def config_index():
"""
Function shall expect no parameters.
Function shall return a config object as a JSON object.
Function shall query the database and obtain the config
object from the db.
"""
# Handle GET /configuration
current_app.logger.debug(str(request))
auth = request.authorization
user = db.get_user(auth.username)
config = {"type": "configuration"}
config.update(db.get_configuration())
config.update({"supportedoperations": db.get_supported_operations()})
current_app.logger.debug(str(config))
return jsonify(config)
def config_index():
'''
Function shall expect no parameters.
Function shall return a config object as a JSON object.
Function shall query the database and obtain the config
object from the db.
'''
# Handle GET /configuration
current_app.logger.debug(str(request))
auth = request.authorization
user = db.get_user(auth.username)
config = {"type": "configuration"}
config.update(db.get_configuration())
config.update({"supportedoperations": db.get_supported_operations()})
current_app.logger.debug(str(config))
return jsonify(config)
def runstate_index():
'''
Function shall handle GET ../runstate.
Function expects no paramaters to be passed in.
Function shall return the state as a JSON object.
This state will contain components from the client
state and the server state.
'''
# Handle GET /runstate request
# Get the user information and server state
current_app.logger.debug(str(request))
auth = request.authorization
user = db.get_user(str(auth.username))
server_state = core_server.GetServerState(user)
client_state = getCurrentClientState(auth.username)
# Start the state object
return_state = {
"type": "state",
"user": user,
"serverstate": server_state,
"clientstate": copy.deepcopy(client_state),
"timestamp": time.time()
}
# Complete with either the run or home states
if server_state["runstate"]["running"]:
return_state.update(
handle_get_state_run(client_state, str(auth.username)))
return_state["clientstate"]["screen"] = "RUN"
else:
return_state.update(
handle_get_state_run(client_state, str(auth.username)))
return_state["clientstate"]["screen"] = "HOME"
return_state["clientstate"]["prompt"]["show"] = False
# Return the state
return jsonify(return_state)
def runstate_index():
"""
Function shall handle GET ../runstate.
Function expects no paramaters to be passed in.
Function shall return the state as a JSON object.
This state will contain components from the client
state and the server state.
"""
# Handle GET /runstate request
# Get the user information and server state
current_app.logger.debug(str(request))
auth = request.authorization
user = db.get_user(str(auth.username))
server_state = core_server.GetServerState(user)
client_state = getCurrentClientState(auth.username)
# Start the state object
return_state = {
"type": "state",
"user": user,
"serverstate": server_state,
"clientstate": copy.deepcopy(client_state),
"timestamp": time.time(),
}
# Complete with either the run or home states
if server_state["runstate"]["running"]:
return_state.update(handle_get_state_run(client_state, str(auth.username)))
return_state["clientstate"]["screen"] = "RUN"
else:
return_state.update(handle_get_state_run(client_state, str(auth.username)))
return_state["clientstate"]["screen"] = "HOME"
return_state["clientstate"]["prompt"]["show"] = False
# Return the state
return jsonify(return_state)
def reagent_index(sequence_id, reagent_ids):
"""
Function expects a sequence id and a reagent id(s) that
is passed in from the web request.
Function returns a reagent(s) object as a JSON object.
This function takes all reagent ids passed in
(seperated by a dot -in the form of .../reagent/1.2.5.6).
For each reagent id, this funcion shall obtain the reagent
information and return all the information as a whole.
"""
current_app.logger.debug(str(request))
auth = request.authorization
user = db.get_user(auth.username)
# Split each reagent id based on a '.'
reagent_ids = str(reagent_ids).split(".")
# Create and return the reagent array
reagents = {}
reagents["type"] = "reagents"
reagents["reagents"] = []
for reagent_id in reagent_ids:
reagents["reagents"].append(sequence_manager.GetReagent(user, int(reagent_id)))
return jsonify(reagents)
def reagent_index(sequence_id, reagent_ids):
'''
Function expects a sequence id and a reagent id(s) that
is passed in from the web request.
Function returns a reagent(s) object as a JSON object.
This function takes all reagent ids passed in
(seperated by a dot -in the form of .../reagent/1.2.5.6).
For each reagent id, this funcion shall obtain the reagent
information and return all the information as a whole.
'''
current_app.logger.debug(str(request))
auth = request.authorization
user = db.get_user(auth.username)
# Split each reagent id based on a '.'
reagent_ids = str(reagent_ids).split(".")
# Create and return the reagent array
reagents = {}
reagents["type"] = "reagents"
reagents["reagents"] = []
for reagent_id in reagent_ids:
reagents["reagents"].append(
sequence_manager.GetReagent(user, int(reagent_id)))
return jsonify(reagents)
def state_index(self=None):
'''
This function requires authentication prior to executing.
Function takes in no parameters.
Function shall direct the client based on the client's
current screen.
Function returns the state to the client as a JSON object.
'''
auth = request.authorization
user = db.get_user(str(auth.username))
server_state = get_server_state(str(auth.username))
client_state = getCurrentClientState(str(auth.username))
current_app.logger.debug(str(request) + "\nClientstate: " + \
str(client_state) + "\nServerstate: " + str(server_state))
# Is the remote user the one that is currently running the system?
if str(auth.username) == server_state["runstate"]["username"]:
# Yes, so make sure the user is on the run screen
if client_state["screen"] != "RUN":
# Update the client state
client_state["screen"] = "RUN"
db.update_user_client_state(str(auth.username), client_state)
return_state = {
"type": "state",
"user": user,
"serverstate": server_state,
"clientstate": client_state,
"timestamp": time.time()
}
# Check which screen is active
choice = str(client_state["screen"])
current_app.logger.debug("Request for state" +
"\nREQUEST: " + str(request) + \
"\nClient state: " + str(client_state) + \
"\nServer state: " + str(server_state))
#current_app.logger.debug("Client State: "+ str(client_state) + \
# "\nChoice from client_state[screen]: " +str(choice))
if choice == "HOME":
return_state.update(handle_get_state_home(auth.username))
elif choice == "SELECT_SAVEDSEQUENCES":
return_state.update(
handle_get_state_select_savedsequences(client_state,
auth.username))
elif choice == "SELECT_RUNHISTORY":
return_state.update(
handle_get_state_select_runhistory(client_state,
auth.username))
elif choice == "VIEW":
return_state.update(
handle_get_state_view(client_state, auth.username))
elif choice == "EDIT":
return_state.update(
handle_get_state_edit(client_state, auth.username))
elif choice == "RUN":
return_state.update(
handle_get_state_run(client_state, auth.username))
else:
current_app.logger.debug("Unknown screen: %s" % str(choice))
raise Exception("Unknown screen: %s" % str(choice))
#current_app.logger.debug("Return state: " + str(return_state))
return jsonify(return_state)
def state_index(self=None):
"""
This function requires authentication prior to executing.
Function takes in no parameters.
Function shall direct the client based on the client's
current screen.
Function returns the state to the client as a JSON object.
"""
auth = request.authorization
user = db.get_user(str(auth.username))
server_state = get_server_state(str(auth.username))
client_state = getCurrentClientState(str(auth.username))
current_app.logger.debug(
str(request) + "\nClientstate: " + str(client_state) + "\nServerstate: " + str(server_state)
)
# Is the remote user the one that is currently running the system?
if str(auth.username) == server_state["runstate"]["username"]:
# Yes, so make sure the user is on the run screen
if client_state["screen"] != "RUN":
# Update the client state
client_state["screen"] = "RUN"
db.update_user_client_state(str(auth.username), client_state)
return_state = {
"type": "state",
"user": user,
"serverstate": server_state,
"clientstate": client_state,
"timestamp": time.time(),
}
# Check which screen is active
choice = str(client_state["screen"])
current_app.logger.debug(
"Request for state"
+ "\nREQUEST: "
+ str(request)
+ "\nClient state: "
+ str(client_state)
+ "\nServer state: "
+ str(server_state)
)
# current_app.logger.debug("Client State: "+ str(client_state) + \
# "\nChoice from client_state[screen]: " +str(choice))
if choice == "HOME":
return_state.update(handle_get_state_home(auth.username))
elif choice == "SELECT_SAVEDSEQUENCES":
return_state.update(handle_get_state_select_savedsequences(client_state, auth.username))
elif choice == "SELECT_RUNHISTORY":
return_state.update(handle_get_state_select_runhistory(client_state, auth.username))
elif choice == "VIEW":
return_state.update(handle_get_state_view(client_state, auth.username))
elif choice == "EDIT":
return_state.update(handle_get_state_edit(client_state, auth.username))
elif choice == "RUN":
return_state.update(handle_get_state_run(client_state, auth.username))
else:
current_app.logger.debug("Unknown screen: %s" % str(choice))
raise Exception("Unknown screen: %s" % str(choice))
# current_app.logger.debug("Return state: " + str(return_state))
return jsonify(return_state)