void AutoImportWindow::executeImport(bool execute) {
if (!execute) {
int choice = QMessageBox::question(this, "Confirm stop", QString("Please select how you want to stop\n\nIf you stop now, the images which are ") +
"being copied will be stopped.\n", "Finish current and stop", "Stop now", "Continue importing", 0, 2);
if(choice == 0) {
continuous->setChecked(false);
toBeImported_.clear();
resetState();
} else if(choice == 1) {
if (process_.state() == QProcess::Running) {
disconnect(&process_, static_cast<void(QProcess::*)(int)>(&QProcess::finished), this, &AutoImportWindow::continueExecution);
process_.kill();
while (!process_.waitForFinished()) process_.kill();
connect(&process_, static_cast<void(QProcess::*)(int)>(&QProcess::finished), this, &AutoImportWindow::continueExecution);
}
finishExecution();
} else {
resetState();
}
} else if(currentlyExecuting_) {
// qDebug() << "Currently importing, skipping this import";
return;
} else if(toBeImported_.isEmpty()) {
resetState();
return;
} else {
currentlyExecuting_ = true;
resetState();
importImage();
}
}
void AutoImportWindow::importImage() {
if(continuous->isChecked()) {
analyzeImport(true);
}
if(toBeImported_.isEmpty()) {
finishExecution();
return;
}
if (imageExecuting_) {
QString numberExec = imageExecuting_->directory();
if (!numberExec.isEmpty()) {
if (dirToRowNumber_.keys().contains(numberExec)) {
if (dirToRowNumber_[numberExec] < resultsTable_->rowCount()) {
if (resultsTable_->item(dirToRowNumber_[numberExec], 0)) {
resultsTable_->item(dirToRowNumber_[numberExec], 0)->setIcon(ApplicationData::icon("process_done"));
}
}
}
}
}
QString number;
number = toBeImported_.keys().first();
QStringList files = toBeImported_[number];
toBeImported_.remove(number);
//Get the original file name used for search
QString baseName = files.first();
//Deduce parameters from baseName
QMap<QString, QString> fileNameParams = FileNameParserDialog::parseFileName(baseName);
QString importGroup_ = projectData.projectParameterData()->getValue("import_target_group");
QString importGroupSuffix = projectData.projectParameterData()->getValue("import_target_group_suffix");
//Add suffix to group name
QString suffix = "";
//case importGroupSuffix=1 => parameter = specimennumber
if(importGroupSuffix == "1") {
//If the file name contains this param take it from there, otherwise search master.cfg
if(fileNameParams.contains("specimennumber")) suffix = fileNameParams["specimennumber"];
else {
suffix = projectData.projectParameterData()->getValue("specimennumber");
}
}
if(suffix == "-") suffix = "";
importGroup_ = importGroup_ + suffix;
if (dirToRowNumber_.keys().contains(number)) {
if (dirToRowNumber_[number] < resultsTable_->rowCount()) {
if(resultsTable_->item(dirToRowNumber_[number], 0)) {
resultsTable_->item(dirToRowNumber_[number], 0)->setIcon(ApplicationData::icon("process_executing"));
resultsTable_->scrollToItem(resultsTable_->item(dirToRowNumber_[number], 0));
}
}
}
statusLabel_->setText(QString("Currently importing and %2 are in queue...").arg(toBeImported_.keys().size()));
projectData.projectParameterData()->set("import_imagenumber", number);
//Create dir
QDir workingDir = QDir(projectData.projectDir().canonicalPath() + "/" + importGroup_ + "/" + number);
//create import group
projectData.projectDir().mkpath(importGroup_);
QFile(projectData.projectDir().absolutePath() + "/merge").link("../2dx_master.cfg", projectData.projectDir().absolutePath() + "/" + importGroup_ + "/2dx_master.cfg");
//create Dir
projectData.projectDir().mkpath(importGroup_ + "/" + number);
workingDir.mkpath("proc");
workingDir.mkpath("LOGS");
//Copy Config File
projectData.projectParameterData()->saveAs(workingDir.canonicalPath() + "/2dx_image.cfg", true);
imageExecuting_ = projectData.addImage(importGroup_, number);
ParametersConfiguration* conf = imageExecuting_->parameters();
conf->set("imagenumber", number, false);
bool hasAveraged = false;
bool hasAligned = false;
bool hasRaw = false;
//Check for the averaged file
if(files.size() > 1 && !files[1].isEmpty()) {
conf->set("imagename", "image_2dx", false);
conf->set("nonmaskimagename", "image_2dx", false);
conf->set("imagename_original", files[1], false);
conf->set("import_original_time", QString::number(QFileInfo(files[1]).created().toMSecsSinceEpoch()), false);
scriptsToBeExecuted_.append("cp -f " + files[1] + " " + workingDir.canonicalPath() + "/" + "image_2dx.mrc");
if(deleteCheck->isChecked()) scriptsToBeExecuted_.append("rm -f " + files[1]);
hasAveraged = true;
}
//Check for aligned file
if (files.size() > 2 && !files[2].isEmpty()) {
conf->set("movie_stackname", "movie_aligned", false);
conf->set("movie_stackname_original", files[2], false);
conf->set("import_original_time", QString::number(QFileInfo(files[2]).created().toMSecsSinceEpoch()), false);
scriptsToBeExecuted_.append("cp -f " + files[2] + " " + workingDir.canonicalPath() + "/" + "movie_aligned.mrcs");
if(deleteCheck->isChecked()) scriptsToBeExecuted_.append("rm -f " + files[2]);
hasAligned = true;
}
//Check for raw file
if (files.size() > 3 && !files[3].isEmpty()) {
int rawOption = conf->getVariant("import_rawstack_type").toInt();
if(rawOption == 1) {
conf->set("import_rawstack", baseName + '.' + QFileInfo(files[3]).suffix(), false);
conf->set("import_rawstack_original", files[3], false);
conf->set("import_original_time", QString::number(QFileInfo(files[3]).created().toMSecsSinceEpoch()), false);
scriptsToBeExecuted_.append("cp -f " + files[3] + " " + workingDir.canonicalPath() + "/" + baseName + '.' + QFileInfo(files[3]).suffix());
if(deleteCheck->isChecked()) scriptsToBeExecuted_.append("rm -f " + files[3]);
hasRaw = true;
} else if (rawOption == 2) {
conf->set("import_rawstack", baseName + '.' + QFileInfo(files[3]).suffix(), false);
conf->set("import_rawstack_original", files[3], false);
conf->set("raw_gaincorrectedstack", "raw_gaincorrectedstack", false);
conf->set("raw_gaincorrectedstack_original", files[3], false);
conf->set("import_original_time", QString::number(QFileInfo(files[3]).created().toMSecsSinceEpoch()), false);
scriptsToBeExecuted_.append("cp -f " + files[3] + " " + workingDir.canonicalPath() + "/" + "raw_gaincorrectedstack.mrcs");
if(deleteCheck->isChecked()) scriptsToBeExecuted_.append("rm -f " + files[3]);
hasRaw = true;
}
}
//Check for defects list file
QString defectsFile = conf->getValue("import_defects_original");
if(QFileInfo(defectsFile).exists()) {
conf->set("import_defects", "../" + QFileInfo(defectsFile).fileName(), false);
scriptsToBeExecuted_.append("rsync -auvP " + defectsFile + " " + workingDir.canonicalPath() + "/../" + QFileInfo(defectsFile).fileName());
}
//Check for gain reference file
QString gainRefFile = conf->getValue("import_gainref_original");
if(QFileInfo(gainRefFile).exists()) {
conf->set("import_gainref", "../" + QFileInfo(gainRefFile).fileName(), false);
scriptsToBeExecuted_.append("rsync -auvP " + gainRefFile + " " + workingDir.canonicalPath() + "/../" + QFileInfo(gainRefFile).fileName());
}
//Set the parameters from filename
for(QString param : fileNameParams.keys()) {
if(parameterMaster.containsParameter(param)) {
conf->set(param, fileNameParams[param], false);
//qDebug() << "Parameter set: " << param << " => " << fileNameParams[param];
}
}
conf->setModified(true);
//Write to status folder if required
if(userPreferenceData.get("status_folder_update") == "y" && QFileInfo(userPreferenceData.get("status_folder")).isDir()) {
long currentMSecs = conf->getValue("import_original_time").toLong();
//Write the last imported data
QFile saveFile(userPreferenceData.get("status_folder") + "/last.txt");
long lastMSecs = 0;
if(saveFile.exists()) {
if (saveFile.open(QIODevice::ReadOnly | QIODevice::Text)) {
while (!saveFile.atEnd()) {
lastMSecs = QString(saveFile.readLine().simplified()).toLong();
}
saveFile.close();
}
saveFile.remove();
}
QString toBeWritten;
if(currentMSecs >= lastMSecs) toBeWritten = QString::number(currentMSecs);
else toBeWritten = QString::number(lastMSecs);
if (saveFile.open(QIODevice::WriteOnly | QIODevice::Text)) {
saveFile.write(toBeWritten.toLatin1());
}
saveFile.close();
//Write the time stamp in the last hour processed data
ProjectData::writeStatisticsToStatusFolder("last_recorded.txt", currentMSecs);
ProjectData::writeStatisticsToStatusFolder("last_imported.txt");
}
//register that this image was imported
ImportFolderSettings(QDir(conf->getValue("import_dir"))).addImportedImage(baseName, importGroup_ + "/" + number, hasAveraged, hasAligned, hasRaw);
//Add the scripts to be executed during import
QStringList scripts = importSelectorDialog.scriptPaths(ProjectPreferences().scripts("import"));
for(QString script : scripts) {
if(!script.isEmpty()) scriptsToBeExecuted_.append("SCRIPT:" + script);
}
continueExecution();
}
int main() {
// Inicializamos la DB
initialize();
// Levantamos los threads del consumidor de escrituras y del administrador de instrucciones
pthread_t instructionsManager;
pthread_create(&instructionsManager, NULL, manageInstructions, NULL);
char * input = NULL;
size_t size;
ssize_t read;
// Si estamos en modo terminal mostramos el caracter >
if(isatty(0))
printf ("> ");
// Leemos lineas desde stdin, si ingresamos un archivo con "./build/db < inputFile" obtendremos un EOF al final
while ((read = getline(&input, &size, stdin)) != -1) {
int length = (strlen(input) -1);
input[length] = '\0';
char command[5];
char word[101];
char *sep;
// Revisamos si tenemos un espacio en la linea
sep = strchr(input, ' ');
if (sep) {
size_t position = sep - input;
// Si es asi separamos lo que esta antes del primer espacio como el comando y lo que esta despues como la palabra o indice
strncpy(command, input, position);
command[position] = '\0';
int wordLength = (strlen(input) - position -1);
strncpy(word, input + position + 1, wordLength);
word[wordLength] = '\0';
// Si el comando es valido:
if (strcmp(command, "save") == 0 || strcmp(command, "find") == 0 || strcmp(command, "get") == 0) {
// Agregamos una entrada al listado de instrucciones
increaseInstructionsList();
// Agregamos los valores necesarios a la instruccion
strcpy(instructions[instructionsCounter].command, command);
strcpy(instructions[instructionsCounter].word, word);
instructions[instructionsCounter].index = instructionsCounter;
// Aumentamos el semaforo de instrucciones
sem_post(Icounter);
} else {
printf("Comando invalido. Los comandos disponibles son: save, find, get, exit.\n");
}
}
else {
if (!(strcmp(input, "") == 0 || strcmp(input, "exit") == 0)) {
printf("Comando invalido. Los comandos disponibles son: save, find, get, exit.\n");
}
else {
break;
}
}
if(isatty(0))
printf ("> ");
}
finishExecution();
return 0;
}
