Replaced OutputStreams with Output objects

numass-core/src/main/java/inr/numass/NumassProperties.java

@@ -21,7 +21,7 @@ import java.util.Properties;
 public class NumassProperties {
 
     private static File getNumassPropertiesFile() throws IOException {
-        File file = new File(Global.instance().getUserDirectory(), "numass");
+        File file = new File(Global.Companion.instance().getUserDirectory(), "numass");
         if (!file.exists()) {
             file.mkdirs();
         }
@@ -54,7 +54,7 @@ public class NumassProperties {
             }
             props.store(new FileOutputStream(store), "");
         } catch (IOException ex) {
-            Global.instance().getLogger().error("Failed to save numass properties", ex);
+            Global.Companion.instance().getLogger().error("Failed to save numass properties", ex);
         }
     }
 }

numass-core/src/main/java/inr/numass/data/api/SimpleNumassPoint.java

@@ -2,7 +2,7 @@ package inr.numass.data.api;
 
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
-import hep.dataforge.utils.MetaHolder;
+import hep.dataforge.meta.MetaHolder;
 
 import java.util.ArrayList;
 import java.util.Collection;

numass-core/src/main/java/inr/numass/data/storage/NumassStorageFactory.java

@@ -69,7 +69,7 @@ public class NumassStorageFactory implements StorageType {
             return new NumassStorage(context, meta, path);
         } else {
             context.getLogger().warn("A storage path not provided. Creating default root storage in the working directory");
-            return new NumassStorage(context, meta, context.getIo().getWorkDirectory());
+            return new NumassStorage(context, meta, context.getIo().getWorkDir());
         }
     }
 

numass-main/src/main/groovy/inr/numass/scripts/workspace/TestActions.groovy

@@ -2,7 +2,7 @@ package inr.numass.scripts.workspace
 
 import hep.dataforge.actions.ActionUtils
 import hep.dataforge.context.Context
-import hep.dataforge.io.IOManager
+import hep.dataforge.context.IOManager
 import inr.numass.NumassPlugin
 
 /**

numass-main/src/main/java/inr/numass/Main.java

@@ -18,8 +18,8 @@ package inr.numass;
 import hep.dataforge.actions.ActionUtils;
 import hep.dataforge.context.Context;
 import hep.dataforge.context.Global;
+import hep.dataforge.context.IOManager;
 import hep.dataforge.data.FileDataFactory;
-import hep.dataforge.io.IOManager;
 import hep.dataforge.io.MetaFileReader;
 import hep.dataforge.meta.Meta;
 import org.apache.commons.cli.*;
@@ -52,7 +52,7 @@ public class Main {
 
     public static void run(Context context, String[] args) throws Exception {
         if(context == null){
-            context = Global.instance();
+            context = Global.Companion.instance();
         }
         Logger logger = LoggerFactory.getLogger("numass-main");
 
@@ -78,7 +78,7 @@ public class Main {
         if (args.length == 0) {
             HelpFormatter formatter = new HelpFormatter();
             formatter.printHelp("java -jar DataReader.jar [OPTIONS]", options);
-            out().println("Trying to use default config location...");
+            Companion.out().println("Trying to use default config location...");
         }
 
         if (line.hasOption("c")) {

numass-main/src/main/java/inr/numass/Numass.java

@@ -31,14 +31,14 @@ import hep.dataforge.meta.Meta;
 public class Numass {
 
     public static Context buildContext(Context parent, Meta meta) {
-        return Context.builder("NUMASS", parent)
+        return Context.Companion.builder("NUMASS", parent)
                 .properties(meta)
                 .plugin(NumassPlugin.class)
                 .build();
     }
 
     public static Context buildContext() {
-        return buildContext(Global.instance(), Meta.empty());
+        return buildContext(Global.Companion.instance(), Meta.empty());
     }
 
     public static void printDescription(Context context) throws DescriptorException {

numass-main/src/main/java/inr/numass/data/MonitorCorrector.java

@@ -39,7 +39,7 @@ public class MonitorCorrector {
     private final List<MonitorPoint> list;
 
     public MonitorCorrector(String path) throws ParseException, IOException {
-        this(Global.instance().getIo().getFile(path));
+        this(Global.Companion.instance().getIo().getFile(path));
     }
 
     public MonitorCorrector(Path monitorFile) throws ParseException, IOException {

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

@@ -40,7 +40,7 @@ public class OldDataReader {
     public static Table readConfig(String path) throws IOException {
         String[] list = {"X", "time", "ushift"};
         ListTable.Builder res = new ListTable.Builder(list);
-        Path file = Global.instance().getIo().getFile(path);
+        Path file = Global.Companion.instance().getIo().getFile(path);
         Scanner sc = new Scanner(file);
         sc.nextLine();
 
@@ -62,7 +62,7 @@ public class OldDataReader {
     public static Table readData(String path, double Elow) {
         SpectrumAdapter factory = new SpectrumAdapter(Meta.empty());
         ListTable.Builder res = new ListTable.Builder(Adapters.getFormat(factory));
-        Path file = Global.instance().getIo().getFile(path);
+        Path file = Global.Companion.instance().getIo().getFile(path);
         double x;
         int count;
         int time;
@@ -114,7 +114,7 @@ public class OldDataReader {
     public static Table readDataAsGun(String path, double Elow) {
         SpectrumAdapter factory = new SpectrumAdapter(Meta.empty());
         ListTable.Builder res = new ListTable.Builder(Adapters.getFormat(factory));
-        Path file = Global.instance().getIo().getFile(path);
+        Path file = Global.Companion.instance().getIo().getFile(path);
         double x;
         long count;
         int time;
@@ -147,7 +147,7 @@ public class OldDataReader {
     public static Table readSpectrumData(String path) {
         SpectrumAdapter factory = new SpectrumAdapter(Meta.empty());
         ListTable.Builder res = new ListTable.Builder(Adapters.getFormat(factory));
-        Path file = Global.instance().getIo().getFile(path);
+        Path file = Global.Companion.instance().getIo().getFile(path);
         double x;
         double count;
         double time;

numass-main/src/main/kotlin/inr/numass/NumassIO.kt

@@ -21,9 +21,9 @@ import ch.qos.logback.classic.spi.ILoggingEvent
 import ch.qos.logback.core.Appender
 import ch.qos.logback.core.FileAppender
 import hep.dataforge.context.Context
+import hep.dataforge.context.DefaultIOManager
+import hep.dataforge.context.IOManager
 import hep.dataforge.fx.plots.plusAssign
-import hep.dataforge.io.BasicIOManager
-import hep.dataforge.io.IOManager
 import hep.dataforge.meta.Meta
 import hep.dataforge.names.Name
 import hep.dataforge.plots.PlotUtils
@@ -45,7 +45,7 @@ import java.util.*
 /**
  * @author Darksnake
  */
-class NumassIO : BasicIOManager() {
+class NumassIO : DefaultIOManager() {
 
     internal var registry = ReferenceRegistry<OutputStream>()
     //    FileAppender<ILoggingEvent> appender;
@@ -63,7 +63,7 @@ class NumassIO : BasicIOManager() {
         ple.context = lc
         ple.start()
         val appender = FileAppender<ILoggingEvent>()
-        appender.file = File(workDirectory.toFile(), meta.getString("logFileName", "numass.log")).toString()
+        appender.file = File(workDir.toFile(), meta.getString("logFileName", "numass.log")).toString()
         appender.encoder = ple
         return appender
     }
@@ -103,7 +103,7 @@ class NumassIO : BasicIOManager() {
 
         val dirName = tokens.joinToString(File.separator)
         val fileName = name.toString() + getExtension(type)
-        val out = buildOut(workDirectory, dirName, fileName)
+        val out = buildOut(workDir, dirName, fileName)
         registry.add(out)
         return out
     }

numass-main/src/main/kotlin/inr/numass/NumassPlugin.kt

@@ -50,7 +50,7 @@ class NumassPlugin : BasicPlugin() {
     override fun attach(context: Context) {
         //        StorageManager.buildFrom(context);
         super.attach(context)
-        context.getPluginManager().load(NumassIO())
+        context.pluginManager.load(NumassIO())
         loadModels(context.getFeature(ModelManager::class.java))
         loadMath(MathPlugin.buildFrom(context))
 

numass-main/src/main/kotlin/inr/numass/NumassUtils.kt

@@ -18,12 +18,14 @@ package inr.numass
 import hep.dataforge.context.Context
 import hep.dataforge.data.DataNode
 import hep.dataforge.data.DataSet
+import hep.dataforge.data.binary.Binary
 import hep.dataforge.io.envelopes.DefaultEnvelopeType
 import hep.dataforge.io.envelopes.Envelope
 import hep.dataforge.io.envelopes.EnvelopeBuilder
 import hep.dataforge.io.envelopes.TaglessEnvelopeType
 import hep.dataforge.io.markup.Markedup
 import hep.dataforge.io.markup.SimpleMarkupRenderer
+import hep.dataforge.kodex.nullable
 import hep.dataforge.meta.Meta
 import hep.dataforge.meta.MetaBuilder
 import hep.dataforge.plots.jfreechart.JFreeChartFrame
@@ -45,7 +47,6 @@ import tornadofx.*
 import java.awt.Color
 import java.awt.Font
 import java.io.IOException
-import java.io.InputStream
 import java.io.OutputStream
 import java.lang.Math.*
 import java.util.*
@@ -165,18 +166,10 @@ object NumassUtils {
 
 fun getFSS(context: Context, meta: Meta): FSS? {
     return if (meta.getBoolean("useFSS", true)) {
-        val fssStream = meta.optString("fssFile")
+        val fssBinary: Binary? = meta.optString("fssFile")
-                .map<InputStream> { fssFile ->
+                .map { fssFile -> context.io.getFile(fssFile).binary }
-                    try {
+                .orElse(context.io.optResource("data/FS.txt").nullable)
-                        context.io.optBinary(fssFile)
+        fssBinary?.let { FSS(it.stream) } ?: throw RuntimeException("Could not load FSS file")
-                                .orElseThrow({ RuntimeException("Could not locate FSS file") })
-                                .stream
-                    } catch (e: IOException) {
-                        throw RuntimeException("Could not load FSS file", e)
-                    }
-                }
-                .orElse(context.io.optResource("data/FS.txt").get().stream)
-        FSS(fssStream)
     } else {
         null
     }

numass-main/src/main/kotlin/inr/numass/actions/MergeDataAction.kt

@@ -120,7 +120,7 @@ class MergeDataAction : ManyToOneAction<Table, Table>() {
     }
 
     companion object {
-        val MERGE_NAME = "mergeName"
+        const val MERGE_NAME = "mergeName"
     }
 
 }

numass-main/src/main/kotlin/inr/numass/tasks/NumassTasks.kt

@@ -175,7 +175,7 @@ val subtractEmptyTask = task("dif") {
 
             res.goal.onComplete { r, _ ->
                 if (r != null) {
-                    context.getIo().out("numass.merge", input.name + "_subtract").use {
+                    context.io.out("numass.merge", input.name + "_subtract").use {
                         NumassUtils.write(it, resMeta, r)
                     }
                 }
@@ -228,7 +228,7 @@ val fitTask = task("fit") {
         configure(meta.getMeta("fit"))
     }
     pipe<Table, FitResult> { data ->
-        context.getIo().out("numass.fit", name).use { out ->
+        context.io.out("numass.fit", name).use { out ->
             val writer = PrintWriter(out)
             writer.printf("%n*** META ***%n")
             writer.println(meta.toString())

numass-main/src/test/java/inr/numass/models/TransmissionInterpolatorTest.java

@@ -30,7 +30,7 @@ public class TransmissionInterpolatorTest {
     public static void main(String[] args) {
         JFreeChartFrame frame = NumassPluginKt.displayJFreeChart("TransmissionInterpolatorTest");
 //JFreeChartFrame.drawFrame("TransmissionInterpolatorTest", null);
-        TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(Global.instance(),
+        TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(Global.Companion.instance(),
                 "d:\\sterile-new\\loss2014-11\\.dataforge\\merge\\empty_sum.onComplete", "Uset", "CR", 15, 0.8, 19002d);
         frame.add(DataPlot.plot("data", interpolator.getX(), interpolator.getY()));
         frame.add(XYFunctionPlot.Companion.plot("interpolated", interpolator.getXmin(), interpolator.getXmax(), 2000, interpolator::value));

numass-server/src/main/java/inr/numass/server/ServerRunner.java

@@ -24,7 +24,7 @@ public class ServerRunner extends SimpleConfigurable implements AutoCloseable {
 //    private static final String NUMASS_REPO_PATH_PROPERTY = "numass.repository.path";
     NumassStorage root;
     NumassServer listener;
-    Context context = Global.getContext("NUMASS_SERVER");
+    Context context = Global.Companion.getContext("NUMASS_SERVER");
 
     public ServerRunner() throws IOException, ParseException {
 //        Global.instance().getPluginManager().load(StorageManager.class);

numass-server/src/main/java/inr/numass/server/TestServer.java

@@ -27,7 +27,7 @@ public class TestServer {
      * @throws hep.dataforge.exceptions.StorageException
      */
     public static void main(String[] args) throws Exception {
-        Context context = Global.getContext("NUMASS-SERVER");
+        Context context = Global.Companion.getContext("NUMASS-SERVER");
 
         StorageManager storageManager = context.getPluginManager().load(StorageManager.class);