void Trajectory::readJSON(const string &filename) {
JSON::Reader reader(filename);
JSON::ValuePtr data = reader.parse();
if (data->isDict()) {
// Units
float scale = 10;
if (data->has("units")) {
string units = String::toUpper(data->getString("units"));
if (units == "NM" || units == "NANOMETERS") scale = 1;
else if (units != "A" && units != "ANGSTROM" && units == "ANGSTROMS")
LOG_WARNING("Unrecognized units '" << data->getString("units") << "'");
}
// Topology
if (data->has("atoms")) {
topology->loadJSON(*data, scale);
topology->setTS();
}
// Positions
if (data->has("positions")) {
JSON::List list = data->getList("positions");
for (unsigned i = 0; i < list.size(); i++)
add(new Positions(list.getList(i), scale));
}
} else add(new Positions(*data, 10));
}
bool JSONAPI::handlePage(HTTP::WebContext &ctx, ostream &stream,
const URI &uri) {
if (!String::startsWith(uri.getPath(), root)) return false;
string cmd = uri.getPath().substr(root.length());
// Look up command
api_t::const_iterator it = api.find(cmd);
if (it == api.end()) return false;
ctx.setDynamic(); // Don't cache
HTTP::Connection &con = ctx.getConnection();
bool jsonp = !jsonpCB.empty() && uri.has(jsonpCB);
if (jsonp) {
con.getResponse().setContentType("application/javascript");
con << uri.get(jsonpCB) << '(';
} else con.getResponse().setContentType("application/json");
JSON::Writer writer(con, 0, !uri.has("pretty"),
uri.has("python_mode") ? JSON::Writer::PYTHON_MODE :
JSON::Writer::JSON_MODE);
try {
// Parse JSON data
JSON::ValuePtr msg;
if (con.getRequest().hasContentType() &&
String::startsWith(con.getRequest().getContentType(),
"application/json")) {
MemoryBuffer &payload = con.getPayload();
if (payload.getFill()) msg = JSON::Reader(payload).parse();
} else if (!uri.empty()) {
msg = new JSON::Dict;
for (URI::const_iterator it = uri.begin(); it != uri.end(); it++)
msg->insert(it->first, it->second);
}
// Dispatch API command
if (msg.isNull()) LOG_DEBUG(5, "JSONAPI Call: " << cmd << "()");
else LOG_DEBUG(5, "JSONAPI Call: " << cmd << '(' << *msg << ')');
it->second->handle(ctx, cmd, msg, writer);
// Make sure JSON stream is complete
writer.close();
} catch (const Exception &e) {
LOG_ERROR(e);
// Clear possibly partial or invalid response
con.clearResponseBuffer();
// jsonp header
if (jsonp) con << uri.get(jsonpCB) << '(';
// Send error message
JSON::Writer writer(con, 0, true);
writer.beginList();
writer.append("error");
writer.append(e.getMessage());
writer.endList();
writer.close();
}
if (jsonp) con << ");";
return true;
}
SmartPointer<Value> Javascript::require(Callback &cb, Value &args) {
string id = args.getString(0);
modules_t::iterator it = modules.find(id);
if (it != modules.end()) return it->second->getExports();
string path = searchPath(id);
if (path.empty()) THROWS("Module '" << id << "' not found");
// Handle package.json
if (String::endsWith(path, "/package.json")) {
JSON::ValuePtr package = JSON::Reader(path).parse();
path = SystemUtilities::absolute(path, package->getString("main"));
}
// Register module
SmartPointer<Module> module = new Module(id, path);
modules.insert(modules_t::value_type(id, module));
SmartPointer<Scope> scope = impl->newScope();
SmartPointer<Factory> factory = getFactory();
SmartPointer<Value> exports = factory->createObject();
if (String::endsWith(path, ".json")) {
// Read JSON data
js::Sink sink(factory);
JSON::Reader(path).parse(sink);
sink.close();
exports = sink.getRoot();
} else {
// Push path
SmartFunctor<Javascript> smartPopPath(this, &Javascript::popPath);
pushPath(path);
// Get global object for this scope
SmartPointer<Value> global = scope->getGlobalObject();
// Inject native properties
global->copyProperties(*nativeProps);
// Create module object
SmartPointer<Value> obj = factory->createObject();
obj->set("id", factory->create(id));
obj->set("exports", exports);
obj->set("filename", factory->create(path));
obj->set("name", factory->create(id));
// Set global vars
global->set("id", factory->create(id));
global->set("exports", exports);
global->set("module", obj);
// Compile & eval code
scope->eval(path);
// Get exports, it may have been reassigned
exports = obj->get("exports");
}
module->setExports(exports->makePersistent());
return exports;
}
bool OAuth2SessionLogin::handlePage(HTTP::WebContext &ctx, ostream &stream,
const URI &uri) {
HTTP::Connection &con = ctx.getConnection();
HTTP::Request &request = con.getRequest();
HTTP::Response &response = con.getResponse();
ctx.setDynamic(); // Don't cache
// Force secure
if (!con.isSecure())
THROWCS("Cannot logon via insecure port",
HTTP::StatusCode::HTTP_UNAUTHORIZED);
// Get session ID
string sid = request.findCookie(sessionManager->getSessionCookie());
if (sid.empty() && uri.has("state")) sid = uri.get("state");
HTTP::SessionPtr session = sessionManager->findSession(ctx, sid);
try {
if (session.isNull() ||
(uri.has("state") && uri.get("state") != session->getID()) ||
(!uri.has("state") && session->getUser().empty())) {
session = sessionManager->openSession(ctx);
sid = session->getID();
URI redirectURL = auth->getRedirectURL(uri.getPath(), sid);
response.redirect(redirectURL);
} else if (session->getUser().empty()) {
// TODO Make sure session is not very old
URI postURI = auth->getVerifyURL(uri, sid);
LOG_DEBUG(5, "Token URI: " << postURI);
// Extract query data
string data = postURI.getQuery();
postURI.setQuery("");
// Verify authorization with OAuth2 server
HTTP::Transaction tran(sslCtx);
tran.post(postURI, data.data(), data.length(),
"application/x-www-form-urlencoded", 1.0);
// Read response
tran.receiveHeader();
JSON::ValuePtr token = JSON::Reader(tran).parse();
LOG_DEBUG(5, "Token Response: \n" << tran.getResponse() << *token);
// Verify token
string accessToken = auth->verifyToken(token);
// Get profile
URI profileURL = auth->getProfileURL(accessToken);
HTTP::Transaction tran2(sslCtx);
tran2.get(profileURL);
// Read response
tran2.receiveHeader();
JSON::ValuePtr profile = JSON::Reader(tran2).parse();
// Process profile
string email = profile->getString("email");
if (!profile->getBoolean("email_verified"))
THROWCS("Email not verified", HTTP::StatusCode::HTTP_UNAUTHORIZED);
session->setUser(email);
LOG_INFO(1, "Authorized: " << email);
// Final redirect to remove auth parameters
response.redirect(uri.getPath());
} else return false; // Already authorized
// Make sure session cookie is set
sessionManager->setSessionCookie(ctx);
} catch (...) {
// Close session on error
if (!sid.empty()) sessionManager->closeSession(ctx, sid);
throw;
}
return true;
}
