Merge pull request #26 from bowring/hotfix

hotfix to handle resources cases local class file vs jar file
CIRDLES · Jun 5, 2015 · 716d53c · 716d53c
2 parents 54e7667 + f60d34b
commit 716d53c
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Showing 17 changed files with 210 additions and 138 deletions.
diff --git a/pom.xml b/pom.xml
@@ -21,7 +21,7 @@
     <groupId>org.cirdles</groupId>
     <artifactId>ET_Redux</artifactId>
     <name>ET_Redux</name>
-    <version>3.2.0</version>
+    <version>3.2.1</version>
     <description>Successor to U-Pb_Redux</description>
     <url>https://cirdles.org</url>
     <inceptionYear>2006</inceptionYear>

diff --git a/src/main/java/org/earthtime/ETRedux.java b/src/main/java/org/earthtime/ETRedux.java
@@ -21,20 +21,18 @@
 package org.earthtime;
 
 import java.awt.Font;
+import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.net.URL;
-import java.util.Scanner;
-import java.util.logging.Level;
-import java.util.logging.Logger;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import javax.help.SwingHelpUtilities;
 import javax.swing.ToolTipManager;
 import javax.swing.UIManager;
 import org.earthtime.UPb_Redux.exceptions.BadLabDataException;
 import org.earthtime.UPb_Redux.user.ReduxPersistentState;
 import org.earthtime.UPb_Redux.utilities.JHelpAction;
 import org.earthtime.exceptions.ETWarningDialog;
-import org.earthtime.ratioDataModels.mineralStandardModels.MineralStandardUPbModel;
 
 /**
  *
@@ -48,12 +46,12 @@ public class ETRedux {
     /**
      * Version 3.0.0 initiates switch to ET_Redux from U-Pb_Redux
      */
-    public static String VERSION;// = "3.x.0";
+    public static String VERSION = "version";
 
     /**
      *
      */
-    public static String RELEASE_DATE;// = "June 2015";
+    public static String RELEASE_DATE = "date";
 
     /**
      * Creates a new instance of UPbRedux
@@ -62,22 +60,19 @@ public class ETRedux {
      */
     public ETRedux(File reduxFile) //throws3 IOException, InvalidPreferencesFormatException 
     {
-        // get version number written by pom.xml
-        URL versionFileURL = MineralStandardUPbModel.class.getClassLoader().getResource("version.txt");
-        File versionFile = new File(versionFileURL.getPath());
-
-        try ( //first use a Scanner to get headers of 4 lines
-                // http://en.wikipedia.org/wiki/Windows-1252
-                Scanner scanner = new Scanner(versionFile, "CP1252")) {
-            String[] versionText = scanner.nextLine().split("=");
+        try {
+            // get version number written by pom.xml
+            InputStream versionFileStreamL = ETRedux.class.getClassLoader().getResourceAsStream("version.txt");
+            BufferedReader reader = new BufferedReader(new InputStreamReader(versionFileStreamL));
+            StringBuilder out = new StringBuilder();
+            String line;
+
+            String[] versionText = reader.readLine().split("=");
             VERSION = versionText[1];
-
-            String[] versionDate = scanner.nextLine().split("=");
+            
+            String[] versionDate = reader.readLine().split("=");
             RELEASE_DATE = versionDate[1];
-
-            scanner.close();
-        } catch (FileNotFoundException ex) {
-            Logger.getLogger(ETRedux.class.getName()).log(Level.SEVERE, null, ex);
+        } catch (IOException iOException) {
         }
 
         // get redux persistent state file
@@ -116,7 +111,7 @@ public ETRedux(File reduxFile) //throws3 IOException, InvalidPreferencesFormatEx
         // installer etc ref
         // http://www.centerkey.com/mac/java/
     }
-        // installer etc ref
+    // installer etc ref
     // http://www.centerkey.com/mac/java/
 
     /**

diff --git a/src/main/java/org/earthtime/UPb_Redux/fractions/AnalysisFraction.java b/src/main/java/org/earthtime/UPb_Redux/fractions/AnalysisFraction.java
@@ -23,7 +23,11 @@
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.converters.ConversionException;
 import com.thoughtworks.xstream.io.xml.DomDriver;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
 import org.earthtime.UPb_Redux.ReduxConstants;
 import org.earthtime.UPb_Redux.fractions.UPbReduxFractions.UPbFraction;
 import org.earthtime.UPb_Redux.fractions.UPbReduxFractions.fractionReduction.UPbFractionReducer;
@@ -34,10 +38,10 @@
 import org.earthtime.UPb_Redux.valueModels.ValueModel;
 import org.earthtime.UPb_Redux.valueModels.ValueModelXMLConverter;
 import org.earthtime.XMLExceptions.BadOrMissingXMLSchemaException;
+import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.exceptions.ETException;
 import org.earthtime.ratioDataModels.initialPbModelsET.InitialPbModelET;
 import org.earthtime.ratioDataModels.initialPbModelsET.InitialPbModelETXMLConverter;
-import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.xmlUtilities.XMLSerializationI;
 
 /**
@@ -180,12 +184,12 @@ public Object readXMLObject ( String filename, boolean doValidate )
                     throw new ETException( null, e.getMessage() );
                 }
 
-                System.out.println( "This is your AnalysisFraction that was just read successfully:\n" );
-
-                String xml2 = getXStreamWriter().toXML( myFraction );
-
-                System.out.println( xml2 );
-                System.out.flush();
+//                System.out.println( "This is your AnalysisFraction that was just read successfully:\n" );
+//
+//                String xml2 = getXStreamWriter().toXML( myFraction );
+//
+//                System.out.println( xml2 );
+//                System.out.flush();
             } else {
                 throw new ETException( null, "XML data file does not conform to schema." );
             }

diff --git a/src/main/java/org/earthtime/UPb_Redux/initialPbModels/InitialPbModel.java b/src/main/java/org/earthtime/UPb_Redux/initialPbModels/InitialPbModel.java
@@ -23,7 +23,12 @@
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.converters.ConversionException;
 import com.thoughtworks.xstream.io.xml.DomDriver;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.Serializable;
 import java.math.BigDecimal;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -34,12 +39,12 @@
 import org.earthtime.UPb_Redux.valueModels.ValueModel;
 import org.earthtime.UPb_Redux.valueModels.ValueModelXMLConverter;
 import org.earthtime.XMLExceptions.BadOrMissingXMLSchemaException;
-import org.earthtime.exceptions.ETException;
+import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.dataDictionaries.DataDictionary;
+import org.earthtime.exceptions.ETException;
 import org.earthtime.ratioDataModels.AbstractRatiosDataModel;
 import org.earthtime.ratioDataModels.initialPbModelsET.InitialPbModelET;
 import org.earthtime.utilities.DateHelpers;
-import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.xmlUtilities.XMLSerializationI;
 
 /**
@@ -520,12 +525,12 @@ public Object readXMLObject ( String filename, boolean doValidate )
                     throw new ETException( null, e.getMessage() );
                 }
 
-                System.out.println( "This is your InitialPbModel that was just read successfully:\n" );
-
-                String xml2 = getXStreamWriter().toXML( myInitialPbModel );
-
-                System.out.println( xml2 );
-                System.out.flush();
+//                System.out.println( "This is your InitialPbModel that was just read successfully:\n" );
+//
+//                String xml2 = getXStreamWriter().toXML( myInitialPbModel );
+//
+//                System.out.println( xml2 );
+//                System.out.flush();
             }
 
         } else {

diff --git a/src/main/java/org/earthtime/UPb_Redux/mineralStandardModels/MineralStandardModel.java b/src/main/java/org/earthtime/UPb_Redux/mineralStandardModels/MineralStandardModel.java
@@ -39,13 +39,13 @@
 import org.earthtime.UPb_Redux.valueModels.ValueModelReferencedXMLConverter;
 import org.earthtime.UPb_Redux.valueModels.ValueModelXMLConverter;
 import org.earthtime.XMLExceptions.BadOrMissingXMLSchemaException;
+import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.dataDictionaries.DataDictionary;
 import org.earthtime.exceptions.ETException;
 import org.earthtime.ratioDataModels.AbstractRatiosDataModel;
 import org.earthtime.ratioDataModels.initialPbModelsET.InitialPbModelET;
 import org.earthtime.ratioDataModels.mineralStandardModels.MineralStandardUPbModel;
 import org.earthtime.utilities.DateHelpers;
-import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.xmlUtilities.XMLSerializationI;
 
 /**
@@ -379,6 +379,7 @@ public void serializeXMLObject ( String filename ) {
      * @throws ETException
      * @throws BadOrMissingXMLSchemaException
      */
+    @Override
     public Object readXMLObject ( String filename, boolean doValidate )
             throws FileNotFoundException,
             ETException,
@@ -404,12 +405,6 @@ public Object readXMLObject ( String filename, boolean doValidate )
                     throw new ETException( null, e.getMessage() );
                 }
 
-                System.out.println( "This is your MineralStandardModel that was just read successfully:\n" );
-
-                String xml2 = getXStreamWriter().toXML( myMineralStandardModel );
-
-                System.out.println( xml2 );
-                System.out.flush();
             } else {
                 throw new FileNotFoundException( "Badly formed or unvalidated XML data file." );
             }

diff --git a/src/main/java/org/earthtime/UPb_Redux/pbBlanks/PbBlank.java b/src/main/java/org/earthtime/UPb_Redux/pbBlanks/PbBlank.java
@@ -23,7 +23,12 @@
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.converters.ConversionException;
 import com.thoughtworks.xstream.io.xml.DomDriver;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.Serializable;
 import java.math.BigDecimal;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -34,12 +39,12 @@
 import org.earthtime.UPb_Redux.valueModels.ValueModel;
 import org.earthtime.UPb_Redux.valueModels.ValueModelXMLConverter;
 import org.earthtime.XMLExceptions.BadOrMissingXMLSchemaException;
-import org.earthtime.exceptions.ETException;
+import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.dataDictionaries.DataDictionary;
+import org.earthtime.exceptions.ETException;
 import org.earthtime.ratioDataModels.AbstractRatiosDataModel;
 import org.earthtime.ratioDataModels.pbBlankICModels.PbBlankICModel;
 import org.earthtime.utilities.DateHelpers;
-import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.xmlUtilities.XMLSerializationI;
 
 /**
@@ -671,12 +676,12 @@ public Object readXMLObject ( String filename, boolean doValidate )
                     throw new ETException( null, e.getMessage() );
                 }
 
-                System.out.println( "This is your PbBlank that was just read successfully:\n" );
-
-                String xml2 = getXStreamWriter().toXML( retPbBlank );
+//                System.out.println( "This is your PbBlank that was just read successfully:\n" );
 
-                System.out.println( xml2 );
-                System.out.flush();
+//                String xml2 = getXStreamWriter().toXML( retPbBlank );
+//
+//                System.out.println( xml2 );
+//                System.out.flush();
             }
 
         } else {

diff --git a/src/main/java/org/earthtime/UPb_Redux/samples/SESARSampleMetadata.java b/src/main/java/org/earthtime/UPb_Redux/samples/SESARSampleMetadata.java
@@ -33,8 +33,8 @@
 import org.earthtime.UPb_Redux.ReduxConstants;
 import org.earthtime.UPb_Redux.user.UPbReduxConfigurator;
 import org.earthtime.XMLExceptions.BadOrMissingXMLSchemaException;
-import org.earthtime.exceptions.ETException;
 import org.earthtime.archivingTools.URIHelper;
+import org.earthtime.exceptions.ETException;
 import org.earthtime.xmlUtilities.XMLSerializationI;
 
 /**
@@ -286,12 +286,12 @@ public Object readXMLObject(String filename, boolean doValidate)
                     throw new ETException(null, e.getMessage());
                 }
 
-                System.out.println("This is your SESARSampleMetadata that was just read successfully:\n");
-
-                String xml2 = getXStreamWriter().toXML(SESARSampleMetadata);
+//                System.out.println("This is your SESARSampleMetadata that was just read successfully:\n");
 
-                System.out.println(xml2);
-                System.out.flush();
+//                String xml2 = getXStreamWriter().toXML(SESARSampleMetadata);
+//
+//                System.out.println(xml2);
+//                System.out.flush();
             } else {
                 throw new ETException( null, "XML data file does not conform to schema." );
             }

diff --git a/src/main/java/org/earthtime/UPb_Redux/samples/SampleMetaData.java b/src/main/java/org/earthtime/UPb_Redux/samples/SampleMetaData.java
@@ -32,8 +32,8 @@
 import org.earthtime.UPb_Redux.fractions.FractionMetaData;
 import org.earthtime.UPb_Redux.user.UPbReduxConfigurator;
 import org.earthtime.XMLExceptions.BadOrMissingXMLSchemaException;
-import org.earthtime.exceptions.ETException;
 import org.earthtime.archivingTools.URIHelper;
+import org.earthtime.exceptions.ETException;
 import org.earthtime.xmlUtilities.XMLSerializationI;
 
 /**
@@ -250,12 +250,12 @@ public Object readXMLObject(String filename, boolean doValidate)
                     throw new ETException(null, e.getMessage());
                 }
 
-                System.out.println("\nThis is your SampleMetaData that was just read successfully:\n");
-
-                String xml2 = getXStreamWriter().toXML(mySampleMetaData);
+//                System.out.println("\nThis is your SampleMetaData that was just read successfully:\n");
 
-                System.out.println(xml2);
-                System.out.flush();
+//                String xml2 = getXStreamWriter().toXML(mySampleMetaData);
+//
+//                System.out.println(xml2);
+//                System.out.flush();
             }
 
         } else {

diff --git a/src/main/java/org/earthtime/UPb_Redux/tracers/Tracer.java b/src/main/java/org/earthtime/UPb_Redux/tracers/Tracer.java
@@ -23,7 +23,12 @@
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.converters.ConversionException;
 import com.thoughtworks.xstream.io.xml.DomDriver;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.Serializable;
 import java.text.DateFormat;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
@@ -36,14 +41,14 @@
 import org.earthtime.UPb_Redux.valueModels.ValueModel;
 import org.earthtime.UPb_Redux.valueModels.ValueModelXMLConverter;
 import org.earthtime.XMLExceptions.BadOrMissingXMLSchemaException;
-import org.earthtime.exceptions.ETException;
+import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.dataDictionaries.DataDictionary;
 import org.earthtime.dataDictionaries.TracerIsotopes;
 import org.earthtime.dataDictionaries.TracerRatiosEnum;
+import org.earthtime.exceptions.ETException;
 import org.earthtime.ratioDataModels.AbstractRatiosDataModel;
 import org.earthtime.ratioDataModels.tracers.TracerUPbModel;
 import org.earthtime.utilities.DateHelpers;
-import org.earthtime.archivingTools.URIHelper;
 import org.earthtime.xmlUtilities.XMLSerializationI;
 
 /**
@@ -939,12 +944,12 @@ public Object readXMLObject ( String filename, boolean doValidate )
                     throw new ETException( null, e.getMessage() );
                 }
 
-                System.out.println( "This is your Tracer that was just read successfully:\n" );
-
-                String xml2 = getXStreamWriter().toXML( myTracer );
+//                System.out.println( "This is your Tracer that was just read successfully:\n" );
 
-                System.out.println( xml2 );
-                System.out.flush();
+//                String xml2 = getXStreamWriter().toXML( myTracer );
+//
+//                System.out.println( xml2 );
+//                System.out.flush();
 
             } else {
                 throw new ETException( null, "Badly formed XML data file." );