Merge pull request #106 from mirpedrol/more-s3

Do not check S3 URL paths

Author: ewels

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### Bug fixes
 
+- Do not check S3 URL paths with `PathValidator` `FilePathValidator` and `DirectoryPathValidator` ([#106](https://github.com/nextflow-io/nf-validation/pull/106))
 - Make monochrome_logs an option in `paramsSummaryLog()`, `paramsSummaryMap()` and `paramsHelp()` instead of a global parameter ([#101](https://github.com/nextflow-io/nf-validation/pull/101))
 
 # Version 0.3.3

plugins/nf-validation/src/main/nextflow/validation/FormatValidators/DirectoryPathValidator.groovy

@@ -1,14 +1,20 @@
 package nextflow.validation
 
 import java.nio.file.Path
+import groovy.util.logging.Slf4j
 
 import org.everit.json.schema.FormatValidator
 import nextflow.Nextflow
 
+@Slf4j
 public class DirectoryPathValidator implements FormatValidator {
 
     @Override
     public Optional<String> validate(final String subject) {
+        if (subject.startsWith('s3://')) {
+            log.debug("S3 paths are not supported by 'DirectoryPathValidator': '${subject}'")
+            return Optional.empty()
+        }
         Path file = Nextflow.file(subject) as Path
         if (file.exists() && !file.isDirectory()) {
             return Optional.of("'${subject}' is not a directory, but a file" as String)

plugins/nf-validation/src/main/nextflow/validation/FormatValidators/FilePathValidator.groovy

@@ -1,14 +1,20 @@
 package nextflow.validation
 
 import java.nio.file.Path
+import groovy.util.logging.Slf4j
 
 import org.everit.json.schema.FormatValidator
 import nextflow.Nextflow
 
+@Slf4j
 public class FilePathValidator implements FormatValidator {
 
     @Override
     public Optional<String> validate(final String subject) {
+        if (subject.startsWith('s3://')) {
+            log.debug("S3 paths are not supported by 'FilePathValidator': '${subject}'")
+            return Optional.empty()
+        }
         Path file = Nextflow.file(subject) as Path  
         if (file.isDirectory()) {
             return Optional.of("'${subject}' is not a file, but a directory" as String)

plugins/nf-validation/src/main/nextflow/validation/FormatValidators/PathValidator.groovy

@@ -1,14 +1,20 @@
 package nextflow.validation
 
 import java.nio.file.Path
+import groovy.util.logging.Slf4j
 
 import org.everit.json.schema.FormatValidator
 import nextflow.Nextflow
 
+@Slf4j
 public class PathValidator implements FormatValidator {
 
     @Override
     public Optional<String> validate(final String subject) {
+        if (subject.startsWith('s3://')) {
+            log.debug("S3 paths are not supported by 'PathValidator': '${subject}'")
+            return Optional.empty()
+        }
         Path file = Nextflow.file(subject) as Path  
         return Optional.empty()
     }