def verify_email(self):
email = self.request.params["email"]
verification = EmailVerification(email)
DBSession.add(verification)
DBSession.flush()
user = verification.email.user
mailer = self.request.registry["mailer"]
message = Message(
recipients=[email],
subject="%s email verification" % self.request.registry.settings["site_title"],
body=render_template(
"../templates/account/verify_email.txt", view=self, request=self.request, verification=verification
),
)
mailer.send(message)
return dict(verification=verification)
def create(self):
# TODO Determine user timezone as default
form = Form(self.request, schema=AccountCreateSchema)
if form.validate():
new_user = form.bind(User())
DBSession.add(new_user)
new_email = form.bind(EmailAddress())
new_email.user = new_user
DBSession.add(new_email)
new_collection = Collection()
new_collection.name = 'Default'
new_collection.owner = new_user.full_name
owner_role = DBSession.query(Role).filter(Role.id == 'owner').one()
new_user.collections[new_collection] = owner_role
return HTTPFound(location=self.request.route_url(
'account_verify_email', _query=dict(email=form.data['email'])))
return dict(form=FormRenderer(form))
def create(self):
form = Form(
self.request,
schema=CollectionCreateSchema,
variable_decode=True,
defaults=dict(owner=self.request.user.full_name))
if form.validate():
new_collection = form.bind(Collection())
# Hard-code ownership to currently authenticated user
new_collection.users[self.request.user] = DBSession.query(Role).\
filter(Role.id==OWNER_ROLE).one()
DBSession.add(new_collection)
DBSession.flush()
return HTTPFound(
location=self.request.route_url(
'collections_view', collection_id=new_collection.id))
return dict(form=FormRenderer(form))
def create(self):
# TODO Determine user timezone as default
form = Form(self.request, schema=AccountCreateSchema)
if form.validate():
new_user = form.bind(User())
DBSession.add(new_user)
new_email = form.bind(EmailAddress())
new_email.user = new_user
DBSession.add(new_email)
new_collection = Collection()
new_collection.name = "Default"
new_collection.owner = new_user.full_name
owner_role = DBSession.query(Role).filter(Role.id == "owner").one()
new_user.collections[new_collection] = owner_role
return HTTPFound(
location=self.request.route_url("account_verify_email", _query=dict(email=form.data["email"]))
)
return dict(form=FormRenderer(form))
def verify_email(self):
email = self.request.params['email']
verification = EmailVerification(email)
DBSession.add(verification)
DBSession.flush()
user = verification.email.user
mailer = self.request.registry['mailer']
message = Message(
recipients=[email],
subject='%s email verification' %
self.request.registry.settings['site_title'],
body=render(renderer_name='../templates/account/verify_email.txt',
value=dict(view=self,
request=self.request,
verification=verification),
request=self.request))
mailer.send(message)
return dict(verification=verification)
def split(self):
sample = self.context.sample
form = Form(
self.request,
schema=SampleSplitSchema,
obj=sample,
defaults=dict(aliquots=2),
variable_decode=True)
if form.validate():
# XXX Check for EDIT_COLLECTION on new collection
aliquots = sample.split(
self.request.user, form.data['collection'],
form.data['aliquots'], form.data['aliquant'],
location=form.data['location'])
for aliquot in aliquots:
DBSession.add(aliquot)
return HTTPFound(
location=self.request.route_url(
'samples_view', sample_id=sample.id))
return dict(form=FormRenderer(form))
def verify_email(self):
email = self.request.params['email']
verification = EmailVerification(email)
DBSession.add(verification)
DBSession.flush()
user = verification.email.user
mailer = self.request.registry['mailer']
message = Message(
recipients=[email],
subject='%s email verification' % self.request.registry.settings['site_title'],
body=render(
renderer_name='../templates/account/verify_email.txt',
value=dict(
view=self,
request=self.request,
verification=verification
),
request=self.request))
mailer.send(message)
return dict(verification=verification)
def split(self):
sample = self.context.sample
form = Form(
self.request,
schema=SampleSplitSchema,
obj=sample,
defaults=dict(aliquots=2),
variable_decode=True)
if form.validate():
# XXX Check for EDIT_COLLECTION on new collection
aliquots = sample.split(
self.request.user, form.data['collection'],
form.data['aliquots'], form.data['aliquant'],
location=form.data['location'])
for aliquot in aliquots:
DBSession.add(aliquot)
return HTTPFound(
location=self.request.route_url(
'samples_view', sample_id=sample.id))
return dict(form=FormRenderer(form))
def create(self):
form = Form(
self.request,
schema=SampleCreateSchema,
variable_decode=True,
multipart=True)
if form.validate():
# XXX Check for EDIT_COLLECTION on selected collection
# XXX Should be using form collection below
new_sample = form.bind(
Sample.create(self.request.user, self.context.collection))
DBSession.add(new_sample)
DBSession.flush() # to generate sample.id
for storage in self.request.POST.getall('attachments'):
if storage:
new_sample.attachments.create(storage.filename, storage.file)
return HTTPFound(
location=self.request.route_url(
'samples_view', sample_id=new_sample.id))
return dict(form=FormRenderer(form))
def init_instances():
with transaction.manager:
admins_group = Group(
id=ADMINS_GROUP, description='Group of administrators')
unlimited_limit = UserLimit(
id='unlimited', collections_limit=1000000, samples_limit=1000000,
templates_limit=1000000, storage_limit=50000 * 1000000)
commercial_limit = UserLimit(
id='commercial', collections_limit=1000, samples_limit=10000,
templates_limit=10, storage_limit=10000 * 1000000)
academic_limit = UserLimit(
id='academic', collections_limit=10, samples_limit=250,
templates_limit=5, storage_limit=100 * 1000000,
email_pattern=r'.*\.(edu|ac\.[a-z][a-z])$')
free_limit = UserLimit(
id='free', collections_limit=3, samples_limit=50,
templates_limit=2, storage_limit=1 * 1000000)
admin_user = User(
salutation='', given_name='Administrator', surname='',
limits_id='unlimited')
admin_email = EmailAddress(
email='*****@*****.**', verified=datetime.utcnow())
admin_collection = Collection(name='Default', owner='Administrator')
owner_role = Role(
id=OWNER_ROLE,
description='Owner and administrator of the collection')
editor_role = Role(
id=EDITOR_ROLE,
description='Can add and remove samples from a collection, but '
'cannot administer members of the collection')
auditor_role = Role(
id=AUDITOR_ROLE,
description='Can audit samples within the collection but cannot '
'manipulate the collection')
viewer_role = Role(
id=VIEWER_ROLE,
description='Can view samples within the collection but cannot '
'manipulate the collection')
DBSession.add(admins_group)
DBSession.add(unlimited_limit)
DBSession.add(commercial_limit)
DBSession.add(academic_limit)
DBSession.add(free_limit)
DBSession.add(admin_user)
DBSession.add(admin_email)
DBSession.add(admin_collection)
DBSession.add(owner_role)
DBSession.add(editor_role)
DBSession.add(auditor_role)
DBSession.add(viewer_role)
admins_group.users.append(admin_user)
admin_user.emails.append(admin_email)
admin_user.password = '******'
admin_user.collections[admin_collection] = owner_role
def init_instances():
with transaction.manager:
admins_group = Group(id=ADMINS_GROUP,
description='Group of administrators')
unlimited_limit = UserLimit(id='unlimited',
collections_limit=1000000,
samples_limit=1000000,
templates_limit=1000000,
storage_limit=50000 * 1000000)
commercial_limit = UserLimit(id='commercial',
collections_limit=1000,
samples_limit=10000,
templates_limit=10,
storage_limit=10000 * 1000000)
academic_limit = UserLimit(id='academic',
collections_limit=10,
samples_limit=250,
templates_limit=5,
storage_limit=100 * 1000000,
email_pattern=r'.*\.(edu|ac\.[a-z][a-z])$')
free_limit = UserLimit(id='free',
collections_limit=3,
samples_limit=50,
templates_limit=2,
storage_limit=1 * 1000000)
admin_user = User(salutation='',
given_name='Administrator',
surname='',
limits_id='unlimited')
admin_email = EmailAddress(email='*****@*****.**',
verified=datetime.utcnow())
admin_collection = Collection(name='Default', owner='Administrator')
owner_role = Role(
id=OWNER_ROLE,
description='Owner and administrator of the collection')
editor_role = Role(
id=EDITOR_ROLE,
description='Can add and remove samples from a collection, but '
'cannot administer members of the collection')
auditor_role = Role(
id=AUDITOR_ROLE,
description='Can audit samples within the collection but cannot '
'manipulate the collection')
viewer_role = Role(
id=VIEWER_ROLE,
description='Can view samples within the collection but cannot '
'manipulate the collection')
DBSession.add(admins_group)
DBSession.add(unlimited_limit)
DBSession.add(commercial_limit)
DBSession.add(academic_limit)
DBSession.add(free_limit)
DBSession.add(admin_user)
DBSession.add(admin_email)
DBSession.add(admin_collection)
DBSession.add(owner_role)
DBSession.add(editor_role)
DBSession.add(auditor_role)
DBSession.add(viewer_role)
admins_group.users.append(admin_user)
admin_user.emails.append(admin_email)
admin_user.password = '******'
admin_user.collections[admin_collection] = owner_role
