Updates to xls generation
modified processing of sections with missing or incorrect template ids
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 75ed50c..1da3c5e 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
@@ -1710,7 +1710,17 @@
}
console.println("Start Section " + section.eClass().getName());
- pss.doSwitch(section);
+ if (!pss.doSwitch(section)) {
+
+ console.println("Error processing section Unknown Template ID ");
+
+ for (II templateId : section.getTemplateIds()) {
+ console.println(
+ "Error processing section Unknown Template ID root : " + templateId.getRoot() +
+ " extension : " + templateId.getExtension());
+ }
+
+ }
console.println("End Section " + stopwatch.elapsed(TimeUnit.MILLISECONDS));
}
diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/ProcessSectionSwitch.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/ProcessSectionSwitch.java
index 1d89d2b..bd43899 100644
--- a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/ProcessSectionSwitch.java
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/ProcessSectionSwitch.java
@@ -11,15 +11,26 @@
*******************************************************************************/
package org.eclipse.mdht.cda.xml.ui.handlers;
+import static org.eclipse.mdht.uml.cda.util.CDAUtil.CDA_ANNOTATION_SOURCE;
+
import java.io.IOException;
+import java.util.HashMap;
import java.util.List;
+import org.apache.commons.lang.StringUtils;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.xssf.streaming.SXSSFWorkbook;
import org.eclipse.core.resources.IFile;
+import org.eclipse.emf.ecore.EAnnotation;
+import org.eclipse.emf.ecore.EClass;
+import org.eclipse.emf.ecore.EClassifier;
+import org.eclipse.emf.ecore.EObject;
+import org.eclipse.emf.ecore.util.EcoreUtil;
import org.eclipse.mdht.cda.xml.ui.handlers.CDAValueUtil.DocumentMetadata;
+import org.eclipse.mdht.cda.xml.ui.internal.Logger;
import org.eclipse.mdht.uml.cda.Act;
+import org.eclipse.mdht.uml.cda.CDAPackage;
import org.eclipse.mdht.uml.cda.Encounter;
import org.eclipse.mdht.uml.cda.Entry;
import org.eclipse.mdht.uml.cda.PatientRole;
@@ -357,7 +368,8 @@
* (non-Javadoc)
*
* @see
- * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseInterventionsSection(org.openhealthtools.mdht.uml.cda.consol.InterventionsSection)
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseInterventionsSection(org.openhealthtools.mdht.uml.cda.consol.
+ * InterventionsSection)
*/
@Override
public Boolean caseInterventionsSection2(InterventionsSection2 section) {
@@ -421,7 +433,8 @@
* (non-Javadoc)
*
* @see
- * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseHealthConcernsSection(org.openhealthtools.mdht.uml.cda.consol.HealthConcernsSection)
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseHealthConcernsSection(org.openhealthtools.mdht.uml.cda.consol.
+ * HealthConcernsSection)
*/
@Override
public Boolean caseHealthConcernsSection(HealthConcernsSection section) {
@@ -796,9 +809,12 @@
// return super.casePlanOfTreatmentSection2(section);
// }
+ HashMap<String, EClass> codeToSection = new HashMap<String, EClass>();
+
/*
* (non-Javadoc)
*
+ *
* @see org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseSection(org.eclipse.mdht.uml.cda.Section)
*/
@Override
@@ -826,4 +842,90 @@
return Boolean.TRUE;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#defaultCase(org.eclipse.emf.ecore.EObject)
+ */
+ @Override
+ public Boolean defaultCase(EObject object) {
+
+ // If not found - try using code
+ Section section = (Section) object;
+
+ Logger.log(Logger.ERROR, "Second Chance");
+
+ if (codeToSection.isEmpty()) {
+ for (EClassifier consolPackageClassifier : ConsolPackage.eINSTANCE.getEClassifiers()) {
+ if (CDAPackage.eINSTANCE.getSection().isSuperTypeOf(CDAPackage.eINSTANCE.getSection())) {
+ EAnnotation annotation = consolPackageClassifier.getEAnnotation(CDA_ANNOTATION_SOURCE);
+ String code = annotation.getDetails().get("code.code");
+ if (!codeToSection.containsKey(code)) {
+ codeToSection.put(code, (EClass) consolPackageClassifier);
+ }
+
+ }
+
+ }
+ }
+
+ boolean processed = false;
+ if (section.getCode() != null && !StringUtils.isEmpty(section.getCode().getCode())) {
+
+ String code = section.getCode().getCode();
+ Logger.log(Logger.ERROR, "Second Chance CODE " + code);
+
+ if (codeToSection.containsKey(code)) {
+ Section newSection = (Section) EcoreUtil.create(codeToSection.get(code));
+ newSection.setText(section.getText());
+ newSection.getEntries().addAll(section.getEntries());
+
+ Logger.log(Logger.ERROR, "Second Chance SECTION " + newSection.toString());
+
+ String secondChanceSheetIndex = currentHandler.getSheet(
+ section.getClinicalDocument().eClass(), String.valueOf(newSection.eClass().getClassifierID()),
+ GenerateCDADataHandler.sheetName(newSection.eClass()), splitOption);
+
+ SectionSwitch secondChanceSwitch = new SectionSwitch(
+ query, wb.getSheet(secondChanceSheetIndex), documentMetadata, patientRole, serviceEvent, encounters,
+ file.getName());
+ secondChanceSwitch.doSwitch(newSection);
+
+ if (currentHandler.shouldCountSection(newSection)) {
+ currentHandler.getSectionHash(
+ section.getClinicalDocument().eClass().getClassifierID(), secondChanceSheetIndex,
+ splitOption).add(file);
+
+ }
+
+ processed = true;
+ }
+
+ }
+
+ // if can not find - process as a section process only narrative
+ if (!processed) {
+ String secondChanceSheetIndex = currentHandler.getSheet(
+ section.getClinicalDocument().eClass(), String.valueOf(section.eClass().getClassifierID()),
+ GenerateCDADataHandler.sheetName(section.eClass()), splitOption);
+
+ SectionSwitch secondChanceSwitch = new SectionSwitch(
+ query, wb.getSheet(secondChanceSheetIndex), documentMetadata, patientRole, serviceEvent, encounters,
+ file.getName());
+ secondChanceSwitch.setFirstpass(false);
+ secondChanceSwitch.doSwitch(section);
+
+ if (currentHandler.shouldCountSection(section)) {
+ currentHandler.getSectionHash(
+ section.getClinicalDocument().eClass().getClassifierID(), secondChanceSheetIndex, splitOption).add(
+ file);
+
+ }
+
+ }
+
+ // TODO Auto-generated method stub
+ return Boolean.FALSE;
+ }
+
}
diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/SectionSwitch.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/SectionSwitch.java
index f448425..648c907 100644
--- a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/SectionSwitch.java
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/SectionSwitch.java
@@ -80,11 +80,29 @@
class SectionSwitch extends ConsolSwitch<Boolean> {
+ boolean firstpass = true;
+
+ /**
+ * @return the firstpass
+ */
+ public boolean isFirstpass() {
+ return firstpass;
+ }
+
+ /**
+ * @param firstpass
+ * the firstpass to set
+ */
+ public void setFirstpass(boolean firstpass) {
+ this.firstpass = firstpass;
+ }
+
/*
* (non-Javadoc)
*
* @see
- * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseHospitalAdmissionMedicationsSectionEntriesOptional(org.openhealthtools.mdht.uml.cda.
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseHospitalAdmissionMedicationsSectionEntriesOptional(org.openhealthtools.mdht.uml.
+ * cda.
* consol.HospitalAdmissionMedicationsSectionEntriesOptional)
*/
@Override
@@ -140,7 +158,8 @@
* (non-Javadoc)
*
* @see
- * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseComplicationsSection(org.openhealthtools.mdht.uml.cda.consol.ComplicationsSection)
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseComplicationsSection(org.openhealthtools.mdht.uml.cda.consol.
+ * ComplicationsSection)
*/
@Override
public Boolean caseComplicationsSection(ComplicationsSection section) {
@@ -407,7 +426,8 @@
/*
* (non-Javadoc)
*
- * @see org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseInstructionsSection(org.openhealthtools.mdht.uml.cda.consol.InstructionsSection)
+ * @see
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseInstructionsSection(org.openhealthtools.mdht.uml.cda.consol.InstructionsSection)
*/
@Override
public Boolean caseInstructionsSection(InstructionsSection section) {
@@ -436,7 +456,8 @@
* (non-Javadoc)
*
* @see
- * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseHealthStatusEvaluationsAndOutcomesSection(org.openhealthtools.mdht.uml.cda.consol.
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseHealthStatusEvaluationsAndOutcomesSection(org.openhealthtools.mdht.uml.cda.
+ * consol.
* HealthStatusEvaluationsAndOutcomesSection)
*/
@Override
@@ -839,7 +860,8 @@
* (non-Javadoc)
*
* @see
- * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseChiefComplaintSection(org.openhealthtools.mdht.uml.cda.consol.ChiefComplaintSection)
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseChiefComplaintSection(org.openhealthtools.mdht.uml.cda.consol.
+ * ChiefComplaintSection)
*/
// @Override
// public Boolean caseChiefComplaintSection(ChiefComplaintSection section) {
@@ -866,7 +888,8 @@
* (non-Javadoc)
*
* @see
- * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseDischargeMedicationsSectionEntriesOptional2(org.openhealthtools.mdht.uml.cda.consol.
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseDischargeMedicationsSectionEntriesOptional2(org.openhealthtools.mdht.uml.cda.
+ * consol.
* DischargeMedicationsSectionEntriesOptional2)
*/
@Override
@@ -924,7 +947,8 @@
/*
* (non-Javadoc)
*
- * @see org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseChiefComplaintAndReasonForVisitSection(org.openhealthtools.mdht.uml.cda.consol.
+ * @see
+ * org.openhealthtools.mdht.uml.cda.consol.util.ConsolSwitch#caseChiefComplaintAndReasonForVisitSection(org.openhealthtools.mdht.uml.cda.consol.
* ChiefComplaintAndReasonForVisitSection)
*/
@Override
@@ -939,7 +963,12 @@
*/
@Override
public Boolean defaultCase(EObject object) {
+
+ if (this.firstpass) {
+ return Boolean.FALSE;
+ }
Section section = (Section) object;
+
if (sheet.getPhysicalNumberOfRows() == 0) {
Row row1 = null; // sheet.createRow(0);
Row row2 = sheet.createRow(0);
@@ -1270,8 +1299,6 @@
offset = SpreadsheetSerializer.appendCode(
row, offset, allergyProblemAct.getSection(), severityCode, severity.getText());
} else {
- // tick up offset becuase appendcode will not populate the text column
- offset++;
offset = SpreadsheetSerializer.appendCode(row, offset, allergyProblemAct.getSection(), null, null);
}
offset = SpreadsheetSerializer.appendOrganizationAndAuthor(row, offset, allergyObservation.getAuthors());
@@ -1442,7 +1469,7 @@
offset = SpreadsheetSerializer.serializeNoEnounterID(row, offset);
- // offset = SpreadsheetSerializer.serializeStrucDocText(row, offset, text);
+ offset = SpreadsheetSerializer.serializeStrucDocText(row, offset, text);
SpreadsheetSerializer.serializeSectionAndFileName(row, offset, (Section) text.eContainer(), fileName);
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 50f9d4d..b180a20 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
@@ -19,6 +19,7 @@
import org.apache.commons.lang.StringUtils;
import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.RichTextString;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.xssf.streaming.SXSSFSheet;
@@ -31,6 +32,7 @@
import org.eclipse.mdht.cda.xml.ui.handlers.AnalyzeCDAHandler.CDAAnalaysisInput.CDAMetrics;
import org.eclipse.mdht.cda.xml.ui.handlers.CDAValueUtil.DocumentMetadata;
import org.eclipse.mdht.cda.xml.ui.handlers.GenerateCDADataHandler.WrapperForZipEnty;
+import org.eclipse.mdht.cda.xml.ui.handlers.html.HTMLToExcel;
import org.eclipse.mdht.uml.cda.Act;
import org.eclipse.mdht.uml.cda.AssignedAuthor;
import org.eclipse.mdht.uml.cda.Author;
@@ -156,9 +158,9 @@
if (text != null && !StringUtils.isEmpty(text.getText())) {
String narrative = text.getText();
- // HTMLToExcel hte = new HTMLToExcel();
- // RichTextString s = hte.fromHtmlToCellValue(narrative, row.getSheet().getWorkbook());
- row.createCell(offset++).setCellValue(narrative);
+ HTMLToExcel hte = new HTMLToExcel();
+ RichTextString s = hte.fromHtmlToCellValue(narrative, row.getSheet().getWorkbook());
+ row.createCell(offset++).setCellValue(s.getString());
} else {
row.createCell(offset++).setCellValue("No Narrative");
}
diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/html/HTMLToExcel.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/html/HTMLToExcel.java
index 827f0bc..d9f510b 100644
--- a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/html/HTMLToExcel.java
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/html/HTMLToExcel.java
@@ -85,12 +85,12 @@
}
RichTextString richText = new XSSFRichTextString(textBuffer.toString());
- for (int i = 0; i < textBuffer.length(); i++) {
- Font currentFont = mergedMap.get(i);
- if (currentFont != null) {
- richText.applyFont(i, i + 1, currentFont);
- }
- }
+ // for (int i = 0; i < textBuffer.length(); i++) {
+ // Font currentFont = mergedMap.get(i);
+ // if (currentFont != null) {
+ // richText.applyFont(i, i + 1, currentFont);
+ // }
+ // }
return richText;
}
