Merge pull request #771 from bowring/joinfix

Joinfix
CIRDLES · Apr 24, 2024 · c1a5a53 · c1a5a53
2 parents b809835 + b168b5d
commit c1a5a53
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Showing 12 changed files with 65 additions and 34 deletions.
diff --git a/common.gradle b/common.gradle
@@ -7,7 +7,7 @@ apply plugin: 'maven-publish'
 
 
 String mavenGroupId = 'org.cirdles'
-String mavenVersion = '2.0.6'
+String mavenVersion = '2.0.7'
 
 [compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
 

diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/ProjectManagerController.java b/squidApp/src/main/java/org/cirdles/squid/gui/ProjectManagerController.java
@@ -51,6 +51,7 @@
  */
 public class ProjectManagerController implements Initializable {
 
+    public Label parametersModelLabel;
     @FXML
     private TextField originalPrawnFileName;
     @FXML
@@ -230,6 +231,8 @@ private void setUpParametersModelsComboBoxes() throws SquidException {
         } else {
             specifyDefaultCommonPbLabel.setVisible(false);
             commonPbModelComboBox.setVisible(false);
+            parametersModelLabel.setVisible(false);
+            useCommonPbModelForUnknownsCheckBox.setVisible(false);
         }
     }
 

diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/TaskEditorController.java b/squidApp/src/main/java/org/cirdles/squid/gui/TaskEditorController.java
@@ -79,11 +79,13 @@ public class TaskEditorController implements Initializable {
     private static final Label instructions = new Label("   Choose numerator and denominator");
     private static final Button addBtn = new Button("Add ratio");
     private static final HBox addBtnHBox = new HBox(addBtn);
+    private static final Button closeBtn = new Button("Close");
+    private static final HBox closeBtnHBox = new HBox(closeBtn);
     private static final Label numLabel = new Label("");
     private static final Label divLabel = new Label("/");
     private static final Label denLabel = new Label("");
     private static final HBox infoLabelHBox = new HBox(numLabel, divLabel, denLabel);
-    private static final VBox addInfo = new VBox(infoLabelHBox, addBtnHBox);
+    private static final VBox addInfo = new VBox(infoLabelHBox, addBtnHBox, closeBtnHBox);
     private static final VBox menuVBox = new VBox(instructions, numDemHBox, addInfo);
     private static final Map<String, Tooltip> tooltipsMap = new HashMap<>();
     private static final ToggleGroup numTG = new ToggleGroup();
@@ -93,6 +95,7 @@ public class TaskEditorController implements Initializable {
     private static Map<String, ExpressionTreeInterface> namedExpressionsMap = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
     private static boolean amGeochronMode;
     private final List<StackPane> undoMassesList = new ArrayList<>();
+    public Text pinkMassesWarningText;
     EventHandler<MouseEvent> mouseEnteredExpressionEventHandler = new EventHandler<MouseEvent>() {
         @Override
         public void handle(MouseEvent event) {
@@ -317,7 +320,21 @@ public void initialize(URL url, ResourceBundle rb) {
             updateAddButton();
         });
 
-//        updateAddButton();
+        closeBtnHBox.setAlignment(Pos.CENTER);
+        closeBtn.setStyle(
+                "-fx-padding: 5 22 5 22;\n"
+                        + "    -fx-border-color: #e2e2e2;"
+                        + "    -fx-border-width: 2;"
+                        + "    -fx-background-radius: 0;"
+                        + "    -fx-background-color: #FB6D42;"
+                        + "    -fx-font-family: SansSerif;"
+                        + "    -fx-font-size: 11pt;"
+                        + "    -fx-text-fill: whitesmoke;"
+                        + "    -fx-background-insets: 0 0 0 0, 0, 1, 2;");
+
+        closeBtn.setOnMouseClicked((event) -> {
+            ADD_RATIOS_STAGE.hide();
+        });
 
         numLabel.setStyle("-fx-font-family: SansSerif bold;-fx-font-size: 18");
         divLabel.setStyle("-fx-font-family: SansSerif bold;-fx-font-size: 18");
@@ -378,6 +395,10 @@ public void changed(ObservableValue<? extends Toggle> ob, Toggle o, Toggle n) {
             }
             amGeochronMode = taskEditor.getTaskType().compareTo(TaskTypeEnum.GEOCHRON) == 0;
 
+            if (taskEditor.getTaskType().equals(TaskTypeEnum.GENERAL)) {
+                pinkMassesWarningText.setText("");
+            }
+
             updateAddButton();
 
             initTaskDesign();
@@ -822,6 +843,7 @@ private ContextMenu createChooseMassesContextMenu() {
 
     @FXML
     private void updateCurrentTaskWithThisTaskAction() throws SquidException {
+        ADD_RATIOS_STAGE.hide();
         if (squidProject.getTask().getTaskType().equals(taskEditor.getTaskType())) {
             // check the mass count
             boolean valid = (squidProject.getTask().getSquidSpeciesModelList().size()
@@ -864,6 +886,7 @@ private void updateCurrentTaskWithThisTaskAction() throws SquidException {
 
     @FXML
     private void saveThisTaskAsXMLFileAction() {
+        ADD_RATIOS_STAGE.hide();
         try {
             TaskInterface task = new Task();
             task.updateTaskFromTaskDesign(taskEditor, true);
@@ -877,6 +900,7 @@ private void saveThisTaskAsXMLFileAction() {
 
     @FXML
     private void viewCurrentTaskAction() {
+        ADD_RATIOS_STAGE.hide();
         MenuItem menuItemTaskManager = ((MenuBar) SquidUI.primaryStage.getScene()
                 .getRoot().getChildrenUnmodifiable().get(0)).getMenus().get(2).getItems().get(0);
         menuItemTaskManager.fire();

diff --git a/squidApp/src/main/resources/org/cirdles/squid/gui/ProjectManager.fxml b/squidApp/src/main/resources/org/cirdles/squid/gui/ProjectManager.fxml
@@ -203,8 +203,8 @@
                     </padding>
                 </HBox>
 
-                <Label alignment="CENTER_RIGHT" prefHeight="24.0" prefWidth="195.0" style="-fx-font-size: 14;"
-                       text="Parameter Models:" GridPane.rowIndex="5"/>
+                <Label fx:id="parametersModelLabel" alignment="CENTER_RIGHT" prefHeight="24.0" prefWidth="195.0"
+                       style="-fx-font-size: 14;" text="Parameter Models:" GridPane.rowIndex="5"/>
                 <HBox prefHeight="100.0" prefWidth="200.0" spacing="10.0" GridPane.columnIndex="1"
                       GridPane.rowIndex="6">
                     <children>
@@ -232,4 +232,4 @@
     <padding>
         <Insets bottom="15.0" left="20.0" right="20.0" top="1.0"/>
     </padding>
-</GridPane>
+</GridPane>
diff --git a/squidApp/src/main/resources/org/cirdles/squid/gui/SquidUIController.fxml b/squidApp/src/main/resources/org/cirdles/squid/gui/SquidUIController.fxml
@@ -48,7 +48,7 @@
                                 <Menu fx:id="openRecentOPFileMenu" mnemonicParsing="false" text="From Recent OP File"/>
                             </items>
                         </Menu>
-                        <Menu mnemonicParsing="false" text="New Squid3 RATIO Project ">
+                        <Menu mnemonicParsing="false" text="New Squid3 GENERAL (Ratio) Project ">
                             <items>
                                 <MenuItem fx:id="newSquidRatioProjectMenuItem" mnemonicParsing="false"
                                           onAction="#newSquidRatioProjectAction" text="From a single Prawn XML file"/>

diff --git a/squidApp/src/main/resources/org/cirdles/squid/gui/TaskEditor.fxml b/squidApp/src/main/resources/org/cirdles/squid/gui/TaskEditor.fxml
@@ -21,8 +21,7 @@
 <?import javafx.scene.layout.*?>
 <?import javafx.scene.shape.Ellipse?>
 <?import javafx.scene.text.*?>
-<GridPane xmlns:fx="http://javafx.com/fxml/1" fx:id="taskManagerGridPane" hgap="15.0" minHeight="660.0"
-          minWidth="1250.0"
+<GridPane xmlns:fx="http://javafx.com/fxml/1" fx:id="taskManagerGridPane" hgap="15.0" minHeight="660.0" minWidth="1250.0"
           prefHeight="660.0" prefWidth="1250.0" styleClass="backgroundCalamari" stylesheets="@css/projectManager.css"
           vgap="10.0" xmlns="http://javafx.com/javafx/17"
           fx:controller="org.cirdles.squid.gui.TaskEditorController">
@@ -229,9 +228,9 @@
         <Label style="-fx-text-fill: #3c77c9; -fx-font-weight: bold;" text="Mass Labels:" GridPane.rowIndex="6"/>
         <HBox alignment="CENTER_LEFT" prefHeight="50.0" GridPane.columnIndex="1" GridPane.rowIndex="6">
             <children>
-                <Button fx:id="chooseMassesButton" minWidth="86.0" mnemonicParsing="false"
-                        prefHeight="27.0" prefWidth="86.0"
-                        style="-fx-padding: 0 0 0 0; -fx-font-size: 10; -fx-font-weight: bold;" text="Add Masses"/>
+                <Button fx:id="chooseMassesButton" minWidth="86.0" mnemonicParsing="false" prefHeight="27.0"
+                        prefWidth="86.0" style="-fx-padding: 0 0 0 0; -fx-font-size: 10; -fx-font-weight: bold;"
+                        text="Add Masses"/>
                 <ScrollPane prefHeight="50.0" prefWidth="1035.0" HBox.hgrow="ALWAYS">
                     <content>
                         <TextFlow fx:id="defaultMassesListTextFlow" minHeight="30.0" minWidth="997.0"
@@ -243,9 +242,9 @@
         <Label style="-fx-text-fill: #3c77c9; -fx-font-weight: bold;" text="Ratios:" GridPane.rowIndex="8"/>
         <HBox alignment="CENTER_LEFT" prefHeight="90.0" GridPane.columnIndex="1" GridPane.rowIndex="8">
             <children>
-                <Button fx:id="chooseRatiosButton" minWidth="86.0" mnemonicParsing="false"
-                        prefHeight="27.0" prefWidth="86.0"
-                        style="-fx-padding: 0 0 0 0; -fx-font-size: 10; -fx-font-weight: bold;" text="Add / Restore"/>
+                <Button fx:id="chooseRatiosButton" minWidth="86.0" mnemonicParsing="false" prefHeight="27.0"
+                        prefWidth="86.0" style="-fx-padding: 0 0 0 0; -fx-font-size: 10; -fx-font-weight: bold;"
+                        text="Add / Restore"/>
                 <ScrollPane HBox.hgrow="ALWAYS">
                     <content>
                         <TextFlow fx:id="defaultRatiosListTextFlow" minHeight="35.0" minWidth="997.0"
@@ -268,7 +267,7 @@
                 </Text>
                 <Spinner fx:id="backgroundIndexSpinner" maxHeight="25.0" minHeight="25.0" prefHeight="25.0"
                          prefWidth="54.0" style="-fx-scale-y: 0.9; -fx-background-color: AQUAMARINE;"/>
-                <Text strokeType="OUTSIDE" strokeWidth="0.0" style="-fx-fill: red;"
+                <Text fx:id="pinkMassesWarningText" strokeType="OUTSIDE" strokeWidth="0.0" style="-fx-fill: red;"
                       text="Note: Pink masses and ratios are required.  Hint: To remove mass or ratio, click its oval in the displayed list."
                       textAlignment="RIGHT" wrappingWidth="578.55224609375">
                     <font>
@@ -304,4 +303,4 @@
     <padding>
         <Insets bottom="15.0" left="20.0" right="20.0" top="1.0"/>
     </padding>
-</GridPane>
+</GridPane>
diff --git a/squidApp/src/main/resources/org/cirdles/squid/gui/expressions/ExpressionBuilder.fxml b/squidApp/src/main/resources/org/cirdles/squid/gui/expressions/ExpressionBuilder.fxml
@@ -21,7 +21,8 @@
 <?import javafx.scene.layout.*?>
 <?import javafx.scene.text.*?>
 <?import javafx.scene.web.WebView?>
-<SplitPane xmlns:fx="http://javafx.com/fxml/1" fx:id="mainPane" dividerPositions="0.25" maxHeight="-Infinity" maxWidth="-Infinity"
+<SplitPane xmlns:fx="http://javafx.com/fxml/1" fx:id="mainPane" dividerPositions="0.25" maxHeight="-Infinity"
+           maxWidth="-Infinity"
            minHeight="660.0" minWidth="1250.0" prefHeight="660.0" prefWidth="1250.0"
            styleClass="backgroundCalamari" stylesheets="@../css/projectManager.css"
            xmlns="http://javafx.com/javafx/17"

diff --git a/squidCore/src/main/java/org/cirdles/squid/constants/Squid3Constants.java b/squidCore/src/main/java/org/cirdles/squid/constants/Squid3Constants.java
@@ -260,7 +260,7 @@ public String getIsotopeCorrectionPrefixString() {
 
     public enum TaskTypeEnum {
         GEOCHRON("GEOCHRON", "Geochron", new ArrayList<>(Arrays.asList("204", "206", "207", "208")), new ArrayList<>(Arrays.asList("204/206", "207/206", "208/206"))),
-        GENERAL("GENERAL", "Ratio", new ArrayList<>(Arrays.asList()), new ArrayList<>(Arrays.asList()));
+        GENERAL("GENERAL", "General (Ratio)", new ArrayList<>(Arrays.asList()), new ArrayList<>(Arrays.asList()));
 
         private final String name;
         private final String projectName;

diff --git a/squidCore/src/main/java/org/cirdles/squid/prawn/RunParameterNames.java b/squidCore/src/main/java/org/cirdles/squid/prawn/RunParameterNames.java
@@ -280,7 +280,15 @@ public enum RunParameterNames implements Serializable {
     @XmlEnumValue("raster_time_sec")
     raster_time_sec("raster_time_sec"),
     @XmlEnumValue("raster_after_burn_time_sec")
-    raster_after_burn_time_sec("raster_after_burn_time_sec");
+    raster_after_burn_time_sec("raster_after_burn_time_sec"),
+
+    @XmlEnumValue("pressure_names")
+    pressure_names("pressure_names"),
+
+    @XmlEnumValue("pressures")
+    pressures("pressures");
+
+
 
     private final String value;
 

diff --git a/squidCore/src/main/java/org/cirdles/squid/projects/SquidProject.java b/squidCore/src/main/java/org/cirdles/squid/projects/SquidProject.java
@@ -225,6 +225,7 @@ public void createNewTask() throws SquidException {
         this.task = new Task(
                 "New Task", prawnFile, prawnFileHandler.getNewReportsEngine());
 
+        this.task.setTaskType(projectType);
         this.task.setDelimiterForUnknownNames(delimiterForUnknownNames);
         this.task.setFilterForConcRefMatSpotNames(filterForConcRefMatSpotNames);
         this.task.setFilterForRefMatSpotNames(filterForRefMatSpotNames);

diff --git a/squidCore/src/main/java/org/cirdles/squid/tasks/Task.java b/squidCore/src/main/java/org/cirdles/squid/tasks/Task.java
@@ -650,19 +650,19 @@ private void generateSpotMetaDataFields() {
     @Override
     public void generateBuiltInExpressions() {
 
-        SortedSet<Expression> generateReferenceMaterialValues = updateReferenceMaterialValuesFromModel((ReferenceMaterialModel) referenceMaterialModel);
-        taskExpressionsOrdered.addAll(generateReferenceMaterialValues);
-
-        SortedSet<Expression> generateConcReferenceMaterialValues = updateConcReferenceMaterialValuesFromModel((ReferenceMaterialModel) concentrationReferenceMaterialModel);
-        taskExpressionsOrdered.addAll(generateConcReferenceMaterialValues);
-
-        SortedSet<Expression> generateCommonLeadParameterValues = updateCommonLeadParameterValuesFromModel(commonPbModel);
-        taskExpressionsOrdered.addAll(generateCommonLeadParameterValues);
-
         SortedSet<Expression> generatePhysicalConstantsValues = updatePhysicalConstantsParameterValuesFromModel((PhysicalConstantsModel) physicalConstantsModel);
         taskExpressionsOrdered.addAll(generatePhysicalConstantsValues);
 
         if (taskType.equals(GEOCHRON)) {
+            SortedSet<Expression> generateReferenceMaterialValues = updateReferenceMaterialValuesFromModel((ReferenceMaterialModel) referenceMaterialModel);
+            taskExpressionsOrdered.addAll(generateReferenceMaterialValues);
+
+            SortedSet<Expression> generateConcReferenceMaterialValues = updateConcReferenceMaterialValuesFromModel((ReferenceMaterialModel) concentrationReferenceMaterialModel);
+            taskExpressionsOrdered.addAll(generateConcReferenceMaterialValues);
+
+            SortedSet<Expression> generateCommonLeadParameterValues = updateCommonLeadParameterValuesFromModel(commonPbModel);
+            taskExpressionsOrdered.addAll(generateCommonLeadParameterValues);
+
             SortedSet<Expression> generatePlaceholderExpressions = generatePlaceholderExpressions(parentNuclide, isDirectAltPD());
             taskExpressionsOrdered.addAll(generatePlaceholderExpressions);
 

diff --git a/.../cirdles/squid/tasks/expressions/builtinExpressions/BuiltInExpressionsDataDictionary.java b/.../cirdles/squid/tasks/expressions/builtinExpressions/BuiltInExpressionsDataDictionary.java
@@ -26,11 +26,6 @@ public class BuiltInExpressionsDataDictionary {
     // **********************  REQUIRED   **************************************
     public static final String DEFAULT_BACKGROUND_MASS_LABEL = "BKG";
 
-//    public static final List<String> REQUIRED_NOMINAL_MASSES
-//            = new ArrayList<>(Arrays.asList("204", "206", "207", "208"));
-//    public static final List<String> REQUIRED_RATIO_NAMES
-//            = new ArrayList<>(Arrays.asList("204/206", "207/206", "208/206"));
-
     // **********************  SPECIAL CONSTANTS ******************************
     // holding spot until models are implemented
     public static final String REF_238U235U_RM_MODEL_NAME = "r238_235s";