Report nf-co2footprint parameters

plugins/nf-co2footprint/src/main/nextflow/co2footprint/CO2FootprintConfig.groovy

@@ -27,15 +27,16 @@ import groovy.util.logging.Slf4j
 @PackageScope
 class CO2FootprintConfig {
 
-    final private String  traceFile
-    final private String  summaryFile
-    final private String  reportFile
-    final private String  location
-    final private Double  ci    // CI: carbon intensity
-    final private Double  pue   // PUE: power usage effectiveness efficiency, coefficient of the data centre
-    final private Double  powerdrawMem  // Power draw of memory [W per GB]
-    final private Boolean ignoreCpuModel
-    final private Double powerdrawCpuDefault
+    private String  traceFile = CO2FootprintFactory.CO2FootprintTextFileObserver.DEF_TRACE_FILE_NAME
+    private String  summaryFile = CO2FootprintFactory.CO2FootprintTextFileObserver.DEF_SUMMARY_FILE_NAME
+    private String  reportFile = CO2FootprintFactory.CO2FootprintReportObserver.DEF_REPORT_FILE_NAME
+    private String  location = null
+    private Double  ci = 475   // CI: carbon intensity
+    private Double  pue = 1.67  // PUE: power usage effectiveness efficiency, coefficient of the data centre
+    private Double  powerdrawMem = 0.3725 // Power draw of memory [W per GB]
+    private Boolean ignoreCpuModel = false
+    private Double  powerdrawCpuDefault = 12.0
+    private String  customCpuTdpFile = null
 
     // Retrieve CI value from file containing CI values for different locations
     protected Double retrieveCi(String location) {
@@ -51,8 +52,9 @@ class CO2FootprintConfig {
             }
         }
         dataReader.close()
-        if (localCi == 0.0)
+        if (localCi == 0.0) {
             throw new IllegalArgumentException("Invalid 'location' parameter: $location. Could not be found in 'CI_aggregated.v2.2.csv'.")
+        }
 
         return localCi
     }
@@ -74,36 +76,77 @@ class CO2FootprintConfig {
 
     CO2FootprintConfig(Map map, Map<String, Double> cpuData){
         def config = map ?: Collections.emptyMap()
-        traceFile = config.traceFile ?: CO2FootprintFactory.CO2FootprintTextFileObserver.DEF_TRACE_FILE_NAME
-        summaryFile = config.summaryFile ?: CO2FootprintFactory.CO2FootprintTextFileObserver.DEF_SUMMARY_FILE_NAME
-        reportFile = config.reportFile ?: CO2FootprintFactory.CO2FootprintReportObserver.DEF_REPORT_FILE_NAME
-        ignoreCpuModel = config.ignoreCpuModel ?: false
-
-        ci = 475
-        if (config.ci && config.location)
+        if (config.traceFile) {
+            traceFile = config.traceFile
+        }
+        if (config.summaryFile) {
+            summaryFile = config.summaryFile
+        }
+        if (config.reportFile) {
+            reportFile = config.reportFile
+        }
+        if (config.ignoreCpuModel) {
+            ignoreCpuModel = config.ignoreCpuModel
+        }
+        if (config.ci && config.location) {
             throw new IllegalArgumentException("Invalid combination of 'ci' and 'location' parameters specified for the CO2Footprint plugin. Please specify either 'ci' or 'location'!")
-        if (config.ci)
+        }
+        if (config.ci) {
             ci = config.ci
+        }
         if (config.location) {
             ci = retrieveCi(config.location)
             location = config.location
         }
-
-        pue = config.pue ?: 1.67
-        powerdrawMem = config.powerdrawMem ?: 0.3725
-        powerdrawCpuDefault = config.powerdrawCpuDefault ?: 12.0
+        if (config.pue) {
+            pue = config.pue
+        }
+        if (config.powerdrawMem) {
+            powerdrawMem = config.powerdrawMem
+        }
+        if (config.powerdrawCpuDefault) {
+            powerdrawCpuDefault = config.powerdrawCpuDefault
+        }
         cpuData['default'] = powerdrawCpuDefault
 
-        if (config.customCpuTdpFile)
+        if (config.customCpuTdpFile) {
+            customCpuTdpFile = config.customCpuTdpFile
             loadCustomCpuTdpData(cpuData, config.customCpuTdpFile)
+        }
     }
 
     String getTraceFile() { traceFile }
     String getSummaryFile() { summaryFile }
     String getReportFile() { reportFile }
     Boolean getIgnoreCpuModel() { ignoreCpuModel }
     String getLocation() { location }
-    Double getCI() { ci }
-    Double getPUE() { pue }
+    Double getCi() { ci }
+    Double getPue() { pue }
     Double getPowerdrawMem() { powerdrawMem }
+    Double getPowerdrawCpuDefault() { powerdrawCpuDefault }
+    String getCustomCpuTdpFile() { customCpuTdpFile }
+
+    // Different functions to collect options for reporting, grouped by purpose
+    SortedMap<String, Object> collectInputFileOptions() {
+        Map<String, Object> newMap = [:]
+        newMap["customCpuTdpFile"] = customCpuTdpFile
+        return newMap.sort()
+    }
+    SortedMap<String, Object> collectOutputFileOptions() {
+        Map<String, Object> newMap = [:]
+        newMap["traceFile"] = traceFile
+        newMap["summaryFile"] = summaryFile
+        newMap["reportFile"] = reportFile
+        return newMap.sort()
+    }
+    SortedMap<String, Object> collectCO2CalcOptions() {
+        Map<String, Object> newMap = [:]
+        newMap["location"] = location
+        newMap["ci"] = ci   // Might be indirectly determined for location parameter
+        newMap["pue"] = pue
+        newMap["powerdrawMem"] = powerdrawMem
+        newMap["powerdrawCpuDefault"] = powerdrawCpuDefault
+        newMap["ignoreCpuModel"] = ignoreCpuModel
+        return newMap.sort()
+    }
 }

plugins/nf-co2footprint/src/main/nextflow/co2footprint/CO2FootprintFactory.groovy

@@ -198,9 +198,9 @@ class CO2FootprintFactory implements TraceObserverFactory {
          * Remaining factors
          */
         // PUE: efficiency coefficient of the data centre
-        Double pue = config.getPUE()
+        Double pue = config.getPue()
         // CI: carbon intensity [gCO2e kWh−1]
-        def ci  = config.getCI()
+        def ci  = config.getCi()
 
         /**
          * Calculate energy consumption [kWh]
@@ -363,6 +363,11 @@ class CO2FootprintFactory implements TraceObserverFactory {
             co2eSummaryFile.println("Lannelongue, L., Grealey, J., Inouye, M., Green Algorithms: Quantifying the Carbon Footprint of Computation. Adv. Sci. 2021, 2100707. https://doi.org/10.1002/advs.202100707")
             co2eSummaryFile.println()
             co2eSummaryFile.println("nf-co2footprint plugin version: ${version}")
+            co2eSummaryFile.println()
+            co2eSummaryFile.println("nf-co2footprint options")
+            config.collectInputFileOptions().each { co2eSummaryFile.println("${it.key}: ${it.value}") }
+            config.collectOutputFileOptions().each { co2eSummaryFile.println("${it.key}: ${it.value}") }
+            config.collectCO2CalcOptions().each { co2eSummaryFile.println("${it.key}: ${it.value}") }
             co2eSummaryFile.flush()
             co2eSummaryFile.close()
 
@@ -737,6 +742,29 @@ class CO2FootprintFactory implements TraceObserverFactory {
             "{ \"trace\":${renderTasksJson()}, \"summary\":${renderSummaryJson()} }"
         }
 
+        /**
+         * @return The options json payload
+         */
+        protected String renderOptionsJson() {
+            final all_options = config.collectInputFileOptions() + config.collectOutputFileOptions() + config.collectCO2CalcOptions()
+            def result = new StringBuilder()
+            result << "["
+            def fields = all_options.keySet() as List
+
+            // Render JSON
+            final QUOTE = '"'
+            for( int i=0; i<fields.size(); i++ ) {
+                if(i) result << ','
+                String name = fields[i]
+                String value = all_options[name].toString()
+                result << "{" << QUOTE << "option" << QUOTE << ":" << QUOTE << name << QUOTE << ","
+                result << QUOTE << "value" << QUOTE << ":" << QUOTE << value << QUOTE << "}"
+            }
+            result << "]"
+
+            return result.toString()
+        }
+
         /**
          * Render the total co2 footprint values for html report
          *
@@ -777,7 +805,8 @@ class CO2FootprintFactory implements TraceObserverFactory {
                             readTemplate('nextflow/trace/assets/moment.min.js'),
                             readTemplate('nextflow/trace/assets/plotly.min.js'),
                             readTemplate('assets/CO2FootprintReportTemplate.js')
-                    ]
+                    ],
+                    options : renderOptionsJson()
             ]
             //log.info "${tpl_fields['payload']}"
             final tpl = readTemplate('CO2FootprintReportTemplate.html')

plugins/nf-co2footprint/src/resources/CO2FootprintReportTemplate.html

@@ -261,6 +261,16 @@ <h2 id="tasks" style="padding-top: 80px;">Tasks</h2>
     </div>
   </div>
 
+  <div class="container">
+    <div id="table-container">
+      <h2 id="options" style="padding-top: 80px;">Options</h2>
+      <p>This table shows the nf-co2footprint plugin options that were used to calculate the CO<sub>2</sub>e footprint measures.</p>
+    </div>
+    <div class="container-fluid">
+      <table class="table small table-striped" id="options_table"></table>
+    </div>
+  </div>
+
   <footer>
     <div class="container-fluid">
       Generated by <a href="https://www.nextflow.io" target="_blank">Nextflow</a>, version ${workflow.nextflow.version}
@@ -272,6 +282,7 @@ <h2 id="tasks" style="padding-top: 80px;">Tasks</h2>
 
   // Nextflow report data
   window.data = $payload;
+  window.options = $options;
 
   </script>
 

plugins/nf-co2footprint/src/resources/assets/CO2FootprintReportTemplate.js

@@ -300,7 +300,7 @@ $(function() {
 
       // Default filter highlight
       $(".buttons-colvisGroup:contains('All')").click();
-    }
+  }
 
   if( window.data.trace==null ) {
       // nascondere
@@ -316,5 +316,24 @@ $(function() {
       make_tasks_table();
   }
 
+  // Create options table
+  function make_options_table(){
+    // reset
+    if ( $.fn.dataTable.isDataTable( '#options_table' ) ) {
+      $('#options_table').DataTable().destroy();
+    }
+
+    var table = $('#options_table').DataTable({
+      data: window.options,
+      columns: [
+          { title: "Option", data: "option" },
+          { title: "Value", data: "value" }
+        ],
+        "deferRender": true,
+        "lengthMenu": [[25, 50, 100, -1], [25, 50, 100, "All"]],
+    });
+  }
 
-});
+  // Make the table on page load
+  make_options_table();
+});