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 get_model_category(model_name):
try:
category = ModelCategory.objects.get(category=model_name).\
origin_type.get_category_display()
except Exception:
chemistry_logger.exception('failed to get model category')
category = ""
return category
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 suite_task_context(sid):
try:
suite_task = SuiteTask.objects.get(sid=sid)
except Exception:
chemistry_logger.exception('failed to get suite task: %s' % sid)
suite_task = None
single_task_lists = []
else:
single_task_lists = SingleTask.objects.filter(sid=sid)
return dict(suite_task=suite_task,
single_task_lists=single_task_lists)
def single_task_context(pid):
try:
single_task = SingleTask.objects.get(pid=pid)
local_search_id = single_task.file_obj.local_search_id
if local_search_id and isinstance(local_search_id, int):
local_search = ChemInfoLocal.objects.get(local_search_id)
else:
local_search = None
except Exception:
chemistry_logger.exception('failed to get single task: %s' % pid)
single_task = None
local_search = None
return dict(single_task=single_task, search_engine=local_search)
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 singletask_details(pid):
from chemistry.tasks import has_temperature
single_task = get_object_or_404(SingleTask, pid=pid)
if not has_temperature(single_task.model.desc):
single_task.temperature = '--'
single_task.result_value, single_task.hi, single_task.hx, single_task.degrade = get_singletask_area(single_task.results)
try:
local_search_id = single_task.file_obj.local_search_id
if local_search_id:
local_search = ChemInfoLocal.objects.get(id=local_search_id)
else:
local_search = None
except Exception:
chemistry_logger.exception('failed to get cheminfo by local_search_id')
local_search = None
return dict(singletask=single_task,
search_engine=local_search)
def fetch_ehomo_by_mopac(name, model):
path = os.path.join(config.MOPAC_PATH, model, name, '%s.out' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch H**O %s by mopac' % path)
return 0.0
with open(path, 'r') as f:
for line in f.readlines():
if EHOMO_MOPAC_RE.search(line):
try:
v = line.split('=')[1].strip().strip('\t').split()[0]
v = float(v)
except:
chemistry_logger.exception('Cannot get EHOMO value %s ' % line)
v = 0.0
finally:
return v
chemistry_logger.error('%s no H**O' % path)
return 0.0
def fetch_ehomo(name, model):
path = os.path.join(config.GAUSSIAN_PATH, model, name, '%s.log' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch H**O %s' % path)
return 0.0
ret = []
with open(path, 'r') as f:
for line in f.readlines():
if EHOMO_RE.search(line):
chemistry_logger.info(line)
ret.append(line)
try:
v = float(ret[-1].split()[-1])
except Exception as e:
chemistry_logger.exception('Cannot get EHOMO value %s ' % line)
v = 0
return v
def fetch_ehomo_by_mopac(name, model):
path = os.path.join(config.MOPAC_PATH, model, name, '%s.out' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch H**O %s by mopac' % path)
return 0.0
with open(path, 'r') as f:
for line in f.readlines():
if EHOMO_MOPAC_RE.search(line):
try:
v = line.split('=')[1].strip().strip('\t').split()[0]
v = float(v)
except:
chemistry_logger.exception('Cannot get EHOMO value %s ' %
line)
v = 0.0
finally:
return v
chemistry_logger.error('%s no H**O' % path)
return 0.0
def fetch_ehomo(name, model):
path = os.path.join(config.GAUSSIAN_PATH, model, name, '%s.log' % name)
if not os.path.exists(path):
chemistry_logger.error('Cannot fetch H**O %s' % path)
return 0.0
ret = []
with open(path, 'r') as f:
for line in f.readlines():
if EHOMO_RE.search(line):
chemistry_logger.info(line)
ret.append(line)
try:
v = float(ret[-1].split()[-1])
except Exception as e:
chemistry_logger.exception('Cannot get EHOMO value %s ' % line)
v = 0
return v