Update to CDA processing

Added validation to spreadsheet

5 files changed, 61 insertions, 7 deletions

diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/DeidentifyCDAHandler.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/DeidentifyCDAHandler.java
index da3e4589..7b4982f9 100644
--- a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/DeidentifyCDAHandler.java
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/DeidentifyCDAHandler.java
@@ -583,7 +583,7 @@ public class DeidentifyCDAHandler extends AbstractHandler {
 
 			int i = file.getName().lastIndexOf(file.getFileExtension());
 
-			IFile df = f.getFile(file.getName().substring(0, i - 1) + "_D" + ".xml");
+			IFile df = f.getFile(file.getName().substring(0, i - 1) + "_DeIdentified.xml");
 
 			try (OutputStream fileOut = Files.newOutputStream(Paths.get(df.getLocation().toOSString()))) {
 				CDAUtil.save(clinicalDocument, fileOut);
diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/GenerateCDADataHandler.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/GenerateCDADataHandler.java
index bb572f33..aa356c0a 100644
--- a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/GenerateCDADataHandler.java
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/GenerateCDADataHandler.java
@@ -268,6 +268,8 @@ public class GenerateCDADataHandler extends GenerateCDABaseHandler {
 
 	static boolean omitUnits = false;
 
+	static boolean omitValidation = false;
+
 	static HashMap<String, String> organizations = new HashMap<String, String>();
 
 	static String preferenceFilters;
@@ -350,6 +352,9 @@ public class GenerateCDADataHandler extends GenerateCDABaseHandler {
 		preferenceFilters = org.eclipse.mdht.uml.cda.ui.internal.Activator.getDefault().getPreferenceStore().getString(
 			MDHTPreferences.CDA_REPORT_DEFAULT_FILTER);
 
+		omitValidation = org.eclipse.mdht.uml.cda.ui.internal.Activator.getDefault().getPreferenceStore().getBoolean(
+			MDHTPreferences.OMIT_VALIDATION_STORE_VALUE);
+
 		final HashSet<EClass> theSections = new HashSet<EClass>();
 
 		final HashMap<EClass, HashSet<EClass>> theSectionCache = new HashMap<EClass, HashSet<EClass>>();
diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/SpreadsheetSerializer.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/SpreadsheetSerializer.java
index d0e0afd7..7883c284 100644
--- a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/SpreadsheetSerializer.java
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/SpreadsheetSerializer.java
@@ -25,6 +25,7 @@ import org.apache.poi.ss.usermodel.Sheet;
 import org.apache.poi.xssf.streaming.SXSSFSheet;
 import org.eclipse.emf.common.util.Diagnostic;
 import org.eclipse.emf.common.util.EList;
+import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.ecore.util.Diagnostician;
 import org.eclipse.emf.ecore.util.EcoreUtil;
 import org.eclipse.mdht.cda.xml.ui.handlers.CDAValueUtil.DocumentMetadata;
@@ -125,7 +126,9 @@ public class SpreadsheetSerializer {
 			Row row = sheet.createRow(sheet.getPhysicalNumberOfRows());
 			int offset = serializePatient(row, 0, documentMetadata, patientRole);
 			offset = serializeEncounter(row, offset, encounter);
-			serializeSectionAndFileName(row, offset, encounter.getSection(), fileName);
+			offset = serializeSectionAndFileName(row, offset, encounter.getSection(), fileName);
+			offset = appendValidation(row, offset, encounter);
+
 		}
 
 	}
@@ -781,7 +784,9 @@ public class SpreadsheetSerializer {
 
 			offset = serializeProcedureActivityProcedure(row, offset, sa);
 
-			serializeSectionAndFileName(row, offset, sa.getSection(), fileName);
+			offset = serializeSectionAndFileName(row, offset, sa.getSection(), fileName);
+
+			offset = appendValidation(row, offset, sa);
 
 		}
 
@@ -802,6 +807,7 @@ public class SpreadsheetSerializer {
 				int offset = serializePatient(row, 0, organizationAndSoftware, patientRole);
 				offset = serializeEncounter(row, offset, encoutner);
 				serializeSectionAndFileName(row, offset, encoutner.getSection(), fileName);
+				offset = appendValidation(row, offset, encoutner);
 			}
 		}
 	}
@@ -948,7 +954,8 @@ public class SpreadsheetSerializer {
 				offset = SpreadsheetSerializer.serializeEnounterID(row, offset, sa, encounters);
 				offset = serializeOrganizer(row, offset, sa, true, false);
 				offset = serializeObservation(row, offset, resultObservation);
-				serializeSectionAndFileName(row, offset, sa.getSection(), fileName);
+				offset = serializeSectionAndFileName(row, offset, sa.getSection(), fileName);
+				offset = appendValidation(row, offset, sa);
 			}
 		}
 	}
@@ -969,7 +976,8 @@ public class SpreadsheetSerializer {
 			offset = serializePatient(row, offset, organizationAndSoftware, patientRole);
 			offset = SpreadsheetSerializer.serializeEnounterID(row, offset, sa, encounters);
 			offset = serializeSubstanceAdministration(row, offset, sa);
-			serializeSectionAndFileName(row, offset, sa.getSection(), fileName);
+			offset = serializeSectionAndFileName(row, offset, sa.getSection(), fileName);
+			offset = appendValidation(row, offset, sa);
 		}
 	}
 
@@ -995,6 +1003,7 @@ public class SpreadsheetSerializer {
 				offset = serializeOrganizer(row, offset, organizer, false, false);
 				offset = serializeObservation(row, offset, observation);
 				serializeSectionAndFileName(row, offset, observation.getSection(), fileName);
+				offset = appendValidation(row, offset, observation);
 			}
 
 		}
@@ -2002,4 +2011,29 @@ public class SpreadsheetSerializer {
 		return offset;
 	}
 
+	public static int appendValidation(Row row, int offset, EObject target) {
+
+		if (!GenerateCDADataHandler.omitValidation) {
+
+			Diagnostic diagnostic = Diagnostician.INSTANCE.validate(target);
+
+			ValidationResult vr = new ValidationResult();
+
+			if (diagnostic.getChildren().size() > 0) {
+				processDiagnostic(diagnostic, vr);
+			}
+
+			StringBuffer sb = new StringBuffer();
+
+			for (Diagnostic dq : vr.getErrorDiagnostics()) {
+
+				sb.append(dq.getMessage()).append("\r");
+
+			}
+			row.createCell(offset++).setCellValue(sb.toString());
+		}
+
+		return offset;
+	}
+
 }
diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/StripCDANarrativeHandler.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/StripCDANarrativeHandler.java
index 0545a5ab..5663ee54 100644
--- a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/StripCDANarrativeHandler.java
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/StripCDANarrativeHandler.java
@@ -213,7 +213,7 @@ public class StripCDANarrativeHandler extends AbstractHandler {
 
 			int i = file.getName().lastIndexOf(file.getFileExtension());
 
-			IFile df = f.getFile(file.getName().substring(0, i - 1) + "_D" + ".xml");
+			IFile df = f.getFile(file.getName().substring(0, i - 1) + "_NoNarrative.xml");
 
 			try (OutputStream fileOut = Files.newOutputStream(Paths.get(df.getLocation().toOSString()))) {
 				CDAUtil.save(clinicalDocument, fileOut);
diff --git a/cda/plugins/org.eclipse.mdht.uml.cda.ui/src/org/eclipse/mdht/uml/cda/ui/editors/MDHTPreferences.java b/cda/plugins/org.eclipse.mdht.uml.cda.ui/src/org/eclipse/mdht/uml/cda/ui/editors/MDHTPreferences.java
index 72ced605..8fdd1074 100644
--- a/cda/plugins/org.eclipse.mdht.uml.cda.ui/src/org/eclipse/mdht/uml/cda/ui/editors/MDHTPreferences.java
+++ b/cda/plugins/org.eclipse.mdht.uml.cda.ui/src/org/eclipse/mdht/uml/cda/ui/editors/MDHTPreferences.java
@@ -84,6 +84,8 @@ public class MDHTPreferences extends PreferencePage implements IWorkbenchPrefere
 
 	public static String OMIT_UNITS_STORE_VALUE = "OmitUnitsCheckValue";
 
+	public static String OMIT_VALIDATION_STORE_VALUE = "OmitValidationStoreValue";
+
 	public static String CDA_REPORT_DEFAULT_FILTER = "CDAReportDefaultFilter";
 
 	private static String OMIT_DOB_CHECK_BOX_LABEL = "Omit DOB and Patient Name from XLS Reports";
@@ -94,10 +96,14 @@ public class MDHTPreferences extends PreferencePage implements IWorkbenchPrefere
 
 	private static String OMIT_UNITS_CHECK_BOX_LABEL = "Omit Quantity Units from XLS Reports";
 
+	private static String OMIT_VALIDATION_CHECK_BOX_LABEL = "Omit CDA Validation from XLS Reports";
+
+	private static String OMIT_VALIDATION_CHECK_BOX_TOOLTIP = "Do not include DCDA Validation in reports";
+
 	/**
 	 * FilterListSelectionDialog
 	 * The dialog buttons were not easily accessible to change the text for OK and Cancel
-	 * 
+	 *
 	 * @TODO This might not be the correct way to do this
 	 * @author seanmuir
 	 *
@@ -141,6 +147,8 @@ public class MDHTPreferences extends PreferencePage implements IWorkbenchPrefere
 
 	private Text cdaReportFilterText;
 
+	private Button omitValidationCheckBox;
+
 	final ArrayList<String> cdaReportfilters = new ArrayList<String>();
 
 	/**
@@ -324,6 +332,10 @@ public class MDHTPreferences extends PreferencePage implements IWorkbenchPrefere
 		Composite dob_composite_textField = createComposite(parent, 2);
 		omitDOBCheckBox = createCheckBox(dob_composite_textField, OMIT_DOB_CHECK_BOX_LABEL, OMIT_DOB_CHECK_BOX_TOOLTIP);
 
+		Composite validateion_composite_textField = createComposite(parent, 2);
+		omitValidationCheckBox = createCheckBox(
+			validateion_composite_textField, OMIT_VALIDATION_CHECK_BOX_LABEL, OMIT_VALIDATION_CHECK_BOX_TOOLTIP);
+
 		Composite units_composite_textField = createComposite(parent, 2);
 		omitUnitsCheckBox = createCheckBox(
 			units_composite_textField, OMIT_UNITS_CHECK_BOX_LABEL, OMIT_UNITS_CHECK_BOX_TOOLTIP);
@@ -372,6 +384,7 @@ public class MDHTPreferences extends PreferencePage implements IWorkbenchPrefere
 		disablePdfGenerationCheckBox.setSelection(store.getBoolean(PDF_GEN_STORE_VALUE));
 		omitDOBCheckBox.setSelection(store.getBoolean(OMIT_DOB_STORE_VALUE));
 		omitUnitsCheckBox.setSelection(store.getBoolean(OMIT_UNITS_STORE_VALUE));
+		omitValidationCheckBox.setSelection(store.getBoolean(OMIT_VALIDATION_STORE_VALUE));
 		cdaReportFilterText.setText(NONE);
 	}
 
@@ -384,6 +397,7 @@ public class MDHTPreferences extends PreferencePage implements IWorkbenchPrefere
 		disablePdfGenerationCheckBox.setSelection(store.getBoolean(PDF_GEN_STORE_VALUE));
 		omitDOBCheckBox.setSelection(store.getBoolean(OMIT_DOB_STORE_VALUE));
 		omitUnitsCheckBox.setSelection(store.getBoolean(OMIT_UNITS_STORE_VALUE));
+		omitValidationCheckBox.setSelection(store.getBoolean(OMIT_VALIDATION_STORE_VALUE));
 		String preferenceFilters = store.getString(CDA_REPORT_DEFAULT_FILTER);
 		cdaReportFilterText.setText(formatFilterNames(Arrays.asList(preferenceFilters.split("\\s*,\\s*"))));
 	}
@@ -409,6 +423,7 @@ public class MDHTPreferences extends PreferencePage implements IWorkbenchPrefere
 		store.setValue(PDF_GEN_STORE_VALUE, disablePdfGenerationCheckBox.getSelection());
 		store.setValue(OMIT_DOB_STORE_VALUE, omitDOBCheckBox.getSelection());
 		store.setValue(OMIT_UNITS_STORE_VALUE, omitUnitsCheckBox.getSelection());
+		store.setValue(OMIT_VALIDATION_STORE_VALUE, omitValidationCheckBox.getSelection());
 		StringBuilder sb = new StringBuilder();
 		for (String filter : cdaReportfilters) {
 			if (sb.length() > 0) {