mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-22 01:48:11 +08:00
bmccandless
907cc634f5
This PR contains a refactoring to make adding new features easier. The new features include supporting the tiledb format, and the multi dataset application. The refactoring includes Simplifying the directory structure and files. a class structure to handle annotations (currently one type: AnnotationsLocalFile). a class to handle application configuration a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb. Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface. The multi dataset option is not fully supported yet, and so the option to use it is hidden. Use "cli launch --dataroot ..." To access this feature. All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
98 lines
2.4 KiB
Python
98 lines
2.4 KiB
Python
# -*- coding: utf-8 -*-
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""" rwlock.py
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A class to implement read-write locks on top of the standard threading
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library.
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This is implemented with two mutexes (threading.Lock instances) as per this
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wikipedia pseudocode:
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https://en.wikipedia.org/wiki/Readers%E2%80%93writer_lock#Using_two_mutexes
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Code written by Tyler Neylon at Unbox Research.
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This file is public domain.
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"""
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# _______________________________________________________________________
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# Imports
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from contextlib import contextmanager
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from threading import Lock
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# _______________________________________________________________________
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# Class
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class RWLock(object):
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""" RWLock class; this is meant to allow an object to be read from by
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multiple threads, but only written to by a single thread at a time. See:
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https://en.wikipedia.org/wiki/Readers%E2%80%93writer_lock
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Usage:
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from rwlock import RWLock
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my_obj_rwlock = RWLock()
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# When reading from my_obj:
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with my_obj_rwlock.r_locked():
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do_read_only_things_with(my_obj)
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# When writing to my_obj:
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with my_obj_rwlock.w_locked():
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mutate(my_obj)
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"""
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def __init__(self):
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self.w_lock = Lock()
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self.num_r_lock = Lock()
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self.num_r = 0
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# ___________________________________________________________________
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# Reading methods.
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def r_acquire(self):
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self.num_r_lock.acquire()
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self.num_r += 1
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if self.num_r == 1:
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self.w_lock.acquire()
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self.num_r_lock.release()
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def r_release(self):
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assert self.num_r > 0
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self.num_r_lock.acquire()
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self.num_r -= 1
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if self.num_r == 0:
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self.w_lock.release()
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self.num_r_lock.release()
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@contextmanager
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def r_locked(self):
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""" This method is designed to be used via the `with` statement. """
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try:
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self.r_acquire()
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yield
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finally:
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self.r_release()
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# ___________________________________________________________________
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# Writing methods.
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def w_acquire(self):
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self.w_lock.acquire()
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def w_release(self):
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self.w_lock.release()
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@contextmanager
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def w_locked(self):
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""" This method is designed to be used via the `with` statement. """
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try:
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self.w_acquire()
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yield
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finally:
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self.w_release()
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