Removing wildcards from Data and DataNodes

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

@@ -22,6 +22,7 @@ import hep.dataforge.data.FileDataFactory;
 import hep.dataforge.io.IOManager;
 import hep.dataforge.io.MetaFileReader;
 import hep.dataforge.meta.Meta;
+import hep.dataforge.providers.Path;
 import org.apache.commons.cli.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -31,6 +32,7 @@ import javax.swing.filechooser.FileFilter;
 import javax.swing.filechooser.FileNameExtensionFilter;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.nio.file.Files;
 import java.util.Locale;
 
 import static hep.dataforge.context.Global.out;
@@ -87,15 +89,15 @@ public class Main {
                 return;
             }
 
-            File configFile = context.io().getFile(cfgPath);
+            java.nio.file.Path configFile = context.io().getFile(cfgPath);
 
-            if (!configFile.exists()) {
+            if (!Files.exists(configFile)) {
                 throw new FileNotFoundException("Configuration file not found");
             }
 
-            Meta config = MetaFileReader.read(configFile).build();
+            Meta config = MetaFileReader.read(configFile);
 
-            context.putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, configFile.getParentFile().toString());
+            context.putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, configFile.getParent().toString());
 
             applyCLItoContext(line, context);
 

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

@@ -28,6 +28,8 @@ import org.apache.commons.io.output.TeeOutputStream;
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -57,7 +59,7 @@ public class NumassIO extends BasicIOManager {
         ple.setContext(lc);
         ple.start();
         FileAppender<ILoggingEvent> appender = new FileAppender<>();
-        appender.setFile(new File(getWorkDirectory(), meta().getString("logFileName", "numass.log")).toString());
+        appender.setFile(new File(getWorkDirectory().toFile(), meta().getString("logFileName", "numass.log")).toString());
         appender.setEncoder(ple);
         return appender;
     }
@@ -97,26 +99,24 @@ public class NumassIO extends BasicIOManager {
         return out;
     }
 
-    private OutputStream buildOut(File parentDir, String dirName, String fileName) {
+    private OutputStream buildOut(Path parentDir, String dirName, String fileName) {
-        File outputFile;
+        Path outputFile;
 
-        if (!parentDir.exists()) {
+        if (!Files.exists(parentDir)) {
             throw new RuntimeException("Working directory does not exist");
         }
         if (dirName != null && !dirName.isEmpty()) {
-            parentDir = new File(parentDir, dirName);
+            parentDir = parentDir.resolve(dirName);
-            if (!parentDir.exists()) {
+            Files.createDirectories(parentDir);
-                parentDir.mkdirs();
-            }
         }
 
 //        String output = source.meta().getString("output", this.meta().getString("output", fileName + ".onComplete"));
-        outputFile = new File(parentDir, fileName);
+        outputFile = parentDir.resolve(fileName);
         try {
             if (getContext().getBoolean("numass.consoleOutput", false)) {
-                return new TeeOutputStream(new FileOutputStream(outputFile), System.out);
+                return new TeeOutputStream(Files.newOutputStream(outputFile), System.out);
             } else {
-                return new FileOutputStream(outputFile);
+                return Files.newOutputStream(outputFile);
             }
         } catch (FileNotFoundException ex) {
             throw new RuntimeException(ex);

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

@@ -21,6 +21,8 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.text.ParseException;
 import java.time.LocalDateTime;
 import java.util.ArrayList;
@@ -42,10 +44,10 @@ public class MonitorCorrector {
         this(Global.instance().io().getFile(path));
     }
 
-    public MonitorCorrector(File monitorFile) throws ParseException, IOException {
+    public MonitorCorrector(Path monitorFile) throws ParseException, IOException {
         list = new ArrayList<>();
         
-        BufferedReader reader = new BufferedReader(new FileReader(monitorFile));
+        BufferedReader reader = new BufferedReader(Files.newBufferedReader(monitorFile));
 //        Scanner sc = new Scanner(monitorFile);
 
         double sum = 0;

numass-main/src/main/java/inr/numass/models/TransmissionInterpolator.java

@@ -29,6 +29,9 @@ import org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -40,10 +43,10 @@ public class TransmissionInterpolator implements UnivariateFunction {
 
     public static TransmissionInterpolator fromFile(Context context, String path, String xName, String yName, int nSmooth, double w, double border) {
         try {
-            File dataFile = context.io().getFile(path);
+            Path dataFile = context.io().getFile(path);
-            ColumnedDataReader reader = new ColumnedDataReader(new FileInputStream(dataFile));
+            ColumnedDataReader reader = new ColumnedDataReader(Files.newInputStream(dataFile));
             return new TransmissionInterpolator(reader, xName, yName, nSmooth, w, border);
-        } catch (FileNotFoundException ex) {
+        } catch (IOException ex) {
             throw new RuntimeException(ex);
         }
     }

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

@@ -63,11 +63,9 @@ public class SterileNeutrinoSpectrum extends AbstractParametricFunction {
         if (configuration.getBoolean("useFSS", true)) {
             InputStream fssStream;
             if (configuration.hasValue("fssFile")) {
-                try {
+                    fssStream = context.io().optBinary(configuration.getString("fssFile"))
-                    fssStream = new FileInputStream(context.io().getFile(configuration.getString("fssFile")));
+                            .orElseThrow(()-> new RuntimeException("Could not locate FSS file"))
-                } catch (FileNotFoundException e) {
+                            .getStream();
-                    throw new RuntimeException("Could not locate FSS file");
-                }
             } else {
                 fssStream = getClass().getResourceAsStream("/data/FS.txt");
             }

numass-main/src/main/java/inr/numass/tasks/NumassFitScanTask.java

@@ -6,6 +6,7 @@
 package inr.numass.tasks;
 
 import hep.dataforge.actions.Action;
+import hep.dataforge.data.Data;
 import hep.dataforge.data.DataNode;
 import hep.dataforge.data.DataTree;
 import hep.dataforge.meta.Meta;

numass-main/src/main/java/inr/numass/tasks/NumassPrepareTask.java

@@ -42,7 +42,7 @@ public class NumassPrepareTask extends AbstractTask<Table> {
 
         //acquiring initial data. Data node could not be empty
 
-        DataFilter filter = new DataFilter().configure(config.getMeta("data"));
+        DataFilter filter = new DataFilter(config.getMeta("data"));
 
         DataNode<NumassSet> data = filter.filter(input.checked(NumassSet.class));