def update_sequence_details(sequence):
# Update the first component id and
# component count of the sequence's fields
# Query for the first component matched
comp = session.query(Component).filter_by(
SequenceID = sequence.SequenceID).first()
sequence.first_component = comp
sequence.Valid = True
session.commit()
def create_sequence(user_id):
# Create a new sequence for the user
new_seq = Sequence()
new_seq.Name = 'Sequence 1'
new_seq.Component = 'Test Sequence'
new_seq.Type = 'Saved'
new_seq.UserID = user_id
session.add(new_seq)
session.commit()
return new_seq
def update_sequence_details(sequence):
# Update the first component id and
# component count of the sequence's fields
# Query for the first component matched
component_id = session.query(Component).filter_by(
SequenceID = sequence.SequenceID).first().ComponentID
sequence.FirstComponentID = component_id
sequence.ComponentCount = 3
sequence.Valid = 1
session.commit()
def create_reagents(cassettes):
# Let's create some empty reagents
# For each of the 3 cassettes, create
# 12 reagents
for cassette in cassettes:
for reg_count in range(1,13):
reagent = Reagent()
reagent.Position = reg_count
reagent.component = cassette
session.add(reagent)
session.commit()
def create_sequence(user):
# Create a new sequence for the user
new_seq = Sequence()
new_seq.Name = 'Sequence 1'
new_seq.Component = 'Test Sequence'
new_seq.Type = 'Saved'
new_seq.user = user
session.add(new_seq)
session.commit()
user.selected_sequence = new_seq
session.commit()
return new_seq
def update_component_details(cassettes):
# Update the details field of each new
# cassette component
# Keep a reactor count
reactor_count = 1
for cassette in cassettes:
cassette.Details = json.dumps(
get_default_component_state(
cassette,
reactor_count))
session.commit()
reactor_count += 1
def create_reagents(sequence_id, cassettes):
# Let's create some empty reagents
# For each of the 3 cassettes, create
# 12 reagents
for cassette in cassettes:
for reg_count in range(1,13):
reagent = Reagents()
reagent.SequenceID = sequence_id
reagent.Position = reg_count
reagent.component = cassette
reagent.ComponentID = cassette.ComponentID
session.add(reagent)
session.commit()
def create_cassette_components(sequence):
# Create a new set of component cassettes
cass_list = []
for cass_count in range(1,4):
new_comp = Component()
new_comp.sequence = sequence
new_comp.Type = 'CASSETTE'
new_comp.Note = ''
# Leave details empty, update later
new_comp.Details = ''
session.add(new_comp)
session.commit()
cass_list.append(new_comp)
return cass_list
def create_user(role):
# Let's create a default user
# Encrypt the password using md5 and reutrn as hex
new_user = User()
new_user.Username = '******'
new_user.Password = hashlib.md5('devel').hexdigest()
new_user.FirstName = 'Sofiebio'
new_user.LastName = 'Developer'
new_user.Email = '*****@*****.**'
new_user.role = role
new_user.ClientState = json.dumps(
get_default_user_client_state())
session.add(new_user)
session.commit()
return new_user
def update_component_details(cassettes):
# Update the details field of each new
# cassette component
# Keep a reactor count
reactor_count = 1
previous_cassette = None
for cassette in cassettes:
cassette.Details = json.dumps(
get_default_component_state(
cassette,
reactor_count))
session.commit()
reactor_count += 1
if not previous_cassette is None:
cassette.previous_component = previous_cassette
session.commit()
previous_cassette.next_component = cassette
session.commit()
previous_cassette = cassette
def create_role():
# Create admin role
role = Role('Administrator', 255)
session.add(role)
session.commit()
return role