def ProcessVisit(user_id, visit_id):
''' Accepts a user_id, visit_id, processes all files for that visit + user '''
PrintTitle('EchoAnalyzer.tasks.ProcessVisit')
# initialize variables:
multiprocess_input = []
result_json_list = []
# get visit by id, start timer:
visit = Visit.objects.get(pk=visit_id)
visit.started_processing_at = datetime.now(timezone.utc)
visit.save()
# get list of files associated to visit:
file_list = list(visit.file_set.all().values_list('id', flat=True))
# set up multiprocessing pool:
number_of_threads = len(file_list)
pool = Pool(number_of_threads)
# iterate over each file:
for file_id in file_list:
# build multiprocess input:
input_point = {
'user_id': user_id,
'visit_id': visit_id,
'file_id': file_id
}
multiprocess_input.append(input_point)
# multiprocess each file:
result_json_list = pool.map(MultiProcessFileList, multiprocess_input)
# delete existing temp data off of server:
shutil.rmtree(result_json_list[0]['VISIT_DIR'])
# pack result list as json:
results = {'results': result_json_list}
# convert results to json object: (handles json strings where there are NaNs)
results = json.loads(json.dumps(results).replace('NaN', 'null'))
# reset database connection for multiprocessing:
ResetDatabaseConnection()
# set completed processing time and save results:
visit = Visit.objects.get(pk=visit_id)
visit.finished_processing_at = datetime.now(timezone.utc)
visit.processing_time = datetime.now(
timezone.utc) - visit.started_processing_at
visit.results = results
visit.save()
def HandleUpload(request, visit_id):
''' Accepts request, visit_id, downloads files and saves them to visit object '''
PrintTitle('EchoAnalyzer.views.HandleUpload')
try:
# debug:
print(
'[EchoAnalyzer.views.HandleUpload]: Got request.FILES.get("filePond") [%s]'
% request.FILES.get('filePond'))
# unpack request:
file_kwargs = {
'file': request.FILES.get('filePond'),
'file_name': request.FILES.get('filePond'),
'dicom_id': None, # update this field later
'user': request.user,
'user_email': request.user.email,
'visit': Visit.objects.get(pk=visit_id, user=request.user),
}
# create file objects and associate to visit:
file = File.objects.create(**file_kwargs)
# update dicom_id field:
file.dicom_id = str(file.file).replace("/staging/", "")
file.save()
success = True
status = 0
internal_message = 'successfully uploaded file [%s]' % file_kwargs[
'file_name']
message = 'Uploaded file successfully.'
except Exception as error:
success = False
status = 1
internal_message = traceback.format_exc()
message = 'Error when uploading file.'
result = {
'success': success,
'status': status,
'message': message,
}
print(
'[EchoAnalyzer.views.HandleUpload]: Status [%d], Internal Message [%s], Message [%s]'
% (status, internal_message, message))
return HttpResponse(json.dumps(result))
def LoadResultsPage(request, visit_id):
''' Accepts request to results/, checks if pipeline completed '''
PrintTitle('EchoAnalyzer.views.LoadResultsPage')
try:
# debug:
print(
'[EchoAnalyzer.views.LoadResultsPage]: Got post request with [%s]'
% request.POST)
# unpack post request:
user = request.user
# get visit object by id:
visit = Visit.objects.get(pk=visit_id, user_id=request.user)
results = visit.results
# add media links to results object: (must be done on load results page)
results = AddMediaLinks(results)
success = True
status = 0
internal_message = 'sent results for visit with id [%s]' % visit_id
message = 'Results sent.'
except Exception as error:
results = -1
success = False
status = 1
internal_message = traceback.format_exc()
message = 'Error, could not find your results.'
result = {
'success': success,
'status': status,
'message': message,
'visit_id': visit_id,
'results': results,
}
print(
'[EchoAnalyzer.views.LoadResultsPage]: Status [%d], Internal Message [%s], Message [%s]'
% (status, internal_message, message))
return render(request, 'temp_results.html', context=result)
def CreateDemo(request, visit_id):
''' Accepts request to demo/, global variable visit id, loads demo page '''
PrintTitle('Demo.views.Demo')
try:
# debug:
print('[Demo.views.Demo]: Got post request with [%s]' % request.POST)
# set demo visit id:
demo_visit_id = visit_id
# get visit object by id:
visit = Visit.objects.get(pk=demo_visit_id)
results = visit.results
# add s3 links to media files:
results = AddMediaLinks(results)
success = True
status = 0
internal_message = 'sent results for visit with id [%s]' % demo_visit_id
message = 'Results sent.'
except Exception as error:
results = -1
success = False
status = 1
internal_message = traceback.format_exc()
message = 'Error, could not find your results.'
result = {
'success': success,
'status': status,
'message': message,
'visit_id': demo_visit_id,
'results': results,
}
print(
'[EchoAnalyzer.views.LoadResultsPage]: Status [%d], Internal Message [%s], Message [%s]'
% (status, internal_message, message))
return render(request, 'temp_results.html', context=result)
def ExecutePipeline(request):
''' Accepts request tp /execute_pipeline, executes production pipeline '''
PrintTitle('EchoAnalyzer.views.ExecutePipeline')
try:
# unpack post request:
user_id = request.user.email
visit_id = request.POST['visit_id']
# get visit object by id:
visit = Visit.objects.get(pk=visit_id, user_id=request.user)
# debug:
print(
'[EchoAnalyzer.views.ExecutePipeline]: Got post request with [%s]'
% request.POST)
# execute pipeline if not already started:
if not visit.started_processing_at:
ProcessVisit(user_id, visit_id)
success = True
status = 0
internal_message = 'pipeline success for visit with id [%s]' % visit_id
message = 'Data processed!'
except Exception as error:
success = False
status = 1
internal_message = traceback.format_exc()
message = 'Error, could not process your data.'
result = {
'success': success,
'status': status,
'message': message,
'visit_id': visit_id,
}
print(
'[EchoAnalyzer.views.ExecutePipeline]: Status [%d], Internal Message [%s], Message [%s]'
% (status, internal_message, message))
return HttpResponse(json.dumps(result), content_type='application/json')
def LoadUploadPage(request):
''' Accepts request from /upload, creates visit object, renders upload page '''
PrintTitle('EchoAnalyzer.views.LoadUploadPage')
# create visit object:
visit = Visit.objects.create(user=request.user,
user_email=request.user.email)
# debug:
print(
'[EchoAnalyzer.views.Upload] Got request from user with user id [%s]' %
request.user)
print(
'[EchoAnalyzer.views.Upload] Got request from user with visit id [%s]'
% visit.pk)
return render(request, 'upload.html', {'visit_id': visit.pk})
def LoadLoaderPage(request, visit_id):
''' Accepts request to /loader, renders loader page '''
PrintTitle('EchoAnalyzer.views.LoadLoaderPage')
try:
# debug:
print(
'[EchoAnalyzer.views.LoadLoaderPage]: Got post request with [%s]' %
request.POST)
# unpack post request:
user_id = request.user
#visit_id = request.POST['visit_id']
success = True
status = 0
internal_message = 'routed to loader with user id [%s] and visit id [%s]' % (
user_id, visit_id)
message = 'We are processing your data.'
except Exception as error:
visit_id = -1
success = False
status = 1
internal_message = error
message = 'Error when rendering loader page.'
result = {
'success': success,
'status': status,
'message': message,
'visit_id': visit_id,
}
print(
'[EchoAnalyzer.views.LoadLoaderPage]: Status [%d], Internal Message [%s], Message [%s]'
% (status, internal_message, message))
return render(request, 'loader.html', context=result)