Merge pull request #134 from nvnieuwk/add-quotes-for-csv

Add support for double quotes in samplesheets
nextflow-io · Nov 21, 2023 · 26f5631 · 26f5631
2 parents bc51bc5 + 5dc7b13
commit 26f5631
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # nextflow-io/nf-validation: Changelog
 
+# Version 1.1.3 - Asahikawa
+
+## Improvements
+
+- Added support for double quotes (`"`) in CSV and TSV samplesheets ([#134](https://github.com/nextflow-io/nf-validation/pull/134))
+
 # Version 1.1.2 - Wakayama
 
 ## Bug fixes

diff --git a/plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy b/plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy
@@ -80,7 +80,7 @@ class SamplesheetConverter {
         }
         else {
             Path fileSamplesheet = Nextflow.file(samplesheetFile) as Path
-            samplesheetList = fileSamplesheet.splitCsv(header:containsHeader ?: ["empty"], strip:true, sep:delimiter, quote:'"')
+            samplesheetList = fileSamplesheet.splitCsv(header:containsHeader ?: ["empty"], strip:true, sep:delimiter, quote:'\"')
         }
 
         // Field checks + returning the channels

diff --git a/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy b/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy
@@ -200,7 +200,7 @@ class SchemaValidator extends PluginExtensionPoint {
             }
         }
         else {
-            fileContent = samplesheetFile.splitCsv(header:containsHeader ?: ["empty"], strip:true, sep:delimiter)
+            fileContent = samplesheetFile.splitCsv(header:containsHeader ?: ["empty"], strip:true, sep:delimiter, quote:'\"')
         }
         def List<Map<String,String>> fileContentCasted = castToType(fileContent, types)
         if (validateFile(false, samplesheetFile.toString(), fileContentCasted, schemaFile.toString(), baseDir, s3PathCheck)) {
@@ -438,7 +438,7 @@ class SchemaValidator extends PluginExtensionPoint {
                         }
                     }
                     else {
-                        fileContent = file_path.splitCsv(header:containsHeader ?: ["empty"], strip:true, sep:delimiter)
+                        fileContent = file_path.splitCsv(header:containsHeader ?: ["empty"], strip:true, sep:delimiter, quote:'\"')
                     }
                     def List<Map<String,String>> fileContentCasted = castToType(fileContent, types)
                     if (validateFile(useMonochromeLogs, key, fileContentCasted, schema_name, baseDir, s3PathCheck)) {

diff --git a/plugins/nf-validation/src/resources/META-INF/MANIFEST.MF b/plugins/nf-validation/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Id: nf-validation
-Plugin-Version: 1.1.2
+Plugin-Version: 1.1.3
 Plugin-Class: nextflow.validation.ValidationPlugin
 Plugin-Provider: nextflow
 Plugin-Requires: >=22.10.0
diff --git a/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy b/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy
@@ -83,7 +83,34 @@ class SamplesheetConverterTest extends Dsl2Spec{
         stdout.contains("[[string1:extraField, string2:extraField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir, unique3, 1, itDoesExist]" as String)
     }
 
-        def 'should work fine - TSV' () {
+    def 'should work fine - quoted CSV' () {
+        given:
+        def SCRIPT_TEXT = '''
+            include { fromSamplesheet } from 'plugin/nf-validation'
+
+            params.input = 'src/testResources/correct_quoted.csv'
+
+            workflow {
+                Channel.fromSamplesheet("input", parameters_schema:"src/testResources/nextflow_schema_with_samplesheet_converter.json").view().first().map {println(it[0].getClass())}
+            }
+        '''
+
+        when:
+        dsl_eval(SCRIPT_TEXT)
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.startsWith('[[') ? it : null }
+
+        then:
+        noExceptionThrown()
+        stdout.contains("[[string1:fullField, string2:fullField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25.12, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/test.txt, unique1, 1, itDoesExist]" as String)
+        stdout.contains("[[string1:value, string2:value, integer1:0, integer2:0, boolean1:true, boolean2:true], string1, 25.08, false, [], [], [], [], [], itDoesExist]")
+        stdout.contains("[[string1:dependentRequired, string2:dependentRequired, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, [], [], [], unique2, 1, itDoesExist]")
+        stdout.contains("[[string1:extraField, string2:extraField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir, unique3, 1, itDoesExist]" as String)
+    }
+
+    def 'should work fine - TSV' () {
         given:
         def SCRIPT_TEXT = '''
             include { fromSamplesheet } from 'plugin/nf-validation'

diff --git a/plugins/nf-validation/src/testResources/correct_quoted.csv b/plugins/nf-validation/src/testResources/correct_quoted.csv
@@ -0,0 +1,5 @@
+field_1,field_2,field_3,field_4,field_5,field_6,field_7,field_8,field_9,field_10,field_11
+"fullField",10,"true","string1",25.12,false,"src/testResources/test.txt",src/testResources/testDir,src/testResources/test.txt,unique1,1
+,,,string1,"25.08",false,"",,,,,
+"dependentRequired",10,true,string1,25,"false",,,,"unique2",1
+"extraField",10,true,string1,25,false,src/testResources/test.txt,"src/testResources/testDir",src/testResources/testDir,unique3,1