void batchSubmission ( ostream& os, ParameterList& paramList )
{
init_html ( os, "Batch Submission" );
if ( paramList.empty () ) {
ErrorHandler::genError ()->error ( "No parameters passed to Prospector program.\n" );
}
string user = paramList.getStringValue ( "user" );
os << "<p>Creating Prospector files.</p>" << endl;
string searchKey = genRandomString ( 16 ); // Selects a unique string for the search
string searchName = paramList.getStringValue ( "search_name" ); // Program (eg batchtag)
string uploadFpath = paramList.getStringValue ( "upload_data_filepath" ); // This is the full path name of the uploaded file as named by PP
string resultsName = paramList.getStringValue ( "output_filename" );
bool searchKeyProblem;
try {
checkConstantAndVariableModCompatibility ( ¶mList );
}
catch ( runtime_error e ) { // Catch database login problems
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( e );
}
try {
searchKeyProblem = MySQLPPSDDBase::instance ().checkSearchKey ( searchKey );// Checks it is unique
}
catch ( runtime_error e ) { // Catch database login problems
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( e );
}
if ( searchKeyProblem ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Search key not unique.\n" );// The search key has to be unique to carry on.
}
if ( resultsName.empty () ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "No results name has been chosen.\n" );
}
string password;
bool passwordFlag = paramList.getValue ( "password", password );
UserInfo* userInfo = MySQLPPSDDBase::instance ().getUserInfo ( user );
if ( !userInfo || ( passwordFlag && userInfo->getPassword () != password ) ) { // Get the user information
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Unknown user and/or password.\n" );
}
if ( user == "root" ) { // Get the user information
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Root user can't do searches.\n" );
}
if ( userInfo->getIsGuest () ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Guest users can't do searches.\n" );
}
if ( !InfoParams::instance ().getBoolValue ( "btag_daemon_remote" ) ) {
try {
startDaemonIfNecessary ();
}
catch ( runtime_error e ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( e );
}
}
string userID = userInfo->getUserID ();
Repository* reposit = new UserRepository ( searchName, userInfo->getDirectoryName () ); // Where to put files given a user. Also creates the directories.
string projectName;
if ( uploadFpath.empty () ) { // The project already exists
projectName = paramList.getStringValue ( "project_name" ); // From a form with a project name option.
}
else {
string uploadFname = paramList.getStringValue ( "upload_data_filename" ); // This is the original file name.
string instrument = paramList.getStringValue ( "instrument_name" );
uploadFname = genFilenameFromPath ( uploadFname ); // IE gives the full path whereas Mozilla give the filename (what we want)
projectName = getProjectName ( uploadFname ); // The project is named after the uploaded file. This has to be unique.
if ( projectName.length () > 58 ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "The project name " + projectName + " is too long.\n" );
}
if ( MySQLPPSDDBase::instance ().checkProject ( userID, projectName ) ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Project already exists.\n" );
}
paramList.setValue ( "data_source", "List of Files" );
paramList.setValue ( "project_name", projectName );
paramList.removeName ( "upload_data_filename" );
paramList.removeName ( "upload_data_filepath" );
string uploadName = genPreprocessFile ( uploadFpath );
if ( uploadName == uploadFpath || isCompressedUpload ( uploadName ) ) { // If the file hasn't been preprocessed or it has just been uncompressed it must be a single file
string shortName = genShortFilenameFromPath ( uploadName );
string newDir = genDirectoryFromPath ( uploadName ) + SLASH + shortName;
if ( newDir == uploadName ) {
newDir += "_1";
}
genCreateDirectory ( newDir );
string newUploadName;
if ( isCompressedUpload ( uploadName ) )
newUploadName = newDir + SLASH + genShortFilenameFromPath ( uploadFname );
else
newUploadName = newDir + SLASH + uploadFname;
genRename ( uploadName, newUploadName );
uploadName = newDir;
}
PPProject ppp ( userInfo->getMaxMSMSSpectra (), userInfo->getAllowRaw (), projectName, uploadName, searchKey, reposit, MSMSDataSetInfo::setChargeRange ( ¶mList ) );
if ( ppp.initialised () ) {
int err = genRename ( uploadName, reposit->getFullDataPath () + SLASH + searchKey );
if ( err ) {
genUnlink ( uploadName );
string e = gen_itoa ( err );
ErrorHandler::genError ()->error ( "Failed to move uploaded file to repository.\nError code = " + e + "\n" );
}
ppp.createProjectFile ( reposit->getFullProjectPath () + SLASH + projectName + ".xml" );
string projectPath = reposit->getProjectPath ();
MySQLPPSDDBase::instance ().submitProject ( userID, projectName, projectName + ".xml", reposit->getProjectPath (), instrument );
}
else {
string err = ppp.getErrMessage ();
if ( ppp.getDeleteFlag () ) { // Known error - delete the upload directory
genUnlinkDirectory ( uploadName );
}
if ( err.empty () )
ErrorHandler::genError ()->error ( "Upload file has an invalid format.\n" );
else
ErrorHandler::genError ()->error ( err + "\n" );
}
}
paramList.removeName ( "user" );
paramList.removeName ( "password" );
paramList.removeName ( "project_name" );
paramList.removeName ( "output_filename" ); // Search results file.
paramList.removeName ( "msms_mod_AA_list" ); // These options are used to load the variable mods
paramList.removeName ( "msms_mod_AA_types" ); // and shouldn't be saved.
paramList.removeName ( "mod_AA_limit" );
paramList.removeName ( "mod_AA_file" );
paramList.removeName ( "motif_offset" );
paramList.removeName ( "motif" );
string projectID = MySQLPPSDDBase::instance ().getProjectID ( userID, projectName );
if ( projectID.empty () ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Project doesn't exist.\n" );
}
if ( MySQLPPSDDBase::instance ().checkResults ( userID, projectID, resultsName ) ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Results file of this name already exists for this project.\n" );
}
paramList.XMLParameterFile ( reposit->getFullResultsPath () + SLASH + searchKey + ".xml" ); // This is the search parameter file
MySQLPPSDDBase::instance ().submitSearch ( searchKey, projectID, resultsName, searchKey + ".xml", reposit->getResultsPath () );
MySQLPPSDDBase::instance ().updateProjectRecordUpdated ( projectID );
genSleep ( 5000 );
ParameterList pList ( "jobStatus", false, false, false, false, false );
pList.addName ( "search_key", searchKey );
refreshJavascript ( os, 0, pList.getURL (), true );
}
// -------------------------------------------------------------------------
int main(int argc, char ** argv)
{
int logLevel = 5;
Logger::setDefaultLogger(Logger::getLogger(logLevel));
string initialStageString("");
string finalStageString("");
string statusFileName("status.txt");
bool resumeFlag = false;
bool gridExecutionFlag = false;
bool runGenoMSFlag = false;
bool runMergedFlag = false;
bool showHelp = false;
for (size_t i = 0; i < argc; i++)
{
string arg(argv[i]);
if (arg.compare("--help") == 0)
{
showHelp = true;
}
}
if (argc < 2 || showHelp)
{
if (showHelp)
{
cout << "Usage: main_flr [PARAM FILE] [OPTION]..." << endl << endl;
cout << "Optional arguments are listed below " << endl;
cout << " -i <intialstage> begin processing at specified stage:"
<< endl;
cout << " begin,pairspectra,lpsolver,flr" << endl;
cout
<< " -f <finalstage> end processing after completing specified stage:"
<< endl;
cout << " lpsolver,flr" << endl;
cout << " -g execution is on a grid" << endl;
cout << " -lf <filename> name of log file for output" << endl;
cout << " -ll <loglevel> log level for debug/warn/error output:"
<< endl;
cout << " 9 for errors only" << endl;
cout << " 5 for warnings and errors" << endl;
cout << " 0 for all debug output" << endl;
cout << " -s execute a single step then exit" << endl;
}
else
{
cerr << "main_specnets: insufficient arguments" << endl;
cerr << "Try \'main_specnets --help\' for more information." << endl
<< endl;
}
cout << PROGRAM_NAME << endl;
cout << "main_specnets 3.0." << XSTR(SPS_VERSION) << endl;
cout << endl;
cout << COPYRIGHT1 << endl;
cout << COPYRIGHT2 << endl;
cout << endl;
return -1;
}
// Parse the command line parameters
vector<CommandLineParser::Option> listOptions;
listOptions.push_back(CommandLineParser::Option("i", "INITIAL_STAGE", 1));
listOptions.push_back(CommandLineParser::Option("f", "FINAL_STAGE", 1));
listOptions.push_back(CommandLineParser::Option("g", "GRID_EXECUTION", 0));
listOptions.push_back(CommandLineParser::Option("lf", "LOG_FILE_NAME", 1));
listOptions.push_back(CommandLineParser::Option("ll", "LOG_LEVEL", 1));
listOptions.push_back(CommandLineParser::Option("s", "SINGLE_STEP", 0));
CommandLineParser clp(argc, argv, 1, listOptions);
string parser_error;
if (!clp.validate(parser_error))
{
ERROR_MSG(parser_error);
return -2;
}
ParameterList commandLineParams;
clp.getOptionsAsParameterList(commandLineParams);
ParameterList ip;
ip.readFromFile(argv[1]);
ip.writeToFile("debug_sps.params");
// Combine the command line parameters to the file ones
// Command line parameters take precedence (hence the overwrite flag set)
ip.addList(commandLineParams, true);
ip.writeToFile("debug_wcommand.params");
logLevel = ip.getValueInt("LOG_LEVEL", 5);
if (ip.exists("LOG_FILE_NAME"))
{
string logFileName = ip.getValue("LOG_FILE_NAME");
Logger::setDefaultLogger(Logger::getLogger(logFileName, logLevel));
}
else
{
Logger::setDefaultLogger(Logger::getLogger(logLevel));
}
// add divert for segfault
addSegFaultDivert();
DEBUG_TRACE;
if (!ip.exists("EXE_DIR"))
{
// extract EXE_DIR from command line
string exeDir(argv[0]);
// find last /, and remove from that point on
size_t found = exeDir.find_last_of("/\\");
string aux = exeDir.substr(0, found);
//string mainSpecnetsStr = "/main_specnets";
//exeDir.erase(exeDir.length() - mainSpecnetsStr.length(), mainSpecnetsStr.length());
// remove /ExecFramework, if it exists
ip.setValue("EXE_DIR", aux);
}
if (ip.exists("INITIAL_STAGE"))
{
initialStageString = commandLineParams.getValue("INITIAL_STAGE");
}
DEBUG_VAR(initialStageString);
if (ip.exists("FINAL_STAGE"))
{
finalStageString = commandLineParams.getValue("FINAL_STAGE");
}
DEBUG_VAR(finalStageString);
addDefaultParameterValues(ip);
ip.writeToFile("debug_default.params");
if (ip.exists("EXE_DIR"))
{
string exeDir = ip.getValue("EXE_DIR");
// if path begins with '~', exit program.
if (exeDir[0] == '~')
{
cout
<< "EXE_DIR path begins with tilde (~). Paths beginning with tilde are not supported."
<< endl;
exit(0);
}
// In case there is a "/" at the end of EXE_DIR.. remove it
if (exeDir.length() > 2 && exeDir[exeDir.length() - 1] == '/')
{
exeDir = exeDir.substr(0, exeDir.length() - 1);
ip.setValue("EXE_DIR", exeDir);
}
}
if (ip.exists("GRID_EXE_DIR"))
{
// In case there is a "/" at the end of EXE_DIR.. remove it
string gridExeDir = ip.getValue("GRID_EXE_DIR");
if (gridExeDir.length() > 2 && gridExeDir[gridExeDir.length() - 1] == '/')
{
gridExeDir = gridExeDir.substr(0, gridExeDir.length() - 1);
ip.setValue("GRID_EXE_DIR", gridExeDir);
}
}
if (ip.exists("GRID_SGE_EXE_DIR"))
{
// In case there is a "/" at the end of GRID_SGE_EXE_DIR.. remove it
string gridSgeExeDir = ip.getValue("GRID_SGE_EXE_DIR");
if (gridSgeExeDir.length() > 2
&& gridSgeExeDir[gridSgeExeDir.length() - 1] == '/')
{
gridSgeExeDir = gridSgeExeDir.substr(0, gridSgeExeDir.length() - 1);
ip.setValue("GRID_SGE_EXE_DIR", gridSgeExeDir);
}
}
if (ip.exists("INITIAL_STAGE"))
{
initialStageString = ip.getValue("INITIAL_STAGE");
}
DEBUG_VAR(initialStageString);
if (initialStageString.empty())
{
initialStageString = "begin";
}
DEBUG_VAR(initialStageString);
if (ip.exists("FINAL_STAGE"))
{
finalStageString = ip.getValue("FINAL_STAGE");
}
DEBUG_VAR(finalStageString);
if (finalStageString.empty())
{
finalStageString = "flr";
}
DEBUG_VAR(finalStageString);
map<string, Stage> map_stage;
map_stage["begin"] = STAGE_BEGIN;
map_stage["pairspectra"] = STAGE_PAIRSPECTRA;
map_stage["lpsolver"] = STAGE_LPSOLVER;
map_stage["flr"] = STAGE_FLR;
if (map_stage.find(initialStageString) == map_stage.end())
{
ERROR_MSG("Unknown starting stage [" << initialStageString << "]");
return -1;
}
if (map_stage.find(finalStageString) == map_stage.end())
{
ERROR_MSG("Unknown final stage [" << finalStageString << "]");
return -1;
}
//Start the status as "running" and write itout
writeStatusFile(statusFileName, "Running");
int initialStage = map_stage[initialStageString];
DEBUG_VAR(initialStage);
int finalStage = map_stage[finalStageString];
DEBUG_VAR(finalStage);
bool res;
res = mkdir_if_not_exist("spectra");
if (res)
{
DEBUG_MSG("Made directory \'spectra\'");
}
// get LD_LIBRARY_PATH from system
char *curLibPath = getenv("LD_LIBRARY_PATH");
// Build the needed library path
string libPath;
libPath = ip.getValue("EXE_DIR");
// set LD_LIBRARY_PATH to EXE_DIR + /libs.
libPath += "/libs";
string fullLibPath;
// check if LD_LIBRARY_PATH is already defined.
if (curLibPath)
{
// if it is, check if it contains the path we want.
fullLibPath = curLibPath;
// if the library path IS NOT contained in the path variable, add it, and set the environment variable.
if (fullLibPath.find(libPath) == string::npos)
{
fullLibPath += ':';
fullLibPath += libPath;
mysetenv("LD_LIBRARY_PATH", fullLibPath.c_str());
}
}
else
{
// if LD_LIBRARY_PATH is not defined,, define it with what we want.
mysetenv("LD_LIBRARY_PATH", libPath.c_str());
}
if (commandLineParams.exists("GRID_EXECUTION"))
{
gridExecutionFlag = true;
}
DEBUG_VAR(gridExecutionFlag);
//---------------------------------
// Load amino acid masses
//---------------------------------
AAJumps jumps(1); // Amino acid masses
if (ip.exists("AMINO_ACID_MASSES"))
{
DEBUG_MSG("Loading amino acid masses from [" << ip.getValue("AMINO_ACID_MASSES") << "]");
if (!jumps.loadJumps(ip.getValue("AMINO_ACID_MASSES").c_str(), true))
{
ERROR_MSG("Unable to load amino acid jumps");
ERROR_MSG("Aborting!");
exit(-1);
}
}
else
{
DEBUG_MSG("No amino acid masses loaded. Using defaults");
}
string exeDir = ip.getValue("EXE_DIR");
string convertCmd = exeDir + "/convert ";
PeptideSpectrumMatchSet peptideResults;
SpecSet filteredSpectra;
if (initialStage == STAGE_BEGIN)
{
DEBUG_TRACE;
//load results
if (!loadPsmResults(ip, peptideResults))
{
return false;
}
if (!loadResultSpectrum(ip,
ip.getValue("INPUT_SPECTRA_FILE_LIST").c_str(),
peptideResults,
filteredSpectra,
ip.getValueBool("REINDEX_SCANS")))
{
return false;
}
if (commandLineParams.exists("SINGLE_STEP"))
{
DEBUG_MSG("Option -s given. Exiting after single step.");
writeStatusFile(statusFileName, "Finished");
exit(0);
}
}
else
{
if (initialStage == STAGE_PAIRSPECTRA)
{
//load results
if (!loadPsmResults(ip, peptideResults))
{
return false;
}
if (!loadSpecsMS(ip.getValue("EXE_DIR"), DEFAULT_INPUT_FILES_LIST, filteredSpectra))
{
ERROR_MSG("loadSpecsMS() exited in error. Exiting program");
exit(0);
}
filteredSpectra.index();
peptideResults.addSpectraByFilename(&filteredSpectra,false);
}
}
DEBUG_VAR(peptideResults.size());
DEBUG_VAR(filteredSpectra.size());
if (finalStage == STAGE_BEGIN)
{
DEBUG_MSG("Option -f given. Exiting after step: " << finalStageString);
writeStatusFile(statusFileName, "Finished");
exit(0);
}
if (initialStage <= STAGE_PAIRSPECTRA)
{
DEBUG_TRACE;
if (!performPairSpectra(ip,
peptideResults,
filteredSpectra,
ip.getValueBool("GRID_EXECUTION")))
{
exit(0);
}
if (commandLineParams.exists("SINGLE_STEP"))
{
DEBUG_MSG("Option -s given. Exiting after single step.");
writeStatusFile(statusFileName, "Finished");
exit(0);
}
}
if (finalStage == STAGE_PAIRSPECTRA)
{
DEBUG_MSG("Option -f given. Exiting after step: " << finalStageString);
writeStatusFile(statusFileName, "Finished");
exit(0);
}
if (initialStage <= STAGE_LPSOLVER)
{
DEBUG_TRACE;
if (!performLpSolver(ip,
ip.getValueBool("GRID_EXECUTION")))
{
exit(0);
}
if (commandLineParams.exists("SINGLE_STEP"))
{
DEBUG_MSG("Option -s given. Exiting after single step.");
writeStatusFile(statusFileName, "Finished");
exit(0);
}
}
if (finalStage == STAGE_LPSOLVER)
{
DEBUG_MSG("Option -f given. Exiting after step: " << finalStageString);
writeStatusFile(statusFileName, "Finished");
exit(0);
}
if (initialStage <= STAGE_FLR)
{
DEBUG_TRACE;
if (!performLpSolver(ip,
ip.getValueBool("GRID_EXECUTION")))
{
exit(0);
}
if (commandLineParams.exists("SINGLE_STEP"))
{
DEBUG_MSG("Option -s given. Exiting after single step.");
writeStatusFile(statusFileName, "Finished");
exit(0);
}
}
if (finalStage == STAGE_FLR)
{
DEBUG_MSG("Option -f given. Exiting after step: " << finalStageString);
writeStatusFile(statusFileName, "Finished");
exit(0);
}
}
