From e46197f33e8264800e75ae3ff1fa6e52429cd891 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 29 Oct 2024 15:37:14 +0100
Subject: [PATCH] add missing depedency for email format support

---
 CHANGELOG.md                                  |  1 +
 plugins/nf-schema/build.gradle                |  1 +
 .../validation/ValidateParametersTest.groovy  | 52 +++++++++++++++++++
 .../src/testResources/nextflow_schema.json    |  4 +-
 4 files changed, 56 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 01759d3..12ef25a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
 ## Bug fixes
 
 1. Fixed a bug in `samplesheetToList` that caused output mixing when the function was used more than once in channel operators.
+2. Added a missing depencency for email format validation.
 
 ## Improvements
 
diff --git a/plugins/nf-schema/build.gradle b/plugins/nf-schema/build.gradle
index 3d72ac6..c4ee257 100644
--- a/plugins/nf-schema/build.gradle
+++ b/plugins/nf-schema/build.gradle
@@ -56,6 +56,7 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.4.1'
     implementation 'org.json:json:20240303'
     implementation 'dev.harrel:json-schema:1.5.0'
+    implementation 'com.sanctionco.jmail:jmail:1.6.3' // Needed for e-mail format validation
 
     // test configuration
     testImplementation "io.nextflow:nextflow:$nextflowVersion"
diff --git a/plugins/nf-schema/src/test/nextflow/validation/ValidateParametersTest.groovy b/plugins/nf-schema/src/test/nextflow/validation/ValidateParametersTest.groovy
index 8636ac0..55448e6 100644
--- a/plugins/nf-schema/src/test/nextflow/validation/ValidateParametersTest.groovy
+++ b/plugins/nf-schema/src/test/nextflow/validation/ValidateParametersTest.groovy
@@ -1095,4 +1095,56 @@ class ValidateParametersTest extends Dsl2Spec{
         !stdout
     }
 
+    def 'should validate an email' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema.json').toAbsolutePath().toString()
+        def SCRIPT = """
+            params.input = 'src/testResource/samplesheet.csv'
+            params.outdir = 'src/testResources/testDir'
+            params.email = "test@domain.com"
+            include { validateParameters } from 'plugin/nf-schema'
+            
+            validateParameters(parameters_schema: '$schema')
+        """
+
+        when:
+        def config = [:]
+        def result = new MockScriptRunner(config).setScript(SCRIPT).execute()
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+        then:
+        noExceptionThrown()
+        !stdout
+    }
+
+    def 'should validate an email - failure' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema.json').toAbsolutePath().toString()
+        def SCRIPT = """
+            params.input = 'src/testResource/samplesheet.csv'
+            params.outdir = 'src/testResources/testDir'
+            params.email = "thisisnotanemail"
+            include { validateParameters } from 'plugin/nf-schema'
+            
+            validateParameters(parameters_schema: '$schema')
+        """
+
+        when:
+        def config = [:]
+        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:
+        def error = thrown(SchemaValidationException)
+        error.message.contains("* --email (thisisnotanemail): \"thisisnotanemail\" is not a valid email address")
+        !stdout
+    }
+
 }
\ No newline at end of file
diff --git a/plugins/nf-schema/src/testResources/nextflow_schema.json b/plugins/nf-schema/src/testResources/nextflow_schema.json
index 7dcf103..1fb1565 100644
--- a/plugins/nf-schema/src/testResources/nextflow_schema.json
+++ b/plugins/nf-schema/src/testResources/nextflow_schema.json
@@ -30,9 +30,9 @@
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",
+                    "format": "email",
                     "fa_icon": "fas fa-envelope",
-                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
-                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run."
                 },
                 "multiqc_title": {
                     "type": "string",