Python neo4j bolt driver loses connection after context switch - python-3.x

I have a backend written in django which uses the neo4j bolt driver to communicate with the neo4j graph db.
I use a Singleton to handle the connection and the bolt driver closes the connection, whenever I access it from another location than where the connection was initially established (e.g. I open the connection in a view, access it in a signal and when I try to save in the view the connection is lost).
I’ve tried to extract the main problem I have come up with and break it down to a small piece of example code below.
I would appreciate any explanation of behavior to or even better a solution ;)
from neo4j.v1 import Driver, GraphDatabase, basic_auth, Session, Transaction
def main():
gm = GraphMapper()
gm.begin_atomic_transaction()
print(f"graph connection closed before method? {gm.is_connection_closed()}") # -> false
fill_transaction() #the context switch
print(f"graph connection closed after method? {gm.is_connection_closed()}") # -> true
if not gm.is_connection_closed():
print(f"graph connection open - try to commit") # -> is never called
gm.commit_atomic_transaction_and_close_session()
def fill_transaction():
gm = GraphMapper()
print(f"graph connection closed in method? {gm.is_connection_closed()}") # -> true
gm.create_update_node("TestNode")
class GraphMapper:
__instance = None
__transaction = None # type: Transaction
__session = None # type: Session
__connection = None # type: Connection
__driver = None # type: Driver
def __new__(cls, *args, **kwargs):
if not isinstance(cls.__instance, cls):
cls.__instance = object.__new__(cls, *args, **kwargs)
return cls.__instance
def __init__(self):
self.__driver = GraphDatabase.driver("bolt://localhost:7687", auth=basic_auth("neo4j", "password"))
def is_connection_closed(self):
return self.__transaction.session._connection._closed
def begin_atomic_transaction(self):
self.__session = self.__driver.session()
self.__transaction = self.__session.begin_transaction()
self.__connection = self.__transaction.session._connection
return self.__transaction
def commit_atomic_transaction_and_close_session(self):
result = self.__transaction.commit()
self.__transaction = None
return result
def create_update_node(self, label):
# Add Cypher statement to transaction
Implementation details: I have a wrapper object "GraphMapper" which encapsulates the connection, session, and transaction of the driver. and is designed as a singleton instance. A transaction is established at a point (A, e.g. a view) but I cannot complete the transaction here. I need to add additional values from location (B, e.g. a post-save signal). However, I cannot pass a reference to the "GraphMapper" A to B. Thus, I came up with the singleton implementation as explained above.
I have ensured that the singleton is exact the same instance on all locations (within one request). But at the moment I exit the context (package, class or method) through a method call and retrieve the "GraphMapper" instance at the very next location, the connection is closed. I even checked the reference count to the "GraphMapper" and its connection and the garbage collector should not delete it. Seldom it says the connection is not closed. But writing to the graph results in a connection refused error.
P.S.: I know there is some useless and unnecessary code, this is for illustrative purposes only and I wanted to make sure that the garbage collector did not kill some objects.

Related

Python multiprocess: run several instances of a class, keep all child processes in memory

First, I'd like to thank the StackOverflow community for the tremendous help it provided me over the years, without me having to ask a single question.
I could not find anything that I can relate to my problem, though it is probably due to my lack of understanding of the subject, rather than the absence of a response on the website. My apologies in advance if this is a duplicate.
I am relatively new to multiprocess; some time ago I succeeded in using multiprocessing.pools in a very simple way, where I didn't need any feedback between the child processes.
Now I am facing a much more complicated problem, and I am just lost in the documentation about multiprocessing. I hence ask for you help, your kindness and your patience.
I am trying to build a parallel tempering monte-carlo algorithm, from a class.
The basic class very roughly goes as follows:
import numpy as np
class monte_carlo:
def __init__(self):
self.x=np.ones((1000,3))
self.E=np.mean(self.x)
self.Elist=[]
def simulation(self,temperature):
self.T=temperature
for i in range(3000):
self.MC_step()
if i%10==0:
self.Elist.append(self.E)
return
def MC_step(self):
x=self.x.copy()
k = np.random.randint(1000)
x[k] = (x[k] + np.random.uniform(-1,1,3))
temp_E=np.mean(self.x)
if np.random.random()<np.exp((self.E-temp_E)/self.T):
self.E=temp_E
self.x=x
return
Obviously, I simplified a great deal (actual class is 500 lines long!), and built fake functions for simplicity: __init__ takes a bunch of parameters as arguments, there are many more lists of measurement else than self.Elist, and also many arrays derived from self.X that I use to compute them. The key point is that each instance of the class contains a lot of informations that I want to keep in memory, and that I don't want to copy over and over again, to avoid dramatic slowing down. Else I would just use the multiprocessing.pool module.
Now, the parallelization I want to do, in pseudo-code:
def proba(dE,pT):
return np.exp(-dE/pT)
Tlist=[1.1,1.2,1.3]
N=len(Tlist)
G=[]
for _ in range(N):
G.append(monte_carlo())
for _ in range(5):
for i in range(N): # this loop should be ran in multiprocess
G[i].simulation(Tlist[i])
for i in range(N//2):
dE=G[i].E-G[i+1].E
pT=G[i].T + G[i+1].T
p=proba(dE,pT) # (proba is a function, giving a probability depending on dE)
if np.random.random() < p:
T_temp = G[i].T
G[i].T = G[i+1].T
G[i+1].T = T_temp
Synthesis: I want to run several instances of my monte-carlo class in parallel child processes, with different values for a parameter T, then periodically pause everything to change the different T's, and run again the child processes/class instances, from where they paused.
Doing this, I want each class-instance/child-process to stay independent from one another, save its current state with all internal variables while it is paused, and do as few copies as possible. This last point is critical, as the arrays inside the class are quite big (some are 1000x1000), and a copy will therefore very quickly become quite time-costly.
Thanks in advance, and sorry if I am not clear...
Edit:
I am using a distant machine with many (64) CPUs, running on Debian GNU/Linux 10 (buster).
Edit2:
I made a mistake in my original post: in the end, the temperatures must be exchanged between the class-instances, and not inside the global Tlist.
Edit3: Charchit answer works perfectly for the test code, on both my personal machine and the distant machine I am usually using for running my codes. I hence check this as the accepted answer.
However, I want to report here that, inserting the actual, more complicated code, instead of the oversimplified monte_carlo class, the distant machine gives me some strange errors:
Unable to init server: Could not connect: Connection refused
(CMC_temper_all.py:55509): Gtk-WARNING **: ##:##:##:###: Locale not supported by C library.
Using the fallback 'C' locale.
Unable to init server: Could not connect: Connection refused
(CMC_temper_all.py:55509): Gdk-CRITICAL **: ##:##:##:###:
gdk_cursor_new_for_display: assertion 'GDK_IS_DISPLAY (display)' failed
(CMC_temper_all.py:55509): Gdk-CRITICAL **: ##:##:##:###: gdk_cursor_new_for_display: assertion 'GDK_IS_DISPLAY (display)' failed
The "##:##:##:###" are (or seems like) IP adresses.
Without the call to set_start_method('spawn') this error shows only once, in the very beginning, while when I use this method, it seems to show at every occurrence of result.get()...
The strangest thing is that the code seems otherwise to work fine, does not crash, produces the datafiles I then ask it to, etc...
I think this would deserve to publish a new question, but I put it here nonetheless in case someone has a quick answer.
If not, I will resort to add one by one the variables, methods, etc... that are present in my actual code but not in the test example, to try and find the origin of the bug. My best guess for now is that the memory space required by each child-process with the actual code, is too large for the distant machine to accept it, due to some restrictions implemented by the admin.
What you are looking for is sharing state between processes. As per the documentation, you can either create shared memory, which is restrictive about the data it can store and is not thread-safe, but offers better speed and performance; or you can use server processes through managers. The latter is what we are going to use since you want to share whole objects of user-defined datatypes. Keep in mind that using managers will impact speed of your code depending on the complexity of the arguments that you pass and receive, to and from the managed objects.
Managers, proxies and pickling
As mentioned, managers create server processes to store objects, and allow access to them through proxies. I have answered a question with better details on how they work, and how to create a suitable proxy here. We are going to use the same proxy defined in the linked answer, with some variations. Namely, I have replaced the factory functions inside the __getattr__ to something that can be pickled using pickle. This means that you can run instance methods of managed objects created with this proxy without resorting to using multiprocess. The result is this modified proxy:
from multiprocessing.managers import NamespaceProxy, BaseManager
import types
import numpy as np
class A:
def __init__(self, name, method):
self.name = name
self.method = method
def get(self, *args, **kwargs):
return self.method(self.name, args, kwargs)
class ObjProxy(NamespaceProxy):
"""Returns a proxy instance for any user defined data-type. The proxy instance will have the namespace and
functions of the data-type (except private/protected callables/attributes). Furthermore, the proxy will be
pickable and can its state can be shared among different processes. """
def __getattr__(self, name):
result = super().__getattr__(name)
if isinstance(result, types.MethodType):
return A(name, self._callmethod).get
return result
Solution
Now we only need to make sure that when we are creating objects of monte_carlo, we do so using managers and the above proxy. For that, we create a class constructor called create. All objects for monte_carlo should be created with this function. With that, the final code looks like this:
from multiprocessing import Pool
from multiprocessing.managers import NamespaceProxy, BaseManager
import types
import numpy as np
class A:
def __init__(self, name, method):
self.name = name
self.method = method
def get(self, *args, **kwargs):
return self.method(self.name, args, kwargs)
class ObjProxy(NamespaceProxy):
"""Returns a proxy instance for any user defined data-type. The proxy instance will have the namespace and
functions of the data-type (except private/protected callables/attributes). Furthermore, the proxy will be
pickable and can its state can be shared among different processes. """
def __getattr__(self, name):
result = super().__getattr__(name)
if isinstance(result, types.MethodType):
return A(name, self._callmethod).get
return result
class monte_carlo:
def __init__(self, ):
self.x = np.ones((1000, 3))
self.E = np.mean(self.x)
self.Elist = []
self.T = None
def simulation(self, temperature):
self.T = temperature
for i in range(3000):
self.MC_step()
if i % 10 == 0:
self.Elist.append(self.E)
return
def MC_step(self):
x = self.x.copy()
k = np.random.randint(1000)
x[k] = (x[k] + np.random.uniform(-1, 1, 3))
temp_E = np.mean(self.x)
if np.random.random() < np.exp((self.E - temp_E) / self.T):
self.E = temp_E
self.x = x
return
#classmethod
def create(cls, *args, **kwargs):
# Register class
class_str = cls.__name__
BaseManager.register(class_str, cls, ObjProxy, exposed=tuple(dir(cls)))
# Start a manager process
manager = BaseManager()
manager.start()
# Create and return this proxy instance. Using this proxy allows sharing of state between processes.
inst = eval("manager.{}(*args, **kwargs)".format(class_str))
return inst
def proba(dE,pT):
return np.exp(-dE/pT)
if __name__ == "__main__":
Tlist = [1.1, 1.2, 1.3]
N = len(Tlist)
G = []
# Create our managed instances
for _ in range(N):
G.append(monte_carlo.create())
for _ in range(5):
# Run simulations in the manager server
results = []
with Pool(8) as pool:
for i in range(N): # this loop should be ran in multiprocess
results.append(pool.apply_async(G[i].simulation, (Tlist[i], )))
# Wait for the simulations to complete
for result in results:
result.get()
for i in range(N // 2):
dE = G[i].E - G[i + 1].E
pT = G[i].T + G[i + 1].T
p = proba(dE, pT) # (proba is a function, giving a probability depending on dE)
if np.random.random() < p:
T_temp = Tlist[i]
Tlist[i] = Tlist[i + 1]
Tlist[i + 1] = T_temp
print(Tlist)
This meets the criteria you wanted. It does not create any copies at all, rather, all arguments to the simulation method call are serialized inside the pool and sent to the manager server where the object is actually stored. It gets executed there, and the results (if any) are serialized and returned in the main process. All of this, with only using the builtins!
Output
[1.2, 1.1, 1.3]
Edit
Since you are using Linux, I encourage you to use multiprocessing.set_start_method inside the if __name__ ... clause to set the start method to "spawn". Doing this will ensure that the child processes do not have access to variables defined inside the clause.

How to invoke methods on the same singleton object in Python?

from __future__ import annotations
import cx_Oracle as oracle
class Connection(oracle.Connection):
__connection = None
#classmethod
def create(cls) -> Connection:
"""Returns a singleton cx_Oracle.Connection object."""
if not cls.__connection:
cls.__connection = oracle.connect(
user="xxx",
password="xxx",
dsn="xxx",
mode=oracle.SYSDBA
)
return cls.__connection
I want to use a singleton database connection object in my project to avoid creating a connection more than one. In this example oracle.connection method returns the instance of the parent class.(which is cx_Oracle.Connection)
My question is how can i return Connection instance (which is the class i created) instead of cx_Oracle.Connection class. Because I want to invoke some methods on my singleton object like;
connection = Connection.create()
connection.execute()
Only my Connection class will have execute method, not the parent class.
This may sound obvious but in order to return an instance, you must first create one - and you don't. So do that and return it:
#classmethod
def create(cls) -> Connection:
""" Sets up a database connection if needed and returns
a new Connection instance.
"""
if not cls.__connection:
cls.__connection = oracle.connect(
user="xxx",
password="xxx",
dsn="xxx",
mode=oracle.SYSDBA
)
instance = Connection()
return instance
Just make sure these instances use the class property __connection whenever they query the database.

How to implement "relationship" caching system in a similar query?

I noticed that when having a Model such as :
class User(Model):
id = ...
books = relationship('Book')
When calling user.books for the first time, SQLAlchemy query the database (when lazy='select' for instance, which is the default), but sub-sequent call to user.books don't call the database. The results seems to have been cached.
I'd like to have the same feature from SQLAlchemy when using a method that query, for instance:
class User:
def get_books(self):
return Book.query.filter(Book.user_id == self.id).all()
But when doing that, if I call 3 times get_books(), SQLAlchemy does call the database 3 times (when setting the ECHO property to True).
How can I change get_books() to use the caching system from SQLAlchemy ?
I insist to mention "from SQLAlchemy" because I believe they handle the refresh/expunge/flush system and changes are then re-queried to the DB if one of these happened. Opposed to if I were to simply create a caching property in the model with a simple:
def get_books(self):
if self._books is None:
self._books = Book.query.filter(Book.user_id == self.id).all()
return self._books
This does not work well with flush/refresh/expunge from SQLAlchemy.
So, How can I change get_books() to use the caching system from SQLAlchemy ?
Edit 1:
I realized that the solution provided under is not perfect, because it caches for the current object. If you have two instances of the same user, and call get_books on both, two queries will be made because the caching applies only on the instance, not globally, contrary to SQLAlchemy.
The reason is simple - I believe - but still unclear how to apply it in my case: The object is defined at the class level, not the instance (books = relationship()), and they build their own query internally, so they can cache it based on the query.
In the solution I gave, the memoize_getter is unaware of the query made, and as such, cannot cache it for the same value accros multiple instance, so any identical call made to another instance will query the database.
Original answer:
I've been trying to wrap my head around SQLAlchemy's code (wow that's dense!), and I think I figured it out!
A relationship, at least when being set as "lazy='select'" (default), is a InstrumentedAttribute, which contains a get function that does the following :
def __get__(self, instance, owner):
if instance is None:
return self
dict_ = instance_dict(instance)
if self._supports_population and self.key in dict_:
return dict_[self.key]
else:
try:
state = instance_state(instance)
except AttributeError as err:
util.raise_(
orm_exc.UnmappedInstanceError(instance),
replace_context=err,
)
return self.impl.get(state, dict_)
So, a basic caching system, respecting SQLAlchemy, would be something like:
from sqlalchemy.orm.base import instance_dict
def get_books(self):
dict_ = instance_dict(self)
if 'books' not in dict_:
dict_['books'] = Book.query.filter(Book.user_id == self.id).all()
return dict_['books']
Now, we can push the vice a bit further, and do ... a decorator (oh sweet):
def memoize_getter(f):
#functools.wraps(f)
def decorator(instance, *args, **kwargs):
property_name = f.__name__.replace('get_', '')
dict_ = instance_dict(instance)
if property_name not in dict_:
dict_[property_name] = f(instance, *args, **kwargs)
return dict_[property_name]
return decorator
Thus transforming the original method to :
class User:
#memoize_getter
def get_books(self):
return Book.query.filter(Book.user_id == self.id).all()
If someone has a better solution, I'm eagerly interested!

flask-sqlalchemy - how to obtain a request-independent db session

I am looking at the best (and correct way) to obtain a request-independent db session.
The problem is the following: I am building a web application that has to access the database. The endpoint exposed accepts a request, performs the first work, then create a thread (that will perform the hard work), starts it, and replies to the client with a unique id for the "job". Meanwhile the thread goes on with its work (and it has to access the database) and the client can perform polling to check the status. I am not using dedicated framework to perform this background job, but only a simple thread. I can only have one single background thread going on at any time, for this reason I am maintaining the state in a singleton.
The application is created with the application factory design https://flask.palletsprojects.com/en/1.1.x/patterns/appfactories/
I am using Gunicorn as WSGI server and sqlite as database.
The basic structure of the code is the following (I am removing the business logic and imports, but the concept remain):
api_jobs.py
#bp.route('/jobs', methods=['POST'])
def create_job():
data = request.get_json(force=True) or {}
name = data['name']
job_controller = JobController() # This is a singleton
job_process = job_controller.start_job(name)
job_process_dict = job_process.to_dict()
return jsonify(job_process_dict)
controller.py
class Singleton(type):
_instances = {}
def __call__(cls, *args, **kwargs):
if cls not in cls._instances:
cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs)
return cls._instances[cls]
class JobController(object):
__metaclass__ = Singleton
def __init__(self):
self.job_thread = None
def start_job(self, name):
if self.job_thread is not None:
job_id = self.job_thread.job_id
job_process = JobProcess.query.get(job_id)
if job_process.status != 'end':
raise ValueError('A job process is already ongoing!')
else:
self.job_thread = None
job_process = JobProcess(name)
db.session.add(job_process)
db.session.commit() # At this step I create the ID
self.job_thread = JobThread(db.session, job_process.id)
self.job_thread.start()
return job_process
class JobThread(threading.Thread):
def __init__(self, db_session, job_id):
self.job_id = job_id
self.db_session = db_session
self.session = self.db_session()
def run(self):
self.job_process = self.session.query(JobProcess).get(self.job_id)
self.job_process.status = 'working'
self.session.commit()
i = 0
while True:
sleep(1)
print('working hard')
i = i +1
if i > 10:
break
self.job_process.status = 'end'
self.session.commit()
self.db_session.remove()
models.py
class JobProcess(db.Model):
id = db.Column(db.Integer, primary_key=True)
status = db.Column(db.String(64))
name = db.Column(db.String(64))
def to_dict(self):
data = {
'id': self.id,
'status': self.status,
'name': self.name,
}
return data
From my understanding, calling self.session = self.db_session() is actually doing nothing (due to the fact that sqlalchemy is using a registry, that is also a proxy, if I am not wrong), however that was the best attempt that I found to create a "new/detached/useful" session.
I checked out https://docs.sqlalchemy.org/en/13/orm/contextual.html#using-thread-local-scope-with-web-applications in order to obtain a request-independent db-session, however even using the suggested method of creating a new session factory (sessionmaker + scoped_session), does not work.
The errors that I obtain, with slight changes to the code, are multiple, in this configuration the error is
DetachedInstanceError: Instance <JobProcess at 0x7f875f81c350> is not bound to a Session; attribute refresh operation cannot proceed (Background on this error at: http://sqlalche.me/e/bhk3)
The basic question remains: Is it possible to create a session that will live inside the thread and that I will take care of creating/tearing down?
The reason that you are encountering the DetachedInstanceError is that you are attempting to pass the session from your main thread to your job thread. Sqlalchemy is using thread local storage to manage the sessions and thus a single session cannot be shared between two threads. You just need to create a new session in the run method of your job thread.

Proper way to start a Trio server that manages multiple TCP Connections

I recently finished a project using a mix of Django and Twisted and realized it's overkill for what I need which is basically just a way for my servers to communicate via TCP sockets. I turned to Trio and so far I'm liking what I see as it's way more direct (for what I need). That said though, I just wanted to be sure I was doing this the right way.
I followed the tutorial which taught the basics but I need a server that could handle multiple clients at once. To this end, I came up with the following code
import trio
from itertools import count
PORT = 12345
BUFSIZE = 16384
CONNECTION_COUNTER = count()
class ServerProtocol:
def __init__(self, server_stream):
self.ident = next(CONNECTION_COUNTER)
self.stream = server_stream
async def listen(self):
while True:
data = await self.stream.receive_some(BUFSIZE)
if data:
print('{} Received\t {}'.format(self.ident, data))
# Process data here
class Server:
def __init__(self):
self.protocols = []
async def receive_connection(self, server_stream):
sp: ServerProtocol = ServerProtocol(server_stream)
self.protocols.append(sp)
await sp.listen()
async def main():
await trio.serve_tcp(Server().receive_connection, PORT)
trio.run(main)
My issue here seems to be that each ServerProtocol runs listen on every cycle instead of waiting for data to be available to be received.
I get the feeling I'm using Trio wrong in which case, is there a Trio best practices that I'm missing?
Your overall structure looks fine to me. The issue that jumps out at me is:
while True:
data = await self.stream.receive_some(BUFSIZE)
if data:
print('{} Received\t {}'.format(self.ident, data))
# Process data here
The guarantee that receive_some makes is: if the other side has closed the connection already, then it immediately returns an empty byte-string. Otherwise, it waits until there is some data to return, and then returns it as a non-empty byte-string.
So your code should work fine... until the other end closes the connection. Then it starts doing an infinite loop, where it keeps checking for data, getting an empty byte-string back (data = b""), so the if data: ... block doesn't run, and it immediately loops around to do it again.
One way to fix this would be (last 3 lines are new):
while True:
data = await self.stream.receive_some(BUFSIZE)
if data:
print('{} Received\t {}'.format(self.ident, data))
# Process data here
else:
# Other side has gone away
break

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