Updates to Generate XLS
Added demographics worksheet
diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/GenerateCDABaseHandler.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/GenerateCDABaseHandler.java
index 341afc2..136d784 100644
--- a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/GenerateCDABaseHandler.java
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/ui/handlers/GenerateCDABaseHandler.java
@@ -63,6 +63,7 @@
import org.eclipse.mdht.uml.cda.Encounter;
import org.eclipse.mdht.uml.cda.InFulfillmentOf;
import org.eclipse.mdht.uml.cda.InformationRecipient;
+import org.eclipse.mdht.uml.cda.LanguageCommunication;
import org.eclipse.mdht.uml.cda.ManufacturedProduct;
import org.eclipse.mdht.uml.cda.Observation;
import org.eclipse.mdht.uml.cda.Organization;
@@ -97,6 +98,7 @@
import org.eclipse.mdht.uml.hl7.datatypes.PQ;
import org.eclipse.mdht.uml.hl7.datatypes.REAL;
import org.eclipse.mdht.uml.hl7.datatypes.SXCM_TS;
+import org.eclipse.mdht.uml.hl7.datatypes.TEL;
import org.eclipse.mdht.uml.hl7.datatypes.util.DatatypesSwitch;
import org.eclipse.mdht.uml.hl7.vocab.x_DocumentEncounterMood;
import org.eclipse.swt.SWT;
@@ -2425,6 +2427,17 @@
return offset;
}
+ static int addCodeHeader2(Row row1, int offset, String prefix) {
+ row1.createCell(offset++).setCellValue(prefix + " Text");
+ row1.createCell(offset++).setCellValue("Code");
+ row1.getSheet().setColumnHidden(offset - 1, true);
+ row1.createCell(offset++).setCellValue("Code System");
+ row1.getSheet().setColumnHidden(offset - 1, true);
+ row1.createCell(offset++).setCellValue("Code System Name");
+ row1.getSheet().setColumnHidden(offset - 1, true);
+ return offset;
+ }
+
static int addSectionHeader(Row row1, int offset) {
row1.createCell(offset++).setCellValue("Section Title");
row1.createCell(offset++).setCellValue("File Name");
@@ -2488,8 +2501,10 @@
static int appendCode(Row row, int offset, Section setion, CD cd, ED ed) {
if (cd != null) {
- // Text
- row.createCell(offset++).setCellValue(getValue(setion, ed));
+ // Text - only try if section or ed is not null
+ if (setion != null || ed != null) {
+ row.createCell(offset++).setCellValue(getValue(setion, ed));
+ }
// Display Name
row.createCell(offset++).setCellValue(getValueAsString(setion, cd));
// Code
@@ -2499,7 +2514,9 @@
// Code System Name
row.createCell(offset++).setCellValue(cd.getCodeSystemName());
} else {
- row.createCell(offset++).setCellValue("");
+ if (setion != null || ed != null) {
+ row.createCell(offset++).setCellValue("");
+ }
row.createCell(offset++).setCellValue("");
row.createCell(offset++).setCellValue("");
row.createCell(offset++).setCellValue("");
@@ -3057,6 +3074,18 @@
return offset;
}
+ static int createDemographicsHeader(Row row1, Row row2, int offset) {
+ row2.createCell(offset++).setCellValue("Name");
+ row2.createCell(offset++).setCellValue("Address");
+ offset = addCodeHeader2(row2, offset, "Race");
+ offset = addCodeHeader2(row2, offset, "Ethnicity");
+ offset = addCodeHeader2(row2, offset, "Gender");
+ offset = addCodeHeader2(row2, offset, "Marital Status");
+ offset = addCodeHeader2(row2, offset, "Langauge");
+ offset = addCodeHeader2(row2, offset, "Telephone");
+ return offset;
+ }
+
static int createPatientHeader2(Row row1, Row row2, int offset) {
row2.createCell(offset++).setCellValue("Recipient Name");
row2.createCell(offset++).setCellValue("Recipient Organization");
@@ -3458,6 +3487,29 @@
} else if (cd.getOriginalText() != null && !StringUtils.isEmpty(cd.getOriginalText().getText())) {
sb.append(cd.getOriginalText().getText());
+ } else if (cd.isNullFlavorDefined()) {
+ sb.append(cd.getNullFlavor());
+ }
+
+ }
+
+ return sb.toString();
+ }
+
+ static String getValueAsString(TEL tel) {
+
+ StringBuffer sb = new StringBuffer();
+
+ if (tel != null) {
+
+ if (!StringUtils.isEmpty(tel.getValue())) {
+ sb.append(tel.getValue());
+ } else if (tel.isNullFlavorDefined()) {
+ sb.append(tel.getNullFlavor());
+ }
+
+ if (!tel.getUses().isEmpty()) {
+ sb.append(" " + tel.getUses().get(0));
}
}
@@ -4256,6 +4308,83 @@
return offset;
}
+ /*
+ * race xx
+ * gender xx
+ * patient name
+ * address
+ * dob XXX
+ * phone #
+ * ethnicity
+ * document id XXX
+ * language
+ * phone #
+ */
+ static int serializePatient2(Row row, int offset, DocumentMetadata documentMetadata, PatientRole patientRole) {
+
+ offset = serializePatient(row, offset, documentMetadata, patientRole);
+
+ if (patientRole != null) {
+ if (patientRole.getPatient() != null) {
+
+ Cell cell = row.createCell(offset++);
+ if (!patientRole.getPatient().getNames().isEmpty()) {
+ cell.setCellValue(getValues(patientRole.getPatient().getNames().get(0)));
+ }
+
+ cell = row.createCell(offset++);
+ if (!patientRole.getAddrs().isEmpty()) {
+ cell.setCellValue(getValues(patientRole.getAddrs().get(0)));
+ }
+
+ if (patientRole.getPatient().getRaceCode() != null) {
+ offset = appendCode(row, offset, null, patientRole.getPatient().getRaceCode(), null);
+ }
+
+ if (patientRole.getPatient().getEthnicGroupCode() != null) {
+ offset = appendCode(row, offset, null, patientRole.getPatient().getEthnicGroupCode(), null);
+ }
+
+ if (patientRole.getPatient().getAdministrativeGenderCode() != null) {
+ offset = appendCode(
+ row, offset, null, patientRole.getPatient().getAdministrativeGenderCode(), null);
+ }
+
+ if (patientRole.getPatient().getMaritalStatusCode() != null) {
+ offset = appendCode(row, offset, null, patientRole.getPatient().getMaritalStatusCode(), null);
+ }
+
+ if (!patientRole.getPatient().getLanguageCommunications().isEmpty()) {
+ LanguageCommunication preferredLanguage = null;
+ for (LanguageCommunication lc : patientRole.getPatient().getLanguageCommunications()) {
+ if (preferredLanguage == null && lc.getLanguageCode() != null) {
+ // get one first one with code as default
+ preferredLanguage = lc;
+ }
+ if (lc.getLanguageCode() != null && lc.getPreferenceInd() != null &&
+ lc.getPreferenceInd().getValue()) {
+ preferredLanguage = lc;
+ // found preferred
+ break;
+ }
+ }
+ if (preferredLanguage != null && preferredLanguage.getLanguageCode() != null) {
+ offset = appendCode(row, offset, null, preferredLanguage.getLanguageCode(), null);
+ }
+ }
+
+ cell = row.createCell(offset++);
+ if (!patientRole.getTelecoms().isEmpty()) {
+ cell.setCellValue(getValueAsString(patientRole.getTelecoms().get(0)));
+ } else {
+ cell.setCellValue("");
+ }
+ }
+
+ }
+ return offset;
+ }
+
static int serializePatient(Row row, int offset, DocumentMetadata documentMetadata, PatientRole patientRole) {
Cell cell = row.createCell(offset++);
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 4ad5c57..343743c 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
@@ -30,6 +30,7 @@
import org.apache.poi.ss.usermodel.CellStyle;
import org.apache.poi.ss.usermodel.Font;
import org.apache.poi.ss.usermodel.IndexedColors;
+import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.util.CellReference;
import org.apache.poi.xssf.streaming.SXSSFRow;
import org.apache.poi.xssf.streaming.SXSSFSheet;
@@ -225,11 +226,28 @@
sheets.put(documentIndex, new HashMap<Integer, String>());
}
if (!sheets.get(documentIndex).containsKey(section.eClass().getClassifierID())) {
+
String sheetName = sheetName(section);
+ /*
+ * get and create appears to not use the same length of string
+ * So walk the collection and see if we have the previous version of section created first
+ *
+ *
+ */
+ for (Integer akey : sheets.get(documentIndex).keySet()) {
+ if (sheetName.startsWith(sheets.get(documentIndex).get(akey))) {
+ sheets.get(documentIndex).put(
+ section.eClass().getClassifierID(), sheets.get(documentIndex).get(akey));
+ return sheets.get(documentIndex).get(akey);
+ }
+ }
+
SXSSFWorkbook wb = getWorkbook(document, splitOption);
+
SXSSFSheet newSheet = wb.createSheet(sheetName);
newSheet.setRandomAccessWindowSize(50);
sheets.get(documentIndex).put(section.eClass().getClassifierID(), newSheet.getSheetName());
+
}
return sheets.get(documentIndex).get(section.eClass().getClassifierID());
@@ -255,6 +273,10 @@
SXSSFSheet sectionsSheet = wb.createSheet("Sections");
+ SXSSFSheet encountersSheet = wb.createSheet("Encounters");
+
+ SXSSFSheet demographicsSheet = wb.createSheet("Demographics");
+
sectionbyfileByDocument.put(documentIndex, new HashMap<String, ArrayList<IFile>>());
SXSSFRow row1 = null;
@@ -262,13 +284,18 @@
offset = createPatientHeader(row1, row2, 0);
createPatientHeader2(row1, row2, offset);
- SXSSFSheet encountersSheet = wb.createSheet("Encounters");
-
row1 = null;
row2 = encountersSheet.createRow(0);
offset = createPatientHeader(row1, row2, 0);
createEncounterHeader(row1, row2, offset);
+
+ row1 = null;
+ row2 = demographicsSheet.createRow(0);
+
+ offset = createPatientHeader(row1, row2, 0);
+ offset = createDemographicsHeader(row1, row2, offset);
+
workbooks.put(documentIndex, wb);
documents.put(documentIndex, document);
}
@@ -394,6 +421,7 @@
clinicalDocument.eClass());
SXSSFSheet documentsSheet = wb.getSheet("Documents");
+ SXSSFSheet demographicsSheet = wb.getSheet("Demographics");
SXSSFSheet encountersSheet = wb.getSheet("Encounters");
List<Encounter> encounters = new ArrayList<Encounter>();
@@ -412,6 +440,8 @@
DocumentMetadata documentMetadata = appendToPatientSheet(
query, documentsSheet, patientRole, ir, iffo, file.getName());
+ appendToDemographicsSheet(query, demographicsSheet, documentMetadata, patientRole);
+
getDMHash(clinicalDocument.eClass().getClassifierID(), splitOption).put(file, documentMetadata);
if (clinicalDocument instanceof GeneralHeaderConstraints) {
@@ -632,6 +662,36 @@
}
+ /**
+ * @param query
+ * @param demographicsSheet
+ * @param patientRole
+ * @param ir
+ * @param iffo
+ * @param string
+ */
+ private void appendToDemographicsSheet(Query query, SXSSFSheet sheet, DocumentMetadata documentMetadata,
+ PatientRole patientRole) {
+
+ Row row = sheet.createRow(sheet.getPhysicalNumberOfRows());
+
+ int offset = serializePatient2(row, 0, documentMetadata, patientRole);
+ /*
+ * race
+ * gender
+ * patient name
+ * address
+ * dob XXX
+ * phone #
+ * ethnicity
+ * document id XXX
+ * language
+ * phone #
+ */
+ serializeSectionAndFileName(row, offset, null, documentMetadata.fileName);
+
+ }
+
/*
* (non-Javadoc)
*
