Fix handling of wave.s5cmdConfigUrl setting [ci fast] (nextflow-io#4707)

Signed-off-by: Dr Marco Claudio De La Pierre <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]> Co-authored-by: Paolo Di Tommaso <[email protected]> Signed-off-by: Niklas Schandry <[email protected]>
nschan · Feb 12, 2024 · 0ec535b · 0ec535b
1 parent a036f1c
commit 0ec535b
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diff --git 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
@@ -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
@@ -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