folly::dynamic ConfigApi::getConfigSourcesInfo() {
folly::dynamic reply_val = folly::dynamic::object;
// we have config_str, write its hash
if (!opts_.config_str.empty()) {
reply_val[kMcrouterConfigKey] = Md5Hash(opts_.config_str);
}
std::lock_guard<std::mutex> lock(fileInfoMutex_);
for (const auto& fileIt : fileInfos_) {
const auto& file = fileIt.second;
switch (file.type) {
case ConfigType::ConfigFile:
reply_val[kConfigFile] = file.path;
reply_val[kMcrouterConfigKey] = file.md5;
break;
case ConfigType::Pool:
if (!reply_val.count("pools")) {
reply_val["pools"] = folly::dynamic::object;
}
reply_val["pools"].insert(file.path, file.md5);
break;
case ConfigType::ConfigImport:
if (!reply_val.count(kConfigImport)) {
reply_val[kConfigImport] = folly::dynamic::object;
}
reply_val[kConfigImport].insert(file.path, file.md5);
break;
}
}
return reply_val;
}
string
Stats::Md5ForSeq(Alignment *alnObj, int s)
{
string seq;
const clustalw::SeqArray* seqArray = alnObj->getSeqArray();
char *hash;
string ret;
for(int l = 1; l <= alnObj->getSeqLength(s); l++)
{
int val = (*seqArray)[s][l];
// continue if gap
if((val < 0) || (val > userParameters->getMaxAA()))
continue;
seq.append(1, clustalw::userParameters->getAminoAcidCode(val));
}
std::transform(seq.begin(), seq.end(), seq.begin(), ::toupper);
hash = Md5Hash(seq.c_str());
if (hash==NULL)
{
ret = "HASHING_FAILURE";
} else {
ret = hash;
}
return ret;
}
bool ConfigApi::FileInfo::checkMd5Changed() {
auto previousHash = md5;
std::string contents;
if (!folly::readFile(path.data(), contents)) {
throw std::runtime_error("Error reading from config file " + path);
}
md5 = Md5Hash(contents);
lastMd5Check = nowWallSec();
return md5 != previousHash;
}
string
Stats::ConcatInputHash(Alignment *alnObj)
{
vector<string> rawSeqArray;
string ret;
char *hash;
// collect all sequences and sort
const clustalw::SeqArray* seqArray = alnObj->getSeqArray();
for(int s = 1; s <= alnObj->getNumSeqs(); s++)
{
string seq;
for(int r = 1; r <= alnObj->getSeqLength(s); r++)
{
int val = (*seqArray)[s][r];
seq.append(1, clustalw::userParameters->getAminoAcidCode(val));
}
rawSeqArray.push_back(seq);
}
std::sort(rawSeqArray.begin(), rawSeqArray.end());
// concatenate sorted seqs
string concatSeq;
std::vector<string>::iterator iter;
for(iter=rawSeqArray.begin(); iter != rawSeqArray.end(); ++iter)
concatSeq.append(*iter);
// build hash and return
hash = Md5Hash(concatSeq.c_str());
if (hash==NULL)
{
ret="HASHING_FAILURE";
} else {
for (int i=0; i<strlen(hash); i++)
ret.append(1, hash[i]);
free(hash);
}
return ret;
}
bool ConfigApi::get(ConfigType type, const std::string& path,
std::string& contents) {
std::string fullPath;
if (type == ConfigType::ConfigImport) {
if (folly::StringPiece(path).startsWith(kAbsoluteFilePrefix)) {
fullPath = path.substr(strlen(kAbsoluteFilePrefix));
} else {
boost::filesystem::path filePath(opts_.config_file);
fullPath = (filePath.parent_path() / path).string();
}
} else if (type == ConfigType::Pool) {
if (folly::StringPiece(path).startsWith(kAbsoluteFilePrefix)) {
fullPath = path.substr(strlen(kAbsoluteFilePrefix));
} else {
return false;
}
} else {
fullPath = path;
}
if (!folly::readFile(fullPath.data(), contents)) {
return false;
}
if (tracking_) {
std::lock_guard<std::mutex> lock(fileInfoMutex_);
auto fileInfoIt = trackedFiles_.emplace(fullPath, FileInfo()).first;
auto& file = fileInfoIt->second;
file.path = fullPath;
file.type = type;
file.lastMd5Check = nowWallSec();
file.md5 = Md5Hash(contents);
}
return true;
}
