Added command line generate xsl
Added new application
modified generation logic
diff --git a/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/HeadlessCDA2XLS.java b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/HeadlessCDA2XLS.java
new file mode 100644
index 0000000..d648494
--- /dev/null
+++ b/cda/plugins/org.eclipse.mdht.cda.xml.ui/src/org/eclipse/mdht/cda/xml/HeadlessCDA2XLS.java
@@ -0,0 +1,33 @@
+package org.eclipse.mdht.cda.xml;
+
+import java.util.Map;
+
+import org.eclipse.equinox.app.IApplication;
+import org.eclipse.equinox.app.IApplicationContext;
+import org.eclipse.mdht.cda.xml.ui.handlers.GenerateCDADataHandler;
+
+public class HeadlessCDA2XLS implements IApplication {
+
+ @Override
+ public Object start(IApplicationContext context) throws Exception {
+
+ final Map<?, ?> args = context.getArguments();
+ final String[] appArgs = (String[]) args.get("application.args");
+ String zipFile = "";
+ for (final String arg : appArgs) {
+ System.out.println(arg);
+ if (arg.startsWith("-Z")) {
+ zipFile = arg.replace("-Z", "");
+ }
+ }
+ GenerateCDADataHandler generateCDADataHandler = new GenerateCDADataHandler();
+ generateCDADataHandler.processCommandLine(zipFile);
+ return IApplication.EXIT_OK;
+ }
+
+ @Override
+ public void stop() {
+
+ }
+
+}
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 7b04b4e..329b2a4 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
@@ -148,7 +148,6 @@
import org.eclipse.ui.console.ConsolePlugin;
import org.eclipse.ui.console.IConsoleManager;
import org.eclipse.ui.console.MessageConsole;
-import org.eclipse.ui.console.MessageConsoleStream;
import org.eclipse.ui.dialogs.ElementListSelectionDialog;
import org.eclipse.ui.handlers.HandlerUtil;
import org.openhealthtools.mdht.uml.cda.consol.ConsolPackage;
@@ -416,7 +415,10 @@
if (object instanceof IFolder) {
IFolder folder = (IFolder) object;
codeMetricsFile = folder.getFile("codemetrics.cfg");
- monitor.beginTask("Generate Spreadsheet", folder.members().length);
+ monitor.beginTask(
+ "Generate Spreadsheet", (folder != null
+ ? folder.members().length
+ : 1));
int worksheetCache = 1000;
if (System.getProperty("org.eclipse.mdht.cda.xls.worksheetcache") != null) {
@@ -424,7 +426,8 @@
}
final SXSSFWorkbook rollupStats = new SXSSFWorkbook(worksheetCache);
- processSelection(folder, null, monitor, splitOption, theSections, theSectionCache, rollupStats);
+ processSelection(
+ folder, null, null, monitor, splitOption, theSections, theSectionCache, rollupStats);
final StringBuffer fileLocation = new StringBuffer();
fileLocation.append(
@@ -444,7 +447,8 @@
IFile zipFile = (IFile) object;
final SXSSFWorkbook rollupStats = new SXSSFWorkbook(10);
- processSelection(null, zipFile, monitor, splitOption, theSections, theSectionCache, rollupStats);
+ processSelection(
+ null, zipFile, null, monitor, splitOption, theSections, theSectionCache, rollupStats);
final StringBuffer fileLocation = new StringBuffer();
fileLocation.append(
@@ -650,7 +654,10 @@
if (o instanceof IFolder) {
IFolder folder = (IFolder) o;
codeMetricsFile = folder.getFile("codemetrics.cfg");
- monitor.beginTask("Generate Spreadsheet", folder.members().length);
+ monitor.beginTask(
+ "Generate Spreadsheet", (folder != null
+ ? folder.members().length
+ : 1));
if (fileLocation.length() == 0) {
fileLocation.append(
@@ -661,7 +668,7 @@
}
processSelection(
- folder, null, monitor, splitOption, theSections, theSectionCache,
+ folder, null, null, monitor, splitOption, theSections, theSectionCache,
rollupStats);
}
@@ -677,7 +684,7 @@
}
processSelection(
- null, zipFile, monitor, splitOption, theSections, theSectionCache,
+ null, zipFile, null, monitor, splitOption, theSections, theSectionCache,
rollupStats);
}
@@ -1373,13 +1380,24 @@
}
- void processSelection(IFolder selectedFolder, IFile selectedFile, IProgressMonitor monitor, String splitOption,
- HashSet<EClass> sectionFilter, HashMap<EClass, HashSet<EClass>> theSectionCache, SXSSFWorkbook rollupStats)
- throws Exception {
+ public void processCommandLine(String selectedFile2) throws Exception {
- MessageConsole mdhtConsole = findConsole(MDHTCONSOLE);
- mdhtConsole.setWaterMarks(1000, 18000);
- MessageConsoleStream console = mdhtConsole.newMessageStream();
+ HashSet<EClass> sectionFilter = new HashSet<EClass>();
+ final HashMap<EClass, HashSet<EClass>> theSectionCache = new HashMap<EClass, HashSet<EClass>>();
+ final SXSSFWorkbook rollupStats = new SXSSFWorkbook(100);
+ processSelection(
+ null, null, selectedFile2, new NullProgressMonitor(), CONSOLIDATED, sectionFilter, theSectionCache,
+ rollupStats);
+
+ }
+
+ void processSelection(IFolder selectedFolder, IFile selectedFile, String selectedFile2, IProgressMonitor monitor,
+ String splitOption, HashSet<EClass> sectionFilter, HashMap<EClass, HashSet<EClass>> theSectionCache,
+ SXSSFWorkbook rollupStats) throws Exception {
+
+ // MessageConsole mdhtConsole = findConsole(MDHTCONSOLE);
+ // mdhtConsole.setWaterMarks(1000, 18000);
+ // MessageConsoleStream console = mdhtConsole.newMessageStream();
/*
* Set Ratio low as to prevent Zip Bomb Detection
@@ -1453,8 +1471,13 @@
IFolder folder = null;
Iterator<IFile> documentsIterator = null;
+
+ String folderTarget = null;
+ String folderName = null;
if (selectedFolder != null) {
folder = selectedFolder;
+ folderTarget = folder.getParent().getLocation().toOSString() + System.getProperty("file.separator");
+ folderName = folder.getName().toUpperCase();
for (IResource resource : folder.members()) {
if (resource instanceof IFile) {
documents.add((IFile) resource);
@@ -1466,17 +1489,27 @@
if (selectedFile != null) {
folder = (IFolder) selectedFile.getParent();
+ folderTarget = folder.getParent().getLocation().toOSString() + System.getProperty("file.separator");
+ folderName = folder.getName().toUpperCase();
documentsIterator = new ZIPIterator(
selectedFile.getName(), new ZipInputStream(selectedFile.getContents()), fileNameFilters);
+
+ }
+
+ if (!StringUtils.isEmpty(selectedFile2)) {
+ java.nio.file.Path zipfile = Paths.get(selectedFile2);
+ folderTarget = zipfile.getParent().toAbsolutePath().toString() + System.getProperty("file.separator");
+ folderName = zipfile.getFileName().toString().toUpperCase().replace(".ZIP", "");
+ documentsIterator = new ZIPIterator(
+ zipfile.getFileName().toString(), new ZipInputStream(Files.newInputStream(zipfile)), fileNameFilters);
}
fileCount = documents.size() + 50;
- String fileLocation2 = folder.getParent().getLocation().toOSString() + System.getProperty("file.separator") +
- CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + folder.getName().toUpperCase() + "performance.log";
+ String fileLocation2 = folderTarget + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + folderName +
+ "performance.log";
- String fileLocation3 = folder.getParent().getLocation().toOSString() + System.getProperty("file.separator") +
- CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + folder.getName().toUpperCase() +
+ String fileLocation3 = folderTarget + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + folderName +
"validatation.csv";
BufferedWriter performance = Files.newBufferedWriter(Paths.get(fileLocation2));
@@ -1539,6 +1572,11 @@
skipSwitch = true;
}
+ boolean ignoreFilter = false;
+ if (System.getProperty("org.eclipse.mdht.cda.xls.ignorefilter") != null) {
+ ignoreFilter = true;
+ }
+
int statfilectr = 0;
int consoldocumentsprocessed = 0;
int outpatientprogressnoteprocessed = 0;
@@ -1549,7 +1587,9 @@
int nonxmldocuments = 0;
int documenterrors = 0;
- int totalFiles = folder.members().length;
+ int totalFiles = (folder != null
+ ? folder.members().length
+ : 1);
while (documentsIterator.hasNext()) {
statfilectr++;
IFile file = documentsIterator.next();
@@ -1569,8 +1609,9 @@
if ("XML".equalsIgnoreCase(file.getFileExtension())) {
files.add(file);
monitor.worked(1);
- double estimatedTimeLeft = ((folder.members().length - filectr) * (currentProcessingTime / filectr)) /
- 1000.0;
+ double estimatedTimeLeft = (((folder != null
+ ? folder.members().length
+ : 1) - filectr) * (currentProcessingTime / filectr)) / 1000.0;
if (estimatedTimeLeft > 60) {
monitor.setTaskName(
@@ -1586,8 +1627,8 @@
try {
- console.println(getMemoryUssage());
- console.println("file : " + file.getName() + " size : " + fileSize);
+ // console.println(getMemoryUssage());
+ // console.println("file : " + file.getName() + " size : " + fileSize);
ClinicalDocument clinicalDocument = null;
@@ -1632,7 +1673,7 @@
}
- console.println("End Load " + stopwatch.elapsed(TimeUnit.MILLISECONDS));
+ // console.println("End Load " + stopwatch.elapsed(TimeUnit.MILLISECONDS));
is.close();
if (!loaded) {
@@ -1714,7 +1755,7 @@
*/
if (clinicalDocument instanceof GeneralHeaderConstraints) {
- console.println("Start Processing ");
+ // console.println("Start Processing ");
consoldocumentsprocessed++;
@@ -1758,7 +1799,7 @@
for (Section section : clinicalDocument.getSections()) {
// This is when a section template is not found
- if (!sectionFilter.isEmpty()) {
+ if (!ignoreFilter && !sectionFilter.isEmpty()) {
if (CDAPackage.eINSTANCE.getSection().isInstance(section)) {
@@ -1801,22 +1842,22 @@
}
}
- console.println("Start Section " + section.eClass().getName());
+ // console.println("Start Section " + section.eClass().getName());
- if (!skipSwitch) {
+ if (!skipSwitch && section != null) {
if (!pss.doSwitch(section)) {
- console.println("Error processing section Unknown Template ID ");
+ // 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(
+ // "Error processing section Unknown Template ID root : " +
+ // templateId.getRoot() + " extension : " + templateId.getExtension());
}
}
}
- console.println("End Section " + stopwatch.elapsed(TimeUnit.MILLISECONDS));
+ // console.println("End Section " + stopwatch.elapsed(TimeUnit.MILLISECONDS));
}
@@ -1830,7 +1871,7 @@
performance.newLine();
performance.flush();
- console.println("End Processing " + stopwatch.elapsed(TimeUnit.MILLISECONDS));
+ // console.println("End Processing " + stopwatch.elapsed(TimeUnit.MILLISECONDS));
} else {
c32documentsprocessed++;
@@ -1906,18 +1947,6 @@
nonxmldocuments++;
}
- // final int STATSFILENAME = 0;
- // final int STATSTOTAL = 1;
- // final int STATSCONSOLIDATED = 2;
- // final int STATSCONTINUITYOFCARE = 3;
- // final int STATSPROGRESSNOTE = 4;
- // final int STATSEPISODENOTE = 5;
- // final int STATSDISCHARGESUMMARY = 6;
- // final int STATSOTHER = 7;
- // final int STATSC32 = 8;
- // final int STATSNONXML = 9;
- // final int STATSERRORS = 10;
-
statrow.createCell(STATSTOTAL).setCellValue(statfilectr);
statrow.createCell(STATSCONSOLIDATED).setCellValue(consoldocumentsprocessed);
statrow.createCell(STATSCONTINUITYOFCARE).setCellValue(continuityofcareprocessed);
@@ -1931,7 +1960,10 @@
stopwatch.stop();
}
- monitor.beginTask("Generate Spreadsheet", folder.members().length);
+ monitor.beginTask(
+ "Generate Spreadsheet", (folder != null
+ ? folder.members().length
+ : 1));
for (Integer eClass : workbooks.keySet()) {
@@ -2030,15 +2062,18 @@
// cell.setCellFormula(strFormula);
// }
+ // folderTarget = zipfile.getParent().toAbsolutePath().toString() + System.getProperty("file.separator");
+ // folderName = zipfile.getFileName().toString().toUpperCase();
+
String fileLocation = "";
if (selectedFile != null) {
- fileLocation = selectedFile.getParent().getLocation().toOSString() +
- System.getProperty("file.separator") + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" +
+ fileLocation = folderTarget + System.getProperty("file.separator") +
+ CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" +
selectedFile.getName().toUpperCase().replace(".ZIP", "") + getFileName(eClass, splitOption) +
"_SA.xlsx";
} else {
- fileLocation = folder.getParent().getLocation().toOSString() + System.getProperty("file.separator") +
- CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + folder.getName().toUpperCase() +
+ fileLocation = folderTarget + System.getProperty("file.separator") +
+ CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + folderName +
getFileName(eClass, splitOption) + "_SA.xlsx";
}
@@ -2050,9 +2085,35 @@
org.apache.commons.io.FileUtils.touch(theFile);
}
- monitor.subTask(
- "Serializing " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + folder.getName().toUpperCase() +
- "_SA.xlsx");
+ monitor.subTask("Serializing " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + fileLocation);
+
+ // String fileLocation = "";
+ // if (selectedFile != null) {
+ // fileLocation = selectedFile.getParent().getLocation().toOSString() +
+ // System.getProperty("file.separator") + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" +
+ // selectedFile.getName().toUpperCase().replace(".ZIP", "") + getFileName(eClass, splitOption) +
+ // "_SA.xlsx";
+ //
+ // } else {
+ // fileLocation = folder.getParent().getLocation().toOSString() + System.getProperty("file.separator") +
+ // CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + (folder != null
+ // ? folder.getName().toUpperCase()
+ // : "XXX") +
+ // getFileName(eClass, splitOption) + "_SA.xlsx";
+ // }
+ //
+ // File theFile = new File(fileLocation);
+
+ // If the file exists, check to see if we can open it
+ // this is the excel
+ if (theFile.exists()) {
+ org.apache.commons.io.FileUtils.touch(theFile);
+ }
+
+ // monitor.subTask(
+ // "Serializing " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + (folder != null
+ // ? folder.getName().toUpperCase()
+ // : "XXX") + "_SA.xlsx");
if (!sectionFilter.isEmpty()) {
/*
@@ -2068,7 +2129,7 @@
wb.removeSheetAt(wb.getSheetIndex("Encounters"));
}
- console.println("Start Saving " + currentProcessingTime);
+ // console.println("Start Saving " + currentProcessingTime);
try (OutputStream fileOut = Files.newOutputStream(Paths.get(fileLocation))) {
wb.write(fileOut);
@@ -2079,25 +2140,30 @@
// FileOutputStream = new FileOutputStream();
- console.println("End Saving " + currentProcessingTime);
+ // console.println("End Saving " + currentProcessingTime);
monitor.subTask(
- "Flushing Memory " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" +
- folder.getName().toUpperCase() + "_SA.xlsx");
+ "Flushing Memory " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + (folder != null
+ ? folder.getName().toUpperCase()
+ : "XXX") + "_SA.xlsx");
monitor.subTask(
- "Reloading " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + folder.getName().toUpperCase() +
- "_SA.xlsx");
+ "Reloading " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + (folder != null
+ ? folder.getName().toUpperCase()
+ : "XXX") + "_SA.xlsx");
/**
* @TODO Add preference for formatting
*/
- if (false && folder.members().length < 50) {
+ if (false && (folder != null
+ ? folder.members().length
+ : 1) < 50) {
format(fileLocation, monitor);
}
monitor.subTask(
- "Completed Saving " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" +
- folder.getName().toUpperCase() + "_SA.xlsx");
+ "Completed Saving " + CDAValueUtil.DATE_FORMAT3.format(new Date()) + "_" + (folder != null
+ ? folder.getName().toUpperCase()
+ : "XXX") + "_SA.xlsx");
}
