def handle_post_reagent(s_id, r_id, client_state, username, body):
'''
Function expects integers sequence id and reagent id.
Function also expects a client state, a string username, and
a string for the body sent with the POST request.
Function calls save client and return then returns the output of the
function called.
'''
# Extract sequence and reagent IDs
sequence_id = int(s_id)
reagent_id = int(r_id)
# Make sure we can edit this sequence
sequence_metadata = db.get_sequence_metadata(sequence_id)
if sequence_metadata["sequencetype"] != "Saved":
raise Exception("Cannot edit sequence")
# Save the reagent
reagent = json.loads(body)
db.update_reagent(
reagent_id,
reagent["name"],
reagent["description"])
# Flag the sequence validation as dirty
db.update_sequence_dirty_flag(sequence_id, True)
# Return the new state
return save_client_state_and_return(client_state, db, username)
def handle_get_state_view(client_state, username):
'''
Handles GET /state for View Sequence
Function expects a client state and a string username.
Function returns the "View Sequence" screen.
'''
server_state = get_server_state(username)
# Do we have a component ID?
if client_state["componentid"] == 0:
# No, the component ID is missing.
# Get the sequence and the ID of the first component
sequence = sequence_manager.GetSequence(username,
client_state["sequenceid"],
False)
client_state["componentid"] = sequence["components"][0]["id"]
# Save client state
db.update_user_client_state(username, client_state)
# Allow editing if this is a saved sequence
sequence_metadata = db.get_sequence_metadata(client_state["sequenceid"])
edit_allowed = (sequence_metadata["sequencetype"] == "Saved")
# Allow running if the system is not in use
run_allowed = (server_state["runstate"]["status"] == "Idle")
# Allow running from here if this is not a cassette
run_here_allowed = False
if run_allowed:
component = sequence_manager.GetComponent(username,
client_state["componentid"],
client_state["sequenceid"])
run_here_allowed = (component["componenttype"] != "CASSETTE")
# Return the state
return {
"buttons": [{
"type": "button",
"id": "SEQUENCER",
"enabled": True
}, {
"type": "button",
"id": "EDITSEQUENCE",
"enabled": edit_allowed
}, {
"type": "button",
"id": "RUNSEQUENCE",
"enabled": run_allowed
}, {
"type": "button",
"id": "RUNSEQUENCEHERE",
"enabled": run_here_allowed
}],
"sequenceid":
client_state["sequenceid"],
"componentid":
client_state["componentid"]
}
def handle_get_state_view(client_state, username):
'''
Handles GET /state for View Sequence
Function expects a client state and a string username.
Function returns the "View Sequence" screen.
'''
server_state = get_server_state(username)
# Do we have a component ID?
if client_state["componentid"] == 0:
# No, the component ID is missing.
# Get the sequence and the ID of the first component
sequence = sequence_manager.GetSequence(
username,
client_state["sequenceid"],
False)
client_state["componentid"] = sequence["components"][0]["id"]
# Save client state
db.update_user_client_state(username, client_state)
# Allow editing if this is a saved sequence
sequence_metadata = db.get_sequence_metadata(
client_state["sequenceid"])
edit_allowed = (sequence_metadata["sequencetype"] == "Saved")
# Allow running if the system is not in use
run_allowed = (server_state["runstate"]["status"] == "Idle")
# Allow running from here if this is not a cassette
run_here_allowed = False
if run_allowed:
component = sequence_manager.GetComponent(username,
client_state["componentid"],
client_state["sequenceid"])
run_here_allowed = (component["componenttype"] != "CASSETTE")
# Return the state
return {"buttons":[{"type":"button",
"id":"SEQUENCER",
"enabled":True},
{"type":"button",
"id":"EDITSEQUENCE",
"enabled":edit_allowed},
{"type":"button",
"id":"RUNSEQUENCE",
"enabled":run_allowed},
{"type":"button",
"id":"RUNSEQUENCEHERE",
"enabled":run_here_allowed}],
"sequenceid":client_state["sequenceid"],
"componentid":client_state["componentid"]}
def handle_post_component(s_id, c_id, unit, client_state, username, body):
'''
Function expects integers sequence id, component id, and insertion id.
Function also expects a client state and a string for the body sent
with the POST request.
Function calls save client and return then returns the output of the
function called.
'''
# Extract sequence and component IDs
current_app.logger.debug("Handle post component.")
sequence_id = int(s_id)
component_id = int(c_id)
insertion_id = unit
# Make sure we can edit this sequence
sequence_metadata = db.get_sequence_metadata(sequence_id)
if sequence_metadata["sequencetype"] != "Saved":
raise Exception("Cannot edit sequence")
# Parse the component JSON if present
component = None
if len(body) != 0:
component = json.loads(body)
# Are we working with an existing component?
if component_id != 0:
# Yes, so update the existing component
sequence_manager.UpdateComponent(
username, int(sequence_id),
int(component_id),
int(insertion_id),
component)
else:
# No, so add a new component
component_id = sequence_manager.AddComponent(
username, int(sequence_id),
int(insertion_id),
component)
# Update the client to show the new component
client_state["componentid"] = component_id
# Return the new state
return save_client_state_and_return(
client_state, username)
def reagent_post_index(s_id, r_id):
'''
Function shall handle all POST .../reagent/<reagent_id>
web requests.
Function expects integers sequence id and reagent id to
be passed in as parameters.
Function returns the output of save client state and
return.
The function obtains the data of the body sent with
the POST request and updates the reagent on the database
before calling save client state and return.
'''
# Get objects
auth = request.authorization
username = str(auth.username)
server_state = get_server_state(username)
client_state = getCurrentClientState(username)
# Get POST object
body = request.data
current_app.logger.debug("Body sent: " + str(body))
# Make sure we can edit this sequence
sequence_metadata = db.get_sequence_metadata(int(s_id))
if sequence_metadata["sequencetype"] != "Saved":
raise Exception("Cannot edit sequence")
# Save the reagent
reagent = json.loads(body)
db.update_reagent(
int(r_id),
reagent["name"],
reagent["description"])
# Flag the sequence validation as dirty
db.update_sequence_dirty_flag(int(s_id), True)
# Return the new state
return save_client_state_and_return(
client_state, username)
def component_post_index(s_id, c_id, unit=None):
'''
This function handles all POST for components from the
client.
Function expects an integer sequence_id, an integer component_id,
and an optional parameter, insertion id.
Function shall return the output of save client and return.
Based on the body sent with the POST request, this function
shall use sequence_manager to update the component passed in.
'''
auth = request.authorization
username = str(auth.username)
server_state = get_server_state(username)
client_state = getCurrentClientState(username)
# Get POST object
body = request.data
insertion_id = None
if unit != None:
insertion_id = int(unit)
current_app.logger.debug('POST /sequence/s_id/component/c_id' +
"\nRequest: " + str(request) + \
"\nBody recieved: " + str(body) + \
"\nInsertion ID: " + str(insertion_id))
sequence_metdata = db.get_sequence_metadata(int(s_id))
if sequence_metdata['sequencetype'] != 'Saved':
raise Exception("Cannot edit sequence!")
component = None
if len(body) != 0:
component = json.loads(body)
if int(c_id) != 0:
current_app.logger.debug("Updating component")
# Check if insertion_id is none
if insertion_id != None:
sequence_manager.UpdateComponent(
username, int(s_id), int(c_id),
int(insertion_id), component)
else:
sequence_manager.UpdateComponent(
username, int(s_id), int(c_id),
None, component)
else:
# Check if insertion_id is None
if insertion_id != None:
c_id = sequence_manager.AddComponent(
username, int(s_id),
int(insertion_id), component)
current_app.logger.debug("Adding component: " + \
str(c_id))
client_state["componentid"] = c_id
else :
c_id = sequence_manager.AddComponent(
username, int(s_id),
None, component)
current_app.logger.debug("Adding component: " + \
str(c_id))
client_state["componentid"] = c_id
return save_client_state_and_return(
client_state, username)