#12290

pending completion

Build # #12290

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/ea15f999cc3dae9f4136511521ca8b5c6b97cf4e">ea15f999c<a href="https://github.com/datajoint/datajoint-python/commit/ea15f999cc3dae9f4136511521ca8b5c6b97cf4e">">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/3c2ac2e73025c1b63134555371707ff41a0673a5">3c2ac2e73</a>">3c2ac2e73</a><a href="https://github.com/datajoint/datajoint-python/commit/ea15f999cc3dae9f4136511521ca8b5c6b97cf4e"> into 0ff34f283">0ff34f283</a>

Run Details

15 of 15 new or added lines in 3 files covered. (100.0%)

3065 of 3386 relevant lines covered (90.52%)

0.91 hits per line

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

81.34

/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__)


# --- 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

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

        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, (
                tqdm(desc="Processes: ", total=nkeys)
                if display_progress
                else contextlib.nullcontext()
            ) as progress_bar:
                for error in pool.imap(_call_populate1, keys, chunksize=1):
                    if error is not None:
                        error_list.append(error)
                    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:
            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	import contextlib	1✔
13
14	# noinspection PyExceptionInherit,PyCallingNonCallable
15
16	logger = logging.getLogger(__name__)	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	make_kwargs=None
163	):
164	"""
165	``table.populate()`` calls ``table.make(key)`` for every primary key in
166	``self.key_source`` for which there is not already a tuple in table.
167
168	:param restrictions: a list of restrictions each restrict
169	(table.key_source - target.proj())
170	:param suppress_errors: if True, do not terminate execution.
171	:param return_exception_objects: return error objects instead of just error messages
172	:param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion
173	:param order: "original"\|"reverse"\|"random" - the order of execution
174	:param limit: if not None, check at most this many keys
175	:param max_calls: if not None, populate at most this many keys
176	:param display_progress: if True, report progress_bar
177	:param processes: number of processes to use. Set to None to use all cores
178	:param make_kwargs: Keyword arguments which do not affect the result of computation
179	to be passed down to each ``make()`` call. Computation arguments should be
180	specified within the pipeline e.g. using a `dj.Lookup` table.
181	:type make_kwargs: dict, optional
182	"""
183	if self.connection.in_transaction:	1✔
184	raise DataJointError("Populate cannot be called during a transaction.")	×
185
186	valid_order = ["original", "reverse", "random"]	1✔
187	if order not in valid_order:	1✔
188	raise DataJointError(	×
189	"The order argument must be one of %s" % str(valid_order)
190	)
191	jobs = (	1✔
192	self.connection.schemas[self.target.database].jobs if reserve_jobs else None
193	)
194
195	# define and set up signal handler for SIGTERM:
196	if reserve_jobs:	1✔
197
198	def handler(signum, frame):	1✔
199	logger.info("Populate terminated by SIGTERM")	×
200	raise SystemExit("SIGTERM received")	×
201
202	old_handler = signal.signal(signal.SIGTERM, handler)	1✔
203
204	keys = (self._jobs_to_do(restrictions) - self.target).fetch("KEY", limit=limit)	1✔
205	if order == "reverse":	1✔
206	keys.reverse()	×
207	elif order == "random":	1✔
208	random.shuffle(keys)	×
209
210	logger.info("Found %d keys to populate" % len(keys))	1✔
211
212	keys = keys[:max_calls]	1✔
213	nkeys = len(keys)	1✔
214	if not nkeys:	1✔
215	return	1✔
216
217	processes = min(_ for _ in (processes, nkeys, mp.cpu_count()) if _)	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	tqdm(desc="Processes: ", total=nkeys)
241	if display_progress
242	else contextlib.nullcontext()
243	) as progress_bar:
244	for error in pool.imap(_call_populate1, keys, chunksize=1):	1✔
245	if error is not None:	1✔
246	error_list.append(error)	×
247	if display_progress:	1✔
248	progress_bar.update()	×
249	self.connection.connect() # reconnect parent process to MySQL server	1✔
250
251	# restore original signal handler:
252	if reserve_jobs:	1✔
253	signal.signal(signal.SIGTERM, old_handler)	1✔
254
255	if suppress_errors:	1✔
256	return error_list	1✔
257
258	def _populate1(	1✔
259	self, key, jobs, suppress_errors, return_exception_objects, make_kwargs=None
260	):
261	"""
262	populates table for one source key, calling self.make inside a transaction.
263	:param jobs: the jobs table or None if not reserve_jobs
264	:param key: dict specifying job to populate
265	:param suppress_errors: bool if errors should be suppressed and returned
266	:param return_exception_objects: if True, errors must be returned as objects
267	:return: (key, error) when suppress_errors=True, otherwise None
268	"""
269	make = self._make_tuples if hasattr(self, "_make_tuples") else self.make	1✔
270
271	if jobs is None or jobs.reserve(self.target.table_name, self._job_key(key)):	1✔
272	self.connection.start_transaction()	1✔
273	if key in self.target: # already populated	1✔
274	self.connection.cancel_transaction()	×
275	if jobs is not None:	×
276	jobs.complete(self.target.table_name, self._job_key(key))	×
277	else:
278	logger.info("Populating: " + str(key))	1✔
279	self.__class__._allow_insert = True	1✔
280	try:	1✔
281	make(dict(key), **(make_kwargs or {}))	1✔
282	except (KeyboardInterrupt, SystemExit, Exception) as error:	1✔
283	try:	1✔
284	self.connection.cancel_transaction()	1✔
285	except LostConnectionError:	×
286	pass	×
287	error_message = "{exception}{msg}".format(	1✔
288	exception=error.__class__.__name__,
289	msg=": " + str(error) if str(error) else "",
290	)
291	if jobs is not None:	1✔
292	# show error name and error message (if any)
293	jobs.error(	1✔
294	self.target.table_name,
295	self._job_key(key),
296	error_message=error_message,
297	error_stack=traceback.format_exc(),
298	)
299	if not suppress_errors or isinstance(error, SystemExit):	1✔
300	raise	1✔
301	else:
302	logger.error(error)	1✔
303	return key, error if return_exception_objects else error_message	1✔
304	else:
305	self.connection.commit_transaction()	1✔
306	if jobs is not None:	1✔
307	jobs.complete(self.target.table_name, self._job_key(key))	×
308	finally:
309	self.__class__._allow_insert = False	1✔
310
311	def progress(self, *restrictions, display=True):	1✔
312	"""
313	Report the progress of populating the table.
314	:return: (remaining, total) -- numbers of tuples to be populated
315	"""
316	todo = self._jobs_to_do(restrictions)	1✔
317	total = len(todo)	1✔
318	remaining = len(todo - self.target)	1✔
319	if display:	1✔
320	print(	1✔
321	"%-20s" % self.__class__.__name__,
322	"Completed %d of %d (%2.1f%%) %s"
323	% (
324	total - remaining,
325	total,
326	100 - 100 * remaining / (total + 1e-12),
327	datetime.datetime.strftime(
328	datetime.datetime.now(), "%Y-%m-%d %H:%M:%S"
329	),
330	),
331	flush=True,
332	)
333	return remaining, total	1✔

datajoint / datajoint-python / #12290

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