Merge pull request #362 from pinin4fjords/fix/config-scope-noarg-constructor

Fix: Add no-arg constructors for v2 config parser scope registration

Author: JosuaCarl

CHANGELOG.md

@@ -1,5 +1,6 @@
 # New
 ## Bug Fixes:
+- Eliminated `Unrecognized config option` warnings under Nextflow's v2 syntax parser by registering `CO2FootprintConfig` as an extension point and aligning the nested file-config scopes with the v2 `ConfigScope` discovery rules
 
 ## Misc:
 

build.gradle

@@ -107,7 +107,8 @@ nextflowPlugin {
     className = 'nextflow.co2footprint.CO2FootprintPlugin'
     extensionPoints = [
             'nextflow.co2footprint.CO2FootprintFactory',
-            'nextflow.co2footprint.CO2FootprintExtension'
+            'nextflow.co2footprint.CO2FootprintExtension',
+            'nextflow.co2footprint.CO2FootprintConfig'
     ]
 
 }

src/main/nextflow/co2footprint/CO2FootprintConfig.groovy

@@ -57,66 +57,68 @@ class CO2FootprintConfig implements ConfigScope {
     private final String timestamp = TraceHelper.launchTimestampFmt()
     private final String executor
 
-    @ConfigOption(types=[Map])
     @Description('Configuration for the trace file.')
     final TraceFileConfig trace
 
-    @ConfigOption(types=[Map])
     @Description('Configuration for the summary file.')
     final SummaryFileConfig summary
 
-    @ConfigOption(types=[Map])
     @Description('Configuration for the report file.')
     final ReportFileConfig report
 
-    @ConfigOption(types=[Map])
     @Description('Configuration for the provenance data/machine-readable file.')
     final ProvenanceFileConfig provenance
 
-    @ConfigOption(types=[GString])
+    @ConfigOption
     @Description('Location GeoCode from Electricity maps.')
     final String location
 
     @ConfigOption(types=[Number, BigDecimal])
     @Description('Location-based carbon intensity (CI).')
     final CiRecord ci
 
-    @ConfigOption(types=[Number])
+    @ConfigOption
     @Description('Market-based carbon intensity (CI).')
     final BigDecimal ciMarket
 
-    @ConfigOption(types=[GString])
+    @ConfigOption
     @Description('Electricity-maps API token.')
     final String emApiKey
 
-    @ConfigOption(types=[Number])
+    @ConfigOption
     @Description('Power usage effectiveness (PUE) of the data centre.')
     BigDecimal pue
 
-    @ConfigOption(types=[Number])
+    @ConfigOption
     @Description('Power draw of memory [W per GB].')
     final BigDecimal powerdrawMem
 
     @ConfigOption
     @Description('Turns off pattern matching of CPU names.')
     final Boolean ignoreCpuModel
 
-    @ConfigOption(types=[Number])
+    @ConfigOption
     @Description('Default powerdraw of the CPU.')
     final BigDecimal powerdrawCpuDefault
 
-    @ConfigOption(types=[String, GString])
+    @ConfigOption
     @Description('Path to a custom CPU TDP file.')
     final Path customCpuTdpFile
 
-    @ConfigOption(types=[GString])
+    @ConfigOption
     @Description('Type of computer on which the workflow is run [\'local\', \'compute cluster\', \'\'].')
     String machineType
 
     @ConfigOption
     @Description('A power model function that takes the parameter `coreUsage`.')
     final Closure<Number> cpuPowerModel
 
+    /**
+     * No-arg constructor required by Nextflow's v2 config parser to
+     * discover and validate config options at parse time.
+     */
+    CO2FootprintConfig() {}
+
     /**
      * Loads configuration from a map and sets up defaults and fallbacks.
      * Also sets up CPU and CI data sources and assigns machine type and PUE.

src/main/nextflow/co2footprint/Config/BaseFileConfig.groovy

@@ -2,9 +2,6 @@ package nextflow.co2footprint.Config
 
 import groovy.util.logging.Slf4j
 import nextflow.co2footprint.CO2FootprintConfig
-import nextflow.config.spec.ConfigOption
-import nextflow.script.dsl.Description
-
 import java.nio.file.Path
 
 /**
@@ -18,36 +15,51 @@ import java.nio.file.Path
 class BaseFileConfig {
     final String name
     final String ending
-
-    @ConfigOption(types=[String, GString])
-    @Description('Path to the file.')
-    final Path file
-
-    @ConfigOption
-    @Description('Whether to enable the file creation.')
-    final Boolean enabled
-
-    @ConfigOption
-    @Description('Whether to overwrite a file if it already exists.')
-    final Boolean overwrite
+    final boolean defaultEnabled
 
     protected final LinkedHashSet<String> usedKeys = [] as LinkedHashSet<String>
 
+
     /**
      * Parses a file-based sub-configuration for nf-co2footprint and sets up defaults and fallbacks.
      *
-     * @param fileConfigMap  User-provided configuration options
-     * @param timestamp      Timestamp for generating default filenames
      * @param subConfigName  Name of the configuration scope
      * @param fileEnding     Output file extension (default: txt)
-     * @param defaultEnabled Whether to enable the file by default (default: true)
      */
-    BaseFileConfig(Map<String, Object> fileConfigMap, String timestamp, String subConfigName, String fileEnding='txt', boolean defaultEnabled=true){
+    BaseFileConfig(String subConfigName, String fileEnding, boolean defaultEnabled=true){
         this.name = subConfigName
         this.ending = fileEnding ?: 'txt'
+        this.defaultEnabled = defaultEnabled
+    }
 
-        file = Path.of(CO2FootprintConfig.getCollect('file', fileConfigMap, usedKeys) as String ?: "co2footprint_${name}_${timestamp}.${ending}")
-        enabled =  fileConfigMap.containsKey('enabled') ? CO2FootprintConfig.getCollect('enabled', fileConfigMap, usedKeys) : defaultEnabled
-        overwrite = fileConfigMap.containsKey('overwrite') ? CO2FootprintConfig.getCollect('overwrite', fileConfigMap, usedKeys) : true
+    /**
+     * Define a file path from the given config map and timestamp, as well as predefined variables.
+     *
+     * @param fileConfig The general config of this file.
+     * @param timestamp A timestamp string.
+     * @return The path to the file.
+     */
+    protected Path defineFile(Map<String, Object> fileConfig, String timestamp) {
+        return Path.of(CO2FootprintConfig.getCollect('file', fileConfig, usedKeys) as String ?: "co2footprint_${name}_${timestamp}.${ending}")
+    }
+
+    /**
+     * Define whether the construction of this file is enabled.
+     *
+     * @param fileConfig The general config of this file.
+     * @return Whether or not to write the file.
+     */
+    protected boolean defineEnabled(Map<String, Object> fileConfig) {
+        return fileConfig.containsKey('enabled') ? CO2FootprintConfig.getCollect('enabled', fileConfig, usedKeys) : defaultEnabled
+    }
+
+    /**
+     * Define whether an existing file should be overwritten.
+     *
+     * @param fileConfig The general config of this file.
+     * @return Whether or not to overwrite the file.
+     */
+    protected boolean defineOverwrite(Map<String, Object> fileConfig) {
+        return fileConfig.containsKey('overwrite') ? CO2FootprintConfig.getCollect('overwrite', fileConfig, usedKeys) : true
     }
 }

src/main/nextflow/co2footprint/Config/ProvenanceFileConfig.groovy

@@ -3,19 +3,35 @@ package nextflow.co2footprint.Config
 import nextflow.co2footprint.CO2FootprintConfig
 import nextflow.config.spec.ConfigOption
 import nextflow.config.spec.ConfigScope
-import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
-@ScopeName('co2footprint.provenance')
+import java.nio.file.Path
+
 @Description('The `co2footprint.provenance` scope allows you to configure the data/machine-actionable file of the `nf-co2footprint` plugin.')
 class ProvenanceFileConfig extends BaseFileConfig implements ConfigScope {
 
+    @ConfigOption
+    @Description('Path to the file.')
+    final Path file
+
+    @ConfigOption
+    @Description('Whether to enable the file creation.')
+    final Boolean enabled
+
+    @ConfigOption
+    @Description('Whether to overwrite a file if it already exists.')
+    final Boolean overwrite
+
     @ConfigOption
     @Description('Whether only emission metrics should be reported in the provenance file.')
     final boolean emissionMetricsOnly
 
     ProvenanceFileConfig(Map provenanceFileConfig, String timestamp=null) {
-        super(provenanceFileConfig, timestamp, 'provenance', 'json', false)
+        super('provenance', 'json', false)
+
+        file = defineFile(provenanceFileConfig, timestamp)
+        enabled = defineEnabled(provenanceFileConfig)
+        overwrite = defineOverwrite(provenanceFileConfig)
 
         emissionMetricsOnly = provenanceFileConfig.containsKey('emissionMetricsOnly') ?
                 CO2FootprintConfig.getCollect('emissionMetricsOnly', provenanceFileConfig, usedKeys) as boolean :

src/main/nextflow/co2footprint/Config/ReportFileConfig.groovy

@@ -3,19 +3,36 @@ package nextflow.co2footprint.Config
 import nextflow.co2footprint.CO2FootprintConfig
 import nextflow.config.spec.ConfigOption
 import nextflow.config.spec.ConfigScope
-import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
-@ScopeName('co2footprint.report')
+import java.nio.file.Path
+
 @Description('The `co2footprint.report` scope allows you to configure the report file of the `nf-co2footprint` plugin.')
-class ReportFileConfig extends BaseFileConfig implements ConfigScope{
+class ReportFileConfig extends BaseFileConfig implements ConfigScope {
+
+    @ConfigOption
+    @Description('Path to the file.')
+    final Path file
+
+    @ConfigOption
+    @Description('Whether to enable the file creation.')
+    final Boolean enabled
+
+    @ConfigOption
+    @Description('Whether to overwrite a file if it already exists.')
+    final Boolean overwrite
 
     @ConfigOption
     @Description('The number of maximum tasks that is displayed in the report.')
     final Integer maxTasks
 
     ReportFileConfig(Map reportFileConfig, String timestamp=null) {
-        super(reportFileConfig, timestamp, 'report', 'html')
+        super('report', 'html')
+
+        file = defineFile(reportFileConfig, timestamp)
+        enabled = defineEnabled(reportFileConfig)
+        overwrite = defineOverwrite(reportFileConfig)
+
         maxTasks = reportFileConfig.containsKey('maxTasks') ?
                 CO2FootprintConfig.getCollect('maxTasks', reportFileConfig, usedKeys) as Integer :
                 10_000

src/main/nextflow/co2footprint/Config/SummaryFileConfig.groovy

@@ -1,15 +1,33 @@
 package nextflow.co2footprint.Config
 
 import nextflow.co2footprint.CO2FootprintConfig
+import nextflow.config.spec.ConfigOption
 import nextflow.config.spec.ConfigScope
-import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
-@ScopeName('co2footprint.summary')
+import java.nio.file.Path
+
 @Description('The `co2footprint.summary` scope allows you to configure the summary file of the `nf-co2footprint` plugin.')
-class SummaryFileConfig extends BaseFileConfig implements ConfigScope{
+class SummaryFileConfig extends BaseFileConfig implements ConfigScope {
+
+    @ConfigOption
+    @Description('Path to the file.')
+    final Path file
+
+    @ConfigOption
+    @Description('Whether to enable the file creation.')
+    final Boolean enabled
+
+    @ConfigOption
+    @Description('Whether to overwrite a file if it already exists.')
+    final Boolean overwrite
+
     SummaryFileConfig(Map summaryFileConfig, String timestamp=null) {
-        super(summaryFileConfig, timestamp, 'summary', 'txt')
+        super('summary', 'txt')
+
+        file = defineFile(summaryFileConfig, timestamp)
+        enabled = defineEnabled(summaryFileConfig)
+        overwrite = defineOverwrite(summaryFileConfig)
 
         CO2FootprintConfig.checkKeyUsage(summaryFileConfig, usedKeys)
     }

src/main/nextflow/co2footprint/Config/TraceFileConfig.groovy

@@ -1,15 +1,33 @@
 package nextflow.co2footprint.Config
 
 import nextflow.co2footprint.CO2FootprintConfig
+import nextflow.config.spec.ConfigOption
 import nextflow.config.spec.ConfigScope
-import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
-@ScopeName('co2footprint.trace')
+import java.nio.file.Path
+
 @Description('The `co2footprint.trace` scope allows you to configure the trace file of the `nf-co2footprint` plugin.')
-class TraceFileConfig extends BaseFileConfig implements ConfigScope{
+class TraceFileConfig extends BaseFileConfig implements ConfigScope {
+
+    @ConfigOption
+    @Description('Path to the file.')
+    final Path file
+
+    @ConfigOption
+    @Description('Whether to enable the file creation.')
+    final Boolean enabled
+
+    @ConfigOption
+    @Description('Whether to overwrite a file if it already exists.')
+    final Boolean overwrite
+
     TraceFileConfig(Map traceFileConfig, String timestamp=null) {
-        super(traceFileConfig, timestamp, 'trace', 'txt')
+        super('trace', 'txt')
+
+        file = defineFile(traceFileConfig, timestamp)
+        enabled = defineEnabled(traceFileConfig)
+        overwrite = defineOverwrite(traceFileConfig)
 
         CO2FootprintConfig.checkKeyUsage(traceFileConfig, usedKeys)
     }