Support cloudgene.report.json on step level

genepi · Sep 18, 2023 · 45011a4 · 45011a4
1 parent 3b26d30
commit 45011a4
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Showing 2 changed files with 35 additions and 3 deletions.
diff --git a/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowStep.java b/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowStep.java
@@ -4,6 +4,7 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -16,6 +17,9 @@
 import cloudgene.mapred.jobs.CloudgeneStep;
 import cloudgene.mapred.jobs.Message;
 import cloudgene.mapred.jobs.workspace.IWorkspace;
+import cloudgene.mapred.plugins.nextflow.report.Report;
+import cloudgene.mapred.plugins.nextflow.report.ReportEvent;
+import cloudgene.mapred.plugins.nextflow.report.ReportEventExecutor;
 import cloudgene.mapred.util.Settings;
 import cloudgene.mapred.wdl.WdlStep;
 import genepi.io.FileUtil;
@@ -152,6 +156,18 @@ public boolean run(WdlStep step, CloudgeneContext context) {
 
 			collector.cleanProcesses(context);
 
+			File report = new File(executionDir, Report.DEFAULT_FILENAME);
+			if (!report.exists()) {
+				return successful;
+			}
+
+			context.log("Load report file from '" + report.getCanonicalPath() + "'");
+			try {
+				parseReport(report);
+			} catch (Exception e) {
+				log.error("[Job {}] Invalid report file.", e);
+			}
+
 			return successful;
 
 		} catch (Exception e) {
@@ -161,6 +177,15 @@ public boolean run(WdlStep step, CloudgeneContext context) {
 
 	}
 
+	private void parseReport(File file) throws IOException {
+		Report report = new Report(file.getAbsolutePath());
+		context.log("Execute " + report.getEvents().size() + " events.");
+		for (ReportEvent event : report.getEvents()) {
+			context.log("Event: " + event);
+			ReportEventExecutor.execute(event, context);
+		}
+	}
+
 	@Override
 	public void updateProgress() {
 

diff --git a/src/main/java/cloudgene/mapred/plugins/nextflow/report/ReportEvent.java b/src/main/java/cloudgene/mapred/plugins/nextflow/report/ReportEvent.java
@@ -65,7 +65,7 @@ public static String format(ReportEvent event) {
 			}
 			case MESSAGE: {
 				String message = (String) event.getParams()[0];
-				int type = ((Integer) event.getParams()[1]);
+				int type = asInteger(event.getParams()[1]);
 				return message(message, type);
 			}
 			case BEGIN_TASK: {
@@ -88,12 +88,12 @@ public static String format(ReportEvent event) {
 			}
 			case END_TASK: {
 				String name = (String) event.getParams()[0];
-				int type = ((Integer) event.getParams()[1]).intValue();
+				int type = asInteger(event.getParams()[1]);
 				return message(name, type);
 			}
 			case INC_COUNTER: {
 				String counter = (String) event.getParams()[0];
-				int value = ((Integer) event.getParams()[1]);
+				int value = asInteger(event.getParams()[1]);
 				return incCounter(counter, value);
 			}
 			default:
@@ -137,5 +137,12 @@ public static String message(String message, int type) {
 
 		}
 	}
+
+	public static int asInteger(Object object) {
+		//groovy writes integers also as doubles
+		Double value = Double.parseDouble(object.toString());
+		return value.intValue();
+
+	}
 
 }