Refactoring and Issue resolution (#703)

bowring · web-flow · commit 32106c46e0d9 · 2022-04-11T13:49:56.000-04:00
* Refactoring * Fixed #701 * Fixed #702 and refactored
diff --git a/common.gradle b/common.gradle
@@ -7,7 +7,7 @@ apply plugin: 'maven-publish'
 
 
 String mavenGroupId = 'org.cirdles'
-String mavenVersion = '1.9.12'
+String mavenVersion = '1.10.0'
 
 [compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
 
diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/commonLeadAssignment/CommonLeadAssignmentController.java b/squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/commonLeadAssignment/CommonLeadAssignmentController.java
@@ -109,6 +109,9 @@ public class CommonLeadAssignmentController implements Initializable {
     @FXML
     private Button viewDetailsButton;
 
+    private int widthOfSelectedAgeColumn = 105;
+    private int ageTypeDisplayTranslationX = 70;
+
     /**
      * Initializes the controller class.
      */
@@ -312,18 +315,20 @@ private void showUnknownsWithOvercountCorrections() throws SquidException {
     }
 
     private void setUpFooter() {
+        int ageLabelWidth = 88;
         footerHBox.getChildren().addAll(
-                makeLabel("", 135, true, 10),
+                makeLabel("", 125, true, 10),
                 makeLabel("206Pb/204Pb", 90, true, 10),
                 makeLabel("207Pb/204Pb", 90, true, 10),
                 makeLabel("208Pb/204Pb", 90, true, 10),
-                makeLabel(PB4CORR + "\n" + PB4COR206_238AGE.replace(PB4CORR, ""), 90, true, 10),
-                makeLabel(PB4CORR + "\n" + PB4COR208_232AGE.replace(PB4CORR, ""), 90, true, 10),
-                makeLabel(PB4CORR + "\n" + PB4COR207_206AGE.replace(PB4CORR, ""), 90, true, 10),
-                makeLabel(PB7CORR + "\n" + PB7COR206_238AGE.replace(PB7CORR, ""), 90, true, 10),
-                makeLabel(PB7CORR + "\n" + PB7COR208_232AGE.replace(PB7CORR, ""), 90, true, 10),
-                makeLabel(PB8CORR + "\n" + PB8COR206_238AGE.replace(PB8CORR, ""), 90, true, 10),
-                makeLabel(PB8CORR + "\n" + PB8COR207_206AGE.replace(PB8CORR, ""), 90, true, 10));
+                makeLabel("", 35, true, 10),
+                makeLabel(PB4CORR + "\n" + PB4COR206_238AGE.replace(PB4CORR, "").replace("_Age", ""), ageLabelWidth, true, 10),
+                makeLabel(PB4CORR + "\n" + PB4COR208_232AGE.replace(PB4CORR, "").replace("_Age", ""), ageLabelWidth, true, 10),
+                makeLabel(PB4CORR + "\n" + PB4COR207_206AGE.replace(PB4CORR, "").replace("_Age", ""), ageLabelWidth, true, 10),
+                makeLabel(PB7CORR + "\n" + PB7COR206_238AGE.replace(PB7CORR, "").replace("_Age", ""), ageLabelWidth, true, 10),
+                makeLabel(PB7CORR + "\n" + PB7COR208_232AGE.replace(PB7CORR, "").replace("_Age", ""), ageLabelWidth, true, 10),
+                makeLabel(PB8CORR + "\n" + PB8COR206_238AGE.replace(PB8CORR, "").replace("_Age", ""), ageLabelWidth, true, 10),
+                makeLabel(PB8CORR + "\n" + PB8COR207_206AGE.replace(PB8CORR, "").replace("_Age", ""), ageLabelWidth, true, 10));
     }
 
     private Label makeLabel(String label, int width, boolean fontIsBold, int fontSize) {
@@ -433,6 +438,10 @@ public void displayData() {
                 addVboxFactory("207Pb/204Pb", spot.getCom_207Pb204Pb(), 0.0);
                 addVboxFactory("208Pb/204Pb", spot.getCom_208Pb204Pb(), 0.0);
 
+                Label aValue = new Label("");
+                aValue.setPrefWidth(35);
+                getChildren().add(aValue);
+
                 addVboxFactory(expPB4COR206_238AGE.getName(),
                         spot.getTaskExpressionsEvaluationsPerSpot().get(expPB4COR206_238AGE)[0][0],
                         spot.getTaskExpressionsEvaluationsPerSpot().get(expPB4COR206_238AGE)[0][1]);
@@ -488,7 +497,7 @@ private void addVboxFactory(String label, double value, double unct) throws Squi
                 aValue.setTextFill(Paint.valueOf("red"));
                 aValue.setFont(Font.font("Monospaced", FontWeight.BOLD, 12));
             }
-            aValue.setPrefWidth(102);
+            aValue.setPrefWidth(widthOfSelectedAgeColumn - 5);
             aValue.setMinWidth(USE_PREF_SIZE);
             aValue.setPrefHeight(20);
             aValue.setMinHeight(USE_PREF_SIZE);
@@ -827,7 +836,7 @@ public void changed(ObservableValue<? extends Boolean> observable, Boolean oldVa
 
             VBox groupDetailsVBox = new VBox(-10);
             HBox ageChoosersHBox = new HBox();
-            ageChoosersHBox.setTranslateX(15);
+            ageChoosersHBox.setTranslateX(ageTypeDisplayTranslationX);
 
             ageChoosersHBox.getChildren().add(ageRadioButtonFactory(sampleGroupName, SampleAgeTypesEnum.PB4COR206_238AGE, PB4CORR));
             ageChoosersHBox.getChildren().add(ageRadioButtonFactory(sampleGroupName, SampleAgeTypesEnum.PB4COR208_232AGE, PB4CORR));
@@ -844,9 +853,9 @@ public void changed(ObservableValue<? extends Boolean> observable, Boolean oldVa
             // be sure we are on sample group toolbar
             if (sampleGroup != null) {
                 weightedMeansHBox = new HBox();
-                weightedMeansHBox.setTranslateX(15);
+                weightedMeansHBox.setTranslateX(ageTypeDisplayTranslationX);
 
-                int wmWidth = 107;
+                int wmWidth = widthOfSelectedAgeColumn;
                 Label weightedMeanLabel = makeRedLabel("", wmWidth, true, 11, 4.0);
                 weightedMeanLabel.setId(SampleAgeTypesEnum.PB4COR206_238AGE.getExpressionName());
                 weightedMeansHBox.getChildren().add(weightedMeanLabel);
@@ -892,7 +901,7 @@ private void updateWeightedMeanLabel(Label wmLabel, String sampleGroupName) {
             Formatter formatter = new Formatter();
             formatter.format("%5.1f", spotSummaryDetails.getValues()[0][0] / 1e6);
             formatter.format(" " + ABS_UNCERTAINTY_DIRECTIVE + "%2.1f", spotSummaryDetails.getValues()[0][1] / 1e6).toString();
-            wmLabel.setText("WM: " + formatter);
+            wmLabel.setText("WM:" + formatter);
 
             // tool tip
             OperationOrFunctionInterface op = ((ExpressionTree) spotSummaryDetails.getExpressionTree()).getOperation();
@@ -943,11 +952,11 @@ public void handle(MouseEvent event) {
          * @param corrString      the value of corrString
          */
         private RadioButton ageRadioButtonFactory(String sampleGroupName, SampleAgeTypesEnum sampleAgeType, String corrString) {
-            RadioButton ageRB = new RadioButton(corrString + "\n" + sampleAgeType.getExpressionName().replace(corrString, ""));
+            RadioButton ageRB = new RadioButton(corrString + "\n" + sampleAgeType.getExpressionName().replace(corrString, "").replace("_Age", ""));
             ageRB.setId(sampleAgeType.getExpressionName());
             ageRB.setToggleGroup(ageRB_ToggleGroup);
             ageRB.setFont(Font.font("Monospaced", FontWeight.BOLD, 10));
-            ageRB.setPrefWidth(107);
+            ageRB.setPrefWidth(widthOfSelectedAgeColumn);
             ageRB.setMinWidth(USE_PREF_SIZE);
             ageRB.setPrefHeight(25);
             ageRB.setMinHeight(USE_PREF_SIZE);
diff --git a/squidApp/src/main/resources/org/cirdles/squid/gui/dateInterpretations/commonLeadAssignment/CommonLeadAssignment.fxml b/squidApp/src/main/resources/org/cirdles/squid/gui/dateInterpretations/commonLeadAssignment/CommonLeadAssignment.fxml
@@ -60,7 +60,8 @@
         </HBox>
         <HBox fx:id="headerHBox" minHeight="25.0" prefHeight="25.0" prefWidth="1200.0" spacing="35.0" styleClass="backgroundCalamari">
             <children>
-                <Label style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;" text="   Common Lead Assignment" translateY="-2.0" />
+                <Label style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;" text="   Common Lead Assignment:" translateY="-2.0" />
+            <Label layoutX="10.0" layoutY="13.0" style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;" text="Age Type:" translateX="260.0" />
             </children>
             <padding>
                 <Insets top="3.0" />
@@ -73,4 +74,4 @@
             </padding>
         </HBox>
     </children>
-</VBox>
+</VBox>
diff --git a/squidApp/src/test/java/org/cirdles/squid/gui/utilities/fileUtilities/FileHandlerTest.java b/squidApp/src/test/java/org/cirdles/squid/gui/utilities/fileUtilities/FileHandlerTest.java
@@ -0,0 +1,30 @@
+package org.cirdles.squid.gui.utilities.fileUtilities;
+
+import junit.framework.TestCase;
+import org.cirdles.squid.constants.Squid3Constants;
+import org.cirdles.squid.exceptions.SquidException;
+import org.cirdles.squid.projects.SquidProject;
+import org.cirdles.squid.utilities.stateUtilities.SquidSerializer;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+
+public class FileHandlerTest extends TestCase {
+
+    public void setUp() throws Exception {
+        super.setUp();
+    }
+
+    public void tearDown() throws Exception {
+    }
+
+    // April 2022 example test for Ian Robinson
+    public void testSelectProjectFile() throws SquidException, IOException {
+        SquidProject myProject = new SquidProject(Squid3Constants.TaskTypeEnum.GENERAL);
+        SquidSerializer.serializeObjectToFile(myProject, "Test.ser");
+        SquidProject myOtherProject = (SquidProject) SquidSerializer.getSerializedObjectFromFile("Test.ser", true);
+        assertEquals(myProject.getProjectName(), myOtherProject.getProjectName());
+        Files.deleteIfExists((new File("Test.ser")).toPath());
+    }
+}
diff --git a/squidCore/src/main/java/org/cirdles/squid/shrimp/ShrimpFraction.java b/squidCore/src/main/java/org/cirdles/squid/shrimp/ShrimpFraction.java
@@ -1034,6 +1034,20 @@ public String getSelectedAgeExpressionName() throws SquidException {
         return expressionName;
     }
 
+    @Override
+    public String getComPbSelectedAgeType() throws SquidException {
+
+        String ageName = getSelectedAgeExpressionName();
+
+        try {
+            ageName.replaceFirst("_Age", "");
+        } catch (Exception e) {
+            //e.printStackTrace();
+        }
+
+        return ageName;
+    }
+
     @Override
     public int hashCode() {
         int result = Objects.hash(getFractionID(), getSpotNumber(), getSpotIndex(), getNameOfMount(),
diff --git a/squidCore/src/main/java/org/cirdles/squid/shrimp/ShrimpFractionExpressionInterface.java b/squidCore/src/main/java/org/cirdles/squid/shrimp/ShrimpFractionExpressionInterface.java
@@ -300,4 +300,11 @@ public interface ShrimpFractionExpressionInterface {
     public String getComPbCorrSKTargetAge();
 
     public String getSelectedAgeExpressionName() throws SquidException;
+
+    /**
+     * Used in custom reports per issue # 701.
+     * @return
+     * @throws SquidException
+     */
+    public String getComPbSelectedAgeType() throws SquidException;
 }
diff --git a/squidCore/src/main/java/org/cirdles/squid/tasks/expressions/builtinExpressions/BuiltInExpressionsFactory.java b/squidCore/src/main/java/org/cirdles/squid/tasks/expressions/builtinExpressions/BuiltInExpressionsFactory.java
@@ -149,6 +149,10 @@ public static Map<String, ExpressionTreeInterface> generateSpotMetaDataFields()
         ExpressionTreeInterface expDateTime = buildSpotNode("getDateTimeMilliseconds");
         spotMetaDataFields.put(expDateTime.getName(), expDateTime);
 
+        // april 2022 issue # 701
+        ExpressionTreeInterface commonLeadAgeType = buildSpotNode("getComPbSelectedAgeType");
+        spotMetaDataFields.put(commonLeadAgeType.getName(), commonLeadAgeType);
+
         return spotMetaDataFields;
     }
 
diff --git a/squidCore/src/main/java/org/cirdles/squid/utilities/stateUtilities/SquidPersistentState.java b/squidCore/src/main/java/org/cirdles/squid/utilities/stateUtilities/SquidPersistentState.java
@@ -63,6 +63,19 @@ public class SquidPersistentState implements Serializable {
     private String MRUTaskXMLFolderPath;
     private File customExpressionsFile;
 
+
+//    private void readObject(ObjectInputStream stream) throws IOException,
+//            ClassNotFoundException {
+//        stream.defaultReadObject();
+//
+//        ObjectStreamClass myObject = ObjectStreamClass.lookup(
+//                Class.forName(SquidPersistentState.class.getCanonicalName()));
+//        long theSUID = myObject.getSerialVersionUID();
+//
+//        System.out.println("Customized De-serialization of SquidPersistentState "
+//                + theSUID);
+//    }
+
     /**
      *
      */
@@ -131,7 +144,7 @@ public static SquidPersistentState getExistingPersistentState() throws SquidExce
             myInstance = new SquidPersistentState();
             myInstance.serializeSelf();
             myInstance.setTaskDesign(new TaskDesign());
-            
+
             // check to update TaskDesign
             TaskDesign sup = myInstance.getTaskDesign();
             if (sup == null) {
@@ -198,7 +211,6 @@ public void setTaskDesign(TaskDesign taskDesign) {
     private void initMRULists() {
         MRUProjectList = new ArrayList<>(MRU_COUNT);
         MRUPrawnFileList = new ArrayList<>(MRU_COUNT);
-//        MRUTaskList = new ArrayList<>(MRU_COUNT);
         MRUExpressionList = new ArrayList<>(MRU_COUNT);
     }
 
diff --git a/squidCore/src/main/java/org/cirdles/squid/utilities/stateUtilities/SquidSerializer.java b/squidCore/src/main/java/org/cirdles/squid/utilities/stateUtilities/SquidSerializer.java
@@ -60,23 +60,6 @@ public static void serializeObjectToFile(Object serializableObject, String fileN
         }
     }
 
-    public static void serializeObjectToFileRAF(Object serializableObject, String fileName) throws SquidException, IOException {
-        ObjectOutputStream objectOutputStream = null;
-        try {
-            RandomAccessFile raf = new RandomAccessFile(fileName, "rwd");
-            FileOutputStream fos = new FileOutputStream(raf.getFD());
-            objectOutputStream = new ObjectOutputStream(fos);
-            objectOutputStream.writeObject(serializableObject);
-        } catch (IOException ex) {
-            throw new SquidException("Cannot serialize object of " + serializableObject.getClass().getSimpleName() + " to: " + fileName);
-
-        } finally {
-            if (objectOutputStream != null) {
-                objectOutputStream.close();
-            }
-        }
-    }
-
     /**
      * @param filename
      * @return
@@ -95,20 +78,15 @@ public static Object getSerializedObjectFromFile(String filename, boolean verbos
             if (verbose) {
                 throw new SquidException("The file you are attempting to open does not exist:\n"
                         + " " + filename);
-//                SquidMessageDialog.showWarningDialog("The file you are attempting to open does not exist:\n"
-//                        + " " + filename, null);
+
             }
         } catch (IOException ex) {
             if (verbose) {
                 throw new SquidException("The file you are attempting to open is not a valid '*.squid' file.");
-//                SquidMessageDialog.showWarningDialog(
-//                        "The file you are attempting to open is not a valid '*.squid' file.", null);
             }
         } catch (ClassNotFoundException | ClassCastException ex) {
             if (verbose) {
                 throw new SquidException("The file you are attempting to open is not compatible with this version of Squid3.");
-//                SquidMessageDialog.showWarningDialog(
-//                        "The file you are attempting to open is not compatible with this version of Squid3.", null);
             }
         }
 
diff --git a/squidCore/src/main/resources/org/cirdles/squid/projects/SQUID3_demo_file.squid b/squidCore/src/main/resources/org/cirdles/squid/projects/SQUID3_demo_file.squid
diff --git a/squidCore/src/main/resources/org/cirdles/squid/projects/Z626611PKPERM1.squid b/squidCore/src/main/resources/org/cirdles/squid/projects/Z626611PKPERM1.squid

Original file line number	Diff line number	Diff line change
`@@ -149,6 +149,10 @@ public static Map<String, ExpressionTreeInterface> generateSpotMetaDataFields()`
`149`	`149`	`ExpressionTreeInterface expDateTime = buildSpotNode("getDateTimeMilliseconds");`
`150`	`150`	`spotMetaDataFields.put(expDateTime.getName(), expDateTime);`
`151`	`151`
	`152`	`+ // april 2022 issue # 701`
	`153`	`+ ExpressionTreeInterface commonLeadAgeType = buildSpotNode("getComPbSelectedAgeType");`
	`154`	`+ spotMetaDataFields.put(commonLeadAgeType.getName(), commonLeadAgeType);`
	`155`	`+`
`152`	`156`	`return spotMetaDataFields;`
`153`	`157`	`}`
`154`	`158`