Fix in logs and io. IOManager is now a genuine plugin

numass-main/src/main/groovy/inr/numass/LaunchGrindShell.groovy

@@ -15,6 +15,10 @@ println cli.usage
 
 String cfgPath = cli.parse(args).c;
 println "Loading config file from $cfgPath"
+//println "Starting numass plugin in GLOBAL"
+//Global.instance().pluginManager().loadPlugin("inr.numass:numass")
+println "Starting Grind shell"
+
 try {
     new GrindShell().launch {
         GrindWorkspaceBuilder numass = new GrindWorkspaceBuilder()
@@ -25,5 +29,5 @@ try {
 } catch (Exception ex) {
     ex.printStackTrace();
 } finally {
-    Global.instance().close();
+    Global.terminate();
 }

numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java

@@ -21,7 +21,7 @@ import hep.dataforge.description.ValueDef;
 import hep.dataforge.exceptions.ContentException;
 import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.io.XMLMetaWriter;
-import hep.dataforge.io.reports.Reportable;
+import hep.dataforge.io.reports.Logable;
 import hep.dataforge.meta.Laminate;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.tables.*;
@@ -142,7 +142,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
      * @param meta
      * @return
      */
-    private double correction(Reportable log, NMPoint point, Laminate meta) {
+    private double correction(Logable log, NMPoint point, Laminate meta) {
         if (meta.hasValue("correction")) {
 //            log.report("Using correction from formula: {}", meta.getString("correction"));
             return evaluateExpression(point, meta.getString("correction"));

numass-main/src/main/java/inr/numass/models/sterile/TestModels.java

@@ -6,17 +6,13 @@
 package inr.numass.models.sterile;
 
 import hep.dataforge.context.Context;
-import hep.dataforge.stat.fit.ParamSet;
-import hep.dataforge.stat.parametric.ParametricFunction;
 import hep.dataforge.maths.MathPlugin;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
+import hep.dataforge.stat.fit.ParamSet;
+import hep.dataforge.stat.parametric.ParametricFunction;
 import inr.numass.Numass;
-import inr.numass.models.BetaSpectrum;
+import inr.numass.models.*;
-import inr.numass.models.ModularSpectrum;
-import inr.numass.models.NBkgSpectrum;
-import inr.numass.models.RangedNamedSetSpectrum;
-import inr.numass.models.ResolutionFunction;
 import org.apache.commons.math3.analysis.BivariateFunction;
 
 /**
@@ -70,7 +66,7 @@ public class TestModels {
         double A = meta.getDouble("resolution", meta.getDouble("resolution.width", 8.3e-5));//8.3e-5
         double from = meta.getDouble("from", 13900d);
         double to = meta.getDouble("to", 18700d);
-        context.getReport().report("Setting up tritium model with real transmission function");
+        context.getLog().report("Setting up tritium model with real transmission function");
         BivariateFunction resolutionTail;
         if (meta.hasValue("resolution.tailAlpha")) {
             resolutionTail = ResolutionFunction.getAngledTail(meta.getDouble("resolution.tailAlpha"), meta.getDouble("resolution.tailBeta", 0));
@@ -81,7 +77,7 @@ public class TestModels {
         RangedNamedSetSpectrum beta = new BetaSpectrum();
         ModularSpectrum sp = new ModularSpectrum(beta, new ResolutionFunction(A, resolutionTail), from, to);
         if (meta.getBoolean("caching", false)) {
-            context.getReport().report("Caching turned on");
+            context.getLog().report("Caching turned on");
             sp.setCaching(true);
         }
         //Adding trapping energy dependence

numass-main/src/main/java/inr/numass/utils/UnderflowCorrection.java

@@ -5,20 +5,21 @@
  */
 package inr.numass.utils;
 
-import hep.dataforge.io.reports.Reportable;
+import hep.dataforge.io.reports.Logable;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.Table;
 import inr.numass.storage.NMPoint;
 import inr.numass.storage.NumassData;
 import inr.numass.storage.RawNMPoint;
-import java.util.List;
-import java.util.stream.Collectors;
 import org.apache.commons.math3.analysis.ParametricUnivariateFunction;
 import org.apache.commons.math3.exception.DimensionMismatchException;
 import org.apache.commons.math3.fitting.SimpleCurveFitter;
 import org.apache.commons.math3.fitting.WeightedObservedPoint;
 
+import java.util.List;
+import java.util.stream.Collectors;
+
 /**
  * A class to calculate underflow correction
  *
@@ -26,7 +27,7 @@ import org.apache.commons.math3.fitting.WeightedObservedPoint;
  */
 public class UnderflowCorrection {
 
-    public double get(Reportable log, Meta meta, NMPoint point) {
+    public double get(Logable log, Meta meta, NMPoint point) {
         if (point.getUset() >= meta.getDouble("underflow.threshold", 17000)) {
             if (meta.hasValue("underflow.function")) {
                 return TritiumUtils.evaluateExpression(point, meta.getString("underflow.function"));

numass-main/src/main/java/inr/numass/workbench/NumassWorkbenchController.java

@@ -167,7 +167,7 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
         // setting io manager
         context.setIO(new WorkbenchIOManager(new NumassIO(), this));
         buildContextPane();
-        context.getReport().addReportListener(new FXReportListener(logPane));
+        context.getLog().addListener(new FXReportListener(logPane));
 
         // display plots iside workbench
         PlotsPlugin.buildFrom(context).setPlotHolderDelegate(this);

numass-main/src/main/java/inr/numass/workbench/WorkbenchIOManager.java

@@ -5,7 +5,7 @@
  */
 package inr.numass.workbench;
 
-import hep.dataforge.context.Context;
+import hep.dataforge.io.BasicIOManager;
 import hep.dataforge.io.IOManager;
 import hep.dataforge.names.Name;
 import org.apache.commons.io.output.TeeOutputStream;
@@ -18,7 +18,7 @@ import java.io.OutputStream;
  * An IOManager wrapper that redirects output to appropriate FX components
  * @author Alexander Nozik <altavir@gmail.com>
  */
-public class WorkbenchIOManager implements IOManager {
+public class WorkbenchIOManager extends BasicIOManager {
     
     private final IOManager manager;
     private final StagePaneHolder holder;
@@ -28,16 +28,6 @@ public class WorkbenchIOManager implements IOManager {
         this.holder = holder;
     }
 
-    @Override
-    public Context getContext() {
-        return manager.getContext();
-    }
-
-    @Override
-    public void setContext(Context context) {
-        manager.setContext(context);
-    }
-
     @Override
     public File getFile(String path) {
         return manager.getFile(path);