/**
* Gets elements depending on the format specified.
*
* @param format The format specification of the elements to be returned.
* @return a List of all elements in MetaDB with the specified format.
*/
public List<Element> getElementList(String format) {
List<Element> elementList = new ArrayList<Element>();
Connection conn = Conn.initialize();
if (conn != null) {
try {
PreparedStatement getElementListQuery = conn.prepareStatement(GET_ELEMENT_LIST_BY_FORMAT);
getElementListQuery.setString(1, format);
ResultSet getElementListQueryResult = getElementListQuery.executeQuery();
while (getElementListQueryResult.next())
elementList.add(
new Element(
getElementListQueryResult.getString(Global.ELEMENT),
getElementListQueryResult.getString(Global.ELEMENT_FORMAT)));
getElementListQueryResult.close();
getElementListQuery.close();
conn.close();
} catch (Exception e) {
MetaDbHelper.logEvent(e);
}
}
return elementList;
}
/** @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response) */
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// TODO Auto-generated method stub
PrintWriter out = response.getWriter();
HttpSession session = request.getSession(false);
if (session != null) {
String projname = (String) session.getAttribute(Global.SESSION_PROJECT);
int id = -1;
try {
id = Integer.parseInt(request.getParameter("id"));
} catch (NumberFormatException e) {
id = -1;
}
String notification = "Attr was deleted before save, or internal error occurred.";
try {
// MetaDbHelper.note("Retrieved attribute ID: "+id);
if (id != -1)
if (AdminDescAttributesDAO.deleteAttribute(id))
notification = "Admin/Desc attr " + id + " deleted successfully, project: " + projname;
out.print(notification);
} catch (Exception e) {
MetaDbHelper.logEvent(this.getClass().toString(), e);
}
} else out.print("Session Expired... Please Login");
out.flush();
}
/**
* Check if an element exists in the system.
*
* @param elementName The element to be checked for existence.
* @return true if the element exists, false otherwise.
*/
public static boolean elementExists(String elementName) {
try {
ArrayList<String> elementList = (ArrayList<String>) getElementList();
for (String element : elementList) {
if (element.equals(elementName)) return true;
}
} catch (Exception e) {
MetaDbHelper.logEvent(e);
}
return false;
}
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// TODO Auto-generated method stub
PrintWriter out = response.getWriter();
HttpSession session = request.getSession(false);
try {
if (session != null) {
String project = (String) session.getAttribute(Global.SESSION_PROJECT);
if (project.equals("") && project == null)
out.println("Please choose a project from the Home tab");
else out.print(project);
}
} catch (Exception e) {
MetaDbHelper.logEvent(this.getClass().toString(), e);
}
out.flush();
}
/** @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response) */
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
try {
String vocabName = request.getParameter("vocab-name");
String filename_ext = ".txt";
File tempDir = (File) getServletContext().getAttribute("javax.servlet.context.tempdir");
// MetaDbHelper.note(tempDir.getCanonicalPath());
// create a temporary file in that directory
File tempFile = File.createTempFile(vocabName, filename_ext, tempDir);
FileWriter fw = new FileWriter(tempFile);
Set<String> vocabList = ControlledVocabDAO.getControlledVocab(vocabName);
for (String v : vocabList) fw.write(v + "\r\n");
fw.flush();
fw.close();
int length = 0;
ServletOutputStream op = response.getOutputStream();
ServletContext context = getServletConfig().getServletContext();
String mimetype = context.getMimeType(tempFile.getName());
response.setContentType((mimetype != null) ? mimetype : "application/x-download");
response.setContentLength((int) tempFile.length());
response.setHeader(
"Content-Disposition", "attachment; filename=\"" + vocabName + filename_ext + "\"");
// MetaDbHelper.note(vocabName + filename_ext);
byte[] bbuf = new byte[1024];
DataInputStream in = new DataInputStream(new FileInputStream(tempFile));
while ((in != null) && ((length = in.read(bbuf)) != -1)) {
op.write(bbuf, 0, length);
}
in.close();
op.flush();
op.close();
if (tempFile.delete()) {
// MetaDbHelper.note("Temp export file deleted");
}
} catch (Exception e) {
MetaDbHelper.logEvent(e);
// MetaDbHelper.logEvent("ExportVocab", "doPost",
// getServletContext().getAttribute("javax.servlet.context.tempdir").toString());
}
}
/**
* Deletes an element from MetaDB.
*
* @param elementName The desired element name to be added
* @return true if the element with name elementName was deleted, false otherwise
*/
public static boolean deleteElement(String elementName) {
Connection conn = Conn.initialize();
if (conn != null) {
try {
PreparedStatement deleteElement = conn.prepareStatement(DELETE_ELEMENT);
deleteElement.setString(1, elementName);
deleteElement.executeUpdate();
deleteElement.close();
conn.close();
return true;
} catch (Exception e) {
MetaDbHelper.logEvent(e);
}
}
return false;
}
/**
* Returns all the elements in the database.
*
* @return a List of all elements in MetaDB.
*/
public static ArrayList<String> getElementList() {
ArrayList<String> elementList = new ArrayList<String>();
Connection conn = Conn.initialize();
if (conn != null) {
try {
PreparedStatement getElementListQuery = conn.prepareStatement(GET_ELEMENT_LIST);
ResultSet getElementListQueryResult = getElementListQuery.executeQuery();
while (getElementListQueryResult.next())
elementList.add(getElementListQueryResult.getString(Global.ELEMENT));
getElementListQueryResult.close();
getElementListQuery.close();
conn.close();
} catch (Exception e) {
MetaDbHelper.logEvent(e);
}
}
return elementList;
}
/** @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response) */
@SuppressWarnings("unchecked")
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// TODO Auto-generated method stub
PrintWriter out = response.getWriter();
JSONObject output = new JSONObject();
String delimiter = "";
String projname = "";
String projnotes = "";
String template = "";
boolean useTemplate = false;
boolean disableQualifier = false;
try {
if (ServletFileUpload.isMultipartContent(request)) {
ServletFileUpload servletFileUpload = new ServletFileUpload(new DiskFileItemFactory());
List fileItemsList = servletFileUpload.parseRequest(request);
DiskFileItemFactory diskFileItemFactory = new DiskFileItemFactory();
diskFileItemFactory.setSizeThreshold(40960); /* the unit is bytes */
Iterator it = fileItemsList.iterator();
InputStream input = null;
while (it.hasNext()) {
FileItem fileItem = (FileItem) it.next();
// MetaDbHelper.note("Field name: "+fileItem.getFieldName());
// MetaDbHelper.note(fileItem.getString());
if (fileItem.isFormField()) {
/*
* The file item contains a simple name-value pair of a
* form field
*/
if (fileItem.getFieldName().equals("delimiter") && delimiter.equals(""))
delimiter = fileItem.getString();
else if (fileItem.getFieldName().equals("projname") && projname.equals(""))
projname = fileItem.getString().replace(" ", "_");
else if (fileItem.getFieldName().equals("projnotes") && projnotes.equals(""))
projnotes = fileItem.getString();
else if (fileItem.getFieldName().equals("project-template-checkbox"))
useTemplate = true;
else if (fileItem.getFieldName().equals("project-template"))
template = fileItem.getString().replace(" ", "_");
// else if (fileItem.getFieldName().equals("disable-qualifier-checkbox"))
// disableQualifier = true;
} else input = fileItem.getInputStream();
}
String userName = Global.METADB_USER;
HttpSession session = request.getSession(false);
if (session != null) {
userName = (String) session.getAttribute(Global.SESSION_USERNAME);
}
// MetaDbHelper.note("Delimiter: "+delimiter+", projname: "+projname+", projnotes:
// "+projnotes+", use template or not? "+useTemplate+" template: "+template);
if (useTemplate) {
ProjectsDAO.createProject(template, projname, projnotes, "");
output.put("projname", projname);
output.put("success", true);
output.put("message", "Project created successfully based on: " + template);
SysLogDAO.log(
userName,
Global.SYSLOG_PROJECT,
"User created project " + projname + " with template from " + template);
} else {
if (ProjectsDAO.createProject(projname, projnotes)) {
output.put("projname", projname);
String delimiterType = "csv";
if (delimiter.equals("tab")) {
delimiterType = "tsv";
disableQualifier = true; // Disable text qualifiers for TSV files.
}
// MetaDbHelper.note("Delim: "+delimiterType+", projname: "+projname+", input: "+input);
if (input != null) {
Result res =
DataImporter.importFile(delimiterType, projname, input, disableQualifier);
output.put("success", res.isSuccess());
if (res.isSuccess()) {
output.put("message", "Data import successfully");
SysLogDAO.log(
userName,
Global.SYSLOG_PROJECT,
"User created project " + projname + " with file import");
} else {
output.put("message", "The following fields have been changed");
SysLogDAO.log(
userName,
Global.SYSLOG_PROJECT,
"User created project " + projname + " with file import");
String fields = "";
ArrayList<String> data = (ArrayList<String>) res.getData();
for (String field : data) fields += field + ',';
output.put("fields", fields);
}
} else {
output.put("success", true);
output.put(
"message", "Project created successfully with default fields. No data imported");
SysLogDAO.log(userName, Global.SYSLOG_PROJECT, "User created project " + projname);
}
} else {
output.put("success", false);
output.put("message", "Cannot create project");
SysLogDAO.log(
userName, Global.SYSLOG_PROJECT, "User failed to create project " + projname);
}
}
} else {
output.put("success", false);
output.put("message", "Form is not multi-part");
}
} catch (NullPointerException e) {
try {
output.put("success", true);
output.put("message", "Project created successfully");
} catch (JSONException e1) {
MetaDbHelper.logEvent(e1);
}
} catch (Exception e) {
MetaDbHelper.logEvent(e);
try {
output.put("success", false);
output.put("message", "Project was not created");
} catch (JSONException e1) {
MetaDbHelper.logEvent(e1);
}
}
out.print(output);
out.flush();
}
