const string off_targets_by_seq(const MongooseRequest& request) {
ots_data_t result;
string sequence;
string species;
string pam_right_param;
vector<uint64_t> matches;
bool pam_right;
string jason_result;
request.getVar("seq", sequence);
request.getVar("species", species);
request.getVar("pam_right", pam_right_param);
pam_right = false;
if ( pam_right_param == "true" ) {
pam_right = true;
}
else if ( pam_right_param == "false" ) {
pam_right = false;
}
else {
throw runtime_error("pam_right must be the string true or false");
}
result = get_util(species)->off_targets_by_seq( sequence, pam_right);
jason_result = util::to_string(result);
return jason_result;
}
const string id_json(const MongooseRequest& request) {
vector<string> seqs;
string ids_text, species;
request.getVar("ids", ids_text);
request.getVar("species", species);
if ( ids_text.empty() )
throw runtime_error("Please provide ids as a comma separated string");
if ( species.empty() )
throw runtime_error("Please provide a species");
util::lc(species);
vector<string> ids = util::split(ids_text);
//should maybe change this to return an object of { id: sequence }
for ( vector<string>::size_type i = 0; i < ids.size(); i++ ) {
cerr << "Getting sequence for " << ids[i] << " (" << species << ")\n";
unsigned long long id;
try {
id = stoull(ids[i]);
}
catch (const invalid_argument &e) {
throw runtime_error("id " + ids[i] + " not an integer");
}
seqs.push_back( "'" + get_util(species)->get_crispr(id) + "'" );
}
return util::to_json_array(seqs);
}
const string generateInfoContent(const MongooseRequest &request) {
string result;
result = "<h1>Sample Info Page</h1>";
result += "<br />Request URI: " + request.getUri();
result += "<br />Your IP: " + ipToString(request.getRemoteIp());
time_t tim;
time(&tim);
result += "<br />Current date & time: " + toString(ctime(&tim));
result += "<br /><br /><a href=\"/\">Index page</a>";
return result;
}
const string find_off_targets(const MongooseRequest& request) {
string species;
string result = "{";
vector<uint64_t> ids_all;
string ids_text;
request.getVar("ids", ids_text);
request.getVar("species", species);
if ( ids_text.empty() )
throw runtime_error("Please provide ids");
if ( species.empty() )
throw runtime_error("Please provide a species");
util::lc(species);
vector<string> ids = util::split(ids_text);
for ( vector<string>::size_type i = 0; i < ids.size(); i++ ) {
unsigned long long id;
try {
id = stoull(ids[i]);
}
catch (const invalid_argument &e) {
throw runtime_error("id " + ids[i] + " not an integer");
}
ids_all.push_back(id);
}
vector<ots_data_t> offs = get_util(species)->find_off_targets(ids_all, true);
for ( uint i = 0; i < offs.size(); ++i ) {
if ( i > 0 ) result += ",";
//we use my to_string here as its a struct we want a string of
result += "\"" + to_string(offs[i].id) + "\":" + util::to_string(offs[i]);
}
result += "}";
//result = "Got data for " + to_string(offs.size()) + " crisprs";
return result;
}
virtual bool handleEvent(ServerHandlingEvent eventCode, MongooseConnection &connection, const MongooseRequest &request, MongooseResponse &response) {
bool res = false;
if (eventCode == MG_NEW_REQUEST) {
if (request.getUri() == string("/info")) {
handleInfo(request, response);
res = true;
}
}
return res;
}
//wrap a json string in jsonp. return true if it was jsonp
bool handle_jsonp(const MongooseRequest& request, string& result) {
string callback;
request.getVar("callback", callback);
if ( callback.empty() ) return false;
callback += "(";
result.insert(0, callback);
result += ");";
return true;
}
void get_matches(const MongooseRequest& request, vector<uint64_t>& matches) {
string seq;
string pam_right_str;
string species;
request.getVar("seq", seq);
request.getVar("pam_right", pam_right_str);
request.getVar("species", species);
//make species lowercase
util::lc( species );
//default pam_right is 2, which means don't consider the pam
if ( pam_right_str.size() == 0 ) pam_right_str = "2";
if ( seq.empty() )
throw runtime_error("Please provide a sequence");
if ( seq.size() != 20 )
throw runtime_error("Sequence must be 20 bases long");
if ( pam_right_str.empty() )
throw runtime_error("Please specify pam right");
int pam_right = atoi( pam_right_str.c_str() );
if ( ! ( pam_right == 0 || pam_right == 1 || pam_right == 2 ) )
throw runtime_error("pam_right must be 0, 1 or 2");
if ( species.empty() )
throw runtime_error("Please specify a species");
cerr << "Searching for " << seq << ", pam_right is " << pam_right << endl;
get_util(species)->search_by_seq( seq, pam_right, matches );
}
const string search(const MongooseRequest& request) {
string result;
result = "<h1>Sample Info Page</h1>";
result += "<br />Request URI: " + request.getUri();
vector<uint64_t> matches;
get_matches(request, matches);
//result += "<br />Seq is: " + seq;
result += "<br />Found " + to_string(matches.size()) + " matches:";
for ( uint i = 0; i < matches.size(); i++ ) {
result += "<br />" + to_string(matches[i]);
}
return result;
}
bool HttpServer::handleEvent(ServerHandlingEvent eventCode,
MongooseConnection &connection,
const MongooseRequest &request,
MongooseResponse &response)
{
bool res = false;
switch (eventCode)
{
case MG_NEW_REQUEST:
// check that we want to handle this.
if (request.getUri().substr(0,strlen("/racka3/")) == "/racka3/")
{
res = handleNewRequest(eventCode,connection,request,response);
}
break;
default:
break;
}
return res;
}
bool HttpServer::handleNewRequest(ServerHandlingEvent eventCode,
MongooseConnection &connection,
const MongooseRequest &request,
MongooseResponse &response)
{
bool res = false;
cJSON* json = 0;
string uri = request.getUri();
bool handled = false;
// if this is a post, get the post data
if (request.getRequestMethod() == "POST")
{
std::string buffer;
char c;
while (connection.read(&c,1))
{
buffer.push_back(c);
}
json = cJSON_Parse(buffer.c_str());
// if we couldnt parse the json? make empty json
if (!json)
{
json = cJSON_CreateObject();
}
}
else
{
// make an empty json object
json = cJSON_CreateObject();
}
// now act depending on the path
if (uri == string("/racka3/getallplugins")) // <-- rack manipulation
{
_pluginHost->getAvailablePlugins(json);
} else if (uri == string("/racka3/addplugin")) {
_pluginHost->addPlugin(json);
} else if (uri == string("/racka3/removeplugin")) {
_pluginHost->removePlugin(json);
} else if (uri == string("/racka3/moveplugin")) {
_pluginHost->movePlugin(json);
} else if (uri == string("/racka3/setparamvalue")) {
_pluginHost->setPluginParam(json);
} else if (uri == string("/racka3/getpluginchain")) {
_pluginHost->getPluginChain(json);
}
else if (uri == string("/racka3/storePluginPreset")) { // <-- plugin presets
_pluginHost->storePluginPreset(json);
} else if (uri == string("/racka3/deletePluginPreset")) {
_pluginHost->deletePluginPreset(json);
}
else if (uri == string("/racka3/storeRackPreset")) { // <-- rack presets
_pluginHost->storeRackPreset(json);
} else if (uri == string("/racka3/deleteRackPreset")) {
_pluginHost->deleteRackPreset(json);
} else if (uri == string("/racka3/loadRackPreset")) {
_pluginHost->loadRackPreset(json);
} else if (uri == string("/racka3/listRackPresets")) {
_pluginHost->listRackPresets(json);
}
else if (uri == string("/racka3/listDevices")) { // <-- soundcard configuration
_soundInterface->listDevices(json);
} else if (uri == string("/racka3/setDevice")) {
if (_pluginHost->getPluginChainSize())
cJSON_AddStringToObject(json,"error","cannot change sound settings unless rack is empty");
else
_soundInterface->init(json);
} else if (uri == string("/racka3/getCurrentDevice")) {
_soundInterface->getCurrent(json);
}
// did we make any json?
if (json->child)
{
// output the json
char * content = cJSON_Print(json);
response.setStatus(200);
response.setContentType("application/json");
response.addContent(content);
free(content);
}
else
{
// no json: error code for you.
response.setStatus(404);
}
response.setCacheDisabled();
response.setConnectionAlive(false);
response.write();
// clean up
cJSON_Delete(json);
return res;
}
virtual bool handleEvent(ServerHandlingEvent eventCode, MongooseConnection& connection, const MongooseRequest& request, MongooseResponse& response) {
bool res = false; //gets set to true if successful
string result, content_type;
if (eventCode == MG_NEW_REQUEST) {
string uri = request.getUri();
//returns 0 if they match
if ( ! uri.compare(0, 4, "/api") ) {
cerr << "API URI: " << uri << endl;
//prefix is api so we know it will be json
content_type = "application/json";
try {
if ( uri == string("/api/search") ) {
result = search_json(request);
res = true;
}
else if ( uri == string("/api/id") ) {
result = id_json(request);
res = true;
}
else if ( uri == string("/api/off_targets") ) {
result = find_off_targets(request);
res = true;
}
else if ( uri == string("/api/off_targets_by_seq") ) {
result = off_targets_by_seq(request);
res = true;
}
else {
cerr << "Couldn't find api URI " << uri << endl;
}
}
catch (const runtime_error& error) {
string e = error.what();
result = json_error( e );
res = true; //we need this or we return 404
}
if ( res ) handle_jsonp(request, result);
}
else {
cerr << "URI: " << uri << endl;
content_type = "text/html";
try {
if ( uri == string("/search") ) {
result = search(request);
}
else {
cerr << "Couldn't find URI " << uri << endl;
}
}
catch (const runtime_error& error) {
result = "<h1>" + string(error.what()) + "</h1>";
}
}
}
if ( res ) {
process_response(request, response, content_type, result);
last_accessed.set(); //update last accessed to now
}
return res;
}
