def detail_matrix(request, matrix_id):
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
matrix = get_object_or_404(Matrix, pk=matrix_id)
matrix_link = get_blog_link_post_url() + matrix.blogpost
matrix_cells = matrix.get_matrix()
columns = matrix.get_columns()
rows = matrix.get_rows()
data.update({
'matrix': matrix,
'matrix_link': matrix_link,
'rows': rows,
'columns': columns,
'matrix_cells': matrix_cells
})
return render(request, 'matrices/detail_matrix.html', data)
def maintenance(request):
if request.user.is_superuser:
data = get_header_data(request.user)
type_list = Type.objects.all()
protocol_list = Protocol.objects.all()
command_list = Command.objects.all()
blog_list = Blog.objects.all()
authority_list = Authority.objects.all()
collection_authority_list = CollectionAuthority.objects.all()
data.update({
'type_list': type_list,
'protocol_list': protocol_list,
'command_list': command_list,
'blog_list': blog_list,
'authority_list': authority_list,
'collection_authority_list': collection_authority_list
})
return render(request, 'host/maintenance.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def show_project(request, server_id, project_id):
"""
Show a project
"""
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
server = get_object_or_404(Server, pk=server_id)
if server.is_omero547() or server.is_omero56():
server_data = server.get_imaging_server_project_json(project_id)
data.update(server_data)
return render(request, 'gallery/show_project.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def add_dataset(request, server_id, dataset_id):
data = get_header_data(request.user)
if not exists_active_collection_for_user(request.user):
return HttpResponseRedirect(reverse('home', args=()))
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
server = get_object_or_404(Server, pk=server_id)
if exists_active_collection_for_user(request.user):
image_ids = request.POST.getlist('checks[]')
for image_id in image_ids:
image = add_image_to_collection(request.user, server, image_id,
0)
else:
messages.error(
request,
"You have no Active Image Collection; Please create a Collection!"
)
return HttpResponseRedirect(
reverse('webgallery_show_dataset', args=(server_id, dataset_id)))
def add_ebi_sca_image(request, server_id, image_id, path_from):
data = get_header_data(request.user)
if not exists_active_collection_for_user(request.user):
return HttpResponseRedirect(reverse('home', args=()))
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
server = get_object_or_404(Server, pk=server_id)
if exists_active_collection_for_user(request.user):
image = add_image_to_collection(request.user, server, image_id, 0)
else:
messages.error(
request,
"You have no Active Image Collection; Please create a Collection!"
)
if server.is_ebi_sca():
if path_from == "show_ebi_sca_image":
return HttpResponseRedirect(
reverse('webgallery_show_ebi_sca_image',
args=(server_id, image_id)))
def show_ebi_widget(request, server_id, experiment_id):
"""
Show the EBI widget
"""
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
server = get_object_or_404(Server, pk=server_id)
if server.is_omero547() or server.is_omero56():
server_data = server.get_ebi_widget_json()
gene = ''
data.update({'experimentAccession': experiment_id, 'geneId': gene})
data.update(server_data)
return render(request, 'ebi/show_widget.html', data)
def show_wordpress(request, server_id, page_id):
"""
Show the Wordpress Server
"""
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
server = get_object_or_404(Server, pk=server_id)
credential = get_credential_for_user(request.user)
if server.is_wordpress():
server_data = server.get_wordpress_json(credential, page_id)
data.update(server_data)
return render(request, 'gallery/show_wordpress.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def add_cell(request, matrix_id):
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
matrix = Matrix.objects.get(id=matrix_id)
authority = get_authority_for_bench_and_user_and_requester(
matrix, request.user)
if authority.is_viewer() == True or authority.is_none() == True:
return HttpResponseRedirect(reverse('home', args=()))
else:
cell_list = Cell.objects.filter(matrix=matrix)
if not cell_list:
cell1 = Cell.create(matrix, "", "", 0, 0, "", None)
cell2 = Cell.create(matrix, "", "", 0, 1, "", None)
cell3 = Cell.create(matrix, "", "", 0, 2, "", None)
cell4 = Cell.create(matrix, "", "", 1, 0, "", None)
cell5 = Cell.create(matrix, "", "", 1, 1, "", None)
cell6 = Cell.create(matrix, "", "", 1, 2, "", None)
cell7 = Cell.create(matrix, "", "", 2, 0, "", None)
cell8 = Cell.create(matrix, "", "", 2, 1, "", None)
cell9 = Cell.create(matrix, "", "", 2, 2, "", None)
cell1.save()
cell2.save()
cell3.save()
cell4.save()
cell5.save()
cell6.save()
cell7.save()
cell8.save()
cell9.save()
matrix.save()
matrix_cells = matrix.get_matrix()
columns = matrix.get_columns()
rows = matrix.get_rows()
data.update({
'matrix': matrix,
'rows': rows,
'columns': columns,
'matrix_cells': matrix_cells
})
return HttpResponseRedirect(reverse('matrix', args=(matrix_id, )))
def new_bench_bench_authorisation(request, matrix_id):
data = get_header_data(request.user)
if request.method == HTTP_POST:
next_page = request.POST.get('next', '/')
form = AuthorisationForm(request.POST)
if form.is_valid():
authorisation = form.save(commit=False)
if authorisation_exists_for_bench_and_permitted(
authorisation.matrix, authorisation.permitted):
authorisation_old = Authorisation.objects.get(
Q(matrix=authorisation.matrix)
& Q(permitted=authorisation.permitted))
if authorisation_old.authority != authorisation.authority:
authorisation_old.authority = authorisation.authority
authorisation_old.save()
else:
authorisation.save()
return HttpResponseRedirect(next_page)
else:
messages.error(request, "Bench Authorisation Form is Invalid!")
form.add_error(None, "Bench Authorisation Form is Invalid!")
text_flag = " for Bench CPW:" + format(int(matrix_id), '06d')
data.update({'text_flag': text_flag, 'form': form})
else:
text_flag = " for Bench CPW:" + format(int(matrix_id), '06d')
form = AuthorisationForm()
form.fields['matrix'] = forms.ModelChoiceField(
Matrix.objects.filter(id=matrix_id))
form.fields['matrix'].initial = matrix_id
form.fields['permitted'] = forms.ModelChoiceField(
User.objects.exclude(id=request.user.id).exclude(
is_superuser=True))
data.update({'text_flag': text_flag, 'form': form})
return render(request, 'permissions/new_bench_authorisation.html', data)
def edit_collection(request, collection_id):
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
collection = get_object_or_404(Collection, pk=collection_id)
if request.method == HTTP_POST:
form = CollectionForm(request.POST, instance=collection)
if form.is_valid():
collection = form.save(commit=False)
if exists_title_for_collection_for_user(
request.user, collection.title):
messages.error(request, "Collection Title NOT Unique!")
form.add_error(None, "Collection Title NOT Unique!")
data.update({'form': form, 'collection': collection})
else:
if collection.is_active():
if exists_active_collection_for_user(request.user):
set_inactive_collection_for_user(request.user)
collection.set_owner(request.user)
collection.save()
return HttpResponseRedirect(
reverse('list_collections', args=()))
else:
messages.error(request, "Collection Form is Invalid!")
form.add_error(None, "Collection Form is Invalid!")
data.update({'form': form, 'collection': collection})
else:
form = CollectionForm(instance=collection)
data.update({'form': form, 'collection': collection})
return render(request, 'matrices/edit_collection.html', data)
def view_user(request, user_id):
data = get_header_data(request.user)
subject = get_object_or_404(User, pk=user_id)
data.update({ 'subject': subject })
return render(request, 'authorisation/detail_user.html', data)
def list_imaging_hosts(request):
data = get_header_data(request.user)
form = SearchUrlForm()
data.update({'form': form, 'search_from': "list_imaging_hosts"})
return render(request, 'host/list_imaging_hosts.html', data)
def collectivization(request):
data = get_header_data(request.user)
if request.user.is_superuser:
user_list = User.objects.all()
out_message_list = list()
for user in user_list:
imageCount = 0
out_message = ""
if exists_image_for_user(user):
image_list = get_images_for_user(user)
if exists_active_collection_for_user(user):
out_message = "Default Collection ALREADY exists for User {}".format(
user.username)
else:
collection = Collection.create("Default Collection",
"Default Collection", True,
user)
collection.save()
for image in image_list:
imageCount = imageCount + 1
Collection.assign_image(image, collection)
out_message = "Default Collection created for {} Images for User {}".format(
imageCount, user.username)
else:
out_message = "NO Default Collection created for User {}".format(
user.username)
out_message_list.append(out_message)
data.update({'out_message_list': out_message_list})
return render(request, 'authorisation/collectivization.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def new_server(request):
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
if request.user.is_superuser:
if request.method == HTTP_POST:
form = ServerForm(request.POST)
if form.is_valid():
server = form.save(commit=False)
server.set_owner(request.user)
cipher = AESCipher(config('NOT_EMAIL_HOST_PASSWORD'))
encryptedPwd = cipher.encrypt(server.pwd).decode()
server.set_pwd(encryptedPwd)
server.save()
return HttpResponseRedirect(
reverse('list_imaging_hosts', args=()))
else:
messages.error(request, "Server Form is Invalid!")
form.add_error(None, "Server Form is Invalid!")
data.update({
'form': form,
})
else:
form = ServerForm()
data.update({
'form': form,
})
return render(request, 'host/new_server.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def add_row_below(request, matrix_id, row_id):
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
matrix = get_object_or_404(Matrix, pk=matrix_id)
authority = get_authority_for_bench_and_user_and_requester(
matrix, request.user)
if authority.is_viewer() == True or authority.is_none() == True:
return HttpResponseRedirect(reverse('home', args=()))
else:
matrix = Matrix.objects.get(id=matrix_id)
oldCells = Cell.objects.filter(matrix=matrix_id).filter(
ycoordinate__gt=row_id)
columns = matrix.get_columns()
new_row_id = int(row_id) + 1
for oldcell in oldCells:
oldcell.increment_y()
oldcell.save()
for i, column in enumerate(columns):
cell = Cell.create(matrix, "", "", i, new_row_id, "", None)
cell.save()
matrix.save()
matrix_cells = matrix.get_matrix()
columns = matrix.get_columns()
rows = matrix.get_rows()
data.update({
'matrix': matrix,
'rows': rows,
'columns': columns,
'matrix_cells': matrix_cells
})
return HttpResponseRedirect(reverse('matrix', args=(matrix_id, )))
def list_bench_authorisation(request):
data = get_header_data(request.user)
authorisation_list = Authorisation.objects.all()
text_flag = ' ALL Permissions, ALL Benches'
matrix_id = ''
data.update({ 'matrix_id': matrix_id, 'text_flag': text_flag, 'authorisation_list': authorisation_list })
return render(request, 'host/list_bench_authorisation.html', data)
def view_bench_authorisation(request, bench_authorisation_id):
data = get_header_data(request.user)
authorisation = get_object_or_404(Authorisation, pk=bench_authorisation_id)
data.update({
'authorisation_id': bench_authorisation_id,
'authorisation': authorisation
})
return render(request, 'permissions/detail_bench_authorisation.html', data)
def list_my_collection_authorisation(request):
data = get_header_data(request.user)
collection_authorisation_list = CollectionAuthorisation.objects.filter(collection__owner=request.user)
text_flag = ' YOUR Collection Permissions'
collection_id = ''
data.update({ 'collection_id': collection_id, 'text_flag': text_flag, 'collection_authorisation_list': collection_authorisation_list })
return render(request, 'host/list_collection_authorisation.html', data)
def list_my_collection_collection_authorisation(request, collection_id, user_id):
data = get_header_data(request.user)
collection_authorisation_list = CollectionAuthorisation.objects.filter(collection__owner=user_id).filter(collection__id=collection_id)
user = get_object_or_404(User, pk=user_id)
text_flag = "Permissions for Collection:" + format(int(collection_id), '06d') + " for User " + user.username
data.update({ 'collection_id': collection_id, 'user_id': user_id, 'text_flag': text_flag, 'collection_authorisation_list': collection_authorisation_list })
return render(request, 'host/list_collection_authorisation.html', data)
def delete_collection(request, collection_id):
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
collection = get_object_or_404(Collection, pk=collection_id)
images = get_images_for_collection(collection)
for image in images:
collection_list = get_collections_for_image(image)
delete_flag = False
for collection_other in collection_list:
if collection != collection_other:
delete_flag = True
if delete_flag == False:
if not exists_image_in_cells(image):
Collection.unassign_image(image, collection)
image.delete()
if exists_bench_for_last_used_collection(collection):
matrix_list = get_benches_for_last_used_collection(collection)
for matrix in matrix_list:
matrix.set_no_last_used_collection()
matrix.save()
if collection.is_active():
set_first_active_collection_for_user(request.user)
collection.delete()
return HttpResponseRedirect(reverse('list_collections', args=()))
def view_collection_authorisation(request, collection_authorisation_id):
data = get_header_data(request.user)
collection_authorisation = get_object_or_404(
CollectionAuthorisation, pk=collection_authorisation_id)
data.update({
'collection_authorisation_id': collection_authorisation_id,
'collection_authorisation': collection_authorisation
})
return render(request, 'permissions/detail_collection_authorisation.html',
data)
def list_user_collection_collection_authorisation(request, user_id):
data = get_header_data(request.user)
collection_authorisation_list = CollectionAuthorisation.objects.filter(matrix__owner=user_id)
user = get_object_or_404(User, pk=user_id)
text_flag = " ALL Collection Permissions for " + user.username
collection_id = ''
data.update({ 'collection_id': collection_id, 'user_id': user_id, 'text_flag': text_flag, 'collection_authorisation_list': collection_authorisation_list })
return render(request, 'host/list_collection_authorisation.html', data)
def edit_collection_authority(request, collection_authority_id):
if request.user.is_superuser:
data = get_header_data(request.user)
collection_authority = get_object_or_404(CollectionAuthority,
pk=collection_authority_id)
if request.method == HTTP_POST:
form = CollectionAuthorityForm(request.POST,
instance=collection_authority)
if form.is_valid():
collection_authority = form.save(commit=False)
collection_authority.set_owner(request.user)
collection_authority.save()
return HttpResponseRedirect(reverse('maintenance', args=()))
else:
messages.error(request,
"Collection Authority Form is Invalid!")
form.add_error(None, "Collection Authority Form is Invalid!")
data.update({
'form': form,
'collection_authority': collection_authority
})
else:
form = CollectionAuthorityForm(instance=collection_authority)
data.update({
'form': form,
'collection_authority': collection_authority
})
return render(request, 'maintenance/edit_collection_authority.html',
data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def show_ebi_sca_image(request, server_id, image_id):
"""
Show a chart from an EBI SCA Server
"""
data = get_header_data(request.user)
if data["credential_flag"] == NO_CREDENTIALS:
return HttpResponseRedirect(reverse('home', args=()))
else:
server = get_object_or_404(Server, pk=server_id)
if server.is_ebi_sca():
image_flag = ''
if exists_active_collection_for_user(request.user):
image_flag = 'ALLOW'
else:
image_flag = 'DISALLOW'
experiment_id = get_an_ebi_sca_experiment_id_from_chart_id(
image_id)
metadata = server.get_ebi_server_experiment_metadata(experiment_id)
chart = get_an_ebi_sca_parameters_from_chart_id(
server.url_server, image_id)
data.update({
'image_flag': image_flag,
'add_from': "show_image",
'server': server,
'chart': chart,
'metadata': metadata,
'add_from': "show_ebi_sca_image"
})
return render(request, 'gallery/show_ebi_sca_image.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def get_context_data(self, **kwargs):
context = super().get_context_data(**kwargs)
data = get_header_data(self.request.user)
data_dict = {'title': self.query_title, 'description': self.query_description, 'created_before': self.query_created_before, 'created_after': self.query_created_after, 'modified_before': self.query_modified_before, 'modified_after': self.query_modified_after, 'owner': self.query_owner, 'authority': self.query_authority, 'paginate_by': self.query_paginate_by }
form = MatrixSummarySearchForm(data_dict)
data.update({ 'form': form, })
context.update(data)
return context
def view_blog_command(request, blog_id):
data = get_header_data(request.user)
blog = get_object_or_404(Blog, pk=blog_id)
if request.user.is_superuser:
data.update({'blog_id': blog_id, 'blog': blog})
return render(request, 'maintenance/detail_blog_command.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def view_protocol(request, protocol_id):
if request.user.is_superuser:
data = get_header_data(request.user)
protocol = get_object_or_404(Protocol, pk=protocol_id)
data.update({'protocol_id': protocol_id, 'protocol': protocol})
return render(request, 'maintenance/detail_protocol.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def list_bench_bench_authorisation(request, matrix_id):
data = get_header_data(request.user)
authorisation_list = Authorisation.objects.filter(matrix__id=matrix_id)
text_flag = "Permissions for Bench CPW:" + format(int(matrix_id), '06d')
data.update({
'matrix_id': matrix_id,
'text_flag': text_flag,
'authorisation_list': authorisation_list
})
return render(request, 'host/list_bench_authorisation.html', data)
def view_command(request, command_id):
if request.user.is_superuser:
data = get_header_data(request.user)
command = get_object_or_404(Command, pk=command_id)
data.update({ 'command_id': command_id, 'command': command })
return render(request, 'maintenance/detail_command.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))
def view_type(request, type_id):
if request.user.is_superuser:
data = get_header_data(request.user)
type = get_object_or_404(Type, pk=type_id)
data.update({'type_id': type_id, 'type': type})
return render(request, 'maintenance/detail_type.html', data)
else:
return HttpResponseRedirect(reverse('home', args=()))