def send_retry_response(request, form, status):
'''Returns the form te be filled out again'''
c = Context({
'form': form,
'status': status,
'subtitle': 'Register Experiment',
'searchDatafileSelectionForm': getNewSearchDatafileSelectionForm()})
return HttpResponse(render_response_index(request,
'tardis_portal/register_experiment.html', c))
def render_response_search(request, url, c):
from tardis.tardis_portal.views import getNewSearchDatafileSelectionForm
links = {}
for app in settings.INSTALLED_APPS:
if app.startswith("tardis.apps."):
view = "%s.views.search" % app
try:
links[app.split(".")[2]] = reverse(view)
except:
pass
c["searchDatafileSelectionForm"] = getNewSearchDatafileSelectionForm(request.GET.get("type", None))
c["links"] = links
return render(request, url, c)
def render_response_search(request, url, c):
from tardis.tardis_portal.views import getNewSearchDatafileSelectionForm
links = {}
for app in settings.INSTALLED_APPS:
if app.startswith('tardis.apps.'):
view = '%s.views.search' % app
try:
links[app.split('.')[2]] = reverse(view)
except:
pass
c['searchDatafileSelectionForm'] = \
getNewSearchDatafileSelectionForm(request.GET.get('type', None))
c['links'] = links
return render(request, url, c)
def render_response_search(request, url, c):
from tardis.tardis_portal.views import getNewSearchDatafileSelectionForm
links = {}
for app in settings.INSTALLED_APPS:
if app.startswith('tardis.apps.'):
view = '%s.views.search' % app
try:
links[app.split('.')[2]] = reverse(view)
except:
pass
c['searchDatafileSelectionForm'] = \
getNewSearchDatafileSelectionForm(request.GET.get('type', None))
c['links'] = links
return render(request, url, c)
def render_response_search(request, *args, **kwargs):
from tardis.tardis_portal.views import getNewSearchDatafileSelectionForm
is_authenticated = request.user.is_authenticated()
if is_authenticated:
is_superuser = request.user.is_superuser
username = request.user.username
else:
is_superuser = False
username = None
links = {}
for app in settings.INSTALLED_APPS:
if app.startswith('tardis.apps.'):
view = '%s.views.search' % app
try:
links[app.split('.')[2]] = reverse(view)
except:
pass
kwargs['context_instance'] = RequestContext(request)
kwargs['context_instance']['is_authenticated'] = is_authenticated
kwargs['context_instance']['is_superuser'] = is_superuser
kwargs['context_instance']['username'] = username
kwargs['context_instance']['searchDatafileSelectionForm'] = \
getNewSearchDatafileSelectionForm(request.GET.get('type', None))
kwargs['context_instance']['links'] = links
staging = get_full_staging_path(
username)
if staging:
kwargs['context_instance']['has_staging_access'] = True
else:
kwargs['context_instance']['has_staging_access'] = False
#if request.mobile:
# template_path = args[0]
# split = template_path.partition('/')
# args = (split[0] + '/mobile/' + split[2], ) + args[1:]
return render_to_response(*args, **kwargs)
def render_response_search(request, *args, **kwargs):
from tardis.tardis_portal.views import getNewSearchDatafileSelectionForm
is_authenticated = request.user.is_authenticated()
if is_authenticated:
is_superuser = request.user.is_superuser
username = request.user.username
else:
is_superuser = False
username = None
links = {}
for app in settings.INSTALLED_APPS:
if app.startswith('tardis.apps.'):
view = '%s.views.search' % app
try:
links[app.split('.')[2]] = reverse(view)
except:
pass
kwargs['context_instance'] = RequestContext(request)
kwargs['context_instance']['is_authenticated'] = is_authenticated
kwargs['context_instance']['is_superuser'] = is_superuser
kwargs['context_instance']['username'] = username
kwargs['context_instance']['searchDatafileSelectionForm'] = \
getNewSearchDatafileSelectionForm(request.GET.get('type', None))
kwargs['context_instance']['links'] = links
staging = get_full_staging_path(username)
if staging:
kwargs['context_instance']['has_staging_access'] = True
else:
kwargs['context_instance']['has_staging_access'] = False
#if request.mobile:
# template_path = args[0]
# split = template_path.partition('/')
# args = (split[0] + '/mobile/' + split[2], ) + args[1:]
return render_to_response(*args, **kwargs)
def render_response_search(request, *args, **kwargs):
from tardis.tardis_portal.views import getNewSearchDatafileSelectionForm
is_authenticated = request.user.is_authenticated()
if is_authenticated:
is_superuser = request.user.is_superuser
username = request.user.username
else:
is_superuser = False
username = None
links = {}
for app in settings.INSTALLED_APPS:
if app.startswith("tardis.apps."):
view = "%s.views.search" % app
try:
links[app.split(".")[2]] = reverse(view)
except:
pass
kwargs["context_instance"] = RequestContext(request)
kwargs["context_instance"]["is_authenticated"] = is_authenticated
kwargs["context_instance"]["is_superuser"] = is_superuser
kwargs["context_instance"]["username"] = username
kwargs["context_instance"]["searchDatafileSelectionForm"] = getNewSearchDatafileSelectionForm(
request.GET.get("type", None)
)
kwargs["context_instance"]["links"] = links
staging = get_full_staging_path(username)
if staging:
kwargs["context_instance"]["has_staging_access"] = True
else:
kwargs["context_instance"]["has_staging_access"] = False
return render(request, *args, **kwargs)
def experiment_datasets(request, experiment_id):
"""View a listing of dataset of an existing experiment as ajax loaded tab.
:param request: a HTTP Request instance
:type request: :class:`django.http.HttpRequest`
:param experiment_id: the ID of the experiment to be edited
:type experiment_id: string
:param template_name: the path of the template to render
:type template_name: string
:rtype: :class:`django.http.HttpResponse`
"""
c = Context({'upload_complete_url':
reverse('tardis.tardis_portal.views.upload_complete'),
'searchDatafileSelectionForm':
getNewSearchDatafileSelectionForm(),
})
try:
experiment = Experiment.safe.get(request, experiment_id)
except PermissionDenied:
return return_response_error(request)
except Experiment.DoesNotExist:
return return_response_not_found(request)
c['experiment'] = experiment
if 'query' in request.GET:
# We've been passed a query to get back highlighted results.
# Only pass back matching datafiles
#
search_query = FacetFixedSearchQuery(backend=HighlightSearchBackend())
sqs = SearchQuerySet(query=search_query)
query = SearchQueryString(request.GET['query'])
facet_counts = sqs.raw_search(query.query_string() + ' AND experiment_id_stored:%i' % (int(experiment_id)), end_offset=1).facet('dataset_id_stored').highlight().facet_counts()
if facet_counts:
dataset_id_facets = facet_counts['fields']['dataset_id_stored']
else:
dataset_id_facets = []
c['highlighted_datasets'] = [ int(f[0]) for f in dataset_id_facets ]
c['file_matched_datasets'] = []
c['search_query'] = query
# replace '+'s with spaces
elif 'datafileResults' in request.session and 'search' in request.GET:
c['highlighted_datasets'] = None
c['highlighted_dataset_files'] = [r.pk for r in request.session['datafileResults']]
c['file_matched_datasets'] = \
list(set(r.dataset.pk for r in request.session['datafileResults']))
c['search'] = True
else:
c['highlighted_datasets'] = None
c['highlighted_dataset_files'] = None
c['file_matched_datasets'] = None
# microtardis change start
if 'session_show_hidden' not in request.session:
request.session['session_show_hidden'] = False
if 'session_hidden_text' not in request.session:
request.session['session_hidden_text'] = "Show Hidden Datasets and Files"
if not request.session['session_show_hidden']:
# hide hidden objects
hidden_datasets = Dataset_Hidden.objects.filter(hidden=True).values_list('dataset', flat=True)
c['datasets'] = Dataset.objects.filter(experiment=experiment_id).exclude(pk__in=hidden_datasets)
hidden_datafiles = Datafile_Hidden.objects.filter(hidden=True).values_list('datafile', flat=True)
datafiles = {}
for dataset in c['datasets']:
datafiles[dataset] = Dataset_File.objects.filter(dataset=dataset.id).exclude(pk__in=hidden_datafiles).count()
c['datafiles'] = datafiles
else:
# show all objects
c['datasets'] = Dataset.objects.filter(experiment=experiment_id)
datafiles = {}
for dataset in c['datasets']:
datafiles[dataset] = Dataset_File.objects.filter(dataset=dataset.id).count()
c['datafiles'] = datafiles
# highlight hidden datasets
hidden_datasets = Dataset_Hidden.objects.filter(hidden=True).values_list('dataset', flat=True)
dataset_objects = Dataset.objects.filter(experiment=experiment_id, pk__in=hidden_datasets)
c['linethrough_datasets'] = [ obj.pk for obj in dataset_objects ]
# highlight datasets which have hidden datafiles
hidden_datafiles = Datafile_Hidden.objects.filter(hidden=True).values_list('datafile', flat=True)
experiment_dataset_objects = Dataset.objects.filter(experiment=experiment_id)
hidden_datafiles_objects = Dataset_File.objects.filter(pk__in=hidden_datafiles, dataset__in=experiment_dataset_objects)
c['file_hidden_datasets'] = list(set(obj.dataset.pk for obj in hidden_datafiles_objects))
# microtardis change end
c['has_write_permissions'] = \
authz.has_write_permissions(request, experiment_id)
c['protocol'] = []
download_urls = experiment.get_download_urls()
for key, value in download_urls.iteritems():
c['protocol'] += [[key, value]]
if 'status' in request.GET:
c['status'] = request.GET['status']
if 'error' in request.GET:
c['error'] = request.GET['error']
return HttpResponse(render_response_index(request,
'tardis_portal/ajax/experiment_datasets.html', c))
def templates(request):
from tardis.tardis_portal.views import getNewSearchDatafileSelectionForm
return {'searchDatafileSelectionForm': getNewSearchDatafileSelectionForm()}
# Seach Views
(r'^search/', include(search_urls)),
# Account Views
(r'^accounts/', include(accounts_urls)),
# Group Views
(r'^groups/$', 'tardis.tardis_portal.views.manage_groups'),
(r'^group/', include(group_urls)),
# Equipment Views
(r'^equipment/$', list_detail.object_list,
{'queryset': Equipment.objects.all(),
'paginate_by': 15,
'extra_context':
{'searchDatafileSelectionForm': getNewSearchDatafileSelectionForm()}}),
(r'^equipment/(?P<object_id>\d+)/$', list_detail.object_detail,
{'queryset': Equipment.objects.all()}),
# Display Views
(r'^displayDatafileImage/', include(display_urls)),
# Login/out
(r'^login/$', 'tardis.tardis_portal.views.login'),
(r'^logout/$', logout, {'next_page': '/'}),
# Media
(r'site_media/(?P<path>.*)$', 'django.views.static.serve',
{'document_root': settings.STATIC_DOC_ROOT}),
(r'media/(?P<path>.*)$', 'django.views.static.serve',
{'document_root': settings.ADMIN_MEDIA_STATIC_DOC_ROOT}),
def register_experiment_ws_xmldata(request):
status = ''
if request.method == 'POST': # If the form has been submitted...
# A form bound to the POST data
form = RegisterExperimentForm(request.POST, request.FILES)
if form.is_valid(): # All validation rules pass
xmldata = request.FILES['xmldata']
username = form.cleaned_data['username']
origin_id = form.cleaned_data['originid']
from_url = form.cleaned_data['from_url']
user = auth_service.authenticate(request=request,
authMethod=localdb_auth_key)
if user:
if not user.is_active:
return return_response_error(request)
else:
return return_response_error(request)
e = Experiment(
title='Placeholder Title',
approved=True,
created_by=user,
)
e.save()
eid = e.id
filename = path.join(e.get_or_create_directory(),
'mets_upload.xml')
f = open(filename, 'wb+')
for chunk in xmldata.chunks():
f.write(chunk)
f.close()
logger.info('=== processing experiment: START')
owners = request.POST.getlist('experiment_owner')
try:
_registerExperimentDocument(filename=filename,
created_by=user,
expid=eid,
owners=owners,
username=username)
logger.info('=== processing experiment %s: DONE' % eid)
except:
logger.exception('=== processing experiment %s: FAILED!' % eid)
return return_response_error(request)
if from_url:
logger.debug('=== sending file request')
logger.info('Sending received_remote signal')
from tardis.tardis_portal.signals import received_remote
received_remote.send(sender=Experiment,
instance=e,
uid=origin_id,
from_url=from_url)
response = HttpResponse(str(eid), status=200)
response['Location'] = request.build_absolute_uri(
'/experiment/view/' + str(eid))
return response
else:
form = RegisterExperimentForm() # An unbound form
c = Context({
'form': form,
'status': status,
'subtitle': 'Register Experiment',
'searchDatafileSelectionForm': getNewSearchDatafileSelectionForm()})
return HttpResponse(render_response_index(request,
'tardis_portal/register_experiment.html', c))
def experiment_samples(request, experiment_id):
"""View a listing of dataset of an existing experiment as ajax loaded tab.
:param request: a HTTP Request instance
:type request: :class:`django.http.HttpRequest`
:param experiment_id: the ID of the experiment to be edited
:type experiment_id: string
:param template_name: the path of the template to render
:type template_name: string
:rtype: :class:`django.http.HttpResponse`
"""
c = Context({'upload_complete_url':
reverse('tardis.tardis_portal.views.upload_complete'),
'searchDatafileSelectionForm':
getNewSearchDatafileSelectionForm(),
})
try:
experiment = Experiment.safe.get(request, experiment_id)
except PermissionDenied:
return return_response_error(request)
except Experiment.DoesNotExist:
return return_response_not_found(request)
c['experiment'] = experiment
if 'query' in request.GET:
# We've been passed a query to get back highlighted results.
# Only pass back matching datafiles
#
search_query = FacetFixedSearchQuery(backend=HighlightSearchBackend())
sqs = SearchQuerySet(query=search_query)
query = SearchQueryString(request.GET['query'])
facet_counts = sqs.raw_search(query.query_string() + ' AND experiment_id_stored:%i' % (int(experiment_id)), end_offset=1).facet('dataset_id_stored').highlight().facet_counts()
if facet_counts:
dataset_id_facets = facet_counts['fields']['dataset_id_stored']
else:
dataset_id_facets = []
c['highlighted_datasets'] = [ int(f[0]) for f in dataset_id_facets ]
c['file_matched_datasets'] = []
c['search_query'] = query
# replace '+'s with spaces
elif 'datafileResults' in request.session and 'search' in request.GET:
c['highlighted_datasets'] = None
c['highlighted_dataset_files'] = [r.pk for r in request.session['datafileResults']]
c['file_matched_datasets'] = \
list(set(r.dataset.pk for r in request.session['datafileResults']))
c['search'] = True
else:
c['highlighted_datasets'] = None
c['highlighted_dataset_files'] = None
c['file_matched_datasets'] = None
c['samples'] = \
Sample.objects.filter(experiment=experiment_id).order_by("id")
c['datasets'] = \
Dataset.objects.filter(experiment=experiment_id)
c['has_write_permissions'] = \
authz.has_write_permissions(request, experiment_id)
c['protocol'] = []
download_urls = experiment.get_download_urls()
for key, value in download_urls.iteritems():
c['protocol'] += [[key, value]]
if 'status' in request.GET:
c['status'] = request.GET['status']
if 'error' in request.GET:
c['error'] = request.GET['error']
return HttpResponse(render_response_index(request,
'tardis_portal/ajax/experiment_samples.html', c))
