def __init__(self, current_user=None, *args, **kwargs):
"""Override for form initialization"""
super().__init__(*args, **kwargs)
self.current_user = current_user
# Default field modifications
self.fields['description'].required = False
self.fields['secret'].widget = forms.TextInput(
attrs={'class': "sodar-code-input"})
self.fields['description'].widget.attrs['rows'] = 4
# Special cases for SOURCE
if settings.PROJECTROLES_SITE_MODE == SITE_MODE_SOURCE:
self.fields['secret'].widget.attrs['readonly'] = True
self.fields['user_display'].widget = forms.CheckboxInput()
elif settings.PROJECTROLES_SITE_MODE == SITE_MODE_TARGET:
self.fields['user_display'].widget = forms.HiddenInput()
self.fields['user_display'].initial = True
# Creation
if not self.instance.pk:
# Generate secret token for target site
if settings.PROJECTROLES_SITE_MODE == SITE_MODE_SOURCE:
self.fields['secret'].initial = build_secret()
# Updating
else:
pass
def update(self, instance, validated_data):
if instance.public_url != bool(
validated_data.get('public_url', instance.public_url)
):
instance.secret = build_secret()
instance.save()
return super().update(instance, validated_data)
def save(self, *args, **kwargs):
"""Override of form saving function"""
obj = super().save(commit=False)
obj.project = self.project
obj.issuer = self.current_user
obj.date_expire = timezone.now() + timezone.timedelta(
days=INVITE_EXPIRY_DAYS)
obj.secret = build_secret()
obj.save()
return obj
def _make_file():
file = self._make_file(
name='file2.txt',
file_name='file2.txt',
file_content=self.file_content,
project=self.project,
folder=None,
owner=self.owner_as.user,
description='',
public_url=True,
secret=build_secret(),
)
file.sodar_uuid = obj_uuid
file.save()
def _make_site(
cls,
name,
url,
mode=SODAR_CONSTANTS['SITE_MODE_TARGET'],
description='',
secret=build_secret(),
):
"""Make and save a RemoteSite"""
values = {
'name': name,
'url': url,
'mode': mode,
'description': description,
'secret': secret,
}
site = RemoteSite(**values)
site.save()
return site
def save(self, *args, **kwargs):
"""Override of form saving function"""
obj = super().save(commit=False)
# Creation
if not self.instance.pk:
obj.name = obj.file.name
obj.owner = self.current_user
obj.project = self.project
if self.folder:
obj.folder = self.folder
obj.secret = build_secret() # Secret string created here
# Updating
else:
old_file = File.objects.get(pk=self.instance.pk)
if old_file.file != self.instance.file:
obj.file = self.instance.file
obj.name = obj.file.name.split('/')[-1]
obj.owner = self.instance.owner
obj.project = self.instance.project
if app_settings.get_app_setting(APP_NAME,
'allow_public_links',
project=self.instance.project):
obj.public_url = self.instance.public_url
else:
obj.public_url = False
obj.secret = self.instance.secret
if self.instance.folder:
obj.folder = self.instance.folder
obj.save()
return obj
def _set_up_as_target(cls, projects):
"""Set up current site as a target site"""
source_site = cls._make_site(
name='Test Source',
url='http://0.0.0.0',
mode=SITE_MODE_SOURCE,
description='',
secret=build_secret(),
)
remote_projects = []
for project in projects:
remote_projects.append(
cls._make_remote_project(
project_uuid=project.sodar_uuid,
project=project,
site=source_site,
level=SODAR_CONSTANTS['REMOTE_LEVEL_READ_ROLES'],
))
return source_site, remote_projects
PROJECT_TYPE_CATEGORY = SODAR_CONSTANTS['PROJECT_TYPE_CATEGORY']
PROJECT_TYPE_PROJECT = SODAR_CONSTANTS['PROJECT_TYPE_PROJECT']
SUBMIT_STATUS_OK = SODAR_CONSTANTS['SUBMIT_STATUS_OK']
SUBMIT_STATUS_PENDING = SODAR_CONSTANTS['SUBMIT_STATUS_PENDING']
SUBMIT_STATUS_PENDING_TASKFLOW = SODAR_CONSTANTS['SUBMIT_STATUS_PENDING']
SITE_MODE_TARGET = SODAR_CONSTANTS['SITE_MODE_TARGET']
SITE_MODE_SOURCE = SODAR_CONSTANTS['SITE_MODE_SOURCE']
REMOTE_LEVEL_VIEW_AVAIL = SODAR_CONSTANTS['REMOTE_LEVEL_VIEW_AVAIL']
REMOTE_LEVEL_READ_INFO = SODAR_CONSTANTS['REMOTE_LEVEL_READ_INFO']
REMOTE_LEVEL_READ_ROLES = SODAR_CONSTANTS['REMOTE_LEVEL_READ_ROLES']
# Local constants
SOURCE_SITE_NAME = 'Test source site'
SOURCE_SITE_URL = 'https://sodar.bihealth.org'
SOURCE_SITE_DESC = 'Source description'
SOURCE_SITE_SECRET = build_secret()
SOURCE_USER_DOMAIN = 'TESTDOMAIN'
SOURCE_USER_USERNAME = '******' + SOURCE_USER_DOMAIN
SOURCE_USER_GROUP = SOURCE_USER_DOMAIN.lower()
SOURCE_USER_NAME = 'Firstname Lastname'
SOURCE_USER_FIRST_NAME = SOURCE_USER_NAME.split(' ')[0]
SOURCE_USER_LAST_NAME = SOURCE_USER_NAME.split(' ')[1]
SOURCE_USER_EMAIL = SOURCE_USER_USERNAME.split('@')[0] + '@example.com'
SOURCE_USER_UUID = str(uuid.uuid4())
SOURCE_CATEGORY_UUID = str(uuid.uuid4())
SOURCE_CATEGORY_TITLE = 'TestCategory'
SOURCE_PROJECT_UUID = str(uuid.uuid4())
SOURCE_PROJECT_TITLE = 'TestProject'
SOURCE_PROJECT_DESCRIPTION = 'Description'
def form_valid(self, form):
"""Override form_valid() for zip file unpacking"""
timeline = get_backend_api('timeline_backend')
######################
# Regular file upload
######################
if not form.cleaned_data.get('unpack_archive'):
return super().form_valid(form)
#####################
# Zip file unpacking
#####################
file = form.cleaned_data.get('file')
folder = form.cleaned_data.get('folder')
project = self.get_project(self.request, self.kwargs)
# Build redirect URL
# TODO: Repetition, put this in a mixin?
if folder:
re_kwargs = {'folder': folder.sodar_uuid}
else:
re_kwargs = {'project': project.sodar_uuid}
redirect_url = reverse('filesfolders:list', kwargs=re_kwargs)
try:
zip_file = ZipFile(file)
except Exception as ex:
messages.error(self.request,
'Unable to extract zip file: {}'.format(ex))
return redirect(redirect_url)
new_folders = []
new_files = []
with transaction.atomic():
for f in [f for f in zip_file.infolist() if not f.is_dir()]:
# Create subfolders if any
current_folder = folder
for zip_folder in f.filename.split('/')[:-1]:
try:
current_folder = Folder.objects.get(
name=zip_folder,
project=project,
folder=current_folder,
)
except Folder.DoesNotExist:
current_folder = Folder.objects.create(
name=zip_folder,
project=project,
folder=current_folder,
owner=self.request.user,
)
new_folders.append(current_folder)
# Save file
file_name_nopath = f.filename.split('/')[-1]
unpacked_file = File(
name=file_name_nopath,
project=project,
folder=current_folder,
owner=self.request.user,
secret=build_secret(),
)
content_file = ContentFile(zip_file.read(f.filename))
unpacked_file.file.save(file_name_nopath, content_file)
unpacked_file.save()
new_files.append(unpacked_file)
# Add timeline events
for new_folder in new_folders:
self._add_item_modify_event(obj=new_folder,
request=self.request,
view_action='create')
for new_file in new_files:
self._add_item_modify_event(obj=new_file,
request=self.request,
view_action='create')
if timeline:
timeline.add_event(
project=project,
app_name=APP_NAME,
user=self.request.user,
event_name='archive_extract',
description='Extract from archive "{}", create {} folders '
'and {} files'.format(file.name, len(new_folders),
len(new_files)),
extra_data={
'new_folders': [f.name for f in new_folders],
'new_files': [f.name for f in new_files],
},
status_type='OK',
)
messages.success(
self.request,
'Extracted {} files in folder "{}" from archive "{}"'.format(
len([f for f in zip_file.infolist() if not f.is_dir()]),
folder.name if folder else 'root',
file.name,
),
)
return redirect(redirect_url)
PROJECT_TYPE_PROJECT = SODAR_CONSTANTS['PROJECT_TYPE_PROJECT']
SUBMIT_STATUS_OK = SODAR_CONSTANTS['SUBMIT_STATUS_OK']
SUBMIT_STATUS_PENDING = SODAR_CONSTANTS['SUBMIT_STATUS_PENDING']
SUBMIT_STATUS_PENDING_TASKFLOW = SODAR_CONSTANTS['SUBMIT_STATUS_PENDING']
SITE_MODE_TARGET = SODAR_CONSTANTS['SITE_MODE_TARGET']
SITE_MODE_SOURCE = SODAR_CONSTANTS['SITE_MODE_SOURCE']
# Settings
INVITE_EXPIRY_DAYS = settings.PROJECTROLES_INVITE_EXPIRY_DAYS
# Local constants
SECRET = 'rsd886hi8276nypuvw066sbvv0rb2a6x'
EXAMPLE_APP_NAME = 'example_project_app'
REMOTE_SITE_NAME = 'Test site'
REMOTE_SITE_URL = 'https://sodar.example.org'
REMOTE_SITE_SECRET = build_secret()
REMOTE_SITE_USER_DISPLAY = True
class ProjectMixin:
"""Helper mixin for Project creation"""
@classmethod
def _make_project(
cls,
title,
type,
parent,
description='',
submit_status=SUBMIT_STATUS_OK,
readme=None,
sodar_uuid=None,
def setUp(self):
super().setUp()
app_settings.set_app_setting(APP_NAME,
'allow_public_links',
True,
project=self.project)
self.file_content = bytes('content'.encode('utf-8'))
self.secret_file_owner = build_secret()
self.secret_file_contributor = build_secret()
# Init folders
# Folder created by project owner
self.folder_owner = self._make_folder(
name='folder_owner',
project=self.project,
folder=None,
owner=self.user_owner,
description='',
)
# File created by project contributor
self.folder_contributor = self._make_folder(
name='folder_contributor',
project=self.project,
folder=None,
owner=self.user_contributor,
description='',
)
# Init files
# File uploaded by project owner
self.file_owner = self._make_file(
name='file_owner.txt',
file_name='file_owner.txt',
file_content=self.file_content,
project=self.project,
folder=None,
owner=self.user_owner,
description='',
public_url=True, # NOTE: Public URL OK
secret=self.secret_file_owner,
)
# File uploaded by project contributor
self.file_contributor = self._make_file(
name='file_contributor.txt',
file_name='file_contributor.txt',
file_content=self.file_content,
project=self.project,
folder=None,
owner=self.user_contributor,
description='',
public_url=False, # NOTE: No public URL
secret=self.secret_file_contributor,
)
# Init hyperlinks
# HyperLink added by project owner
self.hyperlink_owner = self._make_hyperlink(
name='Owner link',
url='https://www.bihealth.org/',
project=self.project,
folder=None,
owner=self.user_owner,
description='',
)
# HyperLink added by project contributor
self.hyperlink_contrib = self._make_hyperlink(
name='Contributor link',
url='http://www.google.com/',
project=self.project,
folder=None,
owner=self.user_contributor,
description='',
)
def create(self, validated_data):
instance = super().create(validated_data)
instance.secret = build_secret()
instance.save()
return instance
