#12586

pending completion

Build # #12586

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

<a href="https://github.com/datajoint/datajoint-python/commit/<a class=hub.com/datajoint/datajoint-python/commit/2ebe8590470dcd21c837ffbe83d8dec988ae0950">2ebe85904<a href="https://github.com/datajoint/datajoint-python/commit/2ebe8590470dcd21c837ffbe83d8dec988ae0950">">Merge </a><a class="double-link" href="https://github.com/datajoint/datajoint-python/commit/<a class="double-link" href="https://github.com/datajoint/datajoint-python/commit/eb827e60eea77a530ab90c3074d8c159ca537a7c">eb827e60e</a>">eb827e60e</a><a href="https://github.com/datajoint/datajoint-python/commit/2ebe8590470dcd21c837ffbe83d8dec988ae0950"> into 77477961b">77477961b</a>

Run Details

18 of 18 new or added lines in 1 file covered. (100.0%)

3105 of 3431 relevant lines covered (90.5%)

0.9 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

83.11

/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
import contextlib

# noinspection PyExceptionInherit,PyCallingNonCallable

logger = logging.getLogger(__name__.split(".")[0])


# --- 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,
        return_success_count=False,
        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 return_success_count: if True, return the count of successful `make()` calls.
            If suppress_errors is also True, returns a tuple: (success_count, errors)
        :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.debug("Found %d keys to populate" % len(keys))

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

        processes = min(_ for _ in (processes, nkeys, mp.cpu_count()) if _)

        error_list = []
        success_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
            ):
                status = self._populate1(key, jobs, **populate_kwargs)
                if status is not None:
                    if isinstance(status, tuple):
                        error_list.append(status)
                    elif status:
                        success_list.append(1)
        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, (
                tqdm(desc="Processes: ", total=nkeys)
                if display_progress
                else contextlib.nullcontext()
            ) as progress_bar:
                for status in pool.imap(_call_populate1, keys, chunksize=1):
                    if status is not None:
                        if isinstance(status, tuple):
                            error_list.append(status)
                        elif status:
                            success_list.append(1)
                    if display_progress:
                        progress_bar.update()
            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 and return_success_count:
            return sum(success_list), error_list
        if suppress_errors:
            return error_list
        if return_success_count:
            return sum(success_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.debug(f"Making {key} -> {self.target.full_table_name}")
                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 "",
                    )
                    logger.debug(
                        f"Error making {key} -> {self.target.full_table_name} - {error_message}"
                    )
                    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()
                    logger.debug(
                        f"Success making {key} -> {self.target.full_table_name}"
                    )
                    if jobs is not None:
                        jobs.complete(self.target.table_name, self._job_key(key))
                    return True
                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	import contextlib	1✔
13
14	# noinspection PyExceptionInherit,PyCallingNonCallable
15
16	logger = logging.getLogger(__name__.split(".")[0])	1✔
17
18
19	# --- helper functions for multiprocessing --
20
21
22	def _initialize_populate(table, jobs, populate_kwargs):	1✔
23	"""
24	Initialize the process for mulitprocessing.
25	Saves the unpickled copy of the table to the current process and reconnects.
26	"""
27	process = mp.current_process()	×
28	process.table = table	×
29	process.jobs = jobs	×
30	process.populate_kwargs = populate_kwargs	×
31	table.connection.connect() # reconnect	×
32
33
34	def _call_populate1(key):	1✔
35	"""
36	Call current process' table._populate1()
37	:key - a dict specifying job to compute
38	:return: key, error if error, otherwise None
39	"""
40	process = mp.current_process()	×
41	return process.table._populate1(key, process.jobs, **process.populate_kwargs)	×
42
43
44	class AutoPopulate:	1✔
45	"""
46	AutoPopulate is a mixin class that adds the method populate() to a Relation class.
47	Auto-populated relations must inherit from both Relation and AutoPopulate,
48	must define the property `key_source`, and must define the callback method `make`.
49	"""
50
51	_key_source = None	1✔
52	_allow_insert = False	1✔
53
54	@property	1✔
55	def key_source(self):	1✔
56	"""
57	:return: the query expression that yields primary key values to be passed,
58	sequentially, to the ``make`` method when populate() is called.
59	The default value is the join of the parent tables references from the primary key.
60	Subclasses may override they key_source to change the scope or the granularity
61	of the make calls.
62	"""
63
64	def _rename_attributes(table, props):	1✔
65	return (	1✔
66	table.proj(
67	**{
68	attr: ref
69	for attr, ref in props["attr_map"].items()
70	if attr != ref
71	}
72	)
73	if props["aliased"]
74	else table.proj()
75	)
76
77	if self._key_source is None:	1✔
78	parents = self.target.parents(	1✔
79	primary=True, as_objects=True, foreign_key_info=True
80	)
81	if not parents:	1✔
82	raise DataJointError(	×
83	"A table must have dependencies "
84	"from its primary key for auto-populate to work"
85	)
86	self._key_source = _rename_attributes(*parents[0])	1✔
87	for q in parents[1:]:	1✔
88	self._key_source = _rename_attributes(q)	1✔
89	return self._key_source	1✔
90
91	def make(self, key):	1✔
92	"""
93	Derived classes must implement method `make` that fetches data from tables
94	above them in the dependency hierarchy, restricting by the given key,
95	computes secondary attributes, and inserts the new tuples into self.
96	"""
97	raise NotImplementedError(	×
98	"Subclasses of AutoPopulate must implement the method `make`"
99	)
100
101	@property	1✔
102	def target(self):	1✔
103	"""
104	:return: table to be populated.
105	In the typical case, dj.AutoPopulate is mixed into a dj.Table class by
106	inheritance and the target is self.
107	"""
108	return self	1✔
109
110	def _job_key(self, key):	1✔
111	"""
112	:param key: they key returned for the job from the key source
113	:return: the dict to use to generate the job reservation hash
114	This method allows subclasses to control the job reservation granularity.
115	"""
116	return key	1✔
117
118	def _jobs_to_do(self, restrictions):	1✔
119	"""
120	:return: the relation containing the keys to be computed (derived from self.key_source)
121	"""
122	if self.restriction:	1✔
123	raise DataJointError(	×
124	"Cannot call populate on a restricted table. "
125	"Instead, pass conditions to populate() as arguments."
126	)
127	todo = self.key_source	1✔
128
129	# key_source is a QueryExpression subclass -- trigger instantiation
130	if inspect.isclass(todo) and issubclass(todo, QueryExpression):	1✔
131	todo = todo()	1✔
132
133	if not isinstance(todo, QueryExpression):	1✔
134	raise DataJointError("Invalid key_source value")	×
135
136	try:	1✔
137	# check if target lacks any attributes from the primary key of key_source
138	raise DataJointError(	1✔
139	"The populate target lacks attribute %s "
140	"from the primary key of key_source"
141	% next(
142	name
143	for name in todo.heading.primary_key
144	if name not in self.target.heading
145	)
146	)
147	except StopIteration:	1✔
148	pass	1✔
149	return (todo & AndList(restrictions)).proj()	1✔
150
151	def populate(	1✔
152	self,
153	*restrictions,
154	suppress_errors=False,
155	return_exception_objects=False,
156	reserve_jobs=False,
157	order="original",
158	limit=None,
159	max_calls=None,
160	display_progress=False,
161	processes=1,
162	return_success_count=False,
163	make_kwargs=None
164	):
165	"""
166	``table.populate()`` calls ``table.make(key)`` for every primary key in
167	``self.key_source`` for which there is not already a tuple in table.
168
169	:param restrictions: a list of restrictions each restrict
170	(table.key_source - target.proj())
171	:param suppress_errors: if True, do not terminate execution.
172	:param return_exception_objects: return error objects instead of just error messages
173	:param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion
174	:param order: "original"\|"reverse"\|"random" - the order of execution
175	:param limit: if not None, check at most this many keys
176	:param max_calls: if not None, populate at most this many keys
177	:param display_progress: if True, report progress_bar
178	:param processes: number of processes to use. Set to None to use all cores
179	:param return_success_count: if True, return the count of successful `make()` calls.
180	If suppress_errors is also True, returns a tuple: (success_count, errors)
181	:param make_kwargs: Keyword arguments which do not affect the result of computation
182	to be passed down to each ``make()`` call. Computation arguments should be
183	specified within the pipeline e.g. using a `dj.Lookup` table.
184	:type make_kwargs: dict, optional
185	"""
186	if self.connection.in_transaction:	1✔
187	raise DataJointError("Populate cannot be called during a transaction.")	×
188
189	valid_order = ["original", "reverse", "random"]	1✔
190	if order not in valid_order:	1✔
191	raise DataJointError(	×
192	"The order argument must be one of %s" % str(valid_order)
193	)
194	jobs = (	1✔
195	self.connection.schemas[self.target.database].jobs if reserve_jobs else None
196	)
197
198	# define and set up signal handler for SIGTERM:
199	if reserve_jobs:	1✔
200
201	def handler(signum, frame):	1✔
202	logger.info("Populate terminated by SIGTERM")	×
203	raise SystemExit("SIGTERM received")	×
204
205	old_handler = signal.signal(signal.SIGTERM, handler)	1✔
206
207	keys = (self._jobs_to_do(restrictions) - self.target).fetch("KEY", limit=limit)	1✔
208	if order == "reverse":	1✔
209	keys.reverse()	×
210	elif order == "random":	1✔
211	random.shuffle(keys)	×
212
213	logger.debug("Found %d keys to populate" % len(keys))	1✔
214
215	keys = keys[:max_calls]	1✔
216	nkeys = len(keys)	1✔
217	if not nkeys:	1✔
218	return	1✔
219
220	processes = min(_ for _ in (processes, nkeys, mp.cpu_count()) if _)	1✔
221
222	error_list = []	1✔
223	success_list = []	1✔
224	populate_kwargs = dict(	1✔
225	suppress_errors=suppress_errors,
226	return_exception_objects=return_exception_objects,
227	make_kwargs=make_kwargs,
228	)
229
230	if processes == 1:	1✔
231	for key in (	1✔
232	tqdm(keys, desc=self.__class__.__name__) if display_progress else keys
233	):
234	status = self._populate1(key, jobs, **populate_kwargs)	1✔
235	if status is not None:	1✔
236	if isinstance(status, tuple):	1✔
237	error_list.append(status)	1✔
238	elif status:	1✔
239	success_list.append(1)	1✔
240	else:
241	# spawn multiple processes
242	self.connection.close() # disconnect parent process from MySQL server	1✔
243	del self.connection._conn.ctx # SSLContext is not pickleable	1✔
244	with mp.Pool(	1✔
245	processes, _initialize_populate, (self, jobs, populate_kwargs)
246	) as pool, (
247	tqdm(desc="Processes: ", total=nkeys)
248	if display_progress
249	else contextlib.nullcontext()
250	) as progress_bar:
251	for status in pool.imap(_call_populate1, keys, chunksize=1):	1✔
252	if status is not None:	1✔
253	if isinstance(status, tuple):	1✔
254	error_list.append(status)	×
255	elif status:	1✔
256	success_list.append(1)	1✔
257	if display_progress:	1✔
258	progress_bar.update()	×
259	self.connection.connect() # reconnect parent process to MySQL server	1✔
260
261	# restore original signal handler:
262	if reserve_jobs:	1✔
263	signal.signal(signal.SIGTERM, old_handler)	1✔
264
265	if suppress_errors and return_success_count:	1✔
266	return sum(success_list), error_list	1✔
267	if suppress_errors:	1✔
268	return error_list	1✔
269	if return_success_count:	1✔
270	return sum(success_list)	1✔
271
272	def _populate1(	1✔
273	self, key, jobs, suppress_errors, return_exception_objects, make_kwargs=None
274	):
275	"""
276	populates table for one source key, calling self.make inside a transaction.
277	:param jobs: the jobs table or None if not reserve_jobs
278	:param key: dict specifying job to populate
279	:param suppress_errors: bool if errors should be suppressed and returned
280	:param return_exception_objects: if True, errors must be returned as objects
281	:return: (key, error) when suppress_errors=True, otherwise None
282	"""
283	make = self._make_tuples if hasattr(self, "_make_tuples") else self.make	1✔
284
285	if jobs is None or jobs.reserve(self.target.table_name, self._job_key(key)):	1✔
286	self.connection.start_transaction()	1✔
287	if key in self.target: # already populated	1✔
288	self.connection.cancel_transaction()	×
289	if jobs is not None:	×
290	jobs.complete(self.target.table_name, self._job_key(key))	×
291	else:
292	logger.debug(f"Making {key} -> {self.target.full_table_name}")	1✔
293	self.__class__._allow_insert = True	1✔
294	try:	1✔
295	make(dict(key), **(make_kwargs or {}))	1✔
296	except (KeyboardInterrupt, SystemExit, Exception) as error:	1✔
297	try:	1✔
298	self.connection.cancel_transaction()	1✔
299	except LostConnectionError:	×
300	pass	×
301	error_message = "{exception}{msg}".format(	1✔
302	exception=error.__class__.__name__,
303	msg=": " + str(error) if str(error) else "",
304	)
305	logger.debug(	1✔
306	f"Error making {key} -> {self.target.full_table_name} - {error_message}"
307	)
308	if jobs is not None:	1✔
309	# show error name and error message (if any)
310	jobs.error(	1✔
311	self.target.table_name,
312	self._job_key(key),
313	error_message=error_message,
314	error_stack=traceback.format_exc(),
315	)
316	if not suppress_errors or isinstance(error, SystemExit):	1✔
317	raise	1✔
318	else:
319	logger.error(error)	1✔
320	return key, error if return_exception_objects else error_message	1✔
321	else:
322	self.connection.commit_transaction()	1✔
323	logger.debug(	1✔
324	f"Success making {key} -> {self.target.full_table_name}"
325	)
326	if jobs is not None:	1✔
327	jobs.complete(self.target.table_name, self._job_key(key))	×
328	return True	1✔
329	finally:
330	self.__class__._allow_insert = False	1✔
331
332	def progress(self, *restrictions, display=True):	1✔
333	"""
334	Report the progress of populating the table.
335	:return: (remaining, total) -- numbers of tuples to be populated
336	"""
337	todo = self._jobs_to_do(restrictions)	1✔
338	total = len(todo)	1✔
339	remaining = len(todo - self.target)	1✔
340	if display:	1✔
341	print(	1✔
342	"%-20s" % self.__class__.__name__,
343	"Completed %d of %d (%2.1f%%) %s"
344	% (
345	total - remaining,
346	total,
347	100 - 100 * remaining / (total + 1e-12),
348	datetime.datetime.strftime(
349	datetime.datetime.now(), "%Y-%m-%d %H:%M:%S"
350	),
351	),
352	flush=True,
353	)
354	return remaining, total	1✔

datajoint / datajoint-python / #12586

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous