void ImportProject::init ( const ParameterList& paramList )
{
string fpath = paramList.getStringValue ( "upload_temp_filepath" );
string user = paramList.getStringValue ( "user" );
if ( user == "root" ) {
genUnlink ( fpath );
throw runtime_error ( "Root user can't create projects." );
}
UserInfo* userInfo = MySQLPPSDDBase::instance ().getUserInfo ( user );
if ( !userInfo ) {
genUnlink ( fpath );
throw runtime_error ( "Unknown user." );
}
userID = userInfo->getUserID ();
if ( !newProjectName.empty () && MySQLPPSDDBase::instance ().checkProject ( userID, newProjectName ) ) {
genUnlink ( fpath );
throw runtime_error ( "Project already exists." );
}
reposit = new UserRepository ( "batchtag", userInfo->getDirectoryName () ); // Where to put files given a user. Also creates the directories.
uploadName = genPreprocessFile ( fpath );
}
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 );
}
