def edit(self):
user = self.request.user
form = Form(self.request, schema=AccountEditSchema, obj=user)
if form.validate():
form.bind(user)
if form.data["password_new"]:
user.password = form.data["password_new"]
return HTTPFound(location=self.request.route_url("account_index"))
return dict(form=FormRenderer(form))
def edit(self):
user = self.request.user
form = Form(self.request, schema=AccountEditSchema, obj=user)
if form.validate():
form.bind(user)
if form.data['password_new']:
user.password = form.data['password_new']
return HTTPFound(location=self.request.route_url('account_index'))
return dict(form=FormRenderer(form))
def add_log(self):
form = Form(self.request, schema=SampleLogEntryCreateSchema)
if form.validate():
new_log_entry = form.bind(SampleLogEntry(creator=self.request.user))
self.context.sample.log.append(new_log_entry)
return HTTPFound(
location=self.request.route_url(
'samples_view',
sample_id=self.context.sample.id,
_anchor='log'))
def add_log(self):
form = Form(self.request, schema=SampleLogEntryCreateSchema)
if form.validate():
new_log_entry = form.bind(SampleLogEntry(creator=self.request.user))
self.context.sample.log.append(new_log_entry)
return HTTPFound(
location=self.request.route_url(
'samples_view',
sample_id=self.context.sample.id,
_anchor='log'))
def destroy(self):
form = Form(
self.request,
defaults=dict(reason='Sample destroyed'),
schema=SampleDestroySchema)
if form.validate():
self.context.sample.destroy(self.request.user, form.data['reason'])
return HTTPFound(
location=self.request.route_url(
'samples_view', sample_id=self.context.sample.id))
return dict(form=FormRenderer(form))
def destroy(self):
form = Form(
self.request,
defaults=dict(reason='Sample destroyed'),
schema=SampleDestroySchema)
if form.validate():
self.context.sample.destroy(self.request.user, form.data['reason'])
return HTTPFound(
location=self.request.route_url(
'samples_view', sample_id=self.context.sample.id))
return dict(form=FormRenderer(form))
def login(self):
referer = self.request.url
if referer == self.request.route_url("account_login"):
referer = self.request.route_url("collections_index")
form = Form(self.request, schema=LoginSchema, came_from=referer)
if form.validate():
username = form.data["username"]
password = form.data["password"]
if authenticate(username, password):
return HTTPFound(location=form.came_from, headers=remember(self.request, username))
else:
self.request.session.flash("Invalid login")
return dict(form=FormRenderer(form))
def edit(self):
collection = self.context.collection
form = Form(
self.request,
schema=CollectionEditSchema,
obj=collection,
variable_decode=True)
if form.validate():
form.bind(collection)
# Ensure the edit cannot change ownership by current user
collection.users[self.request.user] = DBSession.query(Role).\
filter(Role.id==OWNER_ROLE).one()
return HTTPFound(location=form.came_from)
return dict(form=FormRenderer(form))
def login(self):
referer = self.request.url
if referer == self.request.route_url('account_login'):
referer = self.request.route_url('collections_index')
form = Form(self.request, schema=LoginSchema, came_from=referer)
if form.validate():
username = form.data['username']
password = form.data['password']
if authenticate(username, password):
return HTTPFound(location=form.came_from,
headers=remember(self.request, username))
else:
self.request.session.flash('Invalid login')
return dict(form=FormRenderer(form))
def edit(self):
sample = self.context.sample
form = Form(
self.request,
schema=SampleEditSchema,
obj=sample,
variable_decode=True)
if form.validate():
# XXX Check for EDIT_COLLECTION on new collection
form.bind(sample)
return HTTPFound(
location=self.request.route_url(
'samples_view', sample_id=sample.id))
return dict(form=FormRenderer(form))
def edit(self):
sample = self.context.sample
form = Form(
self.request,
schema=SampleEditSchema,
obj=sample,
variable_decode=True)
if form.validate():
# XXX Check for EDIT_COLLECTION on new collection
form.bind(sample)
return HTTPFound(
location=self.request.route_url(
'samples_view', sample_id=sample.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 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):
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))
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 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 combine(self):
form = Form(
self.request,
schema=SampleCombineSchema,
variable_decode=True)
if form.validate():
new_sample = Sample.combine(
self.request.user,
form.data['collection'],
form.data['aliquots'])
return HTTPFound(
location=self.request.route_url(
'samples_view', sample_id=new_sample.id))
return dict(
form=FormRenderer(form),
samples=DBSession.query(Sample).\
filter(Sample.collection==self.context.collection).\
filter(Sample.destroyed==None),
)
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 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 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 export(self):
exporter = CollectionCsvExporter(self.context.collection)
form = Form(
self.request,
obj=exporter,
schema=CollectionCsvExportSchema)
if form.validate():
form.bind(exporter)
response = self.request.response
response.content_type = b'text/csv'
response.headers.add(
str('Content-Disposition'),
str('attachment; filename=%s.csv' % slugify(
self.context.collection.name,
default='collection-%d' % self.context.collection.id)))
exporter.export(response.body_file)
return response
return dict(
exporter=exporter,
form=FormRenderer(form))
def view(self):
return dict(
log_form=FormRenderer(Form(self.request, schema=SampleLogEntryCreateSchema)),
attachment_form=FormRenderer(Form(self.request, multipart=True)))
def home(self):
form = Form(self.request,
schema=LoginSchema,
came_from=self.request.route_url('collections_index'))
return dict(form=FormRenderer(form))
