Ignore Azure paths when validating directories

CHANGELOG.md

@@ -1,5 +1,11 @@
 # nextflow-io/nf-schema: Changelog
 
+# Version 2.6.0
+
+## Bug fixes
+
+1. Fixed a bug where Azure blob storage paths were incorrectly validated as directories.
+
 # Version 2.5.1
 
 ## Bug fixes

src/main/groovy/nextflow/validation/validators/evaluators/FormatDirectoryPathEvaluator.groovy

@@ -24,22 +24,27 @@ class FormatDirectoryPathEvaluator implements Evaluator {
         }
 
         def String value = node.asString()
+
         def Path file
-
         try {
             file = Nextflow.file(value) as Path
             if (!(file instanceof List)) {
                 file.exists() // Do an exists check to see if the file can be correctly accessed
             }
         } catch (Exception e) {
-            return Evaluator.Result.failure("could not validate file format of '${value}': ${e.message}" as String)
+            return Evaluator.Result.failure("could not validate directory format of '${value}': ${e.message}" as String)
         }
 
         // Actual validation logic
         if (file instanceof List) {
             return Evaluator.Result.failure("'${value}' is not a directory, but a file path pattern" as String)
         }
+
         if (file.exists() && !file.isDirectory()) {
+            // If it's an Azure storage path, skip directory validation
+            if (value.startsWith('az://')) {
+                return Evaluator.Result.success()
+            }
             return Evaluator.Result.failure("'${value}' is not a directory, but a file" as String)
         }
         return Evaluator.Result.success()

src/main/groovy/nextflow/validation/validators/evaluators/FormatFilePathEvaluator.groovy

@@ -25,7 +25,6 @@ class FormatFilePathEvaluator implements Evaluator {
 
         def String value = node.asString()
         def Path file
-
         try {
             file = Nextflow.file(value) as Path
             if (!(file instanceof List)) {
@@ -39,7 +38,12 @@ class FormatFilePathEvaluator implements Evaluator {
         if (file instanceof List) {
             return Evaluator.Result.failure("'${value}' is not a file, but a file path pattern" as String)
         }
+
         if (file.exists() && file.isDirectory()) {
+            // If it's an Azure storage path, skip directoryvalidation
+            if(value.startsWith('az://')) {
+                return Evaluator.Result.success()
+            }
             return Evaluator.Result.failure("'${value}' is not a file, but a directory" as String)
         }
         return Evaluator.Result.success()

src/main/groovy/nextflow/validation/validators/evaluators/FormatFilePathPatternEvaluator.groovy

@@ -24,8 +24,8 @@ class FormatFilePathPatternEvaluator implements Evaluator {
         }
 
         def String value = node.asString()
-        def List<Path> files
 
+        def List<Path> files
         try {
             files = Nextflow.files(value)
             files.each { file ->
@@ -41,7 +41,8 @@ class FormatFilePathPatternEvaluator implements Evaluator {
             return Evaluator.Result.failure("No files were found using the glob pattern '${value}'" as String)
         }
         files.each { file ->
-            if (file.isDirectory()) {
+            // If it's an Azure storage path, skip directory validation
+            if (file.isDirectory() && !file.toString().startsWith('az://')) {
                 errors.add("'${file.toString()}' is not a file, but a directory" as String)
             }
         }

src/main/groovy/nextflow/validation/validators/evaluators/SchemaEvaluator.groovy

@@ -44,9 +44,16 @@ class SchemaEvaluator implements Evaluator {
 
         // Actual validation logic
         def Path file = Nextflow.file(value)
-        // Don't validate if the file does not exist or is a directory
-        if(!file.exists() || file.isDirectory()) {
-            log.debug("Could not validate the file ${file.toString()}")
+
+        // Don't validate if the file does not exist
+        if(!file.exists()) {
+            log.debug("Could not validate the file ${file.toString()} - file does not exist")
+            return Evaluator.Result.success()
+        }
+
+        // Skip validation if it's a directory
+        if(file.isDirectory() || value.startsWith('az://')) {
+            log.debug("Could not validate the file ${file.toString()} - path is a directory")
             return Evaluator.Result.success()
         }
 

src/testResources/nextflow_schema_azure_path.json

@@ -0,0 +1,19 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/nf-schema/master/examples/azurepath/nextflow_schema.json",
+    "title": "Azure path validation test",
+    "description": "Test schema for Azure path validation",
+    "type": "object",
+    "properties": {
+        "az_file": {
+            "type": "string",
+            "format": "file-path",
+            "description": "Azure storage file path"
+        },
+        "az_directory": {
+            "type": "string", 
+            "format": "directory-path",
+            "description": "Azure storage directory path"
+        }
+    }
+}