Merge pull request #175 from nextflow-io/patch/url-samplesheets

nvnieuwk · web-flow · commit a547e5cdc33a · 2025-09-03T12:44:33.000+02:00
Patch/url samplesheets
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # nextflow-io/nf-schema: Changelog
 
+# Version 2.5.1
+
+## Bug fixes
+
+1. Fixed a bug where non-local samplesheets couldn't be validated and converted.
+
 # Version 2.5.0
 
 ## New features
diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ Declare the plugin in your Nextflow pipeline configuration file:
 
 ```groovy title="nextflow.config"
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 ```
 
diff --git a/build.gradle b/build.gradle
@@ -8,7 +8,7 @@ dependencies {
     implementation 'com.sanctionco.jmail:jmail:1.6.3' // Needed for e-mail format validation
 }
 
-version = '2.5.0'
+version = '2.5.1'
 
 nextflowPlugin {
     nextflowVersion = '25.04.0'
@@ -31,4 +31,10 @@ nextflowPlugin {
             indexUrl = 'https://github.com/nextflow-io/plugins/blob/main/plugins.json'
         }
     }
+
+    test {
+        jvmArgs += [
+            '--add-opens', 'java.base/sun.net.www.protocol.ftp=ALL-UNNAMED'
+        ]
+    }
 }
diff --git a/examples/helpMessage/pipeline/nextflow.config b/examples/helpMessage/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/examples/paramsHelp/pipeline/nextflow.config b/examples/paramsHelp/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/examples/paramsSummaryLog/pipeline/nextflow.config b/examples/paramsSummaryLog/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/examples/paramsSummaryMap/pipeline/nextflow.config b/examples/paramsSummaryMap/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/examples/samplesheetToListBasic/pipeline/nextflow.config b/examples/samplesheetToListBasic/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/examples/samplesheetToListMeta/pipeline/nextflow.config b/examples/samplesheetToListMeta/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/examples/samplesheetToListOrder/pipeline/nextflow.config b/examples/samplesheetToListOrder/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/examples/validateParameters/pipeline/nextflow.config b/examples/validateParameters/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/examples/validationFailUnrecognisedParams/pipeline/nextflow.config b/examples/validationFailUnrecognisedParams/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 validation.logging.unrecognisedParams = "error"
diff --git a/examples/validationWarnUnrecognisedParams/pipeline/nextflow.config b/examples/validationWarnUnrecognisedParams/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.5.0'
+  id 'nf-schema@2.5.1'
 }
 
 params {
diff --git a/src/main/groovy/nextflow/validation/utils/Files.groovy b/src/main/groovy/nextflow/validation/utils/Files.groovy
@@ -111,7 +111,7 @@ public class Files {
     //
     private static Path sanitize(Path file) {
         // Check if sanitization is needed
-        def BufferedReader reader = new BufferedReader(new FileReader(file.toFile()))
+        def reader = file.newReader()
         def String firstLine = reader.readLine()
         reader.close()
         if (!firstLine.endsWith(",") && !firstLine.endsWith("\t")) {
@@ -123,18 +123,15 @@ public class Files {
 
         def Scanner scanner = new Scanner(file.toFile())
         def PrintWriter writer = new PrintWriter(tempFile)
-        def Boolean headerSanitized = false
-        while (scanner.hasNextLine()) {
-            def String line = scanner.nextLine()
+        file.withReader {
+            def String line
             // Remove trailing commas or tabs from the line
-            if (!headerSanitized) {
-                line = line.replaceAll("[,\\t]*\$", "")
-                headerSanitized = true
+            while( line = it.readLine() ) {
+                def String sanitized_line = line.replaceAll("[,\\t]*\$", "")
+                writer.println(sanitized_line)
             }
-            writer.println(line)
         }
         writer.close()
-        scanner.close()
         return tempFile.toPath()
     }
 
diff --git a/src/test/groovy/nextflow/validation/SamplesheetConverterTest.groovy b/src/test/groovy/nextflow/validation/SamplesheetConverterTest.groovy
@@ -722,5 +722,34 @@ class SamplesheetConverterTest extends Dsl2Spec{
         stdout.contains("[[nullValue:null], 25, defaultString, true, test]")
         stdout.contains("[[nullValue:null], 0, defaultString, true, null]")
     }
+
+    def 'should work fine - CSV from URL' () {
+        given:
+        def SCRIPT_TEXT = '''
+            include { samplesheetToList } from 'plugin/nf-schema'
+
+            params.input = "https://github.com/nextflow-io/nf-schema/raw/refs/heads/master/src/testResources/correct.csv"
+            params.schema = "src/testResources/schema_input.json"
+
+            workflow {
+                Channel.fromList(samplesheetToList(params.input, params.schema))
+                    .view()
+            }
+        '''
+
+        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, ${getRootString()}/src/testResources/test.txt, ${getRootString()}/src/testResources/testDir, ${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, ${getRootString()}/src/testResources/test.txt, ${getRootString()}/src/testResources/testDir, ${getRootString()}/src/testResources/testDir, unique3, 1, itDoesExist]" as String)
+    }
     
 }

Original file line number	Diff line number	Diff line change
`@@ -25,7 +25,7 @@ Declare the plugin in your Nextflow pipeline configuration file:`
`25`	`25`
`26`	`26`	```groovy title="nextflow.config"
`27`	`27`	`plugins {`
`28`		`- id '[email protected].0'`
	`28`	`+ id '[email protected].1'`
`29`	`29`	`}`
`30`	`30`	```
`31`	`31`
Original file line number	Diff line number	Diff line change
`@@ -8,7 +8,7 @@ dependencies {`
`8`	`8`	`implementation 'com.sanctionco.jmail:jmail:1.6.3' // Needed for e-mail format validation`
`9`	`9`	`}`
`10`	`10`
`11`		`-version = '2.5.0'`
	`11`	`+version = '2.5.1'`
`12`	`12`
`13`	`13`	`nextflowPlugin {`
`14`	`14`	`nextflowVersion = '25.04.0'`
`@@ -31,4 +31,10 @@ nextflowPlugin {`
`31`	`31`	`indexUrl = 'https://github.com/nextflow-io/plugins/blob/main/plugins.json'`
`32`	`32`	`}`
`33`	`33`	`}`
	`34`	`+`
	`35`	`+ test {`
	`36`	`+ jvmArgs += [`
	`37`	`+ '--add-opens', 'java.base/sun.net.www.protocol.ftp=ALL-UNNAMED'`
	`38`	`+ ]`
	`39`	`+ }`
`34`	`40`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`plugins {`
`2`		`- id '[email protected].0'`
	`2`	`+ id '[email protected].1'`
`3`	`3`	`}`
`4`	`4`
`5`	`5`	`params {`