void ns_buffered_capture_scheduler::commit_local_changes_to_central_server(ns_local_buffer_connection & local_buffer, ns_sql & central_db) {
ns_acquire_lock_for_scope lock(buffer_capture_scheduler_lock,__FILE__,__LINE__);
local_buffer.clear_query();
central_db.clear_query();
std::string local_time = local_buffer.get_value("SELECT UNIX_TIMESTAMP(NOW())"),
central_time = central_db.get_value("SELECT UNIX_TIMESTAMP(NOW())");
const ns_synchronized_time update_start_time(atol(local_time.c_str()),atol(central_time.c_str()));
//now we update the local buffer to the central node.
commit_all_local_schedule_changes_to_central_db(update_start_time,local_buffer,central_db);
commit_all_local_non_schedule_changes_to_central_db(update_start_time,local_buffer,central_db);
lock.release();
}
bool ns_processing_job_scheduler::run_a_job(ns_sql & sql,bool first_in_first_out_job_queue){
//if we can't talk to the long term storage we're bound to fail, so don't try.
image_server.image_storage.test_connection_to_long_term_storage(true);
if (!image_server.image_storage.long_term_storage_was_recently_writeable())
return false;
ns_image_server_push_job_scheduler push_scheduler;
ns_processing_job job = push_scheduler.request_job(sql,first_in_first_out_job_queue);
if (job.id == 0)
return false;
//refresh flag labels from db
ns_death_time_annotation_flag::get_flags_from_db(sql);
if (job.maintenance_task == ns_maintenance_update_processing_job_queue){
image_server.register_server_event(ns_image_server_event("Updating job queue"),&sql);
sql << "DELETE from processing_jobs WHERE maintenance_task =" << ns_maintenance_update_processing_job_queue;
sql.send_query();
push_scheduler.report_job_as_finished(job,sql);
push_scheduler.discover_new_jobs(sql);
return true;
}
ns_acquire_for_scope<ns_processing_job_processor> processor(
ns_processing_job_processor_factory::generate(job,image_server,this->pipeline->pipeline));
try{
std::string rejection_reason;
if (!processor().job_is_still_relevant(sql,rejection_reason)){
image_server.register_server_event(ns_image_server_event("Encountered a processing job queue that had already been performed or invalidated: ") << rejection_reason << "[" << job.description() << "]",&sql);
push_scheduler.report_job_as_finished(job,sql);
if (processor().delete_job_after_processing())
processor().delete_job(sql);
processor.release();
sql.send_query("COMMIT");
return true;
}
if(idle_timer_running)
image_server.performance_statistics.register_job_duration(ns_performance_statistics_analyzer::ns_idle,idle_timer.stop());
idle_timer_running = false;
ns_high_precision_timer tp;
tp.start();
//mark the subject as busy to prevent multiple jobs running simultaneously on the same data
processor().mark_subject_as_busy(true,sql);
sql.send_query("COMMIT");
//update UI to show job is being performed, if requested.
if (processor().flag_job_as_being_processed_before_processing())
processor().flag_job_as_being_processed(sql);
sql.send_query("COMMIT");
if (processor().run_job(sql))
processor().mark_subject_as_busy(false,sql);
push_scheduler.report_job_as_finished(job,sql);
sql.send_query("COMMIT");
processor().handle_concequences_of_job_completion(sql);
if (processor().delete_job_after_processing())
processor().delete_job(sql);
sql.send_query("COMMIT");
processor.release();
image_server.performance_statistics.register_job_duration(ns_performance_statistics_analyzer::ns_running_a_job,tp.stop());
idle_timer_running = true;
idle_timer.start();
return true;
}
catch(ns_ex & ex){
//we have found an error, handle it by registering it in the
//host_event log, and annotate the current job (and any associated images)
//with a reference to the error that occurred.
sql.clear_query();
processor().mark_subject_as_busy(false,sql);
ns_64_bit error_id(push_scheduler.report_job_as_problem(job,ex,sql));
sql.send_query("COMMIT");
//there are a variety of problems that could cause an exception to be thrown.
//only mark the image itself as problematic if the error doesn't come from
//any of the environmental problems that can crop up.
bool problem_with_long_term_storage(!image_server.image_storage.long_term_storage_was_recently_writeable());
if (!problem_with_long_term_storage &&
ex.type() != ns_network_io &&
ex.type() != ns_sql_fatal &&
ex.type() != ns_memory_allocation &&
ex.type() != ns_cache)
processor().mark_subject_as_problem(error_id,sql);
image_server.performance_statistics.cancel_outstanding_jobs();
if (ex.type() == ns_memory_allocation)
throw; //memory allocation errors can cause big, long-term problems, thus we need to pass
//them downwards to be handled.
else
processor.release();
}
catch(std::exception & e){
ns_ex ex(e);
sql.clear_query();
processor().mark_subject_as_busy(false,sql);
//we have found an error, handle it by registering it in the
//host_event log, and annotate the current job (and any associated images)
//with a reference to the error that occurred.
ns_64_bit error_id(push_scheduler.report_job_as_problem(job,ex,sql));
sql.send_query("COMMIT");
processor().mark_subject_as_problem(error_id,sql);
image_server.performance_statistics.cancel_outstanding_jobs();
processor.release();
if (ex.type() == ns_memory_allocation)
throw; //memory allocation errors can cause big, long-term problems, thus we need to pass
//them downwards to be handled.
}
return true;
}
void ns_buffered_capture_scheduler::update_local_buffer_from_central_server(ns_image_server_device_manager::ns_device_name_list & connected_devices,ns_local_buffer_connection & local_buffer, ns_sql & central_db) {
if (connected_devices.size() == 0)
return;
ns_acquire_lock_for_scope lock(buffer_capture_scheduler_lock,__FILE__,__LINE__);
local_buffer.clear_query();
central_db.clear_query();
std::string local_time = local_buffer.get_value("SELECT UNIX_TIMESTAMP(NOW())"),
central_time = central_db.get_value("SELECT UNIX_TIMESTAMP(NOW())");
const ns_synchronized_time update_start_time(atol(local_time.c_str())-10,atol(central_time.c_str())-10);//go ten seconds into the past
//to make sure all writes
//are committed
//now we update the local buffer to the central node.
commit_all_local_schedule_changes_to_central_db(update_start_time,local_buffer,central_db);
//now that all the local buffer data is reflected in the central database, we check to see if there is any new data in the central database.
//if so, we wipe the local buffer and update everything.
capture_schedule.load_if_needed(¢ral_db);
//get any new or updated capture schedule events
central_db << "SELECT sched.id, samp.id, samp.experiment_id, UNIX_TIMESTAMP(sched.time_stamp),UNIX_TIMESTAMP(samp.time_stamp)";
for (unsigned int i = 0; i < capture_schedule.table_format.column_names.size(); i++)
central_db << ",`sched`.`" << capture_schedule.table_format.column_names[i] << "`";
central_db << " FROM capture_schedule as sched, capture_samples as samp "
<< "WHERE (samp.device_name='" << connected_devices[0].name << "'";
for (unsigned int i = 1; i < connected_devices.size(); i++)
central_db << " OR samp.device_name='" << connected_devices[i].name << "'";
central_db << ")"
<< " AND sched.time_at_start = 0 "
<< " AND sched.sample_id = samp.id "
<< " AND sched.time_at_finish = 0 "
//here, we could bring the entire local database completely up to date
//but only scans in the future will make any difference, so we only download
//those who are still scheduled for the future
//this old command would fully update the database, as time_of_last_update_from_central_db
//would be set to 0
//<< " AND sched.scheduled_time > " << (time_of_last_update_from_central_db.remote_time-image_server.maximum_allowed_local_scan_delay()) //only get events in the future
//however, now we only grab the future, relevant scans.
<< " AND sched.scheduled_time > " << (update_start_time.remote_time-image_server.maximum_allowed_local_scan_delay()) //only get events in the future
<< " AND sched.time_stamp > FROM_UNIXTIME(" << time_of_last_update_from_central_db.remote_time <<") "
<< " AND sched.time_stamp <= FROM_UNIXTIME(" << update_start_time.remote_time << ") "
<< " ORDER BY sched.scheduled_time ASC";
ns_sql_result new_schedule;
central_db.get_rows(new_schedule);
std::set<unsigned long> altered_experiment_ids;
std::set<unsigned long> altered_sample_ids;
for (unsigned int i = 0; i < new_schedule.size(); i++) {
// if (atol(new_schedule[i][4].c_str()) > central_time_of_last_update_from_central_db){
altered_sample_ids.insert(atol(new_schedule[i][1].c_str()));
altered_experiment_ids.insert(atol(new_schedule[i][2].c_str()));
// }
}
const unsigned long new_timestamp(update_start_time.local_time);
if (new_schedule.size() != 0) {
if (new_schedule.size() > 4)
image_server.register_server_event(ns_image_server_event("ns_buffered_capture_scheduler::")
<< new_schedule.size() << " new capture schedule entries found. Updating local buffer.",¢ral_db);
//if samples or experiments have changed or added, update them.
//we need to do this *before* updating the capture schedule,
//as the addition of a capture schedule item might trigger a scan immediately
//and that scan will fail if the sample and experiemnts information isn't already in the local database.
if (altered_sample_ids.size() > 0) {
capture_samples.load_if_needed("capture_samples",¢ral_db);
experiments.load_if_needed("experiments",¢ral_db);
std::string sample_where_clause(std::string(" WHERE ") + ns_compile_sql_where_clause(altered_sample_ids,"id")),
experiment_where_clause(std::string(" WHERE ") + ns_compile_sql_where_clause(altered_experiment_ids,"id"));
ns_sql_result capture_sample_data;
ns_get_all_column_data_from_table("capture_samples",capture_samples.column_names,sample_where_clause,capture_sample_data,¢ral_db);
ns_sql_result experiment_data;
ns_get_all_column_data_from_table("experiments",experiments.column_names,experiment_where_clause,experiment_data,¢ral_db);
std::cerr << "Updating local buffer with information about " << capture_sample_data.size() << " samples\n";
//local_buffer_db.send_query("DELETE FROM buffered_capture_samples");
if (capture_samples.time_stamp_column_id == -1)
throw ns_ex("Could not find capture sample time stamp column!");
long last_displayed_percent(-5);
for(unsigned int i = 0; i < capture_sample_data.size(); i++) {
const long percent((100*i)/capture_sample_data.size());
if (percent >= last_displayed_percent+5) {
std::cerr << percent << "%...";
last_displayed_percent = percent;
}
std::string values;
values += "`";
values += capture_samples.column_names[0] + "`='" + local_buffer.escape_string(capture_sample_data[i][0]) + "'";
for (unsigned int j = 1; j < capture_samples.column_names.size(); j++) {
if (j == capture_samples.time_stamp_column_id) //we need to update the local time stamp here, so that if there might be a clock asynchrony between the
continue; //central server and local server that would allow remote timestamps to be in the future according to local
//which would trigger the local server to update the central in the next check, ad infinitum.
values += std::string(",`") + capture_samples.column_names[j] + "`='" + local_buffer.escape_string(capture_sample_data[i][j]) + "'";
}
values += std::string(",`time_stamp`=FROM_UNIXTIME(") + ns_to_string(new_timestamp) + ")";
local_buffer << "INSERT INTO buffered_capture_samples SET " << values
<< " ON DUPLICATE KEY UPDATE " << values;
local_buffer.send_query();
}
std::cerr << "Done.\n";
//local_buffer.send_query("DELETE FROM buffered_experiments");
for(unsigned int i = 0; i < experiment_data.size(); i++) {
std::string values;
values += "`";
values += experiments.column_names[0] + "`='" + local_buffer.escape_string(experiment_data[i][0]) + "'";
for (unsigned int j = 1; j < experiments.column_names.size(); j++) {
if (experiments.time_stamp_column_id == j)
continue;
values += std::string(",`") + experiments.column_names[j] + "`='" + local_buffer.escape_string(experiment_data[i][j]) + "'";
}
values += std::string(",time_stamp=FROM_UNIXTIME(") + ns_to_string(new_timestamp) + ")";
local_buffer << "INSERT INTO buffered_experiments SET " << values;
local_buffer << " ON DUPLICATE KEY UPDATE " << values;
local_buffer.send_query();
}
}
std::cerr << "Updating local buffer with information about " << new_schedule.size() << " schedule time points...\n";
long last_displayed_percent = -5;
for (unsigned int i = 0; i < new_schedule.size(); i++) {
const long percent((100*i)/new_schedule.size());
if (percent >= last_displayed_percent+5) {
std::cerr << percent << "%...";
last_displayed_percent = percent;
}
std::string all_values;
all_values += "`";
all_values += capture_schedule.table_format.column_names[0] + "`='" + local_buffer.escape_string(new_schedule[i][5]) + "'";
for (unsigned int j = 1; j < capture_schedule.table_format.column_names.size(); j++) {
if (j == capture_schedule.time_stamp_column)
continue;
all_values += std::string( ", `") + capture_schedule.table_format.column_names[j] + "`='" + local_buffer.escape_string(new_schedule[i][5+j]) + "'";
}
all_values+=std::string(",time_stamp=FROM_UNIXTIME(") + ns_to_string(new_timestamp) + ")";
std::string update_values;
update_values += std::string("problem=") + new_schedule[i][5+capture_schedule.problem_column] + ","
+ std::string("scheduled_time=") + new_schedule[i][5+capture_schedule.scheduled_time_column] + ","
+ std::string("missed=") + new_schedule[i][5+capture_schedule.missed_column] + ","
+ std::string("censored=") + new_schedule[i][5+capture_schedule.censored_column] +","
+ std::string("transferred_to_long_term_storage=") + new_schedule[i][5+capture_schedule.transferred_to_long_term_storage_column] +","
+ std::string("time_during_transfer_to_long_term_storage=") + new_schedule[i][5+capture_schedule.time_during_transfer_to_long_term_storage_column] +","
+ std::string("time_during_deletion_from_local_storage=") + new_schedule[i][5+capture_schedule.time_during_deletion_from_local_storage_column] + ","
+ std::string("time_stamp=FROM_UNIXTIME(") + ns_to_string(update_start_time.local_time) + ")";
local_buffer << "INSERT INTO buffered_capture_schedule SET " << all_values
<< " ON DUPLICATE KEY UPDATE " << update_values;
local_buffer.send_query();
}
std::cerr << "Done.\n";
}
//if no changes to the schedule were made, look to see find changes made to any capture samples
else {
ns_sql_result capture_sample_data;
ns_get_all_column_data_from_table("capture_samples",capture_samples.column_names,
std::string("WHERE time_stamp >= FROM_UNIXTIME(") + ns_to_string(time_of_last_update_from_central_db.remote_time) +") "
" AND time_stamp < FROM_UNIXTIME(" + ns_to_string(update_start_time.remote_time) +") "
,capture_sample_data,¢ral_db);
if (capture_sample_data.size() > 0) {
std::cerr << "Copying over " << capture_sample_data.size() << " samples\n";
//local_buffer_db.send_query("DELETE FROM buffered_capture_samples");
for(unsigned int i = 0; i < capture_sample_data.size(); i++) {
std::string values;
values += "`";
values += capture_samples.column_names[0] + "`='" + local_buffer.escape_string(capture_sample_data[i][0]) + "'";
for (unsigned int j = 1; j < capture_samples.column_names.size(); j++)
values += std::string(",`") + capture_samples.column_names[j] + "`='" + local_buffer.escape_string(capture_sample_data[i][j]) + "'";
local_buffer << "INSERT INTO buffered_capture_samples SET " << values
<< " ON DUPLICATE KEY UPDATE " << values;
local_buffer.send_query();
}
}
}
local_buffer.send_query("COMMIT");
//lock.unlock();
commit_all_local_non_schedule_changes_to_central_db(update_start_time,local_buffer,central_db);
central_db << "SELECT k,v FROM constants WHERE time_stamp > FROM_UNIXTIME(" << time_of_last_update_from_central_db.remote_time << ")";
ns_sql_result cres;
central_db.get_rows(cres);
if (cres.size() > 0) {
std::cerr << "Updating " << cres.size() << " constants in local buffer\n";
}
for (unsigned int i = 0; i < cres.size(); i++)
image_server.set_cluster_constant_value(local_buffer.escape_string(cres[i][0]),local_buffer.escape_string(cres[i][1]),&local_buffer,update_start_time.local_time);
time_of_last_update_from_central_db = update_start_time;
store_last_update_time_in_db(time_of_last_update_from_central_db,local_buffer);
lock.release();
}
std::string ns_experiment_capture_specification::submit_schedule_to_db(std::vector<std::string> & warnings,ns_sql & sql,bool actually_write,bool overwrite_previous){
string debug;
if (!device_schedule_produced)
throw ns_ex("ns_experiment_capture_specification::submit_schedule_to_db()::The device schedule has not yet been compiled");
if (name.length() > 40)
throw ns_ex("To avoid lengthy filenames, experiment names must contain 40 characters or less.");
ns_sql_result res;
//check that all devices requested exist
for (unsigned long i = 0; i < capture_schedules.size(); i++){
ns_device_schedule_list & device_schedules(capture_schedules[i].device_schedules);
for (ns_device_schedule_list::iterator p = device_schedules.begin(); p != device_schedules.end(); p++){
sql << "SELECT name FROM devices WHERE name = '" << sql.escape_string(p->second.device_name) << "'";
sql.get_rows(res);
if (res.size() == 0)
throw ns_ex("ns_experiment_capture_specification::submit_schedule_to_db()::Could not find device ") << p->second.device_name << " attached to cluster";
for (ns_device_capture_schedule::ns_sample_group_list::iterator q = p->second.sample_groups.begin(); q!= p->second.sample_groups.end(); ++q){
if (q->second.samples.size() != 4 && q->second.samples.size() != 6){
string warning;
warning+="Device ";
warning+=p->second.device_name + " has " + ns_to_string(q->second.samples.size()) + " samples scheduled on a single device";
warnings.push_back(warning);
debug += "WARNING: ";
debug += warning + ".\n\n";
}
for (unsigned int k = 0; k < q->second.samples.size(); k++){
if (q->second.samples[k]->width < .75 || q->second.samples[k]->height < .75 ||
q->second.samples[k]->width > 2.5 || q->second.samples[k]->height > 10){
string warning;
warning+="Sample ";
warning+=q->second.samples[i]->sample_name + " has unusual dimensions: " + ns_to_string(q->second.samples[i]->width) + "x" + ns_to_string(q->second.samples[i]->height);
warnings.push_back(warning);
debug += "WARNING: ";
debug += warning + ".\n\n";
}
}
if (q->second.schedule->device_capture_period < 10*60 || q->second.schedule->device_capture_period > 20*60){
string warning;
warning+="The schedule contains an unusual device capture period: ";
warning+=ns_to_string(q->second.schedule->device_capture_period/60);
warnings.push_back(warning);
debug += "WARNING: ";
debug += warning + ".\n\n";
}
}
}
}
std::map<std::string,std::string> incubator_assignments;
std::map<std::string,std::string> incubator_location_assignments;
sql << "SELECT device_name, incubator_name, incubator_location FROM device_inventory";
//ns_sql_result res;
sql.get_rows(res);
for (unsigned int i = 0; i < res.size(); ++i){
incubator_assignments[res[i][0]] = res[i][1];
incubator_location_assignments[res[i][0]] = res[i][2];
}
res.resize(0);
sql.clear_query();
sql.send_query("BEGIN");
sql << "SELECT id FROM experiments WHERE name='" << sql.escape_string(name) << "'";
sql.get_rows(res);
if(res.size() == 0){
sql << "INSERT INTO experiments SET name='" << sql.escape_string(name) << "',description='',`partition`='', time_stamp=0";
if (!actually_write){
experiment_id = 0;
debug+="Creating a new experiment named ";
debug+= name + "\n";
}
else experiment_id = sql.send_query_get_id();
}
else{
if (!overwrite_previous)
throw ns_ex("ns_experiment_capture_specification::submit_schedule_to_db::Experiment already exists and overwrite_previous set to false");
if (!actually_write){
debug+="Overwriting an existing experiment named ";
debug+= name + " with id = " + res[0][0] + "\n";
}
experiment_id = atol(res[0][0].c_str());
}
sql.clear_query();
res.resize(0);
try{
for (unsigned int i = 0; i < samples.size(); i++){
sql << "SELECT id, name, device_name,parameters FROM capture_samples WHERE experiment_id = " << experiment_id << " AND name='" << sql.escape_string(samples[i].sample_name) << "'";
sql.get_rows(res);
if(res.size() != 0){
if (!overwrite_previous)
throw ns_ex("ns_experiment_capture_specification::submit_schedule_to_db::Sample ") << samples[i].sample_name << " already exists and overwrite_previous set to false";
samples[i].sample_id = atol(res[0][0].c_str());
ns_processing_job job;
job.sample_id = samples[i].sample_id;
if (!actually_write)
debug+="Deleting previous sample (id=" + ns_to_string(job.sample_id) + ").\n";
else ns_handle_image_metadata_delete_action(job,sql);
}
sql << "INSERT INTO capture_samples SET experiment_id = " << ns_to_string(experiment_id) << ",name='" << sql.escape_string(samples[i].sample_name) << "'"
<< ",device_name='" << sql.escape_string(samples[i].device) << "',parameters='" << sql.escape_string(samples[i].capture_parameters()) << "'"
<< ",position_x=" << samples[i].x_position << ",position_y=" << samples[i].y_position
<< ",size_x=" << samples[i].width << ",size_y="<<samples[i].height
<< ",incubator_name='" << sql.escape_string(incubator_assignments[samples[i].device])
<< "',incubator_location='" << sql.escape_string(incubator_location_assignments[samples[i].device])
<< "',desired_capture_duration_in_seconds=" <<samples[i].desired_minimum_capture_duration
<< ",description='',model_filename='',reason_censored='',image_resolution_dpi='" << samples[i].resolution
<< "',device_capture_period_in_seconds=" << capture_schedules[samples[i].internal_schedule_id].device_capture_period
<< ",number_of_consecutive_captures_per_sample=" << capture_schedules[samples[i].internal_schedule_id].number_of_consecutive_captures_per_sample
<< ", time_stamp=0";
if (!actually_write){
samples[i].sample_id = 0;
debug+="Creating a new sample: name:";
debug += samples[i].sample_name + ", device:" + samples[i].device + "\n\tcapture parameters: \"";
debug += samples[i].capture_parameters() + "\"\n";
}
else{
samples[i].sample_id = sql.send_query_get_id();
}
sql.clear_query();
res.resize(0);
}
sql.clear_query();
res.resize(0);
for (unsigned long i = 0; i < capture_schedules.size(); i++){
unsigned long device_start_offset = 2*60;
unsigned long s_offset(0);
ns_device_schedule_list & device_schedules(capture_schedules[i].device_schedules);
ns_device_start_offset_list & device_start_offsets(capture_schedules[i].device_start_offsets);
for (ns_device_schedule_list::iterator p = device_schedules.begin(); p != device_schedules.end(); p++){
device_start_offsets[p->first] = s_offset;
s_offset+=device_start_offset;
if (s_offset >= 20*60)
s_offset = 0;
}
}
for (unsigned int i = 0; i < capture_schedules.size(); i++){
//compile correct start and stop time for each device.
if (capture_schedules[i].start_time == 0) capture_schedules[i].start_time = ns_current_time() + 2*60;
capture_schedules[i].stop_time = 0;
ns_device_schedule_list & device_schedules(capture_schedules[i].device_schedules);
ns_device_start_offset_list & device_start_offsets(capture_schedules[i].device_start_offsets);
for (ns_device_schedule_list::iterator p = device_schedules.begin(); p != device_schedules.end(); p++){
const string & device_name = p->first;
if (p->second.sample_groups.size() == 0) continue;
p->second.effective_device_period = p->second.sample_groups.begin()->second.schedule->device_capture_period;
p->second.number_of_consecutive_captures_per_sample = p->second.sample_groups.begin()->second.schedule->number_of_consecutive_captures_per_sample;
if (p->second.effective_device_period == 0) throw ns_ex("Device period specified as zero!");
if (p->second.number_of_consecutive_captures_per_sample == 0) throw ns_ex("Number of consecutive_captures_per_sample specified as zero!");
//find earliest start time, stop time
for (ns_device_capture_schedule::ns_sample_group_list::iterator q = p->second.sample_groups.begin(); q != p->second.sample_groups.end(); q++){
if (q->second.schedule->start_time != 0 && q->second.schedule->start_time < ns_current_time())
throw ns_ex("Start time specified is in the past") << q->second.schedule->start_time;
if (q->first->start_time != 0)
q->second.schedule->effective_start_time = q->first->start_time + device_start_offsets[device_name];
else
q->second.schedule->effective_start_time = capture_schedules[i].start_time + device_start_offsets[device_name];
q->second.schedule->effective_stop_time = q->second.schedule->effective_start_time + q->second.schedule->duration + device_start_offsets[device_name];
if (q->second.schedule->effective_start_time < capture_schedules[i].start_time)
capture_schedules[i].start_time = q->second.schedule->effective_start_time;
if (q->second.schedule->effective_stop_time > capture_schedules[i].stop_time)
capture_schedules[i].stop_time = q->second.schedule->effective_stop_time;
if (q->second.schedule->device_capture_period != p->second.effective_device_period)
throw ns_ex("Invalid device capture period specified for device") << p->second.device_name;
if (q->second.schedule->number_of_consecutive_captures_per_sample != p->second.number_of_consecutive_captures_per_sample)
throw ns_ex("Invalid device consecutive samples per sample specified for device") << p->second.device_name;
if (q->second.samples.size() == 0)
throw ns_ex("Empty device sample group found!");
}
}
std::set<string> incubators;
for (ns_device_schedule_list::iterator device = device_schedules.begin(); device != device_schedules.end(); device++){
incubators.insert(incubator_assignments[device->second.device_name]);
}
debug += string("Schedule Involves ") + ns_to_string(device_schedules.size()) + " devices in " + ns_to_string( incubators.size()) + " location";
if (incubators.size() != 1)
debug+="s";
debug +=":";
for(std::set<string>::const_iterator p = incubators.begin(); p != incubators.end(); p++){
debug+=*p;
debug+=",";
}
debug += "\n";
for (ns_device_schedule_list::iterator device = device_schedules.begin(); device != device_schedules.end(); device++){
if (!actually_write){
debug+=string("\tDevice ") + device->second.device_name + " runs between " +
ns_format_time_string_for_human(capture_schedules[i].start_time + device_start_offsets[device->second.device_name]) +
" and " +
ns_format_time_string_for_human(capture_schedules[i].stop_time + device_start_offsets[device->second.device_name]);
debug+=" with a capture period of " + ns_capture_schedule::time_string(device->second.effective_device_period) + "\n";
}
}
}
ns_device_start_offset_list device_stop_times;
ns_device_start_offset_list device_interval_at_stop;
for (unsigned int i = 0; i < capture_schedules.size(); i++){
ns_device_schedule_list & device_schedules(capture_schedules[i].device_schedules);
ns_device_start_offset_list & device_start_offsets(capture_schedules[i].device_start_offsets);
unsigned long number_of_captures(0);
for (ns_device_schedule_list::iterator device = device_schedules.begin(); device != device_schedules.end(); device++){
const string & device_name = device->first;
ns_device_start_offset_list::iterator stop_time(device_stop_times.find(device_name));
if(stop_time == device_stop_times.end()){
device_stop_times[device_name] = 0;
stop_time = device_stop_times.find(device_name);
}
if (!actually_write){
debug+=string("Schedule for device ") + device->second.device_name + ":\n";
}
char have_started(false);
ns_device_capture_schedule::ns_sample_group_list::iterator current_sample_group(device->second.sample_groups.begin());
unsigned long current_sample_id = 0;
for (unsigned long t = capture_schedules[i].start_time+device_start_offsets[device_name]; t < capture_schedules[i].stop_time+device_start_offsets[device_name];){
ns_device_capture_schedule::ns_sample_group_list::iterator loop_start_group = current_sample_group;
unsigned long loop_start_sample_id = current_sample_id;
//find the next active sample at this time
while(true){
if (have_started){
current_sample_id++;
if (current_sample_id >= current_sample_group->second.samples.size()){
current_sample_group++;
current_sample_id = 0;
if (current_sample_group == device->second.sample_groups.end())
current_sample_group = device->second.sample_groups.begin();
}
}
else have_started = true;
if (current_sample_group->second.schedule->effective_start_time <= t+device->second.effective_device_period &&
current_sample_group->second.schedule->effective_stop_time >= t+device->second.effective_device_period)
break;
if (current_sample_group == loop_start_group && current_sample_id == loop_start_sample_id )
break;
}
//schedule the scans
unsigned long dt_total = device->second.effective_device_period*device->second.number_of_consecutive_captures_per_sample;
for (unsigned int dt = 0; dt < dt_total; dt+=device->second.effective_device_period){
sql << "INSERT INTO capture_schedule SET experiment_id = " << experiment_id << ", scheduled_time = " << t+dt << ","
<< "sample_id = " << current_sample_group->second.samples[current_sample_id]->sample_id << ", time_stamp = 0";
if (!actually_write){
sql.clear_query();
debug +="\t";
debug+= current_sample_group->second.samples[current_sample_id]->sample_name + ": " + ns_format_time_string_for_human(t+dt) + "\n";
}
else{
sql.send_query();
number_of_captures++;
}
}
if (t+dt_total> stop_time->second){
stop_time->second = t+dt_total;
device_interval_at_stop[device_name] = device->second.effective_device_period;
}
t+=dt_total;
}
sql << "UPDATE experiments SET num_time_points = " << number_of_captures << ", first_time_point=" << capture_schedules[i].start_time
<< ", last_time_point= " << capture_schedules[i].stop_time << " WHERE id=" << experiment_id;
if (actually_write)
sql.send_query();
sql.clear_query();
}
}
//start autoscans to keep scanners running after the end of the experiment
for (ns_device_start_offset_list::iterator p = device_stop_times.begin(); p != device_stop_times.end(); p++){
sql << "INSERT INTO autoscan_schedule SET device_name='" << p->first
<< "', autoscan_start_time=" << (p->second + device_interval_at_stop[p->first])
<< ", scan_interval = " << device_interval_at_stop[p->first];
if (actually_write)
sql.send_query();
else{
debug+="Scheduling an ";
debug+=ns_to_string(device_interval_at_stop[p->first]) + " second autoscan sequence on device "
+ p->first + " at " + ns_format_time_string_for_human(p->second + device_interval_at_stop[p->first]) + "\n";
}
}
sql.send_query("COMMIT");
sql.send_query("UPDATE experiments SET time_stamp = NOW() WHERE time_stamp = 0");
sql.send_query("UPDATE capture_samples SET time_stamp = NOW() WHERE time_stamp = 0");
sql.send_query("UPDATE capture_schedule SET time_stamp = NOW() WHERE time_stamp = 0");
}
catch(...){
sql.send_query("ROLLBACK");
throw;
}
return debug;
}
