Merge branch '2.2.0-dev' of github.com:nextflow-io/nf-schema into 2.2…

….0-dev
nextflow-io · Oct 30, 2024 · 5d529a6 · 5d529a6
2 parents af9e968 + f4b9caa
commit 5d529a6
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Showing 5 changed files with 64 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@
 
 1. Fixed a bug in `samplesheetToList` that caused output mixing when the function was used more than once in channel operators.
 2. Added a missing depencency for email format validation.
+3. All path formats (with exception to `file-path-pattern`) will now give a proper error message when a `file-path-pattern` has been used.
 
 ## Improvements
 

diff --git a/...-schema/src/main/nextflow/validation/CustomEvaluators/FormatDirectoryPathEvaluator.groovy b/...-schema/src/main/nextflow/validation/CustomEvaluators/FormatDirectoryPathEvaluator.groovy
@@ -33,6 +33,9 @@ class FormatDirectoryPathEvaluator implements Evaluator {
 
         // Actual validation logic
         def Path file = Nextflow.file(value) as Path
+        if (file instanceof List) {
+            return Evaluator.Result.failure("'${value}' is not a directory, but a file path pattern" as String)
+        }
         if (file.exists() && !file.isDirectory()) {
             return Evaluator.Result.failure("'${value}' is not a directory, but a file" as String)
         }

diff --git a/...ns/nf-schema/src/main/nextflow/validation/CustomEvaluators/FormatFilePathEvaluator.groovy b/...ns/nf-schema/src/main/nextflow/validation/CustomEvaluators/FormatFilePathEvaluator.groovy
@@ -33,6 +33,9 @@ class FormatFilePathEvaluator implements Evaluator {
 
         // Actual validation logic
         def Path file = Nextflow.file(value) as Path
+        if (file instanceof List) {
+            return Evaluator.Result.failure("'${value}' is not a file, but a file path pattern" as String)
+        }
         if (file.exists() && file.isDirectory()) {
             return Evaluator.Result.failure("'${value}' is not a file, but a directory" as String)
         }

diff --git a/plugins/nf-schema/src/main/nextflow/validation/CustomEvaluators/FormatPathEvaluator.groovy b/plugins/nf-schema/src/main/nextflow/validation/CustomEvaluators/FormatPathEvaluator.groovy
@@ -33,6 +33,9 @@ class FormatPathEvaluator implements Evaluator {
 
         // Actual validation logic
         def Path file = Nextflow.file(value) as Path
+        if (file instanceof List) {
+            return Evaluator.Result.failure("'${value}' is not a path, but a file path pattern" as String)
+        }
         return Evaluator.Result.success()
     }
 }
diff --git a/plugins/nf-schema/src/test/nextflow/validation/ValidateParametersTest.groovy b/plugins/nf-schema/src/test/nextflow/validation/ValidateParametersTest.groovy
@@ -1097,7 +1097,7 @@ class ValidateParametersTest extends Dsl2Spec{
         given:
         def schema = Path.of('src/testResources/nextflow_schema.json').toAbsolutePath().toString()
         def SCRIPT = """
-            params.input = 'src/testResource/samplesheet.csv'
+            params.input = 'src/testResources/samplesheet.csv'
             params.outdir = 'src/testResources/testDir'
             params.email = "test@domain.com"
             include { validateParameters } from 'plugin/nf-schema'
@@ -1122,7 +1122,7 @@ class ValidateParametersTest extends Dsl2Spec{
         given:
         def schema = Path.of('src/testResources/nextflow_schema.json').toAbsolutePath().toString()
         def SCRIPT = """
-            params.input = 'src/testResource/samplesheet.csv'
+            params.input = 'src/testResources/samplesheet.csv'
             params.outdir = 'src/testResources/testDir'
             params.email = "thisisnotanemail"
             include { validateParameters } from 'plugin/nf-schema'
@@ -1145,4 +1145,56 @@ class ValidateParametersTest extends Dsl2Spec{
         !stdout
     }
 
+    def 'should give an error when a file-path-pattern is used with a file-path format' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema.json').toAbsolutePath().toString()
+        def SCRIPT = """
+            params.input = 'src/testResources/*.csv'
+            params.outdir = 'src/testResources/testDir'
+            include { validateParameters } from 'plugin/nf-schema'
+            
+            validateParameters(parameters_schema: '$schema')
+        """
+
+        when:
+        def config = [:]
+        def result = new MockScriptRunner(config).setScript(SCRIPT).execute()
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+
+        then:
+        def error = thrown(SchemaValidationException)
+        error.message.contains("* --input (src/testResources/*.csv): 'src/testResources/*.csv' is not a file, but a file path pattern")
+        !stdout
+    }
+
+    def 'should give an error when a file-path-pattern is used with a directory-path format' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema.json').toAbsolutePath().toString()
+        def SCRIPT = """
+            params.input = 'src/testResources/samplesheet.csv'
+            params.outdir = 'src/testResources/testDi*'
+            include { validateParameters } from 'plugin/nf-schema'
+            
+            validateParameters(parameters_schema: '$schema')
+        """
+
+        when:
+        def config = [:]
+        def result = new MockScriptRunner(config).setScript(SCRIPT).execute()
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+
+        then:
+        def error = thrown(SchemaValidationException)
+        error.message.contains("* --outdir (src/testResources/testDi*): 'src/testResources/testDi*' is not a directory, but a file path pattern")
+        !stdout
+    }
+
 }