From 3a19386df74a5bfd71025d2dc9b4ded1aa039355 Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Thu, 1 Feb 2024 18:51:22 +0800
Subject: [PATCH] Fix handling of  wave.s5cmdConfigUrl setting [ci fast]
 (#4707)

Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/nextflow/extension/Bolts.groovy         | 12 ++++++++++++
 .../src/test/nextflow/extension/BoltsTest.groovy     | 12 ++++++++++++
 .../test/io/seqera/wave/plugin/WaveClientTest.groovy |  9 +++++++++
 3 files changed, 33 insertions(+)

diff --git a/modules/nf-commons/src/main/nextflow/extension/Bolts.groovy b/modules/nf-commons/src/main/nextflow/extension/Bolts.groovy
index 76622474b8..13d4fc7739 100644
--- a/modules/nf-commons/src/main/nextflow/extension/Bolts.groovy
+++ b/modules/nf-commons/src/main/nextflow/extension/Bolts.groovy
@@ -443,6 +443,12 @@ class Bolts {
         else if( type == RateUnit ) {
             return new RateUnit(self)
         }
+        else if ( type == URL ) {
+            return new URL(self)
+        }
+        else if ( type == URI ) {
+            return URI.create(self)
+        }
 
         StringGroovyMethods.asType(self, type);
     }
@@ -464,6 +470,12 @@ class Bolts {
         else if( type == MemoryUnit ) {
             return new MemoryUnit(self.toString())
         }
+        else if ( type == URL ) {
+            return new URL(self.toString())
+        }
+        else if ( type == URI ) {
+            return URI.create(self.toString())
+        }
 
         StringGroovyMethods.asType(self, type);
     }
diff --git a/modules/nf-commons/src/test/nextflow/extension/BoltsTest.groovy b/modules/nf-commons/src/test/nextflow/extension/BoltsTest.groovy
index ed39bb220d..c569fb9196 100644
--- a/modules/nf-commons/src/test/nextflow/extension/BoltsTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/extension/BoltsTest.groovy
@@ -145,6 +145,18 @@ class BoltsTest extends Specification {
         "$x MB" as MemoryUnit == MemoryUnit.of('5 MB')
     }
 
+    def testAsURL() {
+        expect: 
+        'http://foo.com' as URL == new URL('http://foo.com')
+        'http://foo.com/some/file.txt' as URL == new URL('http://foo.com/some/file.txt')
+    }
+
+    def testAsURI() {
+        expect:
+        'http://foo.com' as URI == URI.create('http://foo.com')
+        'http://foo.com/some/file.txt' as URI == URI.create('http://foo.com/some/file.txt')
+    }
+
     def testConfigToMap  () {
 
         setup:
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 7e70745c27..7155221ee5 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -1248,6 +1248,15 @@ class WaveClientTest extends Specification {
         'linux/arm64/v8'    | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
     }
 
+    def 'should configure custom s5cmd' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [wave:[s5cmdConfigUrl: 'http://host.com/s5cmd.zip']] }
+        when:
+        def wave = Spy(new WaveClient(sess))
+        then:
+        wave.@s5cmdConfigUrl == new URL('http://host.com/s5cmd.zip')
+    }
+
     def 'should check is local conda file' () {
         expect:
         WaveClient.isCondaLocalFile(CONTENT) == EXPECTED