fix: make tests use correct input file for yaml and json tests. Ensur…

…e that boolean values in json/yaml are not treated as null before casting
nextflow-io · Dec 21, 2023 · 8f02b26 · 8f02b26
1 parent 40ffe27
commit 8f02b26
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy b/plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy
@@ -177,15 +177,15 @@ class SamplesheetConverter {
                 def List<String> metaNames = field['value']['meta'] as List<String>
                 if(metaNames) {
                     for(name : metaNames) {
-                        meta[name] = (input != '' && input) ?
+                        meta[name] = (input != '' && input != null) ?
                                 castToNFType(input, field) :
                             field['value']['default'] != null ?
                                 castToNFType(field['value']['default'], field) :
                                 null
                     }
                 }
                 else {
-                    def inputVal = (input != '' && input) ?
+                    def inputVal = (input != '' && input != null) ?
                             castToNFType(input, field) :
                         field['value']['default'] != null ?
                             castToNFType(field['value']['default'], field) :

diff --git a/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy b/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy
@@ -115,7 +115,7 @@ class SamplesheetConverterTest extends Dsl2Spec{
         def SCRIPT_TEXT = '''
             include { fromSamplesheet } from 'plugin/nf-validation'
 
-            params.input = 'src/testResources/correct.csv'
+            params.input = 'src/testResources/correct.tsv'
 
             workflow {
                 Channel.fromSamplesheet("input", parameters_schema:"src/testResources/nextflow_schema_with_samplesheet_converter.json").view()
@@ -142,7 +142,7 @@ class SamplesheetConverterTest extends Dsl2Spec{
         def SCRIPT_TEXT = '''
             include { fromSamplesheet } from 'plugin/nf-validation'
 
-            params.input = 'src/testResources/correct.csv'
+            params.input = 'src/testResources/correct.yaml'
 
             workflow {
                 Channel.fromSamplesheet("input", parameters_schema:"src/testResources/nextflow_schema_with_samplesheet_converter.json").view()

diff --git a/plugins/nf-validation/src/testResources/schema_input.json b/plugins/nf-validation/src/testResources/schema_input.json
@@ -47,7 +47,7 @@
                 "type": "string",
                 "format": "path",
                 "exists": true
-                },
+            },
             "field_10": {
                 "type": "string",
                 "unique": true