        !stdout
+    }
+
+    def 'array errors samplesheet format - TSV' () {
+        given:
+        def SCRIPT_TEXT = '''
+            include { fromSamplesheet } from 'plugin/nf-validation'
+
+            params.input = 'src/testResources/correct.tsv'
+
+            workflow {
+                Channel.fromSamplesheet("input", parameters_schema:"src/testResources/nextflow_schema_with_samplesheet_converter_arrays.json").view()
+            }
+        '''
+
+        when:
+        dsl_eval(SCRIPT_TEXT)
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.startsWith('[[') ? it : null }
+
+        then:
+        def error = thrown(SchemaValidationException)
+        def errorMessages = error.message.readLines()
+        errorMessages[0] == 'Using "type": "array" in schema with a ".tsv" samplesheet is not supported'
+        !stdout
+    }
+
+
     def 'no header - CSV' () {
         given:
         def SCRIPT_TEXT = '''