autopopulate.py

This module defines class dj.AutoPopulate

AutoPopulate

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

Source code in datajoint/autopopulate.py

class AutoPopulate:
    """
    AutoPopulate is a mixin class that adds the method populate() to a Table class.
    Auto-populated tables must inherit from both Table 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 query yielding 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)

        # exclude "error" or "ignore" jobs
        if reserve_jobs:
            exclude_key_hashes = (
                jobs
                & {"table_name": self.target.table_name}
                & 'status in ("error", "ignore")'
            ).fetch("key_hash")
            keys = [key for key in keys if key_hash(key) not in exclude_key_hashes]

        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 = []
        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.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))
                finally:
                    self.__class__._allow_insert = False

    def progress(self, *restrictions, display=False):
        """
        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:
            logger.info(
                "%-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"
                    ),
                ),
            )
        return remaining, total

key_source property

Returns:

Type	Description
	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.

make(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.

Source code in datajoint/autopopulate.py

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`"
    )

target property

Returns:

Type	Description
	table to be populated. In the typical case, dj.AutoPopulate is mixed into a dj.Table class by inheritance and the target is self.

populate(*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.

Parameters:

Name	Type	Description	Default
restrictions		a list of restrictions each restrict (table.key_source - target.proj())	()
suppress_errors		if True, do not terminate execution.	False
return_exception_objects		return error objects instead of just error messages	False
reserve_jobs		if True, reserve jobs to populate in asynchronous fashion	False
order		"original"|"reverse"|"random" - the order of execution	'original'
limit		if not None, check at most this many keys	None
max_calls		if not None, populate at most this many keys	None
display_progress		if True, report progress_bar	False
processes		number of processes to use. Set to None to use all cores	1
make_kwargs	dict, optional	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.	None

Source code in datajoint/autopopulate.py

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)

    # exclude "error" or "ignore" jobs
    if reserve_jobs:
        exclude_key_hashes = (
            jobs
            & {"table_name": self.target.table_name}
            & 'status in ("error", "ignore")'
        ).fetch("key_hash")
        keys = [key for key in keys if key_hash(key) not in exclude_key_hashes]

    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 = []
    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

progress(*restrictions, display=False)

Report the progress of populating the table.

Returns:

Type	Description
	(remaining, total) -- numbers of tuples to be populated

Source code in datajoint/autopopulate.py

def progress(self, *restrictions, display=False):
    """
    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:
        logger.info(
            "%-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"
                ),
            ),
        )
    return remaining, total