def view_signup_page(request):
d = get_common_dict(request, 'Sign Up', signup_page=True)
# If the person is already logged in, go to the homepage
#
if request.user.is_authenticated():
return HttpResponseRedirect(reverse('view_homepage', kwargs={}))
if request.POST:
f = SignUpForm(request.POST)
if f.is_valid():
tb_user = f.create_tb_user()
#return HttpResponse('TB user created: %s' % tb_user)
success_url = reverse('view_signup_success',
kwargs=dict(tb_user_md5=tb_user.md5)
)
return HttpResponseRedirect(success_url)
else:
d['ERROR_FOUND'] = True
else:
#test_data = get_signup_form_test_data()
#f = SignUpForm(initial=test_data)
f = SignUpForm()
d['signup_form'] = f
return render_to_response('tb_users/signup_page.html',
d,
context_instance=RequestContext(request))
def view_login_page(request, just_logged_out=False):
d = get_common_dict(request, 'Log In', login_page=True)
d['JUST_LOGGED_OUT'] = just_logged_out
# If the person is already logged in, go to the homepage
#
if request.user.is_authenticated():
d['ALREADY_LOGGED_IN'] = True
return render_to_response('tb_users/login_page.html',
d,
context_instance=RequestContext(request))
if request.POST:
f = TBUserAuthenticationForm(data=request.POST)
if f.is_valid():
user_obj = f.get_user()
# Log the person in
login(request, f.get_user())
# Go to log in success
success_url = reverse('view_homepage_just_logged_in', kwargs={})
return HttpResponseRedirect(success_url)
else:
d['ERROR_FOUND'] = True
else:
f = TBUserAuthenticationForm()
d['login_form'] = f
return render_to_response('tb_users/login_page.html',
d,
context_instance=RequestContext(request))
def view_map_page(request):
d = get_common_dict(request, 'Map', map_page=True)
return render_to_response('maps/basic_map.html'\
, d\
, context_instance=RequestContext(request))
def view_signup_page(request):
d = get_common_dict(request, 'Sign Up', signup_page=True)
# If the person is already logged in, go to the homepage
#
if request.user.is_authenticated():
return HttpResponseRedirect(reverse('view_homepage', kwargs={}))
if request.POST:
f = SignUpForm(request.POST)
if f.is_valid():
tb_user = f.create_tb_user()
#return HttpResponse('TB user created: %s' % tb_user)
success_url = reverse('view_signup_success',
kwargs=dict(tb_user_md5=tb_user.md5))
return HttpResponseRedirect(success_url)
else:
d['ERROR_FOUND'] = True
else:
#test_data = get_signup_form_test_data()
#f = SignUpForm(initial=test_data)
f = SignUpForm()
d['signup_form'] = f
return render_to_response('tb_users/signup_page.html',
d,
context_instance=RequestContext(request))
def view_dataset_contact(request, dataset_md5):
return HttpResponse('contact here')
d = get_common_dict(request, 'My Dataset Contact', view_my_datasets=True)
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/my_dataset_contact.html',
d,
context_instance=RequestContext(request))
try:
dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
if not request.user == dataset.user.user:
raise Http404('This is not your dataset')
d['dataset'] = dataset
d['dataset_notes'] = PredictDatasetNote.objects.filter(dataset=dataset).all()
d['tb_user'] = dataset.user
return render_to_response('predict/my_dataset_contact.html',
d,
context_instance=RequestContext(request))
def view_explore_page(request):
d = get_common_dict(request, 'Explore', explore_page=True)
explore_link_info = ExploreDataFileInfo.objects.filter(active=True).first()
d.update(dict(explore_link_info=explore_link_info))
return render_to_response('explore.html'\
, d\
, context_instance=RequestContext(request))
def view_explore_page(request):
d = get_common_dict(request, 'Explore', explore_page=True)
explore_link_info = ExploreDataFileInfo.objects.filter(active=True).first()
d.update(dict(explore_link_info=explore_link_info))
return render_to_response('explore.html'\
, d\
, context_instance=RequestContext(request))
def view_homepage(request, just_logged_in=False):
d = get_common_dict(request, 'Home', home_page=True)
d['just_logged_in'] = just_logged_in
#d['page_title'] = 'Phthisis Ravens: TB Project'
return render_to_response('homepage.html'\
, d\
, context_instance=RequestContext(request))
def view_homepage(request, just_logged_in=False):
d = get_common_dict(request, 'Home', home_page=True)
d['just_logged_in'] = just_logged_in
#d['page_title'] = 'Phthisis Ravens: TB Project'
return render_to_response('homepage.html'\
, d\
, context_instance=RequestContext(request))
def view_logout_page(request):
d = get_common_dict(request, 'Log Out', logout_page=True)
# Not logged in, redirect to the log in page
if d[IS_LOGGED_IN_KEY] is False:
d['NOT_LOGGED_IN'] = True
login_url = reverse('view_login_page',
kwargs={})
return HttpResponseRedirect(login_url)
# Log the person out
logout(request)
return view_login_after_logout(request)
def view_my_datasets(request):
d = get_common_dict(request, 'My Datasets', view_my_datasets=True)
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/my_datasets.html',
d,
context_instance=RequestContext(request))
d['datasets'] = PredictDataset.objects.filter(user=request.user.tbuser)
return render_to_response('predict/my_datasets.html',
d,
context_instance=RequestContext(request))
"""
def view_test_upload_success(request):
#print ('msg_or_data', type(msg_or_data))
d = get_common_dict(request, 'Test Predict Upload Success', predict_page=True)
d['UPLOAD_SUCCESS'] = True
d['FILE_PROCESS_SUCCESS'] = True
d['FILE_PROCESS_ERR_OR_DATA'] = { 'test_data' : True }#msg_or_data
#d['shared_file_info'] = shared_file_info
return render_to_response('predict/predict_upload_success.html',
d,
context_instance=RequestContext(request))
def view_test_upload_success(request):
#print ('msg_or_data', type(msg_or_data))
d = get_common_dict(request,
'Test Predict Upload Success',
predict_page=True)
d['UPLOAD_SUCCESS'] = True
d['FILE_PROCESS_SUCCESS'] = True
d['FILE_PROCESS_ERR_OR_DATA'] = {'test_data': True} #msg_or_data
#d['shared_file_info'] = shared_file_info
return render_to_response('predict/predict_upload_success.html',
d,
context_instance=RequestContext(request))
def view_my_datasets(request):
d = get_common_dict(request, 'My Datasets', view_my_datasets=True)
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/my_datasets.html',
d,
context_instance=RequestContext(request))
d['datasets'] = PredictDataset.objects.filter(user=request.user.tbuser)
return render_to_response('predict/my_datasets.html',
d,
context_instance=RequestContext(request))
"""
def view_predict_upload_success(request, dataset_md5):
d = get_common_dict(request, 'Predict Upload Success', predict_page=True)
try:
dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
d['dbox_log'] = DropboxRetrievalLog.objects.filter(dataset=dataset).first()
#print ('get it?', d['dbox_log'])
d['dataset'] = dataset
d['tb_user'] = dataset.user
return render_to_response('predict/predict_upload_success.html',
d,
context_instance=RequestContext(request))
def view_predict_upload_success(request, dataset_md5):
d = get_common_dict(request, 'Predict Upload Success', predict_page=True)
try:
dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
d['dbox_log'] = DropboxRetrievalLog.objects.filter(dataset=dataset).first()
#print ('get it?', d['dbox_log'])
d['dataset'] = dataset
d['tb_user'] = dataset.user
return render_to_response('predict/predict_upload_success.html',
d,
context_instance=RequestContext(request))
def view_single_dataset(request, dataset_md5):
d = get_common_dict(request, 'My Dataset Detail', view_my_datasets=True)
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/my_dataset_detail.html',
d,
context_instance=RequestContext(request))
try:
dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
d['dataset'] = dataset
d['dataset_notes'] = PredictDatasetNote.objects.filter(
dataset=dataset).all()
d['script_runs'] = DatasetScriptRun.objects.filter(dataset=dataset).all()
d['tb_user'] = dataset.user
# Pipeline command
(pipeline_command_found, pipeline_command_or_err
) = PipelineScriptRunner.get_pipeline_command(dataset)
d['pipeline_command_found'] = pipeline_command_found
try:
local_directory_contents = os.listdir(dataset.file_directory)
d['local_directory_contents'] = local_directory_contents
except:
d['local_directory_err'] = "Could not list directory contents"
if pipeline_command_found:
d['pipeline_command'] = pipeline_command_or_err
else:
d['pipeline_command_err'] = pipeline_command_or_err
return render_to_response('predict/my_dataset_detail.html',
d,
context_instance=RequestContext(request))
def view_predict_page(request, previous_attempt_deleted=False):
#logger.info("view_predict_page: info")
#logger.error('ahhh!')
logging.debug("view_predict_page")
d = get_common_dict(request, 'Predict', predict_page=True)
d['PREVIOUS_ATTEMPT_DELETED'] = previous_attempt_deleted
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/predict_upload.html',
d,
context_instance=RequestContext(request))
if request.POST:
f = UploadPredictionDataForm(request.POST)
if f.is_valid():
new_dataset = f.get_dataset(request.user.tbuser)
#kick_off_retrieval(new_dataset)
#get_dropbox_metadata(new_dataset)
#send_new_dataset_message_to_tb_admins(new_dataset)
success_url = reverse('view_predict_upload_step2_confirm',
kwargs=dict(dataset_md5=new_dataset.md5)
)
return HttpResponseRedirect(success_url)
else:
d['ERROR_FOUND'] = True
else:
f = UploadPredictionDataForm(label_suffix='')
d['predict_form'] = f
return render_to_response('predict/predict_upload.html',
d,
context_instance=RequestContext(request))
def view_predict_page(request, previous_attempt_deleted=False):
#logger.info("view_predict_page: info")
#logger.error('ahhh!')
logging.debug("view_predict_page")
d = get_common_dict(request, 'Predict', predict_page=True)
d['PREVIOUS_ATTEMPT_DELETED'] = previous_attempt_deleted
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/predict_upload.html',
d,
context_instance=RequestContext(request))
if request.POST:
f = UploadPredictionDataForm(request.POST)
if f.is_valid():
new_dataset = f.get_dataset(request.user.tbuser)
#kick_off_retrieval(new_dataset)
#get_dropbox_metadata(new_dataset)
#send_new_dataset_message_to_tb_admins(new_dataset)
success_url = reverse('view_predict_upload_step2_confirm',
kwargs=dict(dataset_md5=new_dataset.md5))
return HttpResponseRedirect(success_url)
else:
d['ERROR_FOUND'] = True
else:
f = UploadPredictionDataForm(label_suffix='')
d['predict_form'] = f
return render_to_response('predict/predict_upload.html',
d,
context_instance=RequestContext(request))
def view_single_dataset(request, dataset_md5):
d = get_common_dict(request, 'My Dataset Detail', view_my_datasets=True)
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/my_dataset_detail.html',
d,
context_instance=RequestContext(request))
try:
dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
d['dataset'] = dataset
d['dataset_notes'] = PredictDatasetNote.objects.filter(dataset=dataset).all()
d['script_runs'] = DatasetScriptRun.objects.filter(dataset=dataset).all()
d['tb_user'] = dataset.user
# Pipeline command
(pipeline_command_found, pipeline_command_or_err) = PipelineScriptRunner.get_pipeline_command(dataset)
d['pipeline_command_found'] = pipeline_command_found
try:
local_directory_contents = os.listdir(dataset.file_directory)
d['local_directory_contents'] = local_directory_contents
except:
d['local_directory_err'] = "Could not list directory contents"
if pipeline_command_found:
d['pipeline_command'] = pipeline_command_or_err
else:
d['pipeline_command_err'] = pipeline_command_or_err
return render_to_response('predict/my_dataset_detail.html',
d,
context_instance=RequestContext(request))
def view_signup_success(request, tb_user_md5):
d = get_common_dict(request, 'Sign Up', signup_page=True)
try:
tb_user = TBUser.objects.get(md5=tb_user_md5)
except TBUser.DoesNotExist:
raise Http404('User not found')
# This page should only be seen once, expire it in 10 minutes
#
right_now = timezone.now() #datetime.now()
elapsed = right_now - tb_user.user.date_joined
if elapsed > timedelta(minutes=15):
raise Http404('Page not found')
d['tb_user'] = tb_user.user
d['tb_user_affiliation'] = tb_user.affiliation
return render_to_response('tb_users/signup_success_page.html',
d,
context_instance=RequestContext(request))
def view_signup_success(request, tb_user_md5):
d = get_common_dict(request, 'Sign Up', signup_page=True)
try:
tb_user = TBUser.objects.get(md5=tb_user_md5)
except TBUser.DoesNotExist:
raise Http404('User not found')
# This page should only be seen once, expire it in 10 minutes
#
right_now = timezone.now() #datetime.now()
elapsed = right_now - tb_user.user.date_joined
if elapsed > timedelta(minutes=15):
raise Http404('Page not found')
d['tb_user'] = tb_user.user
d['tb_user_affiliation'] = tb_user.affiliation
return render_to_response('tb_users/signup_success_page.html',
d,
context_instance=RequestContext(request))
def view_data_upload_information(request):
d = get_common_dict(request, 'Data Upload', share_page=True)
return render_to_response('data_upload_instructions.html'\
, d\
, context_instance=RequestContext(request))
def view_data_upload_information(request):
d = get_common_dict(request, 'Data Upload', share_page=True)
return render_to_response('data_upload_instructions.html'\
, d\
, context_instance=RequestContext(request))
def view_share_page(request):
d = get_common_dict(request, 'Share', share_page=True)
return render_to_response('share.html'\
, d\
, context_instance=RequestContext(request))
def view_about_page(request):
d = get_common_dict(request, 'About', about_page=True)
return render_to_response('about.html'\
, d\
, context_instance=RequestContext(request))
def view_predict_upload_step2_confirm(request, dataset_md5):
"""
At this point:
- We have a PredictDataset object and
- Have validated the Dropbox link--it has either .fastq or .vcf files
Now, Ask the user to confirm that these are the files
"""
d = get_common_dict(request, 'Predict Upload - Confirm', predict_page=True)
# Retrieve the PredictDataset
#
try:
predict_dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
d['dataset'] = predict_dataset
d['tb_user'] = predict_dataset.user
# Retrieve the DropboxRetrievalLog
#
dbox_log = DropboxRetrievalLog.objects.filter(dataset=predict_dataset).first()
if dbox_log is None:
raise Http404('DropboxRetrievalLog for PredictDataset not found')
# Handle this better!
if dbox_log.file_metadata_err_msg:
return HttpResponse('DropboxRetrievalLog shows fail: {0}<br />{1}'.format(\
dbox_log.file_metadata_err_msg, 'view_predict_upload_step2_confirm')
)
# Show or validate the confirmation form
#
if request.POST:
f = SimpleConfirmationForm(request.POST)
if f.is_valid():
if f.do_not_use_files():
"""
Delete the info and return to predict Upload page
"""
predict_dataset.delete() # cascades to DropboxRetrievalLog
next_url = reverse('view_predict_upload_delete', args=())
else:
# Cron job will kick off download process
predict_dataset.set_status_confirmed()
next_url = reverse('view_predict_upload_success',
kwargs=dict(dataset_md5=predict_dataset.md5)
)
return HttpResponseRedirect(next_url)
else:
d['ERROR_FOUND'] = True
else:
f = SimpleConfirmationForm()
d['dbox_log'] = dbox_log
d['confirm_form'] = f
return render_to_response('predict/predict_upload_step2.html',
d,
context_instance=RequestContext(request))
def view_share_page(request):
d = get_common_dict(request, 'Share', share_page=True)
return render_to_response('share.html'\
, d\
, context_instance=RequestContext(request))
def view_predict_upload_step2_confirm(request, dataset_md5):
"""
At this point:
- We have a PredictDataset object and
- Have validated the Dropbox link--it has either .fastq or .vcf files
Now, Ask the user to confirm that these are the files
"""
d = get_common_dict(request, 'Predict Upload - Confirm', predict_page=True)
# Retrieve the PredictDataset
#
try:
predict_dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
d['dataset'] = predict_dataset
d['tb_user'] = predict_dataset.user
# Retrieve the DropboxRetrievalLog
#
dbox_log = DropboxRetrievalLog.objects.filter(
dataset=predict_dataset).first()
if dbox_log is None:
raise Http404('DropboxRetrievalLog for PredictDataset not found')
# Handle this better!
if dbox_log.file_metadata_err_msg:
return HttpResponse('DropboxRetrievalLog shows fail: {0}<br />{1}'.format(\
dbox_log.file_metadata_err_msg, 'view_predict_upload_step2_confirm')
)
# Show or validate the confirmation form
#
if request.POST:
f = SimpleConfirmationForm(request.POST)
if f.is_valid():
if f.do_not_use_files():
"""
Delete the info and return to predict Upload page
"""
predict_dataset.delete() # cascades to DropboxRetrievalLog
next_url = reverse('view_predict_upload_delete', args=())
else:
# Cron job will kick off download process
predict_dataset.set_status_confirmed()
next_url = reverse(
'view_predict_upload_success',
kwargs=dict(dataset_md5=predict_dataset.md5))
return HttpResponseRedirect(next_url)
else:
d['ERROR_FOUND'] = True
else:
f = SimpleConfirmationForm()
d['dbox_log'] = dbox_log
d['confirm_form'] = f
return render_to_response('predict/predict_upload_step2.html',
d,
context_instance=RequestContext(request))
def view_about_page(request):
d = get_common_dict(request, 'About', about_page=True)
return render_to_response('about.html'\
, d\
, context_instance=RequestContext(request))