/*******************************************
* WorkflowRunFromCMDLineBase
*******************************************/
WorkflowRunFromCMDLineBase::WorkflowRunFromCMDLineBase()
: Task(tr("Workflow run from cmdline"), TaskFlag_None),
schema(NULL),
optionsStartAt(-1),
loadTask(NULL),
workflowRunTask(NULL)
{
GCOUNTER(cvar,tvar,"workflow_run_from_cmdline");
CMDLineRegistry * cmdLineRegistry = AppContext::getCMDLineRegistry();
// try to process schema without 'task' option (it can only be the first one)
QStringList pureValues = CMDLineRegistryUtils::getPureValues();
if( !pureValues.isEmpty() ) {
QString schemaName = pureValues.first();
processLoadSchemaTask( schemaName, 1 ); // because after program name
}
if( loadTask != NULL ) {
addSubTask( loadTask );
return;
}
// process schema with 'task' option
int taskOptionIdx = CMDLineRegistryUtils::getParameterIndex( WorkflowDesignerPlugin::RUN_WORKFLOW );
if(taskOptionIdx != -1) {
processLoadSchemaTask( cmdLineRegistry->getParameterValue( WorkflowDesignerPlugin::RUN_WORKFLOW, taskOptionIdx ), taskOptionIdx );
}
if( loadTask == NULL ) {
setError( tr( "no task to run" ) );
return;
}
addSubTask( loadTask );
}
void DumpLicenseTask::initHelp() {
CMDLineRegistry * cmdlineRegistry = AppContext::getCMDLineRegistry();
CMDLineHelpProvider * helpSection = new CMDLineHelpProvider(
LICENSE_CMDLINE_OPTION,
tr( "Shows license information." ));
cmdlineRegistry->registerCMDLineHelpProvider(helpSection);
}
void WorkflowRunFromCMDLineBase::run() {
CMDLineRegistry *cmdLineRegistry = AppContext::getCMDLineRegistry();
SAFE_POINT(NULL != cmdLineRegistry, "CMDLineRegistry is NULL", );
CHECK(NULL != workflowRunTask, );
const QString reportFilePath = cmdLineRegistry->getParameterValue(CmdlineTaskRunner::REPORT_FILE_ARG);
CHECK(!reportFilePath.isEmpty(), );
QFile reportFile(reportFilePath);
const bool opened = reportFile.open(QIODevice::WriteOnly);
CHECK_EXT(opened, setError(L10N::errorOpeningFileWrite(reportFilePath)), );
reportFile.write(workflowRunTask->generateReport().toLocal8Bit());
}
Task* GUITestService::createTestSuiteLauncherTask() const {
Q_ASSERT(!testLauncher);
CMDLineRegistry* cmdLine = AppContext::getCMDLineRegistry();
Q_ASSERT(cmdLine);
bool ok;
int suiteNumber = cmdLine->getParameterValue(CMDLineCoreOptions::LAUNCH_GUI_TEST_SUITE).toInt(&ok);
if(!ok){
QString pathToSuite = cmdLine->getParameterValue(CMDLineCoreOptions::LAUNCH_GUI_TEST_SUITE);
Task *task = new GUITestLauncher(pathToSuite);
Q_ASSERT(task);
return task;
}
Task *task = new GUITestLauncher(suiteNumber);
Q_ASSERT(task);
return task;
}
void WorkflowDesignerPlugin::registerCMDLineHelp() {
CMDLineRegistry * cmdLineRegistry = AppContext::getCMDLineRegistry();
assert( NULL != cmdLineRegistry );
CMDLineHelpProvider * taskSection = new CMDLineHelpProvider(
RUN_WORKFLOW,
tr("Runs the specified task."),
tr("Runs the specified task. A path to a user-defined UGENE workflow"
" be used as a task name."),
tr("<task_name> [<task_parameter>=value ...]"));
cmdLineRegistry->registerCMDLineHelpProvider( taskSection );
CMDLineHelpProvider * printSection = new CMDLineHelpProvider(
PRINT,
tr("Prints the content of the specified slot."),
tr("Prints the content of the specified slot. The incoming/outcoming content of"
" specified slot is printed to the standard output."),
tr("<actor_name>.<port_name>.<slot_name>"));
Q_UNUSED(printSection);
CMDLineHelpProvider * galaxyConfigSection = new CMDLineHelpProvider(
GalaxyConfigTask::GALAXY_CONFIG_OPTION,
tr("Creates new Galaxy tool config."),
tr("Creates new Galaxy tool config from existing workflow. Paths to UGENE"
" and Galaxy can be set"),
tr("<uwl-file> [--ugene-path=value] [--galaxy-path=value]"));
cmdLineRegistry->registerCMDLineHelpProvider( galaxyConfigSection );
//CMDLineHelpProvider * remoteMachineSectionArguments = new CMDLineHelpProvider( REMOTE_MACHINE, "<path-to-machine-file>");
//CMDLineHelpProvider * remoteMachineSection = new CMDLineHelpProvider( REMOTE_MACHINE, tr("run provided tasks on given remote machine") );
//TODO: bug UGENE-23
//cmdLineRegistry->registerCMDLineHelpProvider( remoteMachineSectionArguments );
//cmdLineRegistry->registerCMDLineHelpProvider( remoteMachineSection );
}
void PhylipPlugin::processCmdlineOptions() {
CMDLineRegistry *cmdLineRegistry = AppContext::getCMDLineRegistry();
CHECK(cmdLineRegistry->hasParameter(PhylipCmdlineTask::PHYLIP_CMDLINE), );
CHECK(cmdLineRegistry->hasParameter(CmdlineInOutTaskRunner::OUT_DB_ARG), );
CHECK(cmdLineRegistry->hasParameter(CmdlineInOutTaskRunner::IN_DB_ARG), );
CHECK(cmdLineRegistry->hasParameter(CmdlineInOutTaskRunner::IN_ID_ARG), );
CreatePhyTreeSettings settings = fetchSettings();
QString outDbString = cmdLineRegistry->getParameterValue(CmdlineInOutTaskRunner::OUT_DB_ARG);
QString inDbString = cmdLineRegistry->getParameterValue(CmdlineInOutTaskRunner::IN_DB_ARG);
QString idString = cmdLineRegistry->getParameterValue(CmdlineInOutTaskRunner::IN_ID_ARG);
U2OpStatus2Log os;
U2DbiRef outDbiRef = CmdlineInOutTaskRunner::parseDbiRef(outDbString, os);
CHECK_OP(os, );
U2DbiRef inDbiRef = CmdlineInOutTaskRunner::parseDbiRef(inDbString, os);
CHECK_OP(os, );
U2DataId dataId = CmdlineInOutTaskRunner::parseDataId(idString, inDbiRef, os);
CHECK_OP(os, );
Task *t = new PhylipTask(U2EntityRef(inDbiRef, dataId), outDbiRef, settings);
connect(AppContext::getPluginSupport(), SIGNAL(si_allStartUpPluginsLoaded()), new TaskStarter(t), SLOT(registerTask()));
}
void ConsoleLogDriver::setLogSettings() {
CMDLineRegistry *cmd = AppContext::getCMDLineRegistry();
if(cmd->hasParameter(CMDLineCoreOptions::LOG_FORMAT)) {
QString logFormat = cmd->getParameterValue(CMDLineCoreOptions::LOG_FORMAT);
settings.showLevel = logFormat.contains("L", Qt::CaseSensitive);
settings.showCategory = logFormat.contains("C", Qt::CaseSensitive);
settings.showDate = logFormat.contains(QRegExp("[M{2}Y{2,4}d{2}H{2}m{2}s{2}z{3}]"));
settings.logPattern = logFormat;
} else if(cmd->hasParameter( LOG_SHOW_DATE_CMD_OPTION ) || //old options
cmd->hasParameter( LOG_SHOW_LEVEL_CMD_OPTION ) ||
cmd->hasParameter( LOG_SHOW_CATEGORY_CMD_OPTION )){
settings.logPattern = "";
if (cmd->hasParameter( LOG_SHOW_DATE_CMD_OPTION )) {
settings.showDate = true;
settings.logPattern += "[hh:mm]";
}
if (cmd->hasParameter( LOG_SHOW_LEVEL_CMD_OPTION )) {
settings.showLevel = true;
settings.logPattern += "[L]";
}
if (cmd->hasParameter( LOG_SHOW_CATEGORY_CMD_OPTION )) {
settings.showCategory = true;
settings.logPattern += "[C]";
}
} else{
settings.logPattern = "[hh:mm][L]";
}
QString logLevel;
if(cmd->hasParameter(CMDLineCoreOptions::LOG_LEVEL)){
logLevel = cmd->getParameterValue(CMDLineCoreOptions::LOG_LEVEL);
} else if( cmd->hasParameter( LOG_LEVEL_NONE_CMD_OPTION ) ){
logLevel = "NONE";
} else if(cmd->hasParameter( LOG_LEVEL_ERROR_CMD_OPTION )) {
logLevel = "ERROR";
}else if( cmd->hasParameter( LOG_LEVEL_INFO_CMD_OPTION ) ) {
logLevel = "INFO";
} else if( cmd->hasParameter( LOG_LEVEL_DETAILS_CMD_OPTION ) ) {
logLevel = "DETAILS";
} else if( cmd->hasParameter( LOG_LEVEL_TRACE_CMD_OPTION ) ) {
logLevel = "TRACE";
}else {
logLevel = "ERROR";
}
LogServer* ls = LogServer::getInstance();
const QStringList& categoryList = ls->getCategories();
logLevel = logLevel.remove(" ");
QStringList cats = logLevel.split(QRegExp("[,=]"));
LogCategories::init();
if(cats.size() == 1) {
int minLevel = 10;
for (int i=0; i<LogLevel_NumLevels; i++) {
if(getLevelName((LogLevel)i) == logLevel) {
minLevel = i;
}
}
for (int i=0; i<LogLevel_NumLevels; i++) {
settings.activeLevelGlobalFlag[i] = (i >= minLevel);
}
foreach(const QString &str, categoryList) {
LoggerSettings cs;
cs.categoryName = str;
for (int i=0; i<LogLevel_NumLevels; i++) {
cs.activeLevelFlag[i] = (i >= minLevel);
}
settings.categories[str] = cs;
}
void CMDLineRegistryUtils::setCMDLineParams( QList<StringPair> & to ) {
CMDLineRegistry * cmdlineRegistry = AppContext::getCMDLineRegistry();
if( cmdlineRegistry != NULL ) {
to = cmdlineRegistry->getParameters();
}
}
