public void execute(Connection connection) throws XMLDBException, EXistException {
Collection collection = connection.getCollection("/db");
XQueryService service = (XQueryService) collection.getService("XQueryService", "1.0");
service.declareVariable("filename", "");
service.declareVariable("count", "0");
String query = IMPORT + xqueryContent;
System.out.println("query: " + query);
CompiledExpression compiled = service.compile(query);
try {
for (int i = 0; i < count; i++) {
File nextFile = new File(directory, prefix + i + ".xml");
service.declareVariable("filename", nextFile.getName());
service.declareVariable("count", new IntegerValue(i));
ResourceSet results = service.execute(compiled);
Writer out = new OutputStreamWriter(new FileOutputStream(nextFile), "UTF-8");
for (ResourceIterator iter = results.getIterator(); iter.hasMoreResources(); ) {
Resource r = iter.nextResource();
out.write(r.getContent().toString());
}
out.close();
}
} catch (IOException e) {
throw new EXistException("exception while storing generated data: " + e.getMessage(), e);
}
}
private String execQuery(String query) throws XMLDBException {
XQueryService service = (XQueryService) testCollection.getService("XQueryService", "1.0");
service.setProperty("indent", "no");
ResourceSet result = service.query(query);
assertEquals(result.getSize(), 1);
return result.getResource(0).getContent().toString();
}
/** arguments: lines , columns, XQuery string */
public static void main(String[] args) {
String xquery = "";
int lines = 20;
int columns = 20;
if (args.length >= 2) {
lines = Integer.parseInt(args[0]);
columns = Integer.parseInt(args[1]);
}
if (args.length == 3) {
xquery = args[2];
}
if (args.length < 2) {
System.out.println("Taking default values");
}
SAXStorageTest tester = new SAXStorageTest(null);
tester.setUp();
XMLReader dataSource = new TabularXMLReader(lines, columns);
tester.storeSAXEvents(dataSource);
System.out.println("Stored tabular data, " + lines + " lines, " + columns + " columns");
try {
if (xquery != "") {
ResourceSet result = tester.querySingleLine(xquery, "testQueryBigDocument");
System.out.println("result size: " + result.getSize());
}
shutdown(tester.root);
} catch (XMLDBException e) {
fail(e.getMessage());
}
}
/**
* This function makes the call to the XML database and retrieves all the file metadata for use in
* ECGridToolkit. The data is first retrieved in a series of XML blocks, and then they are
* converted into StudyEntry Objects and returned to the user
*
* @param userID - The ID of the user. This is used to check which files the user has submitted
* and thus has access to
* @return The list of StudyEntry Objects taken from the file metadata in the XML database
*/
public ArrayList<StudyEntry> getEntries(String userID) {
ArrayList<StudyEntry> tempList = new ArrayList<StudyEntry>();
try {
// create first query to get the entire studyEntry block, the collection() XQuery function
// does this across
// all documents in the XML Collection
// The goal of this query is to find all the data we need for the StudyEntry object based on
// which user submitted them. For all the documents searched, the query looks to see
// if any files for that subject's ECG repository were submitted by that user. If any files
// were submitted, retrieve their metadata contained in the studyEntry block.
String sQuery =
studyBuilder.defaultFor()
+ studyBuilder.defaultWhere(userID)
+ studyBuilder.defaultOrderBy()
+ studyBuilder.defaultReturn();
System.out.println("Query to be executed = " + sQuery);
ResourceSet resultSet = executeQuery(sQuery);
ResourceIterator iter = resultSet.getIterator();
Resource selection = null;
Resource fileSelection = null;
int listIndex = 0;
int subjectCount = 1;
while (iter.hasMoreResources()) {
selection = iter.nextResource();
String studyEntryResult = (selection.getContent()).toString();
// Now we will create an XStream object and then put that into our StudyEntry objects
// the StudyEntry objects are de-serialized versions of the studyEntry blocks.
XStream xmlStream = new XStream();
xmlStream.alias("studyEntry", StudyEntry.class);
xmlStream.alias("recordDetails", RecordDetails.class);
xmlStream.alias("fileDetails", FileDetails.class);
xmlStream.addImplicitCollection(RecordDetails.class, "fileDetails");
StudyEntry newStudy = (StudyEntry) xmlStream.fromXML(studyEntryResult);
// System.out.println(newStudy);
// Add it to the return array
tempList.add(newStudy);
}
} catch (Exception ex) {
System.out.println(
"StudyEntryUtility.getEntries(): AN EXCEPTION HAS BEEN CAUGHT! IF A LIST IS RETURNED, IT WILL BE EMPTY!!!");
ex.printStackTrace();
}
return tempList;
}
/**
* Store in the new way: the XMLResource stores just a File object before storeResource() stores
* the SAX events in the database.
*
* @throws XMLDBException
*/
public void testQueryBigDocument() {
try {
XMLReader dataSource = new TabularXMLReader();
storeSAXEvents(dataSource);
ResourceSet result = querySingleLine("", "testQueryBigDocument");
assertEquals(1, result.getSize());
} catch (XMLDBException e) {
fail(e.getMessage());
}
}
@Before
public void clearGrammarCache() {
LOG.info("Clearing grammar cache");
ResourceSet results = null;
try {
results = executeQuery("validation:clear-grammar-cache()");
String r = (String) results.getResource(0).getContent();
System.out.println(r);
} catch (Exception e) {
LOG.error(e);
e.printStackTrace();
fail(e.getMessage());
}
}
public ArrayList<String> queryStudyTypes(String userID, String dataName) {
System.out.println("In function queryStudyTypes");
ArrayList<String> tempList = new ArrayList<String>();
try {
// create first query to get the entire studyEntry block, the collection() XQuery function
// does this across
// all documents in the XML Collection
// The goal of this query is to find all the data we need for the StudyEntry object based on
// which user submitted them. For all the documents searched, the query looks to see
// if any files for that subject's ECG repository were submitted by that user. If any files
// were submitted, retrieve their metadata contained in the studyEntry block.
System.out.println("queryDatatypes:");
String sQuery =
studyBuilder.forStudyEntry()
+ studyBuilder.customNameBracket(dataName, EnumStudyTreeNode.DATATYPE)
+ studyBuilder.userDefinedWhere(userID)
+ studyBuilder.customOrderBySubjectID()
+ studyBuilder.returnTreeNodeDistinct(EnumStudyTreeNode.STUDY);
System.out.println("Query to be executed = " + sQuery);
ResourceSet resultSet = executeQuery(sQuery);
ResourceIterator iter = resultSet.getIterator();
Resource selection = null;
tempList = this.checkForDuplicates(iter, selection);
for (String listing : tempList) {
int i = 1;
System.out.println("Entry " + i + " = " + listing);
i++;
}
} catch (Exception ex) {
System.out.println(
"ExistMainDatabase.queryStudies(): AN EXCEPTION HAS BEEN CAUGHT! IF A LIST IS RETURNED, IT WILL BE EMPTY!!!");
ex.printStackTrace();
}
return tempList;
}
private void executeAndEvaluate(String query, String expectedValue) {
LOG.info("Query=" + query);
LOG.info("ExpectedValue=" + query);
try {
ResourceSet results = executeQuery(query);
assertEquals(1, results.getSize());
String r = (String) results.getResource(0).getContent();
LOG.info(r);
assertXpathEvaluatesTo(expectedValue, "//status/text()", r);
} catch (Exception ex) {
LOG.error(ex);
fail(ex.getMessage());
}
}
/**
* Main method of the example class.
*
* @param args (ignored) command-line arguments
* @throws Exception exception
*/
public static void main(final String[] args) throws Exception {
System.out.println("=== XMLDBQuery ===\n");
System.out.println("* Run query via XML:DB:");
// Collection instance
Collection coll = null;
try {
// Register the database
Class<?> c = Class.forName(DRIVER);
Database db = (Database) c.newInstance();
DatabaseManager.registerDatabase(db);
// Receive the database
coll = DatabaseManager.getCollection(DBNAME);
// Receive the XPath query service
XPathQueryService service = (XPathQueryService) coll.getService("XPathQueryService", "1.0");
// Execute the query and receives all results
ResourceSet set = service.query(QUERY);
// Create a result iterator
ResourceIterator iter = set.getIterator();
// Loop through all result items
while (iter.hasMoreResources()) {
// Receive the next results
Resource res = iter.nextResource();
// Write the result to the console
System.out.println(res.getContent());
}
} catch (final XMLDBException ex) {
// Handle exceptions
System.err.println("XML:DB Exception occured " + ex.errorCode);
} finally {
// Close the collection
if (coll != null) coll.close();
}
}
private void insertTags() throws Exception {
XUpdateQueryService service =
(XUpdateQueryService) testCol.getService("XUpdateQueryService", "1.0");
XPathQueryService xquery = (XPathQueryService) testCol.getService("XPathQueryService", "1.0");
String[] tagsWritten = new String[RUNS];
for (int i = 0; i < RUNS; i++) {
String tag = tags[i];
String parent;
if (i > 0 && rand.nextInt(100) < 70) {
parent = "//" + tagsWritten[rand.nextInt(i) / 2];
} else parent = "/root";
String xupdate =
"<xupdate:modifications version=\"1.0\" xmlns:xupdate=\"http://www.xmldb.org/xupdate\">"
+ "<xupdate:append select=\""
+ parent
+ "\">"
+ "<xupdate:element name=\""
+ tag
+ "\"/>"
+ "</xupdate:append>"
+ "</xupdate:modifications>";
long mods = service.updateResource("test.xml", xupdate);
System.out.println("Inserted " + tag + ": " + mods + " ; parent = " + parent);
assertEquals(mods, 1);
tagsWritten[i] = tag;
String query = "//" + tagsWritten[rand.nextInt(i + 1)];
ResourceSet result = xquery.query(query);
assertEquals(result.getSize(), 1);
System.out.println(result.getResource(0).getContent());
}
XMLResource res = (XMLResource) testCol.getResource("test.xml");
assertNotNull(res);
System.out.println(res.getContent());
}
/**
* This method performs an XPath query to the database and returns the results as a Vector of
* Strings.
*
* @param collection The name of the collection to look for the document.
* @param query A string containing an XPath expression which shall act as a query against the
* database.
* @param username The identifier of the user calling the method used for authentication.
* @param password The password of the user calling the method used for authentication.
* @return A Vector containing the answers to the query as Strings.
*/
public Vector query(String collection, String query, String username, String password) {
Vector response = new Vector();
try {
Class cl = Class.forName(_driver);
Database database = (Database) cl.newInstance();
DatabaseManager.registerDatabase(database);
Collection col = DatabaseManager.getCollection(_URI + collection, username, password);
XPathQueryService service = (XPathQueryService) col.getService("XPathQueryService", "1.0");
service.setProperty("indent", "yes");
ResourceSet result = service.query(query);
ResourceIterator i = result.getIterator();
while (i.hasMoreResources()) {
Resource r = i.nextResource();
response.add((String) r.getContent());
}
} catch (Exception e) {
e.printStackTrace();
}
return response;
}
public static void main(String args[]) throws Exception {
String driver = "org.exist.xmldb.DatabaseImpl";
Class cl = Class.forName(driver);
Database database = (Database) cl.newInstance();
DatabaseManager.registerDatabase(database);
Collection col = DatabaseManager.getCollection("xmldb:exist:///db", "admin", "");
XPathQueryService service = (XPathQueryService) col.getService("XPathQueryService", "1.0");
service.setProperty("indent", "yes");
ResourceSet result =
service.query(
"for $s in //intervention/(speaker|writer)/affiliation[@EPparty ='PSE'] return data($s/../../(speech|writing)/@ref)");
ResourceIterator i = result.getIterator();
while (i.hasMoreResources()) {
Resource r = i.nextResource();
System.out.println((String) r.getContent());
}
// shut down the database
DatabaseInstanceManager manager =
(DatabaseInstanceManager) col.getService("DatabaseInstanceManager", "1.0");
manager.shutdown();
}
private void fetchDb() throws Exception {
XPathQueryService xquery = (XPathQueryService) testCol.getService("XPathQueryService", "1.0");
ResourceSet result =
xquery.query(
"for $n in collection('"
+ XmldbURI.ROOT_COLLECTION
+ "/test')//* return local-name($n)");
for (int i = 0; i < result.getSize(); i++) {
Resource r = result.getResource(i);
String tag = r.getContent().toString();
System.out.println("Retrieving " + tag);
ResourceSet result2 = xquery.query("//" + tag);
assertEquals(result2.getSize(), 1);
System.out.println(result2.getResource(0).getContent());
}
}
protected void service(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
if (request.getCharacterEncoding() == null)
try {
request.setCharacterEncoding("UTF-8");
} catch (final IllegalStateException e) {
}
// Try to find the XQuery
final String qpath = getServletContext().getRealPath(query);
final File f = new File(qpath);
if (!(f.canRead() && f.isFile())) {
throw new ServletException("Cannot read XQuery source from " + f.getAbsolutePath());
}
final FileSource source = new FileSource(f, "UTF-8", true);
try {
// Prepare and execute the XQuery
final Collection collection =
DatabaseManager.getCollection(collectionURI.toString(), user, password);
final XQueryService service = (XQueryService) collection.getService("XQueryService", "1.0");
if (!((CollectionImpl) collection).isRemoteCollection()) {
service.declareVariable(
RequestModule.PREFIX + ":request", new HttpRequestWrapper(request, "UTF-8", "UTF-8"));
service.declareVariable(
ResponseModule.PREFIX + ":response", new HttpResponseWrapper(response));
service.declareVariable(
SessionModule.PREFIX + ":session", new HttpSessionWrapper(request.getSession(false)));
}
final ResourceSet result = service.execute(source);
String redirectTo = null;
String servletName = null;
String path = null;
RequestWrapper modifiedRequest = null;
// parse the query result element
if (result.getSize() == 1) {
final XMLResource resource = (XMLResource) result.getResource(0);
Node node = resource.getContentAsDOM();
if (node.getNodeType() == Node.DOCUMENT_NODE) {
node = ((Document) node).getDocumentElement();
}
if (node.getNodeType() != Node.ELEMENT_NODE) {
response.sendError(
HttpServletResponse.SC_BAD_REQUEST,
"Redirect XQuery should return an XML element. Received: " + resource.getContent());
return;
}
Element elem = (Element) node;
if (!(Namespaces.EXIST_NS.equals(elem.getNamespaceURI())
&& "dispatch".equals(elem.getLocalName()))) {
response.sendError(
HttpServletResponse.SC_BAD_REQUEST,
"Redirect XQuery should return an element <exist:dispatch>. Received: "
+ resource.getContent());
return;
}
if (elem.hasAttribute("path")) {
path = elem.getAttribute("path");
} else if (elem.hasAttribute("servlet-name")) {
servletName = elem.getAttribute("servlet-name");
} else if (elem.hasAttribute("redirect")) {
redirectTo = elem.getAttribute("redirect");
} else {
response.sendError(
HttpServletResponse.SC_BAD_REQUEST,
"Element <exist:dispatch> should either provide an attribute 'path' or 'servlet-name'. Received: "
+ resource.getContent());
return;
}
// Check for add-parameter elements etc.
if (elem.hasChildNodes()) {
node = elem.getFirstChild();
while (node != null) {
if (node.getNodeType() == Node.ELEMENT_NODE
&& Namespaces.EXIST_NS.equals(node.getNamespaceURI())) {
elem = (Element) node;
if ("add-parameter".equals(elem.getLocalName())) {
if (modifiedRequest == null) {
modifiedRequest = new RequestWrapper(request);
}
modifiedRequest.addParameter(elem.getAttribute("name"), elem.getAttribute("value"));
}
}
node = node.getNextSibling();
}
}
}
if (redirectTo != null) {
// directly redirect to the specified URI
response.sendRedirect(redirectTo);
return;
}
// Get a RequestDispatcher, either from the servlet context or the request
RequestDispatcher dispatcher;
if (servletName != null && servletName.length() > 0) {
dispatcher = getServletContext().getNamedDispatcher(servletName);
} else {
LOG.debug("Dispatching to " + path);
dispatcher = getServletContext().getRequestDispatcher(path);
if (dispatcher == null) {
dispatcher = request.getRequestDispatcher(path);
}
}
if (dispatcher == null) {
response.sendError(
HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
"Could not create a request dispatcher. Giving up.");
return;
}
if (modifiedRequest != null) {
request = modifiedRequest;
}
// store the original request URI to org.exist.forward.request-uri
request.setAttribute("org.exist.forward.request-uri", request.getRequestURI());
request.setAttribute("org.exist.forward.servlet-path", request.getServletPath());
// finally, execute the forward
dispatcher.forward(request, response);
} catch (final XMLDBException e) {
throw new ServletException(
"An error occurred while initializing RedirectorServlet: " + e.getMessage(), e);
}
}
public final void testXPathQueryServiceSuccess() throws Exception {
XPathQueryService s = (XPathQueryService) this.getService("XPathQueryService");
ResourceSet rs1 = s.query("//author/@id");
assertTrue("Expected a non empty ResourceSet.", rs1.getSize() > 0);
ResourceSet rs2 = s.query("//foo/@bar");
assertTrue("Expected a non empty ResourceSet.", rs2.getSize() > 0);
int id1[] = new int[(int) rs1.getSize()];
for (int i = 0; i < id1.length; i++) {
Resource res = rs1.getResource(i);
assertTrue(
"Expected instance of VirtualResource and not " + res.getClass(),
res instanceof VirtualResource);
Document doc = (Document) ((VirtualResource) res).getContentAsDOM();
Element elem = doc.getDocumentElement();
assertEquals(
"Expected " + NEXDEngineI.QNAME_QUERY_RESULT + " but it is " + elem.getTagName(),
NEXDEngineI.QNAME_QUERY_RESULT,
elem.getTagName());
NamedNodeMap nnm = elem.getAttributes();
String value = elem.getAttribute("id");
id1[i] = Integer.parseInt(value);
}
int id2[] = new int[(int) rs2.getSize()];
for (int i = 0; i < id2.length; i++) {
Resource res = rs2.getResource(i);
assertTrue(
"Expected instance of VirtualResource and not " + res.getClass(),
res instanceof VirtualResource);
Document doc = (Document) ((VirtualResource) res).getContentAsDOM();
Element elem = doc.getDocumentElement();
assertEquals(
"Expected " + NEXDEngineI.QNAME_QUERY_RESULT + " but it is " + elem.getTagName(),
NEXDEngineI.QNAME_QUERY_RESULT,
elem.getTagName());
String value = elem.getAttribute("bar");
id2[i] = Integer.parseInt(value);
}
for (int i = 0; i < id1.length; i++) {
int id = id1[i];
boolean in1 = false;
for (int j = 0; j < id2.length; j++) {
if (id == id2[j]) {
in1 = true;
}
boolean in2 = false;
for (int k = 0; k < id1.length; k++) {
if (id2[j] == id1[k]) {
in2 = true;
}
}
assertTrue("Expected id=" + id2[j] + " is in the first array.", in2);
}
assertTrue("Expected id=" + id + " is in the second array.", in1);
}
}
/**
* This function makes the call to the XML database and retrieves all the file metadata for use in
* ECGridToolkit. The data is first retrieved in a series of XML blocks, and then they are
* converted into StudyEntry Objects and returned to the user
*
* @param userID - The ID of the user. This is used to check which files the user has submitted
* and thus has access to
* @param studyID - The ID of the study selected to search
* @param datatype - The type of data that will be observed
* @return The list of StudyEntry Objects taken from the file metadata in the XML database
*/
public ArrayList<StudyEntry> getEntries(String userID, String studyID, String datatype) {
System.out.println("In function getEntries");
ArrayList<StudyEntry> tempList = new ArrayList<StudyEntry>();
try {
// create first query to get the entire studyEntry block, the collection() XQuery function
// does this across
// all documents in the XML Collection
// The goal of this query is to find all the data we need for the StudyEntry object based on
// which user submitted them. For all the documents searched, the query looks to see
// if any files for that subject's ECG repository were submitted by that user. If any files
// were submitted, retrieve their metadata contained in the studyEntry block.
// CompiledExpression query = subjectQuery.compile("for $x in collection('" +
// allConstants.getDBCollection() + "')//record where collection('" +
// allConstants.getDBCollection() + "')//record/studyEntry/submitterID=\"" + userID + "\"
// order by $x/studyEntry/subjectID return $x/studyEntry");
// ***
// 02/25/2013 - Brandon Benitez: Commented this out temporarily in case the query builder
// version of this failed.
// ***
// String sQuery = "for $x in collection('" + dbHandle.getMainCollection() +
// "')//record/studyEntry[studyID=\"" + studyID + "\"] where $x/submitterID=\"" + userID + "\"
// return $x[datatype=\"" + datatype + "\"]";
String sQuery =
studyBuilder.forStudyEntry()
+
// studyBuilder.customNameBracket(studyID, EnumStudyTreeNode.STUDY) +
studyBuilder.whereUser2(userID)
+ studyBuilder.andWhereStudy(studyID)
+ studyBuilder.customOrderBySubjectID()
+ studyBuilder.returnX()
+ studyBuilder.customNameBracket(datatype, EnumStudyTreeNode.DATATYPE);
System.out.println("Query to be executed = " + sQuery);
ResourceSet resultSet = executeQuery(sQuery);
ResourceIterator iter = resultSet.getIterator();
Resource selection = null;
Resource fileSelection = null;
int listIndex = 0;
int subjectCount = 1;
while (iter.hasMoreResources()) {
selection = iter.nextResource();
String studyEntryResult = (selection.getContent()).toString();
// Now we will create an XStream object and then put that into our StudyEntry objects
// the StudyEntry objects are de-serialized versions of the studyEntry blocks.
XStream xmlStream = new XStream();
xmlStream.alias("studyEntry", StudyEntry.class);
xmlStream.alias("recordDetails", RecordDetails.class);
xmlStream.alias("fileDetails", FileDetails.class);
xmlStream.addImplicitCollection(RecordDetails.class, "fileDetails");
StudyEntry newStudy = (StudyEntry) xmlStream.fromXML(studyEntryResult);
// System.out.println(newStudy);
// Add it to the return array
tempList.add(newStudy);
}
} catch (Exception ex) {
System.out.println(
"StudyEntryUtility.getEntries(): AN EXCEPTION HAS BEEN CAUGHT! IF A LIST IS RETURNED, IT WILL BE EMPTY!!!");
ex.printStackTrace();
}
return tempList;
}
