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78.68

/datajoint/autopopulate.py

"""This module defines class dj.AutoPopulate"""
import logging
import datetime
import traceback
import random
import inspect
from tqdm import tqdm
from .expression import QueryExpression, AndList
from .errors import DataJointError, LostConnectionError
import signal
import multiprocessing as mp

# noinspection PyExceptionInherit,PyCallingNonCallable

logger = logging.getLogger(__name__)


# --- helper functions for multiprocessing --


def _initialize_populate(table, jobs, populate_kwargs):
    """
    Initialize the process for mulitprocessing.
    Saves the unpickled copy of the table to the current process and reconnects.
    """
    process = mp.current_process()
    process.table = table
    process.jobs = jobs
    process.populate_kwargs = populate_kwargs
    table.connection.connect()  # reconnect


def _call_populate1(key):
    """
    Call current process' table._populate1()
    :key - a dict specifying job to compute
    :return: key, error if error, otherwise None
    """
    process = mp.current_process()
    return process.table._populate1(key, process.jobs, **process.populate_kwargs)


class AutoPopulate:
    """
    AutoPopulate is a mixin class that adds the method populate() to a Relation class.
    Auto-populated relations must inherit from both Relation and AutoPopulate,
    must define the property `key_source`, and must define the callback method `make`.
    """

    _key_source = None
    _allow_insert = False

    @property
    def key_source(self):
        """
        :return: the query expression that yields primary key values to be passed,
        sequentially, to the ``make`` method when populate() is called.
        The default value is the join of the parent tables references from the primary key.
        Subclasses may override they key_source to change the scope or the granularity
        of the make calls.
        """

        def _rename_attributes(table, props):
            return (
                table.proj(
                    **{
                        attr: ref
                        for attr, ref in props["attr_map"].items()
                        if attr != ref
                    }
                )
                if props["aliased"]
                else table.proj()
            )

        if self._key_source is None:
            parents = self.target.parents(
                primary=True, as_objects=True, foreign_key_info=True
            )
            if not parents:
                raise DataJointError(
                    "A table must have dependencies "
                    "from its primary key for auto-populate to work"
                )
            self._key_source = _rename_attributes(*parents[0])
            for q in parents[1:]:
                self._key_source *= _rename_attributes(*q)
        return self._key_source

    def make(self, key):
        """
        Derived classes must implement method `make` that fetches data from tables
        above them in the dependency hierarchy, restricting by the given key,
        computes secondary attributes, and inserts the new tuples into self.
        """
        raise NotImplementedError(
            "Subclasses of AutoPopulate must implement the method `make`"
        )

    @property
    def target(self):
        """
        :return: table to be populated.
        In the typical case, dj.AutoPopulate is mixed into a dj.Table class by
        inheritance and the target is self.
        """
        return self

    def _job_key(self, key):
        """
        :param key:  they key returned for the job from the key source
        :return: the dict to use to generate the job reservation hash
        This method allows subclasses to control the job reservation granularity.
        """
        return key

    def _jobs_to_do(self, restrictions):
        """
        :return: the relation containing the keys to be computed (derived from self.key_source)
        """
        if self.restriction:
            raise DataJointError(
                "Cannot call populate on a restricted table. "
                "Instead, pass conditions to populate() as arguments."
            )
        todo = self.key_source

        # key_source is a QueryExpression subclass -- trigger instantiation
        if inspect.isclass(todo) and issubclass(todo, QueryExpression):
            todo = todo()

        if not isinstance(todo, QueryExpression):
            raise DataJointError("Invalid key_source value")

        try:
            # check if target lacks any attributes from the primary key of key_source
            raise DataJointError(
                "The populate target lacks attribute %s "
                "from the primary key of key_source"
                % next(
                    name
                    for name in todo.heading.primary_key
                    if name not in self.target.heading
                )
            )
        except StopIteration:
            pass
        return (todo & AndList(restrictions)).proj()

    def populate(
        self,
        *restrictions,
        suppress_errors=False,
        return_exception_objects=False,
        reserve_jobs=False,
        order="original",
        limit=None,
        max_calls=None,
        display_progress=False,
        processes=1,
        make_kwargs=None
    ):
        """
        ``table.populate()`` calls ``table.make(key)`` for every primary key in
        ``self.key_source`` for which there is not already a tuple in table.

        :param restrictions: a list of restrictions each restrict
            (table.key_source - target.proj())
        :param suppress_errors: if True, do not terminate execution.
        :param return_exception_objects: return error objects instead of just error messages
        :param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion
        :param order: "original"|"reverse"|"random"  - the order of execution
        :param limit: if not None, check at most this many keys
        :param max_calls: if not None, populate at most this many keys
        :param display_progress: if True, report progress_bar
        :param processes: number of processes to use. Set to None to use all cores
        :param make_kwargs: Keyword arguments which do not affect the result of computation
            to be passed down to each ``make()`` call. Computation arguments should be
            specified within the pipeline e.g. using a `dj.Lookup` table.
        :type make_kwargs: dict, optional
        """
        if self.connection.in_transaction:
            raise DataJointError("Populate cannot be called during a transaction.")

        valid_order = ["original", "reverse", "random"]
        if order not in valid_order:
            raise DataJointError(
                "The order argument must be one of %s" % str(valid_order)
            )
        jobs = (
            self.connection.schemas[self.target.database].jobs if reserve_jobs else None
        )

        # define and set up signal handler for SIGTERM:
        if reserve_jobs:

            def handler(signum, frame):
                logger.info("Populate terminated by SIGTERM")
                raise SystemExit("SIGTERM received")

            old_handler = signal.signal(signal.SIGTERM, handler)

        keys = (self._jobs_to_do(restrictions) - self.target).fetch("KEY", limit=limit)
        if order == "reverse":
            keys.reverse()
        elif order == "random":
            random.shuffle(keys)

        logger.info("Found %d keys to populate" % len(keys))

        keys = keys[:max_calls]
        nkeys = len(keys)
        if not nkeys:
            return

        if processes > 1:
            processes = min(processes, nkeys, mp.cpu_count())

        error_list = []
        populate_kwargs = dict(
            suppress_errors=suppress_errors,
            return_exception_objects=return_exception_objects,
            make_kwargs=make_kwargs,
        )

        if processes == 1:
            for key in (
                tqdm(keys, desc=self.__class__.__name__) if display_progress else keys
            ):
                error = self._populate1(key, jobs, **populate_kwargs)
                if error is not None:
                    error_list.append(error)
        else:
            # spawn multiple processes
            self.connection.close()  # disconnect parent process from MySQL server
            del self.connection._conn.ctx  # SSLContext is not pickleable
            with mp.Pool(
                processes, _initialize_populate, (self, jobs, populate_kwargs)
            ) as pool:
                if display_progress:
                    with tqdm(desc="Processes: ", total=nkeys) as pbar:
                        for error in pool.imap(_call_populate1, keys, chunksize=1):
                            if error is not None:
                                error_list.append(error)
                            pbar.update()
                else:
                    for error in pool.imap(_call_populate1, keys):
                        if error is not None:
                            error_list.append(error)
            self.connection.connect()  # reconnect parent process to MySQL server

        # restore original signal handler:
        if reserve_jobs:
            signal.signal(signal.SIGTERM, old_handler)

        if suppress_errors:
            return error_list

    def _populate1(
        self, key, jobs, suppress_errors, return_exception_objects, make_kwargs=None
    ):
        """
        populates table for one source key, calling self.make inside a transaction.
        :param jobs: the jobs table or None if not reserve_jobs
        :param key: dict specifying job to populate
        :param suppress_errors: bool if errors should be suppressed and returned
        :param return_exception_objects: if True, errors must be returned as objects
        :return: (key, error) when suppress_errors=True, otherwise None
        """
        make = self._make_tuples if hasattr(self, "_make_tuples") else self.make

        if jobs is None or jobs.reserve(self.target.table_name, self._job_key(key)):
            self.connection.start_transaction()
            if key in self.target:  # already populated
                self.connection.cancel_transaction()
                if jobs is not None:
                    jobs.complete(self.target.table_name, self._job_key(key))
            else:
                logger.info("Populating: " + str(key))
                self.__class__._allow_insert = True
                try:
                    make(dict(key), **(make_kwargs or {}))
                except (KeyboardInterrupt, SystemExit, Exception) as error:
                    try:
                        self.connection.cancel_transaction()
                    except LostConnectionError:
                        pass
                    error_message = "{exception}{msg}".format(
                        exception=error.__class__.__name__,
                        msg=": " + str(error) if str(error) else "",
                    )
                    if jobs is not None:
                        # show error name and error message (if any)
                        jobs.error(
                            self.target.table_name,
                            self._job_key(key),
                            error_message=error_message,
                            error_stack=traceback.format_exc(),
                        )
                    if not suppress_errors or isinstance(error, SystemExit):
                        raise
                    else:
                        logger.error(error)
                        return key, error if return_exception_objects else error_message
                else:
                    self.connection.commit_transaction()
                    if jobs is not None:
                        jobs.complete(self.target.table_name, self._job_key(key))
                finally:
                    self.__class__._allow_insert = False

    def progress(self, *restrictions, display=True):
        """
        Report the progress of populating the table.
        :return: (remaining, total) -- numbers of tuples to be populated
        """
        todo = self._jobs_to_do(restrictions)
        total = len(todo)
        remaining = len(todo - self.target)
        if display:
            print(
                "%-20s" % self.__class__.__name__,
                "Completed %d of %d (%2.1f%%)   %s"
                % (
                    total - remaining,
                    total,
                    100 - 100 * remaining / (total + 1e-12),
                    datetime.datetime.strftime(
                        datetime.datetime.now(), "%Y-%m-%d %H:%M:%S"
                    ),
                ),
                flush=True,
            )
        return remaining, total

1	"""This module defines class dj.AutoPopulate"""
2	import logging	1✔
3	import datetime	1✔
4	import traceback	1✔
5	import random	1✔
6	import inspect	1✔
7	from tqdm import tqdm	1✔
8	from .expression import QueryExpression, AndList	1✔
9	from .errors import DataJointError, LostConnectionError	1✔
10	import signal	1✔
11	import multiprocessing as mp	1✔
12
13	# noinspection PyExceptionInherit,PyCallingNonCallable
14
15	logger = logging.getLogger(__name__)	1✔
16
17
18	# --- helper functions for multiprocessing --
19
20
21	def _initialize_populate(table, jobs, populate_kwargs):	1✔
22	"""
23	Initialize the process for mulitprocessing.
24	Saves the unpickled copy of the table to the current process and reconnects.
25	"""
26	process = mp.current_process()	×
27	process.table = table	×
28	process.jobs = jobs	×
29	process.populate_kwargs = populate_kwargs	×
30	table.connection.connect() # reconnect	×
31
32
33	def _call_populate1(key):	1✔
34	"""
35	Call current process' table._populate1()
36	:key - a dict specifying job to compute
37	:return: key, error if error, otherwise None
38	"""
39	process = mp.current_process()	×
40	return process.table._populate1(key, process.jobs, **process.populate_kwargs)	×
41
42
43	class AutoPopulate:	1✔
44	"""
45	AutoPopulate is a mixin class that adds the method populate() to a Relation class.
46	Auto-populated relations must inherit from both Relation and AutoPopulate,
47	must define the property `key_source`, and must define the callback method `make`.
48	"""
49
50	_key_source = None	1✔
51	_allow_insert = False	1✔
52
53	@property	1✔
54	def key_source(self):
55	"""
56	:return: the query expression that yields primary key values to be passed,
57	sequentially, to the ``make`` method when populate() is called.
58	The default value is the join of the parent tables references from the primary key.
59	Subclasses may override they key_source to change the scope or the granularity
60	of the make calls.
61	"""
62
63	def _rename_attributes(table, props):	1✔
64	return (	1✔
65	table.proj(
66	**{
67	attr: ref
68	for attr, ref in props["attr_map"].items()
69	if attr != ref
70	}
71	)
72	if props["aliased"]
73	else table.proj()
74	)
75
76	if self._key_source is None:	1✔
77	parents = self.target.parents(	1✔
78	primary=True, as_objects=True, foreign_key_info=True
79	)
80	if not parents:	1✔
81	raise DataJointError(	×
82	"A table must have dependencies "
83	"from its primary key for auto-populate to work"
84	)
85	self._key_source = _rename_attributes(*parents[0])	1✔
86	for q in parents[1:]:	1✔
87	self._key_source = _rename_attributes(q)	1✔
88	return self._key_source	1✔
89
90	def make(self, key):	1✔
91	"""
92	Derived classes must implement method `make` that fetches data from tables
93	above them in the dependency hierarchy, restricting by the given key,
94	computes secondary attributes, and inserts the new tuples into self.
95	"""
96	raise NotImplementedError(	×
97	"Subclasses of AutoPopulate must implement the method `make`"
98	)
99
100	@property	1✔
101	def target(self):
102	"""
103	:return: table to be populated.
104	In the typical case, dj.AutoPopulate is mixed into a dj.Table class by
105	inheritance and the target is self.
106	"""
107	return self	1✔
108
109	def _job_key(self, key):	1✔
110	"""
111	:param key: they key returned for the job from the key source
112	:return: the dict to use to generate the job reservation hash
113	This method allows subclasses to control the job reservation granularity.
114	"""
115	return key	1✔
116
117	def _jobs_to_do(self, restrictions):	1✔
118	"""
119	:return: the relation containing the keys to be computed (derived from self.key_source)
120	"""
121	if self.restriction:	1✔
122	raise DataJointError(	×
123	"Cannot call populate on a restricted table. "
124	"Instead, pass conditions to populate() as arguments."
125	)
126	todo = self.key_source	1✔
127
128	# key_source is a QueryExpression subclass -- trigger instantiation
129	if inspect.isclass(todo) and issubclass(todo, QueryExpression):	1✔
130	todo = todo()	1✔
131
132	if not isinstance(todo, QueryExpression):	1✔
133	raise DataJointError("Invalid key_source value")	×
134
135	try:	1✔
136	# check if target lacks any attributes from the primary key of key_source
137	raise DataJointError(	1✔
138	"The populate target lacks attribute %s "
139	"from the primary key of key_source"
140	% next(
141	name
142	for name in todo.heading.primary_key
143	if name not in self.target.heading
144	)
145	)
146	except StopIteration:	1✔
147	pass	1✔
148	return (todo & AndList(restrictions)).proj()	1✔
149
150	def populate(	1✔
151	self,
152	*restrictions,
153	suppress_errors=False,
154	return_exception_objects=False,
155	reserve_jobs=False,
156	order="original",
157	limit=None,
158	max_calls=None,
159	display_progress=False,
160	processes=1,
161	make_kwargs=None
162	):
163	"""
164	``table.populate()`` calls ``table.make(key)`` for every primary key in
165	``self.key_source`` for which there is not already a tuple in table.
166
167	:param restrictions: a list of restrictions each restrict
168	(table.key_source - target.proj())
169	:param suppress_errors: if True, do not terminate execution.
170	:param return_exception_objects: return error objects instead of just error messages
171	:param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion
172	:param order: "original"\|"reverse"\|"random" - the order of execution
173	:param limit: if not None, check at most this many keys
174	:param max_calls: if not None, populate at most this many keys
175	:param display_progress: if True, report progress_bar
176	:param processes: number of processes to use. Set to None to use all cores
177	:param make_kwargs: Keyword arguments which do not affect the result of computation
178	to be passed down to each ``make()`` call. Computation arguments should be
179	specified within the pipeline e.g. using a `dj.Lookup` table.
180	:type make_kwargs: dict, optional
181	"""
182	if self.connection.in_transaction:	1✔
183	raise DataJointError("Populate cannot be called during a transaction.")	×
184
185	valid_order = ["original", "reverse", "random"]	1✔
186	if order not in valid_order:	1✔
187	raise DataJointError(	×
188	"The order argument must be one of %s" % str(valid_order)
189	)
190	jobs = (	1✔
191	self.connection.schemas[self.target.database].jobs if reserve_jobs else None
192	)
193
194	# define and set up signal handler for SIGTERM:
195	if reserve_jobs:	1✔
196
197	def handler(signum, frame):	1✔
198	logger.info("Populate terminated by SIGTERM")	×
199	raise SystemExit("SIGTERM received")	×
200
201	old_handler = signal.signal(signal.SIGTERM, handler)	1✔
202
203	keys = (self._jobs_to_do(restrictions) - self.target).fetch("KEY", limit=limit)	1✔
204	if order == "reverse":	1✔
205	keys.reverse()	×
206	elif order == "random":	1✔
207	random.shuffle(keys)	×
208
209	logger.info("Found %d keys to populate" % len(keys))	1✔
210
211	keys = keys[:max_calls]	1✔
212	nkeys = len(keys)	1✔
213	if not nkeys:	1✔
214	return	1✔
215
216	if processes > 1:	1✔
217	processes = min(processes, nkeys, mp.cpu_count())	1✔
218
219	error_list = []	1✔
220	populate_kwargs = dict(	1✔
221	suppress_errors=suppress_errors,
222	return_exception_objects=return_exception_objects,
223	make_kwargs=make_kwargs,
224	)
225
226	if processes == 1:	1✔
227	for key in (	1✔
228	tqdm(keys, desc=self.__class__.__name__) if display_progress else keys
229	):
230	error = self._populate1(key, jobs, **populate_kwargs)	1✔
231	if error is not None:	1✔
232	error_list.append(error)	1✔
233	else:
234	# spawn multiple processes
235	self.connection.close() # disconnect parent process from MySQL server	1✔
236	del self.connection._conn.ctx # SSLContext is not pickleable	1✔
237	with mp.Pool(	1✔
238	processes, _initialize_populate, (self, jobs, populate_kwargs)
239	) as pool:
240	if display_progress:	1✔
241	with tqdm(desc="Processes: ", total=nkeys) as pbar:	×
242	for error in pool.imap(_call_populate1, keys, chunksize=1):	×
243	if error is not None:	×
244	error_list.append(error)	×
245	pbar.update()	×
246	else:
247	for error in pool.imap(_call_populate1, keys):	1✔
248	if error is not None:	1✔
249	error_list.append(error)	×
250	self.connection.connect() # reconnect parent process to MySQL server	1✔
251
252	# restore original signal handler:
253	if reserve_jobs:	1✔
254	signal.signal(signal.SIGTERM, old_handler)	1✔
255
256	if suppress_errors:	1✔
257	return error_list	1✔
258
259	def _populate1(	1✔
260	self, key, jobs, suppress_errors, return_exception_objects, make_kwargs=None
261	):
262	"""
263	populates table for one source key, calling self.make inside a transaction.
264	:param jobs: the jobs table or None if not reserve_jobs
265	:param key: dict specifying job to populate
266	:param suppress_errors: bool if errors should be suppressed and returned
267	:param return_exception_objects: if True, errors must be returned as objects
268	:return: (key, error) when suppress_errors=True, otherwise None
269	"""
270	make = self._make_tuples if hasattr(self, "_make_tuples") else self.make	1✔
271
272	if jobs is None or jobs.reserve(self.target.table_name, self._job_key(key)):	1✔
273	self.connection.start_transaction()	1✔
274	if key in self.target: # already populated	1✔
275	self.connection.cancel_transaction()	×
276	if jobs is not None:	×
277	jobs.complete(self.target.table_name, self._job_key(key))	×
278	else:
279	logger.info("Populating: " + str(key))	1✔
280	self.__class__._allow_insert = True	1✔
281	try:	1✔
282	make(dict(key), **(make_kwargs or {}))	1✔
283	except (KeyboardInterrupt, SystemExit, Exception) as error:	1✔
284	try:	1✔
285	self.connection.cancel_transaction()	1✔
286	except LostConnectionError:	×
287	pass	×
288	error_message = "{exception}{msg}".format(	1✔
289	exception=error.__class__.__name__,
290	msg=": " + str(error) if str(error) else "",
291	)
292	if jobs is not None:	1✔
293	# show error name and error message (if any)
294	jobs.error(	1✔
295	self.target.table_name,
296	self._job_key(key),
297	error_message=error_message,
298	error_stack=traceback.format_exc(),
299	)
300	if not suppress_errors or isinstance(error, SystemExit):	1✔
301	raise	1✔
302	else:
303	logger.error(error)	1✔
304	return key, error if return_exception_objects else error_message	1✔
305	else:
306	self.connection.commit_transaction()	1✔
307	if jobs is not None:	1✔
308	jobs.complete(self.target.table_name, self._job_key(key))	×
309	finally:
310	self.__class__._allow_insert = False	1✔
311
312	def progress(self, *restrictions, display=True):	1✔
313	"""
314	Report the progress of populating the table.
315	:return: (remaining, total) -- numbers of tuples to be populated
316	"""
317	todo = self._jobs_to_do(restrictions)	1✔
318	total = len(todo)	1✔
319	remaining = len(todo - self.target)	1✔
320	if display:	1✔
321	print(	1✔
322	"%-20s" % self.__class__.__name__,
323	"Completed %d of %d (%2.1f%%) %s"
324	% (
325	total - remaining,
326	total,
327	100 - 100 * remaining / (total + 1e-12),
328	datetime.datetime.strftime(
329	datetime.datetime.now(), "%Y-%m-%d %H:%M:%S"
330	),
331	),
332	flush=True,
333	)
334	return remaining, total	1✔

datajoint / datajoint-python / #12217

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