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);
}
}
/**
* 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;
}
/**
* 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 ArrayList<String> checkForDuplicates(ResourceIterator iter, Resource selection) {
ArrayList<String> tempList = new ArrayList<String>();
HashMap<String, Integer> duplicateFilter = new HashMap<String, Integer>();
try {
while (iter.hasMoreResources()) {
selection = iter.nextResource();
String studyNameResult = (selection.getContent()).toString();
if (duplicateFilter.isEmpty()) {
// Add it to the return array
tempList.add(studyNameResult);
duplicateFilter.put(studyNameResult, 1);
} else {
boolean duplicateCheck = duplicateFilter.containsKey(studyNameResult);
if (!duplicateCheck) {
// Add it to the return array
tempList.add(studyNameResult);
duplicateFilter.put(studyNameResult, 1);
} else {
// Otherwise, increment the count
Integer increaseCount = duplicateFilter.get(studyNameResult);
duplicateFilter.put(studyNameResult, increaseCount++);
}
}
System.out.println("The size of the duplicate filter is " + duplicateFilter.size());
}
} catch (XMLDBException e) {
System.out.println("An XML Exception has been caught in the checkForDuplicates() method");
e.printStackTrace();
}
return tempList;
}
/**
* 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();
}
/**
* 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;
}
