Fixed #680 and #681 (#682)

bowring · web-flow · commit 108e68e218dc · 2022-02-04T06:39:34.000-05:00
* Updated dependency per Snyk * fixed issue #680 * fixed issue #681 * New version
diff --git a/common.gradle b/common.gradle
@@ -7,7 +7,7 @@ apply plugin: 'maven-publish'
 
 
 String mavenGroupId = 'org.cirdles'
-String mavenVersion = '1.9.6'
+String mavenVersion = '1.9.7'
 
 [compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
 
diff --git a/squidAPI/src/main/java/org/cirdles/squid/Squid3API.java b/squidAPI/src/main/java/org/cirdles/squid/Squid3API.java
@@ -104,7 +104,7 @@ void newSquid3GeochronProjectFromDataFileOP(Path dataFileOPSourcePath)
 
     void setUseLinearRegression(boolean doUse) throws SquidException;
 
-    void setPreferredIndexIsotope(Squid3Constants.IndexIsoptopesEnum isotope);
+    void setPreferredIndexIsotope(Squid3Constants.IndexIsoptopesEnum isotope) throws SquidException;
 
     void setAutoExcludeSpots(boolean doAutoExclude) throws SquidException;
 
diff --git a/squidAPI/src/main/java/org/cirdles/squid/Squid3Ink.java b/squidAPI/src/main/java/org/cirdles/squid/Squid3Ink.java
@@ -389,7 +389,7 @@ public void setUseLinearRegression(boolean doUse) throws SquidException {
     }
 
     @Override
-    public void setPreferredIndexIsotope(Squid3Constants.IndexIsoptopesEnum isotope) {
+    public void setPreferredIndexIsotope(Squid3Constants.IndexIsoptopesEnum isotope) throws SquidException {
         squid3Project.setSelectedIndexIsotope(isotope);
         SquidProject.setProjectChanged(true);
         TaskInterface task = squid3Project.getTask();
diff --git a/squidApp/build.gradle b/squidApp/build.gradle
@@ -10,10 +10,8 @@
 // prefer. In this case NetBeans will not add these tasks but you may rely on
 // your own implementation.
 
-//apply plugin: "application"
 plugins {
     id 'application'
-   // id "org.openjfx.javafxplugin" version "0.0.10"
 }
 
 if (!hasProperty('mainClass')) {
@@ -22,16 +20,11 @@ if (!hasProperty('mainClass')) {
 
 mainClassName = 'org.cirdles.squid.gui.SquidUI'
 
-//javafx {
-//    version = "17"
-//    modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web' ]
-//}
-
 dependencies {
     implementation 'org.jetbrains:annotations:22.0.0'
     implementation project(":squidCore")
     implementation group: 'org.apache.xmlgraphics', name: 'batik-svg-dom', version: '1.14'
-    implementation group: 'org.apache.xmlgraphics', name: 'fop', version: '2.6'
+    implementation group: 'org.apache.xmlgraphics', name: 'fop', version: '2.7'
     implementation 'com.github.cirdles:topsoil:87d2f107c0'
     // https://mvnrepository.com/artifact/commons-io/commons-io
     implementation group: 'commons-io', name: 'commons-io', version: '2.11.0'
diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/ProjectManagerController.java b/squidApp/src/main/java/org/cirdles/squid/gui/ProjectManagerController.java
@@ -348,21 +348,21 @@ private void spotAverageRatioCalcRadioButtonAction(ActionEvent event) {
     }
 
     @FXML
-    private void pb204RadioButtonAction(ActionEvent event) {
+    private void pb204RadioButtonAction(ActionEvent event) throws SquidException {
         squidProject.setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum.PB_204);
         SquidProject.setProjectChanged(true);
         task.setChanged(true);
     }
 
     @FXML
-    private void pb207RadioButtonAction(ActionEvent event) {
+    private void pb207RadioButtonAction(ActionEvent event) throws SquidException {
         squidProject.setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum.PB_207);
         SquidProject.setProjectChanged(true);
         task.setChanged(true);
     }
 
     @FXML
-    private void pb208RadioButtonAction(ActionEvent event) {
+    private void pb208RadioButtonAction(ActionEvent event) throws SquidException {
         squidProject.setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum.PB_208);
         SquidProject.setProjectChanged(true);
         task.setChanged(true);
diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/SquidUIController.java b/squidApp/src/main/java/org/cirdles/squid/gui/SquidUIController.java
@@ -748,6 +748,8 @@ private void openProject(String aProjectFileName) throws IOException, SquidExcep
 
                 // fixes #624 by correcting out of synch tasks
                 squidProject.getTask().setSelectedIndexIsotope(squidProject.getSelectedIndexIsotope());
+                squidProject.getTask().setChanged(true);
+                squidProject.getTask().setupSquidSessionSpecsAndReduceAndReport(false);
 
                 ((Task) squidProject.getTask()).buildExpressionDependencyGraphs();
                 ((Task) squidProject.getTask()).updateSquidSpeciesModelsGeochronMode();
diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/plots/plotControllers/RefMatCalibrationConstantWMToolBoxNode.java b/squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/plots/plotControllers/RefMatCalibrationConstantWMToolBoxNode.java
@@ -128,13 +128,25 @@ public void changed(ObservableValue<? extends Toggle> observable, Toggle oldValu
                 correction = ((String) isotopeGroup.getSelectedToggle().getUserData());
                 switch (correction.substring(0, 1)) {
                     case "4":
-                        squidProject.setSelectedIndexIsotope(PB_204);
+                        try {
+                            squidProject.setSelectedIndexIsotope(PB_204);
+                        } catch (SquidException e) {
+                            e.printStackTrace();
+                        }
                         break;
                     case "7":
-                        squidProject.setSelectedIndexIsotope(PB_207);
+                        try {
+                            squidProject.setSelectedIndexIsotope(PB_207);
+                        } catch (SquidException e) {
+                            e.printStackTrace();
+                        }
                         break;
                     default: // case 8
-                        squidProject.setSelectedIndexIsotope(PB_208);
+                        try {
+                            squidProject.setSelectedIndexIsotope(PB_208);
+                        } catch (SquidException e) {
+                            e.printStackTrace();
+                        }
                 }
                 squidProject.getTask().setChanged(true);
 
diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/plots/plotControllers/RefMatConcordiaToolBoxNode.java b/squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/plots/plotControllers/RefMatConcordiaToolBoxNode.java
@@ -108,13 +108,25 @@ public void changed(ObservableValue<? extends Toggle> observable, Toggle oldValu
                 correction = ((String) isotopeGroup.getSelectedToggle().getUserData());
                 switch (correction.substring(0, 1)) {
                     case "4":
-                        squidProject.setSelectedIndexIsotope(PB_204);
+                        try {
+                            squidProject.setSelectedIndexIsotope(PB_204);
+                        } catch (SquidException e) {
+                            e.printStackTrace();
+                        }
                         break;
                     case "7":
-                        squidProject.setSelectedIndexIsotope(PB_207);
+                        try {
+                            squidProject.setSelectedIndexIsotope(PB_207);
+                        } catch (SquidException e) {
+                            e.printStackTrace();
+                        }
                         break;
                     default: // case 8
-                        squidProject.setSelectedIndexIsotope(PB_208);
+                        try {
+                            squidProject.setSelectedIndexIsotope(PB_208);
+                        } catch (SquidException e) {
+                            e.printStackTrace();
+                        }
                 }
 
                 squidProject.getTask().setChanged(true);
diff --git a/squidCore/build.gradle b/squidCore/build.gradle
@@ -26,7 +26,7 @@ dependencies {
     implementation "org.apache.commons:commons-math3:3.6.1"
     implementation group: 'com.google.guava', name: 'guava', version: '31.0.1-jre'
 
-    implementation group: 'com.thoughtworks.xstream', name: 'xstream', version: '1.4.18'
+    implementation group: 'com.thoughtworks.xstream', name: 'xstream', version: '1.4.19'
 
     antlr 'org.antlr:antlr4:4.9.3'
     implementation group: 'org.antlr', name: 'antlr4-runtime', version: '4.9.3'
diff --git a/squidCore/src/main/java/org/cirdles/squid/projects/Squid3ProjectBasicAPI.java b/squidCore/src/main/java/org/cirdles/squid/projects/Squid3ProjectBasicAPI.java
@@ -164,7 +164,7 @@ public boolean setupPrawnOPFile(File opFileNew)
     /**
      * @param selectedIndexIsotope the selectedIndexIsotope to set
      */
-    void setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum selectedIndexIsotope);
+    void setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum selectedIndexIsotope) throws SquidException;
 
     /**
      * @return the sessionDurationHours
diff --git a/squidCore/src/main/java/org/cirdles/squid/projects/SquidProject.java b/squidCore/src/main/java/org/cirdles/squid/projects/SquidProject.java
@@ -227,6 +227,7 @@ public void createNewTask() throws SquidException {
         this.task.setCommonPbModel(commonPbModel);
         this.task.setPhysicalConstantsModel(physicalConstantsModel);
         this.task.setSelectedIndexIsotope(selectedIndexIsotope);
+        this.task.setupSquidSessionSpecsAndReduceAndReport(false);
         this.task.setSquidAllowsAutoExclusionOfSpots(squidAllowsAutoExclusionOfSpots);
         this.task.setExtPErrU(extPErrU);
         this.task.setExtPErrTh(extPErrTh);
@@ -1339,9 +1340,11 @@ public Squid3Constants.IndexIsoptopesEnum getSelectedIndexIsotope() {
     /**
      * @param selectedIndexIsotope the selectedIndexIsotope to set
      */
-    public void setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum selectedIndexIsotope) {
+    public void setSelectedIndexIsotope(Squid3Constants.IndexIsoptopesEnum selectedIndexIsotope) throws SquidException {
         if (task != null) {
             task.setSelectedIndexIsotope(selectedIndexIsotope);
+            task.setChanged(true);
+            task.setupSquidSessionSpecsAndReduceAndReport(false);
         }
         this.selectedIndexIsotope = selectedIndexIsotope;
     }
diff --git a/squidCore/src/main/java/org/cirdles/squid/tasks/Task.java b/squidCore/src/main/java/org/cirdles/squid/tasks/Task.java
@@ -3389,11 +3389,11 @@ public IndexIsoptopesEnum getSelectedIndexIsotope() {
     @Override
     public void setSelectedIndexIsotope(IndexIsoptopesEnum selectedIndexIsotope) {
         this.selectedIndexIsotope = selectedIndexIsotope;
-        try {
-            changed = true;
-            setupSquidSessionSpecsAndReduceAndReport(false);
-        } catch (SquidException squidException) {
-        }
+//        try {
+//            changed = true;
+//            setupSquidSessionSpecsAndReduceAndReport(false);
+//        } catch (SquidException squidException) {
+//        }
     }
 
     @Override
@@ -3872,7 +3872,11 @@ public int hashCode() {
      */
     public String getxAxisExpressionName() {
         if (xAxisExpressionName == null) {
-            xAxisExpressionName = "204/206";
+            if (namedExpressionsMap.containsKey("LnUOU")) {
+                xAxisExpressionName = "LnUOU";
+            } else {
+                xAxisExpressionName = "204/206";
+            }
         }
         return xAxisExpressionName;
     }
@@ -3889,7 +3893,11 @@ public void setxAxisExpressionName(String xAxisExpressionName) {
      */
     public String getyAxisExpressionName() {
         if (yAxisExpressionName == null) {
-            yAxisExpressionName = "204/206";
+            if (namedExpressionsMap.containsKey("LnPbU")) {
+                yAxisExpressionName = "LnPbU";
+            } else {
+                yAxisExpressionName = "204/206";
+            }
         }
         return yAxisExpressionName;
     }

Original file line number	Diff line number	Diff line change
`@@ -389,7 +389,7 @@ public void setUseLinearRegression(boolean doUse) throws SquidException {`
`389`	`389`	`}`
`390`	`390`
`391`	`391`	`@Override`
`392`		`- public void setPreferredIndexIsotope(Squid3Constants.IndexIsoptopesEnum isotope) {`
	`392`	`+ public void setPreferredIndexIsotope(Squid3Constants.IndexIsoptopesEnum isotope) throws SquidException {`
`393`	`393`	`squid3Project.setSelectedIndexIsotope(isotope);`
`394`	`394`	`SquidProject.setProjectChanged(true);`
`395`	`395`	`TaskInterface task = squid3Project.getTask();`