Merge pull request #63 from nextflow-io/fix/unique

Fix `uniqueEntries` on empty optional values

Author: nvnieuwk

CHANGELOG.md

@@ -5,6 +5,12 @@
 ## Bug fixes
 
 1. The directory `nf_test_output` is now an ignored parameter during validation to support use of both `nf_test` and `nf_schema`.
+2. `uniqueEntries` will now skip unique checks when all values in the requested array properties are empty. This had to be implemented to allow optional values to work with the `uniqueEntries` check. Partially filled in array properties will still fail (and that's how it's meant to be). Be sure to use `oneOf` to properly configure all possible combinations in case this causes some issues.
+3. Improved the error messages produced by `uniqueEntries`.
+
+## Documentation
+
+1. Fix some faults in the docs
 
 # Version 2.1.1
 

README.md

@@ -25,7 +25,7 @@ Declare the plugin in your Nextflow pipeline configuration file:
 
 ```groovy title="nextflow.config"
 plugins {
-  id '[email protected].1'
+  id '[email protected].2'
 }
 ```
 

plugins/nf-schema/src/main/nextflow/validation/CustomEvaluators/UniqueEntriesEvaluator.groovy

@@ -43,8 +43,8 @@ class UniqueEntriesEvaluator implements Evaluator {
                 .findAll { k,v -> uniqueEntries.contains(k) }
                 .collectEntries { k,v -> [k, v.asString()] }
             for (uniqueNode : uniques) {
-                if(filteredNodes.equals(uniqueNode)) {
-                    return Evaluator.Result.failure("Entry ${count}: Detected non-unique combination of the following fields: ${uniqueEntries}" as String)
+                if(filteredNodes.equals(uniqueNode) && filteredNodes != [:]) {
+                    return Evaluator.Result.failure("Entry ${count}: Detected duplicate entries: ${filteredNodes}" as String)
                 }
             }
             uniques.add(filteredNodes)

plugins/nf-schema/src/resources/META-INF/MANIFEST.MF

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Id: nf-schema
-Plugin-Version: 2.1.1
+Plugin-Version: 2.1.2
 Plugin-Class: nextflow.validation.ValidationPlugin
 Plugin-Provider: nextflow
 Plugin-Requires: >=23.10.0

plugins/nf-schema/src/test/nextflow/validation/ValidateParametersTest.groovy

@@ -990,12 +990,37 @@ class ValidateParametersTest extends Dsl2Spec{
         error.message == '''The following invalid input values have been detected:
 
 * --input (src/testResources/samplesheet_non_unique.csv): Validation of file failed:
-	-> Entry 3: Detected non-unique combination of the following fields: [sample, fastq_1]
+	-> Entry 3: Detected duplicate entries: [fastq_1:test2_fastq1.fastq.gz, sample:test_2]
 
 '''
         !stdout
     }
 
+    def 'should not fail because of non-unique empty entries' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema_with_samplesheet_uniqueEntries.json').toAbsolutePath().toString()
+        def SCRIPT = """
+            params.input = "src/testResources/samplesheet_non_unique_empty.csv"
+            include { validateParameters } from 'plugin/nf-schema'
+
+            validateParameters(parameters_schema: '$schema')
+        """
+
+        when:
+        def config = ["validation": [
+            "monochromeLogs": true
+        ]]
+        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:
+        noExceptionThrown()
+        !stdout
+    }
+
     def 'should validate nested params - pass' () {
         given:
         def SCRIPT = """

plugins/nf-schema/src/testResources/samplesheet_non_unique_empty.csv

@@ -0,0 +1,6 @@
+sample,fastq_1,fastq_2,strandedness
+test_1,test1_fastq1.fastq.gz,test1_fastq2.fastq.gz,forward
+test_2,,,unstranded
+test_3,test2_fastq1.fastq.gz,,forward
+,,,forward
+,,,unstranded