Improved SquidInkAPI and fixed a bug.

common.gradle

@@ -6,7 +6,7 @@ apply plugin: 'java'
 apply plugin: 'maven'
 
 String mavenGroupId = 'org.cirdles'
-String mavenVersion = '1.7.3'
+String mavenVersion = '1.7.4'
 
 sourceCompatibility = '1.8'
 [compileJava, compileTestJava]*.options*.encoding = 'UTF-8'

squidAPI/src/main/java/org/cirdles/squid/Squid3API.java

@@ -38,23 +38,23 @@ public interface Squid3API {
     public Squid3ProjectBasicAPI getSquid3Project();
 
     /**
-     * 
+     *
      * @param prawnXMLFileSourcePath
      * @throws IOException
      * @throws JAXBException
      * @throws SAXException
-     * @throws SquidException 
+     * @throws SquidException
      */
     public void newSquid3GeochronProjectFromPrawnXML(Path prawnXMLFileSourcePath)
             throws IOException, JAXBException, SAXException, SquidException;
-    
+
     /**
-     * 
+     *
      * @param prawnXMLFileSourcePath
      * @throws IOException
      * @throws JAXBException
      * @throws SAXException
-     * @throws SquidException 
+     * @throws SquidException
      */
     public void newSquid3GeochronProjectFromZippedPrawnXML(Path prawnXMLFileSourcePath)
             throws IOException, JAXBException, SAXException, SquidException;
@@ -93,10 +93,45 @@ public void newSquid3GeochronProjectFromZippedPrawnXML(Path prawnXMLFileSourcePa
     public void saveAsSquid3Project(File squid3ProjectFileTarget) throws IOException, SquidException;
 
     // reports management ++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    /**
+     * 
+     * @return
+     * @throws IOException 
+     */
+    public Path generateReferenceMaterialSummaryExpressionsReport() throws IOException;
+
+    /**
+     * 
+     * @return
+     * @throws IOException 
+     */
+    public Path generateUnknownsSummaryExpressionsReport() throws IOException;
+
+    /**
+     * 
+     * @return
+     * @throws IOException 
+     */
+    public Path generateTaskSummaryReport() throws IOException;
+
+    /**
+     * 
+     * @return
+     * @throws IOException 
+     */
+    public Path generateProjectAuditReport() throws IOException;
+
+    /**
+     * 
+     * @return
+     * @throws IOException 
+     */
+    public Path generatePerScanReports() throws IOException;
+
     /**
      *
      * @throws IOException
      */
-    public void generateAllSquid3ProjectReports() throws IOException;
+    public Path generateAllSquid3ProjectReports() throws IOException;
 
 }

squidAPI/src/main/java/org/cirdles/squid/Squid3Ink.java

@@ -19,9 +19,12 @@
 import java.io.IOException;
 import java.nio.file.Path;
 import java.util.List;
+import javafx.event.ActionEvent;
+import javafx.fxml.FXML;
 import javax.xml.bind.JAXBException;
 import static org.cirdles.squid.constants.Squid3Constants.DEMO_SQUID_PROJECTS_FOLDER;
 import static org.cirdles.squid.constants.Squid3Constants.TaskTypeEnum.GEOCHRON;
+import org.cirdles.squid.dialogs.SquidMessageDialog;
 import org.cirdles.squid.exceptions.SquidException;
 import org.cirdles.squid.parameters.ParametersModelComparator;
 import org.cirdles.squid.parameters.parameterModels.commonPbModels.CommonPbModel;
@@ -264,15 +267,58 @@ public void saveAsSquid3Project(File squid3ProjectFileTarget) throws IOException
 
     // REPORTS +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     /**
-     * This method first checks to see if reports folder is initialized
      *
-     * @throws IOException
+     * @return @throws IOException
      */
     @Override
-    public void generateAllSquid3ProjectReports() throws IOException {
-        if (squid3Project.hasReportsFolder()) {
-            ((Squid3ProjectReportingAPI) squid3Project).generateAllReports();
-        }
+    public Path generateReferenceMaterialSummaryExpressionsReport() throws IOException {
+        return ((Squid3ProjectReportingAPI) squid3Project).generateReferenceMaterialSummaryExpressionsReport();
+    }
+
+    /**
+     *
+     * @return @throws IOException
+     */
+    @Override
+    public Path generateUnknownsSummaryExpressionsReport() throws IOException {
+        return ((Squid3ProjectReportingAPI) squid3Project).generateUnknownsSummaryExpressionsReport();
+    }
+
+    /**
+     *
+     * @return @throws IOException
+     */
+    @Override
+    public Path generateTaskSummaryReport() throws IOException {
+        return ((Squid3ProjectReportingAPI) squid3Project).generateTaskSummaryReport();
+    }
+
+    /**
+     *
+     * @return @throws IOException
+     */
+    @Override
+    public Path generateProjectAuditReport() throws IOException {
+        return ((Squid3ProjectReportingAPI) squid3Project).generateProjectAuditReport();
+    }
+
+    /**
+     *
+     * @return @throws IOException
+     */
+    @Override
+    public Path generateAllSquid3ProjectReports() throws IOException {
+        return ((Squid3ProjectReportingAPI) squid3Project).generateAllReports();
+    }
+
+    /**
+     * 
+     * @return
+     * @throws IOException 
+     */
+    @Override
+    public Path generatePerScanReports() throws IOException {
+        return ((Squid3ProjectReportingAPI) squid3Project).generatePerScanReports();
     }
 
     /**
@@ -285,20 +331,24 @@ public void generateAllSquid3ProjectReports() throws IOException {
     public static void main(String[] args) throws IOException, SquidException, JAXBException, SAXException {
         Squid3API squid3Ink = Squid3Ink.spillSquid3Ink();
 
-        //squid3Ink.openDemonstrationSquid3Project();
+        squid3Ink.openDemonstrationSquid3Project();
 //        squid3Ink.newSquid3GeochronProjectFromPrawnXML(
 //                (new File("Squid3_Resources/ExamplePrawnXMLFiles/836_1_2016_Nov_28_09.50.xml")).toPath());
-        squid3Ink.newSquid3GeochronProjectFromZippedPrawnXML(
-                (new File("zippy/836_1_2016_Nov_28_09.50.xml.zip")).toPath());
-
+//        squid3Ink.newSquid3GeochronProjectFromZippedPrawnXML(
+//                (new File("zippy/836_1_2016_Nov_28_09.50.xml.zip")).toPath());
+//        
         squid3Ink.generateAllSquid3ProjectReports();
         System.out.println(squid3Ink.getSquid3Project().getProjectName()
-                + "   " + squid3Ink.getSquid3Project().getPrawnFileHandler().getReportsEngine().makeReportFolderStructure());
-
-        squid3Ink.saveAsSquid3Project(new File("XXXXXX.squid"));
-        squid3Ink.generateAllSquid3ProjectReports();
-        System.out.println(squid3Ink.getSquid3Project().getProjectName()
-                + "   " + squid3Ink.getSquid3Project().getPrawnFileHandler().getReportsEngine().makeReportFolderStructure());
+                + "\n" + squid3Ink.getSquid3Project().getPrawnFileHandler().getReportsEngine().makeReportFolderStructure());
+        try {
+            System.out.println(squid3Ink.generateReferenceMaterialSummaryExpressionsReport().toString());
+            System.out.println(squid3Ink.generatePerScanReports().toString());
+        } catch (IOException iOException) {
+        }
+//        squid3Ink.saveAsSquid3Project(new File("XXXXXX.squid"));
+//        squid3Ink.generateAllSquid3ProjectReports();
+//        System.out.println(squid3Ink.getSquid3Project().getProjectName()
+//                + "   " + squid3Ink.getSquid3Project().getPrawnFileHandler().getReportsEngine().makeReportFolderStructure());
 
         System.out.println(squid3Ink.retrieveSquid3ProjectListMRU());
     }

squidCore/src/main/java/org/cirdles/squid/projects/Squid3ProjectReportingAPI.java

@@ -14,5 +14,74 @@
  */
 public interface Squid3ProjectReportingAPI {
 
+    public default boolean generateReportsValid() {
+        return (!((SquidProject) this).getTask().getNominalMasses().isEmpty())
+                && ((SquidProject) this).hasReportsFolder()
+                && ((SquidProject) this).prawnFileExists();
+    }
+
+    public default Path generateReferenceMaterialSummaryExpressionsReport() throws IOException {
+        Path summaryFilePath = null;
+        if (generateReportsValid()) {
+            summaryFilePath
+                    = ((SquidProject) this).getPrawnFileHandler().getReportsEngine().writeSummaryReportsForReferenceMaterials().toPath();
+        }
+        if (summaryFilePath == null) {
+            throw new IOException("Squid3 unable to generateReferenceMaterialSummaryExpressionsReport");
+        } else {
+            return summaryFilePath;
+        }
+    }
+
+    public default Path generateUnknownsSummaryExpressionsReport() throws IOException {
+        Path summaryFilePath = null;
+        if (generateReportsValid()) {
+            summaryFilePath
+                    = ((SquidProject) this).getPrawnFileHandler().getReportsEngine().writeSummaryReportsForUnknowns().toPath();
+        }
+        if (summaryFilePath == null) {
+            throw new IOException("Squid3 unable to generateUnknownsSummaryExpressionsReport");
+        } else {
+            return summaryFilePath;
+        }
+    }
+
+    public default Path generateTaskSummaryReport() throws IOException {
+        Path taskAuditFilePath = null;
+        if (generateReportsValid()) {
+            taskAuditFilePath = ((SquidProject) this).getPrawnFileHandler().getReportsEngine().writeTaskAudit().toPath();
+        }
+        if (taskAuditFilePath == null) {
+            throw new IOException("Squid3 unable to generateTaskSummaryReport");
+        } else {
+            return taskAuditFilePath;
+        }
+    }
+
+    public default Path generateProjectAuditReport() throws IOException {
+        Path projectAuditFilePath = null;
+        if (generateReportsValid()) {
+            projectAuditFilePath = ((SquidProject) this).getPrawnFileHandler().getReportsEngine().writeProjectAudit().toPath();
+        }
+        if (projectAuditFilePath == null) {
+            throw new IOException("Squid3 unable to generateProjectAuditReport");
+        } else {
+            return projectAuditFilePath;
+        }
+    }
+
+    public default Path generatePerScanReports() throws IOException {
+        Path projectScanReportsPath = null;
+        if (generateReportsValid()) {
+            projectScanReportsPath = ((SquidProject) this).getTask().producePerScanReportsToFiles().toPath();
+        }
+        if (projectScanReportsPath == null) {
+            throw new IOException("Squid3 unable to generatePerScanReports");
+        } else {
+            return projectScanReportsPath;
+        }
+    }
+
     public Path generateAllReports() throws IOException;
+
 }

squidCore/src/main/java/org/cirdles/squid/projects/SquidProject.java

@@ -873,27 +873,29 @@ public String[] splitPrawnFileAtRun(Run run, boolean useOriginalData)
         return retVal;
     }
 
+    @Override
     public Path generateAllReports() throws IOException {
-        if (prawnFileExists()) {
-            if (filterForConcRefMatSpotNames.length() > 0) {
-                prawnFileHandler.getReportsEngine().writeProjectAudit();
-                prawnFileHandler.getReportsEngine().writeTaskAudit();
-
-                prawnFileHandler.getReportsEngine().writeSummaryReportsForReferenceMaterials();
-                produceReferenceMaterialPerSquid25CSV(true);
-                produceSelectedReferenceMaterialReportCSV();
-
-                prawnFileHandler.getReportsEngine().writeSummaryReportsForUnknowns();
-                produceUnknownsPerSquid25CSV(true);
-                produceUnknownsBySampleForETReduxCSV(true);
-                produceSelectedUnknownsReportCSV();
-                produceUnknownsWeightedMeanSortingFieldsCSV();
-            }
 
+        if (prawnFileExists()) {
             // these are raw data reports
             getTask().producePerScanReportsToFiles();
         }
 
+        if (generateReportsValid()) {
+            prawnFileHandler.getReportsEngine().writeProjectAudit();
+            prawnFileHandler.getReportsEngine().writeTaskAudit();
+
+            prawnFileHandler.getReportsEngine().writeSummaryReportsForReferenceMaterials();
+            produceReferenceMaterialPerSquid25CSV(true);
+            produceSelectedReferenceMaterialReportCSV();
+
+            prawnFileHandler.getReportsEngine().writeSummaryReportsForUnknowns();
+            produceUnknownsPerSquid25CSV(true);
+            produceUnknownsBySampleForETReduxCSV(true);
+            produceSelectedUnknownsReportCSV();
+            produceUnknownsWeightedMeanSortingFieldsCSV();
+        }
+
         return (new File(prawnFileHandler.getReportsEngine().makeReportFolderStructure())).toPath();
     }
 

squidCore/src/main/java/org/cirdles/squid/squidReports/squidReportColumns/SquidReportColumn.java

@@ -23,7 +23,6 @@
 import org.cirdles.squid.tasks.expressions.expressionTrees.ExpressionTree;
 import org.cirdles.squid.tasks.expressions.expressionTrees.ExpressionTreeInterface;
 import org.cirdles.squid.tasks.expressions.isotopes.ShrimpSpeciesNode;
-import org.cirdles.squid.tasks.expressions.operations.Divide;
 import org.cirdles.squid.tasks.expressions.spots.SpotFieldNode;
 import org.cirdles.squid.tasks.expressions.variables.VariableNodeForSummary;
 
@@ -37,7 +36,6 @@
 import static org.cirdles.squid.squidReports.squidReportColumns.SquidReportColumnInterface.formatBigDecimalForPublicationSigDigMode;
 import static org.cirdles.squid.squidReports.squidReportTables.SquidReportTable.DEFAULT_COUNT_OF_SIGNIFICANT_DIGITS;
 import static org.cirdles.squid.squidReports.squidReportTables.SquidReportTable.HEADER_ROW_COUNT;
-import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.R204PB_206PB;
 
 /**
  * @author James F. Bowring, CIRDLES.org, and Earth-Time.org
@@ -121,11 +119,11 @@ public void initReportColumn(TaskInterface task) {
             expressionNameCustom = "total_" + expressionName + "_cts_/sec";
         }
 
-        amIsotopicRatio = false;
-        if (((ExpressionTree) expTree).getLeftET() instanceof ShrimpSpeciesNode) {
-            // Check for isotopic ratios
-            amIsotopicRatio = (((ExpressionTree) expTree).getOperation() instanceof Divide);
-        }
+        amIsotopicRatio = ((ExpressionTree) expTree).amIsotopicRatio();
+//        if (((ExpressionTree) expTree).getLeftET() instanceof ShrimpSpeciesNode) {
+//            // Check for isotopic ratios
+//            amIsotopicRatio = (((ExpressionTree) expTree).getOperation() instanceof Divide);
+//        }
 
         // propose column headers by splitting on underscores in name
         // row 0 is reserved for category displayname
@@ -180,7 +178,7 @@ public void initReportColumn(TaskInterface task) {
 
         uncertaintyColumn = null;
         if ((uncertaintyDirective.length() == 0)
-                && expTree.builtAsValueModel()
+                && ( expTree.builtAsValueModel() || amIsotopicRatio)
 //                && (!expressionName.toUpperCase().contains("PCT"))
 //                && (!expressionName.toUpperCase().contains("ERR"))
 //                && (!expressionName.toUpperCase().contains("CONCEN"))