def calculateTask(task, sid, model):
try:
generate_mol_image(task)
suite = SuiteTask.objects.get(sid=sid)
map_model_name = get_model_name(model['model'])
smile = task.file_obj.smiles.encode(
'utf-8') if task.file_obj.file_type != 'mol' else ''
# smile, mol_fpath 输入只选择一种方式(优先smile)
mol_fpath = os.path.join(
settings.SETTINGS_ROOT,
task.file_obj.file_obj.path) if not smile else None
try:
temperature = float(model.get('temperature'))
except:
temperature = DEFAULT_TEMPERATURE_ARGS
chemistry_logger.info(
'PredictionModel calculating: model name(%s),'
'smile(%s) mol path(%s) temperature(%s)', map_model_name, smile,
mol_fpath, temperature)
# 后台模型计算入口
predict_results = prediction_model_calculate(map_model_name, smile,
mol_fpath, temperature)
if task.file_obj.file_type == 'mol':
name = os.path.basename(mol_fpath).split('.')[0]
else:
name = smile
result = predict_results[name][map_model_name]
chemistry_logger.info('[task]result %s' % result)
except KeyError:
chemistry_logger.exception('still cannot support this model')
result = None
task.result_state = "We don't support this model now"
task.status = StatusCategory.objects.get(category=STATUS_FAILED)
suite.status_id = StatusCategory.objects.get(category=STATUS_FAILED)
except Exception as e:
chemistry_logger.exception('failed to submit task to prediction model')
result = None
task.result_state = str(e)
task.status = StatusCategory.objects.get(category=STATUS_FAILED)
suite.status_id = StatusCategory.objects.get(category=STATUS_FAILED)
else:
chemistry_logger.info("calculate Successfully in celery queue!")
task.result_state = "Calculate Successfully!"
task.status = StatusCategory.objects.get(category=STATUS_SUCCESS)
suite.status_id = StatusCategory.objects.get(category=STATUS_WORKING)
task.end_time = utils.get_real_now()
task.results = json.dumps(result)
suite.save()
task.save()
add_counter(suite.sid)
return result
def activation_key_expired(self):
"""
Determine whether this ``RegistrationProfile``'s activation
key has expired, returning a boolean -- ``True`` if the key
has expired.
"""
expiration_date = datetime.timedelta(days=settings.ACCOUNT_ACTIVATION_DAYS)
return self.activation_key == "ALREADY_ACTIVATED" or \
(self.user.date_joined + expiration_date <= get_real_now())
def calculateTask(task, sid, model):
try:
generate_mol_image(task)
suite = SuiteTask.objects.get(sid=sid)
map_model_name = get_model_name(model['model'])
smile = task.file_obj.smiles.encode('utf-8') if task.file_obj.file_type != 'mol' else ''
# smile, mol_fpath 输入只选择一种方式(优先smile)
mol_fpath = os.path.join(settings.SETTINGS_ROOT, task.file_obj.file_obj.path) if not smile else None
try:
temperature = float(model.get('temperature'))
except:
temperature = DEFAULT_TEMPERATURE_ARGS
chemistry_logger.info('PredictionModel calculating: model name(%s),'
'smile(%s) mol path(%s) temperature(%s)',
map_model_name, smile, mol_fpath, temperature)
# 后台模型计算入口
predict_results = prediction_model_calculate(map_model_name, smile,
mol_fpath, temperature)
if task.file_obj.file_type == 'mol':
name = os.path.basename(mol_fpath).split('.')[0]
else:
name = smile
result = predict_results[name][map_model_name]
chemistry_logger.info('[task]result %s' % result)
except KeyError:
chemistry_logger.exception('still cannot support this model')
result = None
task.result_state = "We don't support this model now"
task.status = StatusCategory.objects.get(category=STATUS_FAILED)
suite.status_id = StatusCategory.objects.get(category=STATUS_FAILED)
except Exception as e:
chemistry_logger.exception('failed to submit task to prediction model')
result = None
task.result_state = str(e)
task.status = StatusCategory.objects.get(category=STATUS_FAILED)
suite.status_id = StatusCategory.objects.get(category=STATUS_FAILED)
else:
chemistry_logger.info("calculate Successfully in celery queue!")
task.result_state = "Calculate Successfully!"
task.status = StatusCategory.objects.get(category=STATUS_SUCCESS)
suite.status_id = StatusCategory.objects.get(category=STATUS_WORKING)
task.end_time = utils.get_real_now()
task.results = json.dumps(result)
suite.save()
task.save()
add_counter(suite.sid)
return result
def generate_calculate_task(models, smile, draw_mol_data, files_id_list,
sid, local_search_id):
from chemistry.tasks import send_email_task
try:
for model in models:
handle_smile_task(smile, model, sid, local_search_id)
handle_moldraw_task(draw_mol_data, model, sid)
handle_files_task(files_id_list, model, sid)
except Exception:
chemistry_logger.exception('failed to generate suite_task:%s' % sid)
s = SuiteTask.objects.get(sid=sid)
s.end_time = utils.get_real_now()
s.status_id = StatusCategory.objects.get(category=STATUS_FAILED)
s.save()
send_email_task(s.email, s.sid)
def submit_calculate_task(user, smile=None, draw_mol_data=None,
task_notes=None, task_name=None,
files_id_list=None, models=None,
local_search_id=None):
chemistry_logger.info("smile: %s" % smile)
chemistry_logger.info("draw_mol_data: %s" % draw_mol_data)
chemistry_logger.info("files_id_list: %s" % files_id_list)
chemistry_logger.info("models: %s" % models)
tasks_num = calculate_tasks(files_id_list, smile, draw_mol_data, models)
if tasks_num == 0:
status = False
info = "请至少选择一种输入方式和计算模型!"
id = None
return (status, info, id)
try:
s = SuiteTask()
s.sid = id = str(uuid.uuid4())
s.user = UserProfile.objects.get(user=user)
s.total_tasks = tasks_num
s.has_finished_tasks = 0
s.start_time = utils.get_real_now()
s.name = task_name
s.notes = task_notes
s.models_str, s.models_category_str = parse_models(models)
s.status = StatusCategory.objects.get(category=STATUS_WORKING)
s.email = user.email
s.save()
chemistry_logger.info('~~~~~~~~ s:%s' % s.start_time)
generate_calculate_task.delay(models, smile, draw_mol_data,
files_id_list, id, local_search_id)
except:
chemistry_logger.exception('failed to generate suite_task')
s.delete()
status = False
info = "计算任务添加不成功，将重试或联系网站管理员!"
id = None
else:
status = True
info = "恭喜,计算任务已经提交!"
return (status, info, id)
def save_record(f, model, sid, source_type, smile=None, local_search_id=None):
from chemistry.tasks import calculateTask, DEFAULT_TEMPERATURE_ARGS
task = SingleTask()
task.start_time = utils.get_real_now()
task.sid = SuiteTask.objects.get(sid=sid)
task.pid = str(uuid.uuid4())
task.model = ModelCategory.objects.get(category=model['model'])
temperature = model.get('temperature')
task.temperature = float(temperature) if temperature else DEFAULT_TEMPERATURE_ARGS
if source_type == ORIGIN_UPLOAD:
# here, f is ProcessedFile record instance
f.file_source = FileSourceCategory.objects.get(category=source_type)
f.file_type = "mol"
task.file_obj = f
f.save()
elif source_type in (ORIGIN_SMILE, ORIGIN_DRAW):
# here, f is a file path
processed_f = ProcessedFile()
obj = File(open(f, "r"))
processed_f.title = os.path.basename(obj.name)
processed_f.file_type = source_type
processed_f.file_source = FileSourceCategory.objects.get(category=source_type)
processed_f.file_obj = obj
if smile:
processed_f.smiles = smile
if source_type == ORIGIN_SMILE and local_search_id is not None:
processed_f.local_search_id = int(local_search_id)
processed_f.save()
task.file_obj = processed_f
obj.close()
else:
raise ErrorCalculateType('Cannot recongize this source type')
task.status = StatusCategory.objects.get(category=STATUS_WORKING)
task.save()
chemistry_logger.info('~~~~~~~~ t:%s' % task.start_time)
calculateTask.delay(task, sid, model)
def add_counter(suite_id):
"""
use filter to get task numbers
"""
finished_count = SingleTask.objects.filter(sid=suite_id)\
.exclude(status=StatusCategory.objects.get(category=STATUS_WORKING))\
.count()
suite = SuiteTask.objects.get(sid=suite_id)
if finished_count == suite.total_tasks:
suite.has_finished_tasks = suite.total_tasks
suite.status_id = StatusCategory.objects.get(category=STATUS_SUCCESS)
suite.end_time = utils.get_real_now()
suite.save()
send_email_task(suite.email, suite.sid)
else:
suite.has_finished_tasks = finished_count
suite.save()
chemistry_logger.info('~~~~~~~~ s-e:%s' % suite.end_time)
def add_counter(suite_id):
"""
use filter to get task numbers
"""
finished_count = SingleTask.objects.filter(sid=suite_id)\
.exclude(status=StatusCategory.objects.get(category=STATUS_WORKING))\
.count()
suite = SuiteTask.objects.get(sid=suite_id)
if finished_count == suite.total_tasks:
suite.has_finished_tasks = suite.total_tasks
suite.status_id = StatusCategory.objects.get(category=STATUS_SUCCESS)
suite.end_time = utils.get_real_now()
suite.save()
send_email_task(suite.email, suite.sid)
else:
suite.has_finished_tasks = finished_count
suite.save()
chemistry_logger.info('~~~~~~~~ s-e:%s' % suite.end_time)