Merge pull request #65 from mirpedrol/path-missing-param

Print param name when path does not exist

CHANGELOG.md

@@ -8,7 +8,9 @@
 - Only validate a file with a schema if the file path is provided ([#51](https://github.com/nextflow-io/nf-validation/pull/51))
 - Handle errors when sample sheet not provided or doesn't have a schema ([#56](https://github.com/nextflow-io/nf-validation/pull/56))
 - Silently ignore samplesheet fields that are not defined in samplesheet schema ([#59](https://github.com/nextflow-io/nf-validation/pull/59))
-- Correctly handle double-quoted fields containing commas in csv files by `.fromSamplesheet()` [#63](https://github.com/nextflow-io/nf-validation/pull/63))
+- Correctly handle double-quoted fields containing commas in csv files by `.fromSamplesheet()` ([#63](https://github.com/nextflow-io/nf-validation/pull/63))
+- Print param name when path does not exist ([#65](https://github.com/nextflow-io/nf-validation/pull/65))
+- Fix file or directory does not exist error not printed when it was the only error in a samplesheet ([#65](https://github.com/nextflow-io/nf-validation/pull/65))
 - Do not return parameter in summary if it has no default in the schema and is set to 'false' ([#66](https://github.com/nextflow-io/nf-validation/pull/66))
 
 ## Version 0.2.1

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

@@ -279,7 +279,7 @@ class SchemaValidator extends PluginExtensionPoint {
         def List<String> pathsToCheck = (List) collectExists(schemaParams)
         pathsToCheck.each {
             if (params[it] != null) {
-                pathExists(params[it].toString())
+                pathExists(params[it].toString(), it.toString())
             }
         }
 
@@ -510,12 +510,11 @@ class SchemaValidator extends PluginExtensionPoint {
         //=====================================================================//
         // Check if files or directories exist
         def List<String> pathsToCheck = (List) collectExists(schemaParams)
-        pathsToCheck.each { fieldName ->
-            def String filedName = fieldName
+        pathsToCheck.each { String fieldName ->
             for (int i=0; i < arrayJSON.size(); i++) {
                 def JSONObject entry = arrayJSON.getJSONObject(i)
-                if ( entry.has(filedName) ) {
-                    pathExists(entry[filedName].toString())
+                if ( entry.has(fieldName) ) {
+                    pathExists(entry[fieldName].toString(), " Entry ${(i+1).toString()} - ${fieldName.toString()}")
                 }
             }
         }
@@ -528,6 +527,13 @@ class SchemaValidator extends PluginExtensionPoint {
                 .primitiveValidationStrategy(PrimitiveValidationStrategy.LENIENT)
                 .build();
             validator.performValidation(schema, arrayJSON);
+            if (this.hasErrors()) {
+                // Needed for custom errors such as pathExists() errors
+                def colors = logColours(monochrome_logs)
+                def msg = "${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()
@@ -546,10 +552,10 @@ class SchemaValidator extends PluginExtensionPoint {
     //
     // Function to check if a file or directory exists
     //
-    List pathExists(String path) {
+    List pathExists(String path, String paramName) {
         def Path file = Nextflow.file(path) as Path
         if (!file.exists()) {
-            errors << "* The file or directory '${path}' does not exist.".toString()
+            errors << "* --${paramName}: the file or directory '${path}' does not exist.".toString()
         }
     }
 

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

@@ -352,8 +352,8 @@ class SamplesheetConverterTest extends Dsl2Spec{
         def error = thrown(SchemaValidationException)
         def errorMessages = error.message.readLines() 
         errorMessages[0] == "\033[0;31mThe following errors have been detected:"
-        errorMessages[2] == "* The file or directory 'non_existing_path' does not exist."
-        errorMessages[3] == "* The file or directory 'non_existing_file.tsv' does not exist."
+        errorMessages[2] == "* -- Entry 1 - field_9: the file or directory 'non_existing_path' does not exist."
+        errorMessages[3] == "* -- Entry 1 - field_7: the file or directory 'non_existing_file.tsv' does not exist."
         errorMessages[4] == '* -- Entry 1 - field_7: string [non_existing_file.tsv] does not match pattern ^.*\\.txt$ (non_existing_file.tsv)'
         errorMessages[5] == "* -- Entry 1 - field_8: 'src/testResources/test.txt' is not a directory, but a file (src/testResources/test.txt)"
         errorMessages[6] == "* -- Entry 1 - field_5: expected type: Number, found: String (string)"