From 4977ec097afac7fdc047c87fd4358f3858fa2320 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 20 Mar 2024 16:01:36 +0100
Subject: [PATCH] convert fromSamplesheet to an operator

---
 .../validation/SchemaValidator.groovy         | 90 ++++++-------------
 1 file changed, 27 insertions(+), 63 deletions(-)

diff --git a/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy b/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy
index 5ab0573f..646ea620 100644
--- a/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy
+++ b/plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy
@@ -12,6 +12,7 @@ import java.nio.file.Path
 import java.util.regex.Matcher
 import java.util.regex.Pattern
 import nextflow.extension.CH
+import nextflow.extension.DataflowHelper
 import nextflow.Channel
 import nextflow.Global
 import nextflow.Nextflow
@@ -138,73 +139,36 @@ class SchemaValidator extends PluginExtensionPoint {
     public DataflowWriteChannel fromSamplesheet(
         final DataflowReadChannel source,
         final Path schema,
-        final Map options = null,
+        final Map options = null
     ) {
-        def Map params = session.params
-
-        // Set defaults for optional inputs
-        def String schemaFilename = options?.containsKey('parameters_schema') ? options.parameters_schema as String : 'nextflow_schema.json'
-        def String baseDir = session.baseDir.toString()
-
-        // Get the samplesheet schema from the parameters schema
-        def slurper = new JsonSlurper()
-        def Map parsed = (Map) slurper.parse( Path.of(Utils.getSchemaPath(baseDir, schemaFilename)) )
-        def Map samplesheetValue = (Map) findDeep(parsed, samplesheetParam)
-        def Path samplesheetFile = params[samplesheetParam] as Path
-
-        // Some safeguard to make sure the channel factory runs correctly
-        if (samplesheetValue == null) {
-            log.error """
-Parameter '--$samplesheetParam' was not found in the schema ($schemaFilename). 
-Unable to create a channel from it.
-
-Please make sure you correctly specified the inputs to `.fromSamplesheet`:
-
---------------------------------------------------------------------------------------
-Channel.fromSamplesheet("input")
---------------------------------------------------------------------------------------
-
-This would create a channel from params.input using the schema specified in the parameters JSON schema for this parameter.
-"""
-            throw new SchemaValidationException("", [])
-        }
-        else if (samplesheetFile == null) {
-            log.error "Parameter '--$samplesheetParam' was not provided. Unable to create a channel from it."
-            throw new SchemaValidationException("", [])
-        }
-        else if (!samplesheetValue.containsKey('schema')) {
-            log.error "Parameter '--$samplesheetParam' does not contain a schema in the parameter schema ($schemaFilename). Unable to create a channel from it."
-            throw new SchemaValidationException("", [])
-        }
-        
-        // Convert to channel
-        final channel = CH.create()
-        def List arrayChannel = []
-        try {
-            def Path schemaFile = Path.of(Utils.getSchemaPath(baseDir, samplesheetValue['schema'].toString()))
-            def SamplesheetConverter converter = new SamplesheetConverter(samplesheetFile, schemaFile)
-            arrayChannel = converter.convertToList()
-        } catch (Exception e) {
-            log.error(
-                """ Following error has been found during samplesheet conversion:
-    ${e}
-    ${e.getStackTrace().join("\n\t")}
-
-Please run validateParameters() first before trying to convert a samplesheet to a channel.
-Reference: https://nextflow-io.github.io/nf-schema/parameters/validation/
-
-Also make sure that the same schema is used for validation and conversion of the samplesheet
-""" as String
-            )
-        }
-
-        session.addIgniter {
+        def params = session.params
+        final target = CH.createBy(source)
+        final validator = new JsonSchemaValidator()
+        final next = {
+            def JSONArray samplesheet = Utils.fileToJsonArray(it as Path, schema)
+            def List<String> validationErrors = validator.validate(samplesheet, schema.text)
+            this.errors.addAll(validationErrors)
+            if (validationErrors) {
+                def Boolean useMonochromeLogs = options?.containsKey('monochrome_logs') ? options.monochrome_logs as Boolean :
+                    params.monochrome_logs ? params.monochrome_logs as Boolean : 
+                    params.monochromeLogs  ? params.monochromeLogs as Boolean :
+                    false
+                def colors = logColours(useMonochromeLogs)
+                def msg = "${colors.red}The following errors have been detected in ${it.toString()}:\n\n" + validationErrors.join('\n').trim() + "\n${colors.reset}\n"
+                log.error("Validation of samplesheet failed!")
+                throw new SchemaValidationException(msg, this.getErrors())
+            }
+            def SamplesheetConverter converter = new SamplesheetConverter(it as Path, schema)
+            def List arrayChannel = converter.convertToList()
             arrayChannel.each { 
-                channel.bind(it) 
+                target.bind(it)
             }
-            channel.bind(Channel.STOP)
         }
-        return channel
+        final done = {
+            target.bind(Channel.STOP)
+        }
+        DataflowHelper.subscribeImpl(source, [onNext: next, onComplete: done])
+        return target
     }