/**
* Generates html page containing the NGL canvas.
*
* @param directory path to the job directory
* @param inputName the input: either a PDB id or the file name as input by user
* @param strucFile the file with the AU structure (can be cif or pdb and gzipped or not)
* @param strucURI URL to reach auCifFile within the browser
* @param title Page title [default: structure name]
* @param size the canvas size
* @param jsonURI path to the json dataURL
* @param interfaces List of all interfaces to build the latticegraph
* @param requestedIfaces subset of the interfaces to display
* @param out Stream to output the HTML page
* @param urlMolViewer path to the libURL
* @throws StructureException For errors parsing the input structure
* @throws IOException For errors reading or writing files
*/
public static void generateHTMLPage(
File directory,
String inputName,
File strucFile,
String strucURI,
String title,
String size,
String jsonURL,
List<Interface> interfaces,
Collection<Integer> requestedIfaces,
PrintWriter out,
String urlMolViewer)
throws IOException, StructureException {
logger.info("JSON URL for {}: {}", inputName, jsonURL);
logger.info("Structure URL for {}: {}", inputName, strucURI);
MustacheFactory mf = new DefaultMustacheFactory();
String template = LatticeGUIMustache.expandTemplatePath(TEMPLATE_LATTICE_GUI_NGL_LAZY);
Mustache mustache = mf.compile(template);
LazyLatticeGUIMustache3D page = new LazyLatticeGUIMustache3D();
page.setSize(size);
page.setTitle(title);
page.setDataURL(jsonURL);
page.setLibURL(urlMolViewer);
page.setStrucURL(strucURI);
try {
mustache.execute(out, page).flush();
} catch (IOException e) {
logger.error("Error generating output from template " + template, e);
}
}
public void renderAndWrite() throws IOException, ConfigurationException {
readConfig();
removeOld();
InputStreamReader reader;
BufferedReader bufferedReader;
File template = new File(templatePath);
if (!template.isFile() || !template.exists()) {
LOGGER.error("template for logstash config doesn't exist! ");
throw new IOException("template for logstash config doesn't exist! ");
}
reader = new InputStreamReader(new FileInputStream(template));
bufferedReader = new BufferedReader(reader);
File newConf = new File(logstashConfPath);
Writer writer = new OutputStreamWriter(new FileOutputStream(newConf));
HashMap<String, Object> m = new HashMap<String, Object>();
// Add redis host
m.put("redisHost", redisHost);
m.put("elasticSearchHost", elasticSearchHost);
m.put("elasticSearchHttpPort", elasticSearchHttpPort);
MustacheFactory mf = new DefaultMustacheFactory();
// TODO: what's the meaning of this tag in mustache's compile
Mustache mustache = mf.compile(bufferedReader, "example");
mustache.execute(writer, m);
writer.flush();
bufferedReader.close();
reader.close();
}
public String render(Review review) throws IOException {
MustacheFactory mf = new DefaultMustacheFactory();
Mustache mustache = mf.compile(TEMPLATE_MUSTACHE);
Writer sink = new StringWriter();
mustache.execute(sink, review).flush();
return sink.toString();
}
public static void main(String[] args) {
CompiledMustacheTemplates cmt = getInstance();
Mustache m = cmt.getProcessesMustache();
try {
m.execute(new PrintWriter(System.out), BASFProcess.getNameToProcessMap().values()).flush();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
private String getDefaultTemplate(BinaryResource binaryResource, String uuid) throws IOException {
MustacheFactory mf = new DefaultMustacheFactory();
Mustache mustache = mf.compile("com/docdoku/server/viewers/default_viewer.mustache");
Map<Object, Object> scopes = new HashMap<>();
scopes.put("uriResource", ViewerUtils.getURI(binaryResource, uuid));
scopes.put("fileName", binaryResource.getName());
StringWriter templateWriter = new StringWriter();
mustache.execute(templateWriter, scopes).flush();
return ViewerUtils.getViewerTemplate(
dataManager, binaryResource, uuid, templateWriter.toString());
}
private Mustache customCompile(String filename, Res resource) {
Map<String, Mustache> cache = partialCache.get();
try {
Mustache mustache = cache.get(filename);
if (mustache == null) {
String template = preprocess(resource.getContent());
InputStreamReader reader =
new InputStreamReader(new ByteArrayInputStream(template.getBytes()));
mustache = mc.compile(reader, filename, SM, EM);
cache.put(filename, mustache);
mustache.init();
}
return mustache;
} finally {
cache.remove(filename);
}
}
protected Writer handleFunction(Writer writer, Function function, Object[] scopes) {
StringWriter sw = new StringWriter();
runIdentity(sw);
Object newtemplate = function.apply(sw.toString());
if (newtemplate != null) {
if (function instanceof TemplateFunction) {
String templateText = newtemplate.toString();
Mustache mustache = cf.getTemplate(templateText);
if (mustache == null) {
mustache =
cf.compile(new StringReader(templateText), tc.file(), tc.startChars(), tc.endChars());
cf.putTemplate(templateText, mustache);
}
writer = mustache.execute(writer, scopes);
} else {
try {
writer.write(newtemplate.toString());
} catch (IOException e) {
throw new MustacheException("Failed to write function result", e);
}
}
}
return writer;
}
@Override
public void handle(HttpServletRequest request, HttpServletResponse response, DataObject user)
throws IOException, ServletException {
if (request.getMethod().equals("POST")) {
String fullname = request.getParameter("fullname");
String email = request.getParameter("email");
String password = request.getParameter("password");
String password2 = request.getParameter("password2");
if (email != null) {
DataObject data = new DataObject();
data.put("email", email);
DataObject query = new DataObject();
query.put("data", data);
query = ds.fetch(query);
DataList lista = query.getDataObject("response").getDataList("data");
if (lista.size() == 0) {
if (password != null) {
if (password.equals(password2)) {
DataObject obj = new DataObject();
obj.put("fullname", fullname);
obj.put("email", email);
obj.put("password", password);
obj.put("registeredAt", ZonedDateTime.now().toString());
obj.put("confirmed", "false");
obj.put("emailSent", "false");
Address userAddr = new InternetAddress(email, fullname, "utf-8");
DataObject dao = ds.addObj(obj);
dao =
dao.getDataObject("response")
.getDataObject("data"); // System.out.println("dao:"+dao);
String content =
MessageFormat.format(
Utils.textInputStreamToString(
LoginHandler.class.getResourceAsStream(
"/templates/confirmationMail.template"),
"utf-8"),
fullname,
TokenGenerator.nextTokenByUserId(dao.getNumId()),
email);
MailSender.send(userAddr, "Cloudino confirmation email", content, dao.getNumId());
logger.log(Level.FINE, "Register and send mail to: {0}", email);
Map<String, Object> register = new HashMap<>();
Map<String, Object> scope = new HashMap<>();
scope.put("ctx", request.getContextPath());
register.put("confirm", scope);
response.setCharacterEncoding("utf-8");
mustache.execute(response.getWriter(), register);
}
}
} else {
Map<String, Object> register = new HashMap<>();
Map<String, Object> scope = new HashMap<>();
scope.put("error", "Email was already registered");
scope.put("ctx", request.getContextPath());
register.put("register", scope);
response.setCharacterEncoding("utf-8");
mustache.execute(response.getWriter(), register);
}
}
} else {
Map<String, Object> register = new HashMap<>();
Map<String, Object> scope = new HashMap<>();
scope.put("ctx", request.getContextPath());
register.put("register", scope);
response.setCharacterEncoding("utf-8");
mustache.execute(response.getWriter(), register);
}
}