int main (int argc,char *argv[]){
// all args are meant to be brought
if (argc!=1) {
char file_name[4096];
char file_addr[4096];
char wrk_dir[4096];
int i;
// get file path
if (getWorkingDir(&wrk_dir)==0) {
if (DEBUG) printf ("[debug] wrk_dir = %s\n",wrk_dir);
}
if (DEBUG) printf("[debug] sizeof(argc)=%d\n",sizeof(argc));
for (i = 1; i < argc; i++) {
strcpy(file_name,argv[i]);
if (DEBUG) printf("[debug] file_name = %s\n",file_name);
fileExist(file_name);
sprintf(file_addr,strcat(strcat(wrk_dir,"/"),file_name));
if (DEBUG) printf("[debug] file_addr=%s\n",file_addr);
// add a comma if more than 1 exists
if (argc-i!=0)
storePath(strcat(file_addr,","));
else
storePath(file_addr);
}
return 0;
} else {
// if none, drop
// check for file waiting to be dropped
if (bring_it()!=0){
printf("No file to be brought.\n");
}
}
if (DEBUG) printf("[debug] returning\n");
return 0;
}
void LLDir::dumpCurrentDirectories()
{
LL_DEBUGS2("AppInit","Directories") << "Current Directories:" << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " CurPath: " << getCurPath() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " AppName: " << getAppName() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " ExecutableFilename: " << getExecutableFilename() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " ExecutableDir: " << getExecutableDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " ExecutablePathAndName: " << getExecutablePathAndName() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " WorkingDir: " << getWorkingDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " AppRODataDir: " << getAppRODataDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " OSUserDir: " << getOSUserDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " OSUserAppDir: " << getOSUserAppDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " LindenUserDir: " << getLindenUserDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " TempDir: " << getTempDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " CAFile: " << getCAFile() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " SkinBaseDir: " << getSkinBaseDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " SkinDir: " << getSkinDir() << LL_ENDL;
}
void LLDir::dumpCurrentDirectories()
{
LL_DEBUGS2("AppInit","Directories") << "Current Directories:" << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " CurPath: " << getCurPath() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " AppName: " << getAppName() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " ExecutableFilename: " << getExecutableFilename() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " ExecutableDir: " << getExecutableDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " ExecutablePathAndName: " << getExecutablePathAndName() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " WorkingDir: " << getWorkingDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " AppRODataDir: " << getAppRODataDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " OSUserDir: " << getOSUserDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " OSUserAppDir: " << getOSUserAppDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " LindenUserDir: " << getLindenUserDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " TempDir: " << getTempDir() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " CAFile: " << getCAFile() << LL_ENDL;
LL_DEBUGS2("AppInit","Directories") << " SkinDir: " << getSkinDir() << LL_ENDL;
#if LL_LIBXUL_ENABLED
LL_DEBUGS2("AppInit","Directories") << " HTML Path: " << getExpandedFilename( LL_PATH_HTML, "" ) << llendl;
LL_DEBUGS2("AppInit","Directories") << " Mozilla Profile Path: " << getExpandedFilename( LL_PATH_MOZILLA_PROFILE, "" ) << llendl;
#endif
}
/**
* @internal
* @brief Mac version. Extracts the user application execution and data path.
*
* They are stored in userDataPath and userExecPath attributes.
*/
void ResourceManager::extractUserAppPathMAC()
{
char bundlePath[2048];
char exePath[2048];
char resourcesPath[2048];
CFBundleRef mainBundle = CFBundleGetMainBundle();
assert( mainBundle );
// Get URLs
CFURLRef mainBundleURL = CFBundleCopyBundleURL( mainBundle);
assert( mainBundleURL);
CFURLRef exeURL = CFBundleCopyExecutableURL( mainBundle);
assert( exeURL);
CFURLRef resourcesURL = CFBundleCopyResourcesDirectoryURL( mainBundle);
assert( resourcesURL);
// Get Paths into strings
CFStringRef cfStringRef = CFURLCopyFileSystemPath( mainBundleURL, kCFURLPOSIXPathStyle);
assert( cfStringRef);
CFStringRef cfExePathRef = CFURLCopyFileSystemPath( exeURL, kCFURLPOSIXPathStyle);
assert( cfExePathRef);
CFStringRef cfResourcesPathRef = CFURLCopyFileSystemPath( resourcesURL, kCFURLPOSIXPathStyle);
assert( cfResourcesPathRef);
CFStringGetCString( cfStringRef, bundlePath, 1024, kCFStringEncodingASCII);
CFStringGetCString( cfExePathRef, exePath, 1024, kCFStringEncodingASCII);
CFStringGetCString( cfResourcesPathRef, resourcesPath, 1024, kCFStringEncodingASCII);
// Release resources
CFRelease( mainBundleURL);
CFRelease( exeURL);
CFRelease( cfStringRef);
CFRelease( cfExePathRef);
CFRelease( cfResourcesPathRef);
userExecPath = bundlePath;
//userExecPath = exePath;
std::string::size_type lastSlashPos = userExecPath.find_last_of("/");
userExecPath = userExecPath.substr(0, lastSlashPos);
userExecPath = userExecPath + "/";
//userDataPath = userExecPath + userResourcesDirName;
resourcesPathInBundle = String(bundlePath) + "/" + String(resourcesPath) + "/";
//userDataPath = String(bundlePath) + "/" + String(resourcesPath) + "/data/";
userDataPath = String(bundlePath) + "/" + userResourcesDirName;
//libDataPath = String(bundlePath) + "/" + String(resourcesPath) + "/cing_bin/data/";
libDataPath = String(bundlePath) + "/../../../../cing_bin/data/";
// Log some info
LOG( "Exec Path %s", exePath );
LOG( "Bundle Path %s", bundlePath );
LOG( "Resources Path %s", resourcesPath );
LOG( "User Data Path %s", userDataPath.c_str() );
const char* curentDir = getWorkingDir().c_str();
LOG( "Current Working Dir: %s", getWorkingDir().c_str() );
}
bool MolecularFileDialog::writeFile()
{
list<Composite*>& selection = getMainControl()->getMolecularControlSelection();
if (selection.size() != 1 || !RTTI::isKindOf<System> (*selection.begin()))
{
setStatusbarText((String)tr("Not a single system selected! Aborting writing..."), true);
return false;
}
const System& system = *(const System*) (*selection.begin());
String file_name = getWorkingDir();
file_name += FileSystem::PATH_SEPARATOR;
file_name += system.getName();
file_name += ".pdb";
QString s = QFileDialog::getSaveFileName(
0,
tr("Choose a filename to save the selected system"),
file_name.c_str(),
getSupportedFileFormats().c_str());
if (s == QString::null) return false;
setStatusbarText((String)tr("writing file..."));
String filename = ascii(s);
setWorkingDirFromFilename_(filename);
String filter(filename);
while (filter.has(FileSystem::PATH_SEPARATOR))
{
filter = filter.after(FileSystem::PATH_SEPARATOR);
}
String filename_without_path = filter;
while (filter.has('.'))
{
filter = filter.after(".");
}
bool result = false;
if (filter == "PDB" || filter == "pdb" ||
filter == "ent" || filter == "ENT" ||
filter == "brk" || filter == "BRK")
{
result = writePDBFile(filename, system);
}
else if (filter.hasSubstring("HIN") || filter.hasSubstring("hin"))
{
result = writeHINFile(filename, system);
}
else if (filter.hasSubstring("MOL2") || filter.hasSubstring("mol2"))
{
result = writeMOL2File(filename, system);
}
else if (filter.hasSubstring("MOL") || filter.hasSubstring("mol"))
{
result = writeMOLFile(filename, system);
}
else if (filter.hasSubstring("SDF") || filter.hasSubstring("sdf"))
{
result = writeSDFile(filename, system);
}
else if (filter.hasSubstring("AC") || filter.hasSubstring("ac"))
{
result = writeACFile(filename, system);
}
else if (filter.hasSubstring("XYZ") || filter.hasSubstring("xyz"))
{
result = writeXYZFile(filename, system);
}
else
{
if (filter == filename_without_path)
{
filename += ".pdb";
result = writePDBFile(filename, system);
}
else
{
setStatusbarText((String)tr("Unknown file format, please set the file extension accordingly to type, aborting..."), true);
return false;
}
}
if (!result)
{
return false;
}
setStatusbarText(String(system.countAtoms()) + " " + (String)tr("atoms written to file") + " \"" + filename + "\"", true);
return true;
}
void Awstats::config(HttpVHost *pVHost, int val, char* achBuf, const XmlNode *pAwNode,
char* iconURI, const char* vhDomain, int vhAliasesLen )
{
const char *pURI;
const char *pValue;
char *p;
int handlerType;
int len = strlen( achBuf );
int iChrootLen = 0;
if ( HttpGlobals::s_psChroot != NULL )
iChrootLen = HttpGlobals::s_psChroot->len();
setMode( val );
if ( achBuf[len - 1] == '/' )
achBuf[len - 1] = 0;
setWorkingDir( achBuf );
pURI = pAwNode->getChildValue( "awstatsURI" );
if ( ( !pURI ) || ( *pURI != '/' ) || ( * ( pURI + strlen( pURI ) - 1 ) != '/' )
|| ( strlen( pURI ) > 100 ) )
{
ConfigCtx::getCurConfigCtx()->log_warn( "AWStats URI is invalid"
", use default [/awstats/]." );
iconURI[9] = 0;;
pURI = iconURI;
}
setURI( pURI );
if ( val == AWS_STATIC )
{
handlerType = HandlerType::HT_NULL;
strcat( achBuf, "/html/" );
}
else
{
ConfigCtx::getCurConfigCtx()->getValidPath( achBuf, "$SERVER_ROOT/add-ons/awstats/wwwroot/cgi-bin/",
"AWStats CGI-BIN directory" );
if ( pVHost->getRootContext().determineMime( "pl", NULL )->getHandler()->getHandlerType() )
handlerType = HandlerType::HT_NULL;
else
handlerType = HandlerType::HT_CGI;
}
HttpContext *pContext =
pVHost->addContext( pURI, handlerType, &achBuf[iChrootLen], NULL, 1 );
p = achBuf;
if ( ConfigCtx::getCurConfigCtx()->getLongValue( pAwNode, "securedConn", 0, 1, 0 ) == 1 )
{
p += safe_snprintf( achBuf, 8192,
"rewriteCond %%{HTTPS} !on\n"
"rewriteCond %%{HTTP:X-Forwarded-Proto} !https\n"
"rewriteRule ^(.*)$ https://%%{SERVER_NAME}%%{REQUEST_URI} [R,L]\n" );
}
if ( val == AWS_STATIC )
{
safe_snprintf( p, &achBuf[8192] - p,
"RewriteRule ^$ awstats.%s.html\n",
pVHost->getName() );
}
else
{
safe_snprintf( p, &achBuf[8192] - p,
"RewriteRule ^$ awstats.pl\n"
"RewriteCond %%{QUERY_STRING} !configdir=\n"
"RewriteRule ^awstats.pl "
"$0?config=%s&configdir=%s/conf [QSA]\n",
pVHost->getName(),
getWorkingDir() + iChrootLen );
pContext->setUidMode( UID_DOCROOT );
}
pContext->enableRewrite( 1 );
pContext->configRewriteRule( pVHost->getRewriteMaps(), achBuf );
pValue = pAwNode->getChildValue( "realm" );
if ( pValue )
pVHost->configAuthRealm( pContext, pValue );
pValue = pAwNode->getChildValue( "siteDomain" );
if ( !pValue )
{
ConfigCtx::getCurConfigCtx()->log_warn( "SiteDomain configuration is invalid"
", use default [%s].", vhDomain );
pValue = vhDomain;
}
else
{
ConfigCtx::getCurConfigCtx()->expandDomainNames( pValue, achBuf, 4096 );
pValue = achBuf;
}
setSiteDomain( pValue );
pValue = pAwNode->getChildValue( "siteAliases" );
int needConvert = 1;
if ( !pValue )
{
if ( vhAliasesLen == 0 )
{
safe_snprintf( achBuf, 8192, "127.0.0.1 localhost REGEX[%s]",
getSiteDomain() );
ConfigCtx::getCurConfigCtx()->log_warn( "SiteAliases configuration is invalid"
", use default [%s].", achBuf );
pValue = achBuf;
needConvert = 0;
}
else
pValue = "$vh_aliases";
}
if ( needConvert )
{
ConfigCtx::getCurConfigCtx()->expandDomainNames( pValue, &achBuf[4096], 4096, ' ' );
ConfigCtx::getCurConfigCtx()->convertToRegex( &achBuf[4096], achBuf, 4096 );
pValue = achBuf;
ConfigCtx::getCurConfigCtx()->log_info( "SiteAliases is set to '%s'", achBuf );
}
setAliases( pValue );
val = ConfigCtx::getCurConfigCtx()->getLongValue( pAwNode, "updateInterval", 3600, 3600 * 24, 3600 * 24 );
if ( val % 3600 != 0 )
val = ( ( val + 3599 ) / 3600 ) * 3600;
setInterval( val );
val = ConfigCtx::getCurConfigCtx()->getLongValue( pAwNode, "updateOffset", 0, LONG_MAX, 0 );
if ( val > getInterval() )
val %= getInterval();
setOffset( val );
pVHost->setAwstats( this );
}
void AbstractEngine::writeRestartFile() {
GreasyTask *task;
map<int,GreasyTask*>::iterator it;
list<int> dependants;
set<GreasyTask*> invalidTasks;
list<int>::iterator lit;
set<GreasyTask*>::iterator sit;
int nindex;
ofstream rstfile( restartFile.c_str(), ios_base::out);
log->record(GreasyLog::devel, "AbstractEngine::writeRestartFile", "Entering...");
if (!rstfile.is_open()) {
log->record(GreasyLog::error, "Could not create restart file " + restartFile);
return;
}
log->record(GreasyLog::info, "Creating restart file " + restartFile + "...");
string logFile = "Standard Error";
if (config->keyExists("LogFile")&&((config->getValue("LogFile") != ""))) {
logFile = config->getValue("LogFile");
//Check for a relative path
if ((GreasyRegex::match(logFile,"^[:blank:]*/(.*)$")==""))
logFile = getWorkingDir() + logFile;
}
rstfile << "# " << endl;
rstfile << "# Greasy restart file generated at "<< GreasyTimer::now() << endl;
rstfile << "# Original task file: " << getWorkingDir() << "/" << taskFile << endl;
rstfile << "# Log file: " << logFile << endl;
rstfile << "# " << endl;
rstfile << endl;
nindex = 7;
for (it=taskMap.begin();it!=taskMap.end(); it++) {
task = it->second;
// Completed tasks will not be recorded in the restart file
if (task->getTaskState() == GreasyTask::completed) continue;
// Invalid tasks will be treated at the end
if (task->getTaskState() == GreasyTask::invalid) {
invalidTasks.insert(task);
continue;
}
if (task->getTaskState() == GreasyTask::failed) {
rstfile << "# Warning: Task " << task->getTaskId() << " failed" << endl;
nindex++;
}
if (task->getTaskState() == GreasyTask::cancelled) {
rstfile << "# Warning: Task " << task->getTaskId() << " was cancelled due to a dependency failure" << endl;
nindex++;
}
// Write the task in the restart with its dependencies if any
if (task->hasDependencies()) {
rstfile << "[# " << task->dumpDependencies() << " #] ";
}
rstfile << ((*it).second)->getCommand() << endl;
//Update indexes of dependencies to the new lines in the restart
dependants = revDepMap[task->getTaskId()];
if (!dependants.empty()) {
for(lit=dependants.begin();lit!=dependants.end();lit++) {
taskMap[*lit]->removeDependency(task->getTaskId());
taskMap[*lit]->addDependency(nindex);
}
}
nindex++;
}
if (!invalidTasks.empty()) {
rstfile << endl << "# Invalid tasks were found. Check these lines on " << taskFile << ": " << endl << "# ";
bool first = true;
for (sit=invalidTasks.begin();sit!=invalidTasks.end(); sit++) {
task = *sit;
if (first) {
rstfile << toString(task->getTaskId());
first = false;
} else {
rstfile << ", " << toString(task->getTaskId());
}
}
rstfile << endl;
}
rstfile << endl << "# End of restart file" << endl;
// close restart file;
rstfile.close();
log->record(GreasyLog::info, "Restart file created");
log->record(GreasyLog::devel, "AbstractEngine::writeRestartFile", "Exiting...");
}
QString NewProjectDialog::getProjectFullPath() const
{
return QDir::fromNativeSeparators(QDir(getWorkingDir()+"/"+getProjectName()).path());
}
