Updates to processing Zip Archive
Added the ability to process zip of zips
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 1e2be10..7d4737f 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
@@ -14,6 +14,7 @@
import java.io.BufferedReader;
import java.io.BufferedWriter;
+import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
@@ -34,7 +35,6 @@
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
-import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
@@ -45,6 +45,7 @@
import java.util.concurrent.TimeUnit;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
+import java.util.zip.ZipInputStream;
import javax.swing.text.html.HTMLEditorKit;
@@ -154,6 +155,7 @@
import org.openhealthtools.mdht.uml.cda.hitsp.HITSPPackage;
import com.google.common.base.Stopwatch;
+import com.google.common.io.ByteStreams;
public class GenerateCDADataHandler extends GenerateCDABaseHandler {
@@ -556,8 +558,14 @@
}
- }
- if (selection instanceof IStructuredSelection) {
+ if (completed) {
+ for (IProject project : ResourcesPlugin.getWorkspace().getRoot().getProjects()) {
+ project.refreshLocal(IResource.DEPTH_INFINITE, new NullProgressMonitor());
+ }
+ PlatformUI.getWorkbench().getActiveWorkbenchWindow();
+ }
+
+ } else if (selection instanceof IStructuredSelection) {
final IStructuredSelection iss = (IStructuredSelection) selection;
@@ -1117,6 +1125,34 @@
return path;
}
+ private void processZipFile(String prefix, ArrayList<IFile> documents, ZipInputStream zipInputStream)
+ throws IOException {
+
+ ZipEntry entry;
+ while ((entry = zipInputStream.getNextEntry()) != null) {
+ /*
+ * What is not obvious from the documentation on ZipInputStream
+ * is the getNextEntry() modifies the zipInputStream state such that the input stream itself is now the entry
+ *
+ */
+ if (!entry.isDirectory()) {
+ if ("XML".equalsIgnoreCase(FilenameUtils.getExtension(entry.getName()))) {
+ // zipInputStream is now the input stream for the xml document
+ byte[] buffer = ByteStreams.toByteArray(zipInputStream);
+ ByteArrayInputStream byteArrayInputStream = new ByteArrayInputStream(buffer);
+ WrapperForZipEnty wrapper = new WrapperForZipEnty(prefix, entry, byteArrayInputStream);
+ documents.add(wrapper);
+ }
+ if ("ZIP".equalsIgnoreCase(FilenameUtils.getExtension(entry.getName()))) {
+ // zipInputStream is now the input stream of the archive
+ ZipInputStream embeddedZipInputStream = new ZipInputStream(zipInputStream);
+ processZipFile(prefix + "/" + entry.getName(), documents, embeddedZipInputStream);
+ }
+ }
+ }
+
+ }
+
void processSelection(IFolder selectedFolder, IFile selectedFile, IProgressMonitor monitor, String splitOption,
HashSet<EClass> sectionFilter, HashMap<EClass, HashSet<EClass>> theSectionCache) throws Exception {
@@ -1185,20 +1221,6 @@
}
};
- /*
- * zipFile
- *
- * for (Enumeration e = zp.entries(); e.hasMoreElements();) {
- * ZipEntry zipEntry = (ZipEntry) e.nextElement();
- * ClinicalDocument cd = CDAUtil.load(zp.getInputStream(zipEntry));
- * CDAUtil.save(cd, System.out);
- *
- *
- * }
- */
-
- // zipFile.entries().
- // folder.members().length + 50
ArrayList<IFile> documents = new ArrayList<IFile>();
IFolder folder = null;
@@ -1213,18 +1235,8 @@
}
if (selectedFile != null) {
-
folder = (IFolder) selectedFile.getParent();
- ZipFile zipFile = new ZipFile(selectedFile.getLocation().toOSString());
-
- WrapperForZipEnty.zipFile = zipFile;
-
- for (Enumeration<?> e = zipFile.entries(); e.hasMoreElements();) {
- ZipEntry zipEntry = (ZipEntry) e.nextElement();
-
- WrapperForZipEnty wrapper = new WrapperForZipEnty(zipEntry);
- documents.add(wrapper);
- }
+ processZipFile(selectedFile.getName(), documents, new ZipInputStream(selectedFile.getContents()));
}
fileCount = documents.size() + 50;
@@ -1298,8 +1310,6 @@
if (!omitValidation) {
vr = new ValidationResult();
}
- // ValidationResult result = new ValidationResult();
- // System.out.println("\n***** Sample validation results *****");
clinicalDocument = CDAUtil.load(is, vr);
console.println("End Load " + stopwatch.elapsed(TimeUnit.MILLISECONDS));
@@ -1687,17 +1697,30 @@
*/
private static class WrapperForZipEnty implements IFile {
- static ZipFile zipFile;
+ ZipFile zipFile;
ZipEntry zipEntry;
+ InputStream inputStream;
+
+ String prefix = "";
+
/**
* @param zipEntry
*/
- public WrapperForZipEnty(ZipEntry zipEntry) {
+ public WrapperForZipEnty(ZipFile zipFile, ZipEntry zipEntry) {
+ this.zipFile = zipFile;
this.zipEntry = zipEntry;
}
+ public WrapperForZipEnty(String prefix, ZipEntry zipEntry, InputStream inputStream) {
+ this.prefix = prefix;
+ this.zipEntry = zipEntry;
+ this.inputStream = inputStream;
+ // this.zipFile = zipFile;
+ // this.zipEntry = zipEntry;
+ }
+
/*
* (non-Javadoc)
*
@@ -1802,7 +1825,11 @@
@Override
public InputStream getContents() throws CoreException {
try {
- return zipFile.getInputStream(this.zipEntry);
+ if (this.inputStream != null) {
+ return this.inputStream;
+ } else {
+ return zipFile.getInputStream(this.zipEntry);
+ }
} catch (IOException e) {
throw new CoreException(null);
}
@@ -2701,7 +2728,7 @@
*/
@Override
public String getName() {
- return zipEntry.getName();
+ return prefix + zipEntry.getName();
}
/*
