Add defaults configuration settings

modules/nextflow/src/main/groovy/nextflow/config/scope/nextflow/DefaultOpts.groovy

@@ -0,0 +1,39 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.config.scope.nextflow
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+
+/**
+ * Model nextflow default options
+ * 
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@ToString(includePackage = false, includeNames = true)
+@EqualsAndHashCode
+@CompileStatic
+class DefaultOpts {
+
+    final PublishDirOpts publishDir
+
+    DefaultOpts(Map opts) {
+        publishDir = new PublishDirOpts( opts.publishDir as Map ?: Map.of())
+    }
+}

modules/nextflow/src/main/groovy/nextflow/config/scope/nextflow/NextflowOpts.groovy

@@ -0,0 +1,40 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.config.scope.nextflow
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+
+/**
+ * Model nextflow options
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@ToString(includePackage = false, includeNames = true)
+@EqualsAndHashCode
+@CompileStatic
+class NextflowOpts {
+
+    final DefaultOpts defaults
+
+    NextflowOpts(Map<String,Object> opts) {
+        defaults = new DefaultOpts(opts.defaults as Map<String,Object> ?: Map.<String,Object>of())
+    }
+
+}

modules/nextflow/src/main/groovy/nextflow/config/scope/nextflow/PublishDirOpts.groovy

@@ -0,0 +1,62 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.config.scope.nextflow
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+
+/**
+ * Model publishDir options
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@ToString(includePackage = false, includeNames = true)
+@EqualsAndHashCode
+@CompileStatic
+class PublishDirOpts {
+
+    static final public PublishDirOpts EMPTY = new PublishDirOpts(Map.of())
+
+
+    final String mode
+    final Boolean enabled
+    final Boolean failOnError
+    final String pattern
+    final Object contentType
+    final Boolean overwrite
+    final String storageClass
+    final Map<String,String> tags
+
+    PublishDirOpts(Map opts) {
+        mode = opts.mode
+        enabled = asBool(opts.enabled)
+        failOnError = asBool(opts.failOnError)
+        overwrite = asBool(opts.overwrite)
+        pattern = opts.pattern
+        contentType = opts.contentType
+        storageClass = opts.storageClass
+        tags = opts.tags as Map<String,String>
+    }
+
+    private Boolean asBool(Object value) {
+        if( value==null )
+            return null
+        return Boolean.valueOf(value as String)
+    }
+}

modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy

@@ -37,6 +37,7 @@ import groovy.util.logging.Slf4j
 import nextflow.Global
 import nextflow.NF
 import nextflow.Session
+import nextflow.config.scope.nextflow.PublishDirOpts
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.file.TagAwareFile
@@ -178,41 +179,55 @@ class PublishDir {
      * @return An instance of {@link PublishDir} class
      */
     @CompileDynamic
-    static PublishDir create( Map params ) {
+    static PublishDir create( Map params, PublishDirOpts defaults=PublishDirOpts.EMPTY ) {
         assert params
 
         def result = new PublishDir()
         if( params.path )
             result.path = params.path
 
-        if( params.mode )
-            result.mode = params.mode
+        final mode = params.mode as String ?: defaults.mode
+        if( mode )
+            result.setMode(mode as String)
 
-        if( params.pattern )
-            result.pattern = params.pattern
+        final pattern = params.pattern ?: defaults.pattern
+        if( pattern )
+            result.pattern = pattern
 
-        if( params.overwrite != null )
-            result.overwrite = Boolean.parseBoolean(params.overwrite.toString())
+        final overwrite = params.overwrite!=null
+            ? Boolean.parseBoolean(params.overwrite.toString())
+            : defaults.overwrite
+        if( overwrite != null )
+            result.overwrite = overwrite
 
         if( params.saveAs )
             result.saveAs = (Closure) params.saveAs
 
-        if( params.enabled != null )
-            result.enabled = Boolean.parseBoolean(params.enabled.toString())
-
-        if( params.failOnError != null )
-            result.failOnError = Boolean.parseBoolean(params.failOnError.toString())
-
-        if( params.tags != null )
-            result.tags = params.tags
-
-        if( params.contentType instanceof Boolean )
-            result.contentType = params.contentType
-        else if( params.contentType )
-            result.contentType = params.contentType as String
-
-        if( params.storageClass )
-            result.storageClass = params.storageClass as String
+        final enabled  = params.enabled!=null
+            ? Boolean.parseBoolean(params.enabled.toString())
+            : defaults.enabled
+        if( enabled != null )
+            result.enabled = enabled
+
+        final failOnError = params.failOnError!=null
+            ? Boolean.parseBoolean(params.failOnError.toString())
+            : defaults.failOnError
+        if( failOnError != null )
+            result.failOnError = failOnError
+
+        final tags = params.tags ?: defaults.tags
+        if( tags != null )
+            result.tags = tags
+
+        final contentType = params.contentType!=null ? params.contentType : defaults.contentType
+        if( contentType instanceof Boolean )
+            result.contentType = contentType
+        else if( contentType )
+            result.contentType = contentType as String
+
+        final storageClass = params.storageClass as String ?: defaults.storageClass
+        if( storageClass )
+            result.storageClass = storageClass
 
         return result
     }

modules/nextflow/src/test/groovy/nextflow/config/scope/nextflow/DefaultOptsTest.groovy

@@ -0,0 +1,41 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.config.scope.nextflow
+
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+class DefaultOptsTest extends Specification {
+
+    def 'should validate equals and hashcode' () {
+        given:
+        def o1 = new DefaultOpts([publishDir: [mode:'foo']])
+        def o2 = new DefaultOpts([publishDir: [mode:'foo']])
+        def o3 = new DefaultOpts([publishDir: [mode:'bar']])
+
+        expect:
+        o1 == o2
+        o1 != o3
+        and:
+        o1.hashCode() == o2.hashCode()
+        o1.hashCode() != o3.hashCode()
+    }
+}

modules/nextflow/src/test/groovy/nextflow/config/scope/nextflow/NextflowOptsTest.groovy

@@ -0,0 +1,80 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.config.scope.nextflow
+
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+class NextflowOptsTest extends Specification {
+
+    def 'should validate equals and hashcode' () {
+        given:
+        def o1 = new NextflowOpts([defaults: [publishDir: [mode:'foo']]])
+        def o2 = new NextflowOpts([defaults: [publishDir: [mode:'foo']]])
+        def o3 = new NextflowOpts([defaults: [publishDir: [mode:'bar']]])
+
+        expect:
+        o1 == o2
+        o1 != o3
+        and:
+        o1.hashCode() == o2.hashCode()
+        o1.hashCode() != o3.hashCode()
+    }
+
+    def 'should create empty nextflow opts' () {
+        when:
+        def nextflow = new NextflowOpts([:])
+        then:
+        !nextflow.defaults.publishDir.enabled
+        !nextflow.defaults.publishDir.mode
+        !nextflow.defaults.publishDir.failOnError
+        !nextflow.defaults.publishDir.contentType
+        !nextflow.defaults.publishDir.overwrite
+        !nextflow.defaults.publishDir.contentType
+        !nextflow.defaults.publishDir.storageClass
+        !nextflow.defaults.publishDir.tags
+    }
+
+    def 'should create nextflow publishdir opts' () {
+        when:
+        def nextflow = new NextflowOpts([
+            defaults: [
+                publishDir: [
+                    mode:'foo',
+                    enabled: 'true',
+                    failOnError: 'true',
+                    contentType: 'some-content',
+                    overwrite: 'true',
+                    storageClass: 'some-storage',
+                    tags: ['this':'one', 'that': 'two']
+                ]
+            ]])
+        then:
+        nextflow.defaults.publishDir.mode == 'foo'
+        nextflow.defaults.publishDir.enabled
+        nextflow.defaults.publishDir.failOnError
+        nextflow.defaults.publishDir.contentType == 'some-content'
+        nextflow.defaults.publishDir.overwrite
+        nextflow.defaults.publishDir.storageClass == 'some-storage'
+        nextflow.defaults.publishDir.tags == ['this':'one', 'that': 'two']
+    }
+
+}