def __init__(self, collection):
self.collection = collection
self.delimiter = self._delimiter_map[csv.excel.delimiter]
self.lineterminator = self._lineterminator_map[
csv.excel.lineterminator]
self.quotechar = self._quotechar_map[csv.excel.quotechar]
self.quoting = self._quoting_map[csv.excel.quoting]
self.doublequote = csv.excel.doublequote
self.dateformat = '%Y-%m-%d'
self.all_columns = [
('id', 'Identifier'),
('description', 'Description'),
('created', 'Created'),
('destroyed', 'Destroyed'),
('location', 'Location'),
# XXX Figure out a reasonable cross-database way of including this
# (SQLite supports GROUP_CONCAT, PostgreSQL has a string_agg but
# only in 9+, or we could use Python expressions if we don't care
# about efficieny...)
#('parents' , 'Parents') ,
#('children' , 'Children') ,
]
self.all_columns.extend(
DBSession.query('code_' + SampleCode.name, SampleCode.name).\
join(Sample).\
join(Collection).\
filter(Collection.id==collection.id).\
distinct().all())
self.columns = [name for (name, title) in self.all_columns]
self.all_columns = dict(self.all_columns)
def __init__(self, collection):
self.collection = collection
self.delimiter = self._delimiter_map[csv.excel.delimiter]
self.lineterminator = self._lineterminator_map[csv.excel.lineterminator]
self.quotechar = self._quotechar_map[csv.excel.quotechar]
self.quoting = self._quoting_map[csv.excel.quoting]
self.doublequote = csv.excel.doublequote
self.dateformat = '%Y-%m-%d'
self.all_columns = [
('id' , 'Identifier') ,
('description' , 'Description') ,
('created' , 'Created') ,
('destroyed' , 'Destroyed') ,
('location' , 'Location') ,
# XXX Figure out a reasonable cross-database way of including this
# (SQLite supports GROUP_CONCAT, PostgreSQL has a string_agg but
# only in 9+, or we could use Python expressions if we don't care
# about efficieny...)
#('parents' , 'Parents') ,
#('children' , 'Children') ,
]
self.all_columns.extend(
DBSession.query('code_' + SampleCode.name, SampleCode.name).\
join(Sample).\
join(Collection).\
filter(Collection.id==collection.id).\
distinct().all())
self.columns = [name for (name, title) in self.all_columns]
self.all_columns = dict(self.all_columns)
def __init__(self, request):
super(CollectionContextFactory, self).__init__(request)
self.collection = DBSession.query(Collection).\
filter_by(id=request.matchdict['collection_id']).one()
# If the collection has an open-license grant view permission to anyone
if self.collection.license.is_open:
self.__acl__.append((Allow, Everyone, (VIEW_COLLECTION, )))
def __init__(self, request):
super(CollectionContextFactory, self).__init__(request)
self.collection = DBSession.query(Collection).\
filter_by(id=request.matchdict['collection_id']).one()
# If the collection has an open-license grant view permission to anyone
if self.collection.license.is_open:
self.__acl__.append(
(Allow, Everyone, (VIEW_COLLECTION,))
)
def open(self):
return dict(
title='Open Collections',
# XXX Perform the open filter with a query
collections=[
collection for collection in DBSession.query(Collection)
if collection.license.is_open
]
)
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 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 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 export(self, output_file):
"""
Export the collection to the specified file.
`output_file` : a file-like object which the CSV will be written to
"""
columns = []
aliases = []
for column in self.columns:
if column.startswith('code_'):
alias = aliased(SampleCode)
aliases.append((alias, column[len('code_'):]))
columns.append(getattr(alias, 'value'))
elif column in ('parents', 'children'):
raise NotImplementedError
else:
columns.append(Sample.__table__.columns[column])
query = DBSession.query(*columns).select_from(Sample).\
filter(Sample.collection_id==self.collection.id)
for alias, name in aliases:
query = query.\
outerjoin(alias,
(Sample.id==getattr(alias, 'sample_id')) &
(getattr(alias, 'name')==name)
)
writer = csv.writer(
output_file,
delimiter=self._delimiter_inv[self.delimiter],
lineterminator=self._lineterminator_inv[self.lineterminator],
quotechar=self._quotechar_inv[self.quotechar],
quoting=self._quoting_inv[self.quoting],
doublequote=self.doublequote)
for row in query:
# Rewrite the format of datetime values to exclude microseconds
# (which confuse several spreadsheet parsers and which it's
# unlikely anyone cares about)
row = [
value.strftime(self.dateformat)
if isinstance(value, datetime) else value for value in row
]
writer.writerow(row)
def export(self, output_file):
"""
Export the collection to the specified file.
`output_file` : a file-like object which the CSV will be written to
"""
columns = []
aliases = []
for column in self.columns:
if column.startswith('code_'):
alias = aliased(SampleCode)
aliases.append((alias, column[len('code_'):]))
columns.append(getattr(alias, 'value'))
elif column in ('parents', 'children'):
raise NotImplementedError
else:
columns.append(Sample.__table__.columns[column])
query = DBSession.query(*columns).select_from(Sample).\
filter(Sample.collection_id==self.collection.id)
for alias, name in aliases:
query = query.\
outerjoin(alias,
(Sample.id==getattr(alias, 'sample_id')) &
(getattr(alias, 'name')==name)
)
writer = csv.writer(output_file,
delimiter=self._delimiter_inv[self.delimiter],
lineterminator=self._lineterminator_inv[self.lineterminator],
quotechar=self._quotechar_inv[self.quotechar],
quoting=self._quoting_inv[self.quoting],
doublequote=self.doublequote)
for row in query:
# Rewrite the format of datetime values to exclude microseconds
# (which confuse several spreadsheet parsers and which it's
# unlikely anyone cares about)
row = [
value.strftime(self.dateformat)
if isinstance(value, datetime) else value
for value in row
]
writer.writerow(row)
def roles(self):
return [
(role.id, role.id.title())
for role in DBSession.query(Role)
]
def open_collections(self):
return [
collection
for collection in DBSession.query(Collection).all()
if collection.license.is_open
]
