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bd808/python-iptools | iptools/__init__.py | IpRange.index | def index(self, item):
"""
Return the 0-based position of `item` in this IpRange.
>>> r = IpRange('127.0.0.1', '127.255.255.255')
>>> r.index('127.0.0.1')
0
>>> r.index('127.255.255.255')
16777214
>>> r.index('10.0.0.1')
Traceback (most recent call last):
...
ValueError: 10.0.0.1 is not in range
:param item: Dotted-quad ip address.
:type item: str
:returns: Index of ip address in range
"""
item = self._cast(item)
offset = item - self.startIp
if offset >= 0 and offset < self._len:
return offset
raise ValueError('%s is not in range' % self._ipver.long2ip(item)) | python | def index(self, item):
"""
Return the 0-based position of `item` in this IpRange.
>>> r = IpRange('127.0.0.1', '127.255.255.255')
>>> r.index('127.0.0.1')
0
>>> r.index('127.255.255.255')
16777214
>>> r.index('10.0.0.1')
Traceback (most recent call last):
...
ValueError: 10.0.0.1 is not in range
:param item: Dotted-quad ip address.
:type item: str
:returns: Index of ip address in range
"""
item = self._cast(item)
offset = item - self.startIp
if offset >= 0 and offset < self._len:
return offset
raise ValueError('%s is not in range' % self._ipver.long2ip(item)) | [
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>>> r.index('127.0.0.1')
0
>>> r.index('127.255.255.255')
16777214
>>> r.index('10.0.0.1')
Traceback (most recent call last):
...
ValueError: 10.0.0.1 is not in range
:param item: Dotted-quad ip address.
:type item: str
:returns: Index of ip address in range | [
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torfsen/service | src/service/__init__.py | _detach_process | def _detach_process():
"""
Detach daemon process.
Forks the current process into a parent and a detached child. The
child process resides in its own process group, has no controlling
terminal attached and is cleaned up by the init process.
Returns ``True`` for the parent and ``False`` for the child.
"""
# To detach from our process group we need to call ``setsid``. We
# can only do that if we aren't a process group leader. Therefore
# we fork once, which makes sure that the new child process is not
# a process group leader.
pid = os.fork()
if pid > 0:
# Parent process
# Use waitpid to "collect" the child process and avoid Zombies
os.waitpid(pid, 0)
return True
os.setsid()
# We now fork a second time and let the second's fork parent exit.
# This makes the second fork's child process an orphan. Orphans are
# cleaned up by the init process, so we won't end up with a zombie.
# In addition, the second fork's child is no longer a session
# leader and can therefore never acquire a controlling terminal.
pid = os.fork()
if pid > 0:
os._exit(os.EX_OK)
return False | python | def _detach_process():
"""
Detach daemon process.
Forks the current process into a parent and a detached child. The
child process resides in its own process group, has no controlling
terminal attached and is cleaned up by the init process.
Returns ``True`` for the parent and ``False`` for the child.
"""
# To detach from our process group we need to call ``setsid``. We
# can only do that if we aren't a process group leader. Therefore
# we fork once, which makes sure that the new child process is not
# a process group leader.
pid = os.fork()
if pid > 0:
# Parent process
# Use waitpid to "collect" the child process and avoid Zombies
os.waitpid(pid, 0)
return True
os.setsid()
# We now fork a second time and let the second's fork parent exit.
# This makes the second fork's child process an orphan. Orphans are
# cleaned up by the init process, so we won't end up with a zombie.
# In addition, the second fork's child is no longer a session
# leader and can therefore never acquire a controlling terminal.
pid = os.fork()
if pid > 0:
os._exit(os.EX_OK)
return False | [
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torfsen/service | src/service/__init__.py | _block | def _block(predicate, timeout):
"""
Block until a predicate becomes true.
``predicate`` is a function taking no arguments. The call to
``_block`` blocks until ``predicate`` returns a true value. This
is done by polling ``predicate``.
``timeout`` is either ``True`` (block indefinitely) or a timeout
in seconds.
The return value is the value of the predicate after the
timeout.
"""
if timeout:
if timeout is True:
timeout = float('Inf')
timeout = time.time() + timeout
while not predicate() and time.time() < timeout:
time.sleep(0.1)
return predicate() | python | def _block(predicate, timeout):
"""
Block until a predicate becomes true.
``predicate`` is a function taking no arguments. The call to
``_block`` blocks until ``predicate`` returns a true value. This
is done by polling ``predicate``.
``timeout`` is either ``True`` (block indefinitely) or a timeout
in seconds.
The return value is the value of the predicate after the
timeout.
"""
if timeout:
if timeout is True:
timeout = float('Inf')
timeout = time.time() + timeout
while not predicate() and time.time() < timeout:
time.sleep(0.1)
return predicate() | [
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torfsen/service | src/service/__init__.py | _PIDFile.read_pid | def read_pid(self):
"""
Return the PID of the process owning the lock.
Returns ``None`` if no lock is present.
"""
try:
with open(self._path, 'r') as f:
s = f.read().strip()
if not s:
return None
return int(s)
except IOError as e:
if e.errno == errno.ENOENT:
return None
raise | python | def read_pid(self):
"""
Return the PID of the process owning the lock.
Returns ``None`` if no lock is present.
"""
try:
with open(self._path, 'r') as f:
s = f.read().strip()
if not s:
return None
return int(s)
except IOError as e:
if e.errno == errno.ENOENT:
return None
raise | [
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torfsen/service | src/service/__init__.py | Service._get_logger_file_handles | def _get_logger_file_handles(self):
"""
Find the file handles used by our logger's handlers.
"""
handles = []
for handler in self.logger.handlers:
# The following code works for logging's SysLogHandler,
# StreamHandler, SocketHandler, and their subclasses.
for attr in ['sock', 'socket', 'stream']:
try:
handle = getattr(handler, attr)
if handle:
handles.append(handle)
break
except AttributeError:
continue
return handles | python | def _get_logger_file_handles(self):
"""
Find the file handles used by our logger's handlers.
"""
handles = []
for handler in self.logger.handlers:
# The following code works for logging's SysLogHandler,
# StreamHandler, SocketHandler, and their subclasses.
for attr in ['sock', 'socket', 'stream']:
try:
handle = getattr(handler, attr)
if handle:
handles.append(handle)
break
except AttributeError:
continue
return handles | [
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torfsen/service | src/service/__init__.py | Service.is_running | def is_running(self):
"""
Check if the daemon is running.
"""
pid = self.get_pid()
if pid is None:
return False
# The PID file may still exist even if the daemon isn't running,
# for example if it has crashed.
try:
os.kill(pid, 0)
except OSError as e:
if e.errno == errno.ESRCH:
# In this case the PID file shouldn't have existed in
# the first place, so we remove it
self.pid_file.release()
return False
# We may also get an exception if we're not allowed to use
# kill on the process, but that means that the process does
# exist, which is all we care about here.
return True | python | def is_running(self):
"""
Check if the daemon is running.
"""
pid = self.get_pid()
if pid is None:
return False
# The PID file may still exist even if the daemon isn't running,
# for example if it has crashed.
try:
os.kill(pid, 0)
except OSError as e:
if e.errno == errno.ESRCH:
# In this case the PID file shouldn't have existed in
# the first place, so we remove it
self.pid_file.release()
return False
# We may also get an exception if we're not allowed to use
# kill on the process, but that means that the process does
# exist, which is all we care about here.
return True | [
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torfsen/service | src/service/__init__.py | Service._get_signal_event | def _get_signal_event(self, s):
'''
Get the event for a signal.
Checks if the signal has been enabled and raises a
``ValueError`` if not.
'''
try:
return self._signal_events[int(s)]
except KeyError:
raise ValueError('Signal {} has not been enabled'.format(s)) | python | def _get_signal_event(self, s):
'''
Get the event for a signal.
Checks if the signal has been enabled and raises a
``ValueError`` if not.
'''
try:
return self._signal_events[int(s)]
except KeyError:
raise ValueError('Signal {} has not been enabled'.format(s)) | [
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torfsen/service | src/service/__init__.py | Service.send_signal | def send_signal(self, s):
"""
Send a signal to the daemon process.
The signal must have been enabled using the ``signals``
parameter of :py:meth:`Service.__init__`. Otherwise, a
``ValueError`` is raised.
"""
self._get_signal_event(s) # Check if signal has been enabled
pid = self.get_pid()
if not pid:
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os.kill(pid, s) | python | def send_signal(self, s):
"""
Send a signal to the daemon process.
The signal must have been enabled using the ``signals``
parameter of :py:meth:`Service.__init__`. Otherwise, a
``ValueError`` is raised.
"""
self._get_signal_event(s) # Check if signal has been enabled
pid = self.get_pid()
if not pid:
raise ValueError('Daemon is not running.')
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torfsen/service | src/service/__init__.py | Service.stop | def stop(self, block=False):
"""
Tell the daemon process to stop.
Sends the SIGTERM signal to the daemon process, requesting it
to terminate.
If ``block`` is true then the call blocks until the daemon
process has exited. This may take some time since the daemon
process will complete its on-going backup activities before
shutting down. ``block`` can either be ``True`` (in which case
it blocks indefinitely) or a timeout in seconds.
The return value is ``True`` if the daemon process has been
stopped and ``False`` otherwise.
.. versionadded:: 0.3
The ``block`` parameter
"""
self.send_signal(signal.SIGTERM)
return _block(lambda: not self.is_running(), block) | python | def stop(self, block=False):
"""
Tell the daemon process to stop.
Sends the SIGTERM signal to the daemon process, requesting it
to terminate.
If ``block`` is true then the call blocks until the daemon
process has exited. This may take some time since the daemon
process will complete its on-going backup activities before
shutting down. ``block`` can either be ``True`` (in which case
it blocks indefinitely) or a timeout in seconds.
The return value is ``True`` if the daemon process has been
stopped and ``False`` otherwise.
.. versionadded:: 0.3
The ``block`` parameter
"""
self.send_signal(signal.SIGTERM)
return _block(lambda: not self.is_running(), block) | [
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torfsen/service | src/service/__init__.py | Service.kill | def kill(self, block=False):
"""
Kill the daemon process.
Sends the SIGKILL signal to the daemon process, killing it. You
probably want to try :py:meth:`stop` first.
If ``block`` is true then the call blocks until the daemon
process has exited. ``block`` can either be ``True`` (in which
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Returns ``True`` if the daemon process has (already) exited and
``False`` otherwise.
The PID file is always removed, whether the process has already
exited or not. Note that this means that subsequent calls to
:py:meth:`is_running` and :py:meth:`get_pid` will behave as if
the process has exited. If you need to be sure that the process
has already exited, set ``block`` to ``True``.
.. versionadded:: 0.5.1
The ``block`` parameter
"""
pid = self.get_pid()
if not pid:
raise ValueError('Daemon is not running.')
try:
os.kill(pid, signal.SIGKILL)
return _block(lambda: not self.is_running(), block)
except OSError as e:
if e.errno == errno.ESRCH:
raise ValueError('Daemon is not running.')
raise
finally:
self.pid_file.release() | python | def kill(self, block=False):
"""
Kill the daemon process.
Sends the SIGKILL signal to the daemon process, killing it. You
probably want to try :py:meth:`stop` first.
If ``block`` is true then the call blocks until the daemon
process has exited. ``block`` can either be ``True`` (in which
case it blocks indefinitely) or a timeout in seconds.
Returns ``True`` if the daemon process has (already) exited and
``False`` otherwise.
The PID file is always removed, whether the process has already
exited or not. Note that this means that subsequent calls to
:py:meth:`is_running` and :py:meth:`get_pid` will behave as if
the process has exited. If you need to be sure that the process
has already exited, set ``block`` to ``True``.
.. versionadded:: 0.5.1
The ``block`` parameter
"""
pid = self.get_pid()
if not pid:
raise ValueError('Daemon is not running.')
try:
os.kill(pid, signal.SIGKILL)
return _block(lambda: not self.is_running(), block)
except OSError as e:
if e.errno == errno.ESRCH:
raise ValueError('Daemon is not running.')
raise
finally:
self.pid_file.release() | [
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torfsen/service | src/service/__init__.py | Service.start | def start(self, block=False):
"""
Start the daemon process.
The daemon process is started in the background and the calling
process returns.
Once the daemon process is initialized it calls the
:py:meth:`run` method.
If ``block`` is true then the call blocks until the daemon
process has started. ``block`` can either be ``True`` (in which
case it blocks indefinitely) or a timeout in seconds.
The return value is ``True`` if the daemon process has been
started and ``False`` otherwise.
.. versionadded:: 0.3
The ``block`` parameter
"""
pid = self.get_pid()
if pid:
raise ValueError('Daemon is already running at PID %d.' % pid)
# The default is to place the PID file into ``/var/run``. This
# requires root privileges. Since not having these is a common
# problem we check a priori whether we can create the lock file.
try:
self.pid_file.acquire()
finally:
self.pid_file.release()
# Clear previously received SIGTERMs. This must be done before
# the calling process returns so that the calling process can
# call ``stop`` directly after ``start`` returns without the
# signal being lost.
self.clear_signal(signal.SIGTERM)
if _detach_process():
# Calling process returns
return _block(lambda: self.is_running(), block)
# Daemon process continues here
self._debug('Daemon has detached')
def on_signal(s, frame):
self._debug('Received signal {}'.format(s))
self._signal_events[int(s)].set()
def runner():
try:
# We acquire the PID as late as possible, since its
# existence is used to verify whether the service
# is running.
self.pid_file.acquire()
self._debug('PID file has been acquired')
self._debug('Calling `run`')
self.run()
self._debug('`run` returned without exception')
except Exception as e:
self.logger.exception(e)
except SystemExit:
self._debug('`run` called `sys.exit`')
try:
self.pid_file.release()
self._debug('PID file has been released')
except Exception as e:
self.logger.exception(e)
os._exit(os.EX_OK) # FIXME: This seems redundant
try:
setproctitle.setproctitle(self.name)
self._debug('Process title has been set')
files_preserve = (self.files_preserve +
self._get_logger_file_handles())
signal_map = {s: on_signal for s in self._signal_events}
signal_map.update({
signal.SIGTTIN: None,
signal.SIGTTOU: None,
signal.SIGTSTP: None,
})
with DaemonContext(
detach_process=False,
signal_map=signal_map,
files_preserve=files_preserve):
self._debug('Daemon context has been established')
# Python's signal handling mechanism only forwards signals to
# the main thread and only when that thread is doing something
# (e.g. not when it's waiting for a lock, etc.). If we use the
# main thread for the ``run`` method this means that we cannot
# use the synchronization devices from ``threading`` for
# communicating the reception of SIGTERM to ``run``. Hence we
# use a separate thread for ``run`` and make sure that the
# main loop receives signals. See
# https://bugs.python.org/issue1167930
thread = threading.Thread(target=runner)
thread.start()
while thread.is_alive():
time.sleep(1)
except Exception as e:
self.logger.exception(e)
# We need to shutdown the daemon process at this point, because
# otherwise it will continue executing from after the original
# call to ``start``.
os._exit(os.EX_OK) | python | def start(self, block=False):
"""
Start the daemon process.
The daemon process is started in the background and the calling
process returns.
Once the daemon process is initialized it calls the
:py:meth:`run` method.
If ``block`` is true then the call blocks until the daemon
process has started. ``block`` can either be ``True`` (in which
case it blocks indefinitely) or a timeout in seconds.
The return value is ``True`` if the daemon process has been
started and ``False`` otherwise.
.. versionadded:: 0.3
The ``block`` parameter
"""
pid = self.get_pid()
if pid:
raise ValueError('Daemon is already running at PID %d.' % pid)
# The default is to place the PID file into ``/var/run``. This
# requires root privileges. Since not having these is a common
# problem we check a priori whether we can create the lock file.
try:
self.pid_file.acquire()
finally:
self.pid_file.release()
# Clear previously received SIGTERMs. This must be done before
# the calling process returns so that the calling process can
# call ``stop`` directly after ``start`` returns without the
# signal being lost.
self.clear_signal(signal.SIGTERM)
if _detach_process():
# Calling process returns
return _block(lambda: self.is_running(), block)
# Daemon process continues here
self._debug('Daemon has detached')
def on_signal(s, frame):
self._debug('Received signal {}'.format(s))
self._signal_events[int(s)].set()
def runner():
try:
# We acquire the PID as late as possible, since its
# existence is used to verify whether the service
# is running.
self.pid_file.acquire()
self._debug('PID file has been acquired')
self._debug('Calling `run`')
self.run()
self._debug('`run` returned without exception')
except Exception as e:
self.logger.exception(e)
except SystemExit:
self._debug('`run` called `sys.exit`')
try:
self.pid_file.release()
self._debug('PID file has been released')
except Exception as e:
self.logger.exception(e)
os._exit(os.EX_OK) # FIXME: This seems redundant
try:
setproctitle.setproctitle(self.name)
self._debug('Process title has been set')
files_preserve = (self.files_preserve +
self._get_logger_file_handles())
signal_map = {s: on_signal for s in self._signal_events}
signal_map.update({
signal.SIGTTIN: None,
signal.SIGTTOU: None,
signal.SIGTSTP: None,
})
with DaemonContext(
detach_process=False,
signal_map=signal_map,
files_preserve=files_preserve):
self._debug('Daemon context has been established')
# Python's signal handling mechanism only forwards signals to
# the main thread and only when that thread is doing something
# (e.g. not when it's waiting for a lock, etc.). If we use the
# main thread for the ``run`` method this means that we cannot
# use the synchronization devices from ``threading`` for
# communicating the reception of SIGTERM to ``run``. Hence we
# use a separate thread for ``run`` and make sure that the
# main loop receives signals. See
# https://bugs.python.org/issue1167930
thread = threading.Thread(target=runner)
thread.start()
while thread.is_alive():
time.sleep(1)
except Exception as e:
self.logger.exception(e)
# We need to shutdown the daemon process at this point, because
# otherwise it will continue executing from after the original
# call to ``start``.
os._exit(os.EX_OK) | [
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.. versionadded:: 0.3
The ``block`` parameter | [
"Start",
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] | d0dd824fce9237825c1943b30cd14f7b0f5957a6 | https://github.com/torfsen/service/blob/d0dd824fce9237825c1943b30cd14f7b0f5957a6/src/service/__init__.py#L439-L544 | train |
datacats/datacats | datacats/cli/create.py | create | def create(opts):
"""Create a new environment
Usage:
datacats create [-bin] [--interactive] [-s NAME] [--address=IP] [--syslog]
[--ckan=CKAN_VERSION] [--no-datapusher] [--site-url SITE_URL]
[--no-init-db] ENVIRONMENT_DIR [PORT]
Options:
--address=IP Address to listen on (Linux-only)
--ckan=CKAN_VERSION Use CKAN version CKAN_VERSION [default: 2.4]
-b --bare Bare CKAN site with no example extension
-i --image-only Create the environment but don't start containers
--interactive Doesn't detach from the web container
--no-datapusher Don't install/enable ckanext-datapusher
--no-init-db Don't initialize the database. Useful for importing CKANs.
-n --no-sysadmin Don't prompt for an initial sysadmin user account
-s --site=NAME Pick a site to create [default: primary]
--site-url SITE_URL The site_url to use in API responses (e.g. http://example.org:{port}/)
--syslog Log to the syslog
ENVIRONMENT_DIR is a path for the new environment directory. The last
part of this path will be used as the environment name.
"""
if opts['--address'] and is_boot2docker():
raise DatacatsError('Cannot specify address on boot2docker.')
return create_environment(
environment_dir=opts['ENVIRONMENT_DIR'],
port=opts['PORT'],
create_skin=not opts['--bare'],
start_web=not opts['--image-only'],
create_sysadmin=not opts['--no-sysadmin'],
site_name=opts['--site'],
ckan_version=opts['--ckan'],
address=opts['--address'],
log_syslog=opts['--syslog'],
datapusher=not opts['--no-datapusher'],
site_url=opts['--site-url'],
interactive=opts['--interactive'],
init_db=not opts['--no-init-db'],
) | python | def create(opts):
"""Create a new environment
Usage:
datacats create [-bin] [--interactive] [-s NAME] [--address=IP] [--syslog]
[--ckan=CKAN_VERSION] [--no-datapusher] [--site-url SITE_URL]
[--no-init-db] ENVIRONMENT_DIR [PORT]
Options:
--address=IP Address to listen on (Linux-only)
--ckan=CKAN_VERSION Use CKAN version CKAN_VERSION [default: 2.4]
-b --bare Bare CKAN site with no example extension
-i --image-only Create the environment but don't start containers
--interactive Doesn't detach from the web container
--no-datapusher Don't install/enable ckanext-datapusher
--no-init-db Don't initialize the database. Useful for importing CKANs.
-n --no-sysadmin Don't prompt for an initial sysadmin user account
-s --site=NAME Pick a site to create [default: primary]
--site-url SITE_URL The site_url to use in API responses (e.g. http://example.org:{port}/)
--syslog Log to the syslog
ENVIRONMENT_DIR is a path for the new environment directory. The last
part of this path will be used as the environment name.
"""
if opts['--address'] and is_boot2docker():
raise DatacatsError('Cannot specify address on boot2docker.')
return create_environment(
environment_dir=opts['ENVIRONMENT_DIR'],
port=opts['PORT'],
create_skin=not opts['--bare'],
start_web=not opts['--image-only'],
create_sysadmin=not opts['--no-sysadmin'],
site_name=opts['--site'],
ckan_version=opts['--ckan'],
address=opts['--address'],
log_syslog=opts['--syslog'],
datapusher=not opts['--no-datapusher'],
site_url=opts['--site-url'],
interactive=opts['--interactive'],
init_db=not opts['--no-init-db'],
) | [
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[--no-init-db] ENVIRONMENT_DIR [PORT]
Options:
--address=IP Address to listen on (Linux-only)
--ckan=CKAN_VERSION Use CKAN version CKAN_VERSION [default: 2.4]
-b --bare Bare CKAN site with no example extension
-i --image-only Create the environment but don't start containers
--interactive Doesn't detach from the web container
--no-datapusher Don't install/enable ckanext-datapusher
--no-init-db Don't initialize the database. Useful for importing CKANs.
-n --no-sysadmin Don't prompt for an initial sysadmin user account
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--site-url SITE_URL The site_url to use in API responses (e.g. http://example.org:{port}/)
--syslog Log to the syslog
ENVIRONMENT_DIR is a path for the new environment directory. The last
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datacats/datacats | datacats/cli/create.py | reset | def reset(environment, opts):
"""Resets a site to the default state. This will re-initialize the
database and recreate the administrator account.
Usage:
datacats reset [-iyn] [-s NAME] [ENVIRONMENT]
Options:
-i --interactive Don't detach from the web container
-s --site=NAME The site to reset [default: primary]
-y --yes Respond yes to all questions
-n --no-sysadmin Don't prompt for a sysadmin password"""
# pylint: disable=unused-argument
if not opts['--yes']:
y_or_n_prompt('Reset will remove all data related to the '
'site {} and recreate the database'.format(opts['--site']))
print 'Resetting...'
environment.stop_supporting_containers()
environment.stop_ckan()
clean_pyc(environment)
# Save the port.
saved_port = environment.port
environment.purge_data([opts['--site']], never_delete=True)
init({
'ENVIRONMENT_DIR': opts['ENVIRONMENT'],
'--site': opts['--site'],
'PORT': saved_port,
'--syslog': None,
'--address': None,
'--image-only': False,
'--interactive': opts['--interactive'],
'--no-init-db': False,
'--no-sysadmin': opts['--no-sysadmin'],
'--site-url': None
}, no_install=True) | python | def reset(environment, opts):
"""Resets a site to the default state. This will re-initialize the
database and recreate the administrator account.
Usage:
datacats reset [-iyn] [-s NAME] [ENVIRONMENT]
Options:
-i --interactive Don't detach from the web container
-s --site=NAME The site to reset [default: primary]
-y --yes Respond yes to all questions
-n --no-sysadmin Don't prompt for a sysadmin password"""
# pylint: disable=unused-argument
if not opts['--yes']:
y_or_n_prompt('Reset will remove all data related to the '
'site {} and recreate the database'.format(opts['--site']))
print 'Resetting...'
environment.stop_supporting_containers()
environment.stop_ckan()
clean_pyc(environment)
# Save the port.
saved_port = environment.port
environment.purge_data([opts['--site']], never_delete=True)
init({
'ENVIRONMENT_DIR': opts['ENVIRONMENT'],
'--site': opts['--site'],
'PORT': saved_port,
'--syslog': None,
'--address': None,
'--image-only': False,
'--interactive': opts['--interactive'],
'--no-init-db': False,
'--no-sysadmin': opts['--no-sysadmin'],
'--site-url': None
}, no_install=True) | [
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Options:
-i --interactive Don't detach from the web container
-s --site=NAME The site to reset [default: primary]
-y --yes Respond yes to all questions
-n --no-sysadmin Don't prompt for a sysadmin password | [
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datacats/datacats | datacats/cli/create.py | init | def init(opts, no_install=False, quiet=False):
"""Initialize a purged environment or copied environment directory
Usage:
datacats init [-in] [--syslog] [-s NAME] [--address=IP] [--interactive]
[--site-url SITE_URL] [ENVIRONMENT_DIR [PORT]] [--no-init-db]
Options:
--address=IP Address to listen on (Linux-only)
--interactive Don't detach from the web container
-i --image-only Create the environment but don't start containers
--no-init-db Don't initialize the database. Useful for importing other CKANs
-n --no-sysadmin Don't prompt for an initial sysadmin user account
-s --site=NAME Pick a site to initialize [default: primary]
--site-url SITE_URL The site_url to use in API responses (e.g. http://example.org:{port}/)
--syslog Log to the syslog
ENVIRONMENT_DIR is an existing datacats environment directory. Defaults to '.'
"""
if opts['--address'] and is_boot2docker():
raise DatacatsError('Cannot specify address on boot2docker.')
environment_dir = opts['ENVIRONMENT_DIR']
port = opts['PORT']
address = opts['--address']
start_web = not opts['--image-only']
create_sysadmin = not opts['--no-sysadmin']
site_name = opts['--site']
site_url = opts['--site-url']
interactive = opts['--interactive']
init_db = not opts['--no-init-db']
environment_dir = abspath(environment_dir or '.')
log_syslog = opts['--syslog']
environment = Environment.load(environment_dir, site_name)
if address:
environment.address = address
if port:
environment.port = int(port)
if site_url:
environment.site_url = site_url
try:
if environment.sites and site_name in environment.sites:
raise DatacatsError('Site named {0} already exists.'
.format(site_name))
# There are a couple of steps we can/must skip if we're making a sub-site only
making_full_environment = not environment.data_exists()
if not quiet:
write('Creating environment {0}/{1} '
'from existing environment directory "{0}"'
.format(environment.name, environment.site_name))
steps = [
lambda: environment.create_directories(create_project_dir=False)] + ([
environment.save,
environment.create_virtualenv
] if making_full_environment else []) + [
environment.save_site,
environment.start_supporting_containers,
environment.fix_storage_permissions,
]
for fn in steps:
fn()
if not quiet:
write('.')
if not quiet:
write('\n')
except:
if not quiet:
print
raise
return finish_init(environment, start_web, create_sysadmin,
log_syslog=log_syslog, do_install=not no_install,
quiet=quiet, site_url=site_url, interactive=interactive,
init_db=init_db) | python | def init(opts, no_install=False, quiet=False):
"""Initialize a purged environment or copied environment directory
Usage:
datacats init [-in] [--syslog] [-s NAME] [--address=IP] [--interactive]
[--site-url SITE_URL] [ENVIRONMENT_DIR [PORT]] [--no-init-db]
Options:
--address=IP Address to listen on (Linux-only)
--interactive Don't detach from the web container
-i --image-only Create the environment but don't start containers
--no-init-db Don't initialize the database. Useful for importing other CKANs
-n --no-sysadmin Don't prompt for an initial sysadmin user account
-s --site=NAME Pick a site to initialize [default: primary]
--site-url SITE_URL The site_url to use in API responses (e.g. http://example.org:{port}/)
--syslog Log to the syslog
ENVIRONMENT_DIR is an existing datacats environment directory. Defaults to '.'
"""
if opts['--address'] and is_boot2docker():
raise DatacatsError('Cannot specify address on boot2docker.')
environment_dir = opts['ENVIRONMENT_DIR']
port = opts['PORT']
address = opts['--address']
start_web = not opts['--image-only']
create_sysadmin = not opts['--no-sysadmin']
site_name = opts['--site']
site_url = opts['--site-url']
interactive = opts['--interactive']
init_db = not opts['--no-init-db']
environment_dir = abspath(environment_dir or '.')
log_syslog = opts['--syslog']
environment = Environment.load(environment_dir, site_name)
if address:
environment.address = address
if port:
environment.port = int(port)
if site_url:
environment.site_url = site_url
try:
if environment.sites and site_name in environment.sites:
raise DatacatsError('Site named {0} already exists.'
.format(site_name))
# There are a couple of steps we can/must skip if we're making a sub-site only
making_full_environment = not environment.data_exists()
if not quiet:
write('Creating environment {0}/{1} '
'from existing environment directory "{0}"'
.format(environment.name, environment.site_name))
steps = [
lambda: environment.create_directories(create_project_dir=False)] + ([
environment.save,
environment.create_virtualenv
] if making_full_environment else []) + [
environment.save_site,
environment.start_supporting_containers,
environment.fix_storage_permissions,
]
for fn in steps:
fn()
if not quiet:
write('.')
if not quiet:
write('\n')
except:
if not quiet:
print
raise
return finish_init(environment, start_web, create_sysadmin,
log_syslog=log_syslog, do_install=not no_install,
quiet=quiet, site_url=site_url, interactive=interactive,
init_db=init_db) | [
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Options:
--address=IP Address to listen on (Linux-only)
--interactive Don't detach from the web container
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--no-init-db Don't initialize the database. Useful for importing other CKANs
-n --no-sysadmin Don't prompt for an initial sysadmin user account
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datacats/datacats | datacats/cli/create.py | finish_init | def finish_init(environment, start_web, create_sysadmin, log_syslog=False,
do_install=True, quiet=False, site_url=None, interactive=False,
init_db=True):
"""
Common parts of create and init: Install, init db, start site, sysadmin
"""
if not init_db:
start_web = False
create_sysadmin = False
if do_install:
install_all(environment, False, verbose=False, quiet=quiet)
if init_db:
if not quiet:
write('Initializing database')
environment.install_postgis_sql()
environment.ckan_db_init()
if not quiet:
write('\n')
if site_url:
try:
site_url = site_url.format(address=environment.address, port=environment.port)
environment.site_url = site_url
environment.save_site(False)
except (KeyError, IndexError, ValueError) as e:
raise DatacatsError('Could not parse site_url: {}'.format(e))
if start_web:
environment.start_ckan(log_syslog=log_syslog)
if not quiet and not interactive:
write('Starting web server at {0} ...\n'.format(
environment.web_address()))
if create_sysadmin:
try:
adminpw = confirm_password()
environment.create_admin_set_password(adminpw)
except KeyboardInterrupt:
print
if not start_web:
environment.stop_supporting_containers() | python | def finish_init(environment, start_web, create_sysadmin, log_syslog=False,
do_install=True, quiet=False, site_url=None, interactive=False,
init_db=True):
"""
Common parts of create and init: Install, init db, start site, sysadmin
"""
if not init_db:
start_web = False
create_sysadmin = False
if do_install:
install_all(environment, False, verbose=False, quiet=quiet)
if init_db:
if not quiet:
write('Initializing database')
environment.install_postgis_sql()
environment.ckan_db_init()
if not quiet:
write('\n')
if site_url:
try:
site_url = site_url.format(address=environment.address, port=environment.port)
environment.site_url = site_url
environment.save_site(False)
except (KeyError, IndexError, ValueError) as e:
raise DatacatsError('Could not parse site_url: {}'.format(e))
if start_web:
environment.start_ckan(log_syslog=log_syslog)
if not quiet and not interactive:
write('Starting web server at {0} ...\n'.format(
environment.web_address()))
if create_sysadmin:
try:
adminpw = confirm_password()
environment.create_admin_set_password(adminpw)
except KeyboardInterrupt:
print
if not start_web:
environment.stop_supporting_containers() | [
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datacats/datacats | datacats/userprofile.py | UserProfile.save | def save(self):
"""
Save profile settings into user profile directory
"""
config = self.profiledir + '/config'
if not isdir(self.profiledir):
makedirs(self.profiledir)
cp = SafeConfigParser()
cp.add_section('ssh')
cp.set('ssh', 'private_key', self.ssh_private_key)
cp.set('ssh', 'public_key', self.ssh_public_key)
with open(config, 'w') as cfile:
cp.write(cfile) | python | def save(self):
"""
Save profile settings into user profile directory
"""
config = self.profiledir + '/config'
if not isdir(self.profiledir):
makedirs(self.profiledir)
cp = SafeConfigParser()
cp.add_section('ssh')
cp.set('ssh', 'private_key', self.ssh_private_key)
cp.set('ssh', 'public_key', self.ssh_public_key)
with open(config, 'w') as cfile:
cp.write(cfile) | [
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datacats/datacats | datacats/userprofile.py | UserProfile.generate_ssh_key | def generate_ssh_key(self):
"""
Generate a new ssh private and public key
"""
web_command(
command=["ssh-keygen", "-q", "-t", "rsa", "-N", "", "-C",
"datacats generated {0}@{1}".format(
getuser(), gethostname()),
"-f", "/output/id_rsa"],
rw={self.profiledir: '/output'},
) | python | def generate_ssh_key(self):
"""
Generate a new ssh private and public key
"""
web_command(
command=["ssh-keygen", "-q", "-t", "rsa", "-N", "", "-C",
"datacats generated {0}@{1}".format(
getuser(), gethostname()),
"-f", "/output/id_rsa"],
rw={self.profiledir: '/output'},
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datacats/datacats | datacats/userprofile.py | UserProfile.create | def create(self, environment, target_name):
"""
Sends "create project" command to the remote server
"""
remote_server_command(
["ssh", environment.deploy_target, "create", target_name],
environment, self,
clean_up=True,
) | python | def create(self, environment, target_name):
"""
Sends "create project" command to the remote server
"""
remote_server_command(
["ssh", environment.deploy_target, "create", target_name],
environment, self,
clean_up=True,
) | [
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datacats/datacats | datacats/userprofile.py | UserProfile.admin_password | def admin_password(self, environment, target_name, password):
"""
Return True if password was set successfully
"""
try:
remote_server_command(
["ssh", environment.deploy_target,
"admin_password", target_name, password],
environment, self,
clean_up=True
)
return True
except WebCommandError:
return False | python | def admin_password(self, environment, target_name, password):
"""
Return True if password was set successfully
"""
try:
remote_server_command(
["ssh", environment.deploy_target,
"admin_password", target_name, password],
environment, self,
clean_up=True
)
return True
except WebCommandError:
return False | [
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datacats/datacats | datacats/userprofile.py | UserProfile.deploy | def deploy(self, environment, target_name, stream_output=None):
"""
Return True if deployment was successful
"""
try:
remote_server_command(
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],
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stream_output=stream_output,
clean_up=True,
)
except WebCommandError as e:
raise DatacatsError(
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" datacats was not able to copy data to the remote server"
.format((target_name,)),
parent_exception=e
)
try:
remote_server_command(
[
"ssh", environment.deploy_target, "install", target_name,
],
environment, self,
clean_up=True,
)
return True
except WebCommandError as e:
raise DatacatsError(
"Unable to deploy `{0}` to remote server for some reason:\n"
"datacats copied data to the server but failed to register\n"
"(or `install`) the new catalog"
.format((target_name,)),
parent_exception=e
) | python | def deploy(self, environment, target_name, stream_output=None):
"""
Return True if deployment was successful
"""
try:
remote_server_command(
[
"rsync", "-lrv", "--safe-links", "--munge-links",
"--delete", "--inplace", "--chmod=ugo=rwX",
"--exclude=.datacats-environment",
"--exclude=.git",
"/project/.",
environment.deploy_target + ':' + target_name
],
environment, self,
include_project_dir=True,
stream_output=stream_output,
clean_up=True,
)
except WebCommandError as e:
raise DatacatsError(
"Unable to deploy `{0}` to remote server for some reason:\n"
" datacats was not able to copy data to the remote server"
.format((target_name,)),
parent_exception=e
)
try:
remote_server_command(
[
"ssh", environment.deploy_target, "install", target_name,
],
environment, self,
clean_up=True,
)
return True
except WebCommandError as e:
raise DatacatsError(
"Unable to deploy `{0}` to remote server for some reason:\n"
"datacats copied data to the server but failed to register\n"
"(or `install`) the new catalog"
.format((target_name,)),
parent_exception=e
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Britefury/batchup | batchup/sampling.py | num_batches | def num_batches(n, batch_size):
"""Compute the number of mini-batches required to cover a data set of
size `n` using batches of size `batch_size`.
Parameters
----------
n: int
the number of samples in the data set
batch_size: int
the mini-batch size
Returns
-------
int: the number of batches required
"""
b = n // batch_size
if n % batch_size > 0:
b += 1
return b | python | def num_batches(n, batch_size):
"""Compute the number of mini-batches required to cover a data set of
size `n` using batches of size `batch_size`.
Parameters
----------
n: int
the number of samples in the data set
batch_size: int
the mini-batch size
Returns
-------
int: the number of batches required
"""
b = n // batch_size
if n % batch_size > 0:
b += 1
return b | [
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the mini-batch size
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Britefury/batchup | batchup/sampling.py | StandardSampler.num_indices_generated | def num_indices_generated(self):
"""
Get the number of indices that would be generated by this
sampler.
Returns
-------
int, `np.inf` or `None`.
An int if the number of samples is known, `np.inf` if it is
infinite or `None` if the number of samples is unknown.
"""
if self.repeats == -1:
return np.inf
else:
return self.length * self.repeats | python | def num_indices_generated(self):
"""
Get the number of indices that would be generated by this
sampler.
Returns
-------
int, `np.inf` or `None`.
An int if the number of samples is known, `np.inf` if it is
infinite or `None` if the number of samples is unknown.
"""
if self.repeats == -1:
return np.inf
else:
return self.length * self.repeats | [
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Britefury/batchup | batchup/sampling.py | StandardSampler.in_order_indices_batch_iterator | def in_order_indices_batch_iterator(self, batch_size):
"""
Create an iterator that generates in-order mini-batches of sample
indices. The batches will have `batch_size` elements, with the
exception of the final batch which will have less if there are not
enough samples left to fill it.
The generated mini-batches indices take the form of 1D NumPy integer
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Parameters
----------
batch_size: int
Mini-batch size
Returns
-------
iterator
An iterator that generates mini-batches in the form of 1D NumPy
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"""
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yield np.arange(i, min(i + batch_size, self.length))
else:
repeats = self.repeats
i = 0
while True:
j = i + batch_size
if j <= self.length:
# Within size of data
yield np.arange(i, j)
i = j
elif j <= self.length * 2:
# One restart is required
# Reduce the number of remaining repeats
if repeats != -1:
repeats -= 1
if repeats == 0:
# Finished; emit remaining elements
if i < self.length:
yield np.arange(i, self.length)
break
# Wrap over
# Compute number of elements required to make up
# the batch
k = batch_size - (self.length - i)
yield np.append(np.arange(i, self.length),
np.arange(0, k), axis=0)
i = k
else:
# Multiple restarts required to fill the batch
batch_ndx = np.arange(0)
# i = 0
while len(batch_ndx) < batch_size:
# Wrap over
k = min(batch_size - len(batch_ndx), self.length - i)
batch_ndx = np.append(
batch_ndx, np.arange(i, i + k), axis=0)
i += k
if i >= self.length:
i -= self.length
# Reduce the number of remaining repeats
if repeats != -1:
repeats -= 1
if repeats == 0:
break
if len(batch_ndx) > 0:
yield batch_ndx
if repeats == 0:
break | python | def in_order_indices_batch_iterator(self, batch_size):
"""
Create an iterator that generates in-order mini-batches of sample
indices. The batches will have `batch_size` elements, with the
exception of the final batch which will have less if there are not
enough samples left to fill it.
The generated mini-batches indices take the form of 1D NumPy integer
arrays.
Parameters
----------
batch_size: int
Mini-batch size
Returns
-------
iterator
An iterator that generates mini-batches in the form of 1D NumPy
integer arrays.
"""
if self.repeats == 1:
for i in range(0, self.length, batch_size):
yield np.arange(i, min(i + batch_size, self.length))
else:
repeats = self.repeats
i = 0
while True:
j = i + batch_size
if j <= self.length:
# Within size of data
yield np.arange(i, j)
i = j
elif j <= self.length * 2:
# One restart is required
# Reduce the number of remaining repeats
if repeats != -1:
repeats -= 1
if repeats == 0:
# Finished; emit remaining elements
if i < self.length:
yield np.arange(i, self.length)
break
# Wrap over
# Compute number of elements required to make up
# the batch
k = batch_size - (self.length - i)
yield np.append(np.arange(i, self.length),
np.arange(0, k), axis=0)
i = k
else:
# Multiple restarts required to fill the batch
batch_ndx = np.arange(0)
# i = 0
while len(batch_ndx) < batch_size:
# Wrap over
k = min(batch_size - len(batch_ndx), self.length - i)
batch_ndx = np.append(
batch_ndx, np.arange(i, i + k), axis=0)
i += k
if i >= self.length:
i -= self.length
# Reduce the number of remaining repeats
if repeats != -1:
repeats -= 1
if repeats == 0:
break
if len(batch_ndx) > 0:
yield batch_ndx
if repeats == 0:
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The generated mini-batches indices take the form of 1D NumPy integer
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Mini-batch size
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Britefury/batchup | batchup/sampling.py | StandardSampler.shuffled_indices_batch_iterator | def shuffled_indices_batch_iterator(self, batch_size, shuffle_rng):
"""
Create an iterator that generates randomly shuffled mini-batches of
sample indices. The batches will have `batch_size` elements, with the
exception of the final batch which will have less if there are not
enough samples left to fill it.
The generated mini-batches indices take the form of 1D NumPy integer
arrays.
Parameters
----------
batch_size: int
Mini-batch size
shuffle_rng: a `numpy.random.RandomState` that will be used to
randomise element order.
Returns
-------
iterator
An iterator that generates mini-batches in the form of 1D NumPy
integer arrays.
"""
if self.repeats == 1:
indices = shuffle_rng.permutation(self.length)
for i in range(0, self.length, batch_size):
yield indices[i:i + batch_size]
else:
repeats = self.repeats
indices = shuffle_rng.permutation(self.length)
i = 0
while True:
j = i + batch_size
if j <= self.length:
# Within size of data
yield indices[i:j]
i = j
else:
# Multiple restarts required to fill the batch
batch_ndx = np.arange(0)
while len(batch_ndx) < batch_size:
# Wrap over
k = min(batch_size - len(batch_ndx), self.length - i)
batch_ndx = np.append(
batch_ndx, indices[i:i + k], axis=0)
i += k
if i >= self.length:
# Loop over; new permutation
indices = shuffle_rng.permutation(self.length)
i -= self.length
# Reduce the number of remaining repeats
if repeats != -1:
repeats -= 1
if repeats == 0:
break
if len(batch_ndx) > 0:
yield batch_ndx
if repeats == 0:
break | python | def shuffled_indices_batch_iterator(self, batch_size, shuffle_rng):
"""
Create an iterator that generates randomly shuffled mini-batches of
sample indices. The batches will have `batch_size` elements, with the
exception of the final batch which will have less if there are not
enough samples left to fill it.
The generated mini-batches indices take the form of 1D NumPy integer
arrays.
Parameters
----------
batch_size: int
Mini-batch size
shuffle_rng: a `numpy.random.RandomState` that will be used to
randomise element order.
Returns
-------
iterator
An iterator that generates mini-batches in the form of 1D NumPy
integer arrays.
"""
if self.repeats == 1:
indices = shuffle_rng.permutation(self.length)
for i in range(0, self.length, batch_size):
yield indices[i:i + batch_size]
else:
repeats = self.repeats
indices = shuffle_rng.permutation(self.length)
i = 0
while True:
j = i + batch_size
if j <= self.length:
# Within size of data
yield indices[i:j]
i = j
else:
# Multiple restarts required to fill the batch
batch_ndx = np.arange(0)
while len(batch_ndx) < batch_size:
# Wrap over
k = min(batch_size - len(batch_ndx), self.length - i)
batch_ndx = np.append(
batch_ndx, indices[i:i + k], axis=0)
i += k
if i >= self.length:
# Loop over; new permutation
indices = shuffle_rng.permutation(self.length)
i -= self.length
# Reduce the number of remaining repeats
if repeats != -1:
repeats -= 1
if repeats == 0:
break
if len(batch_ndx) > 0:
yield batch_ndx
if repeats == 0:
break | [
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Britefury/batchup | batchup/sampling.py | WeightedSampler.shuffled_indices_batch_iterator | def shuffled_indices_batch_iterator(self, batch_size, shuffle_rng):
"""
Create an iterator that generates randomly shuffled mini-batches of
sample indices. The batches will have `batch_size` elements.
The generated mini-batches indices take the form of 1D NumPy integer
arrays.
Parameters
----------
batch_size: int
Mini-batch size
shuffle_rng: a `numpy.random.RandomState` that will be used to
randomise element order.
Returns
-------
iterator
An iterator that generates mini-batches in the form of 1D NumPy
integer arrays.
"""
while True:
yield shuffle_rng.choice(len(self.weights), size=(batch_size,),
p=self.weights) | python | def shuffled_indices_batch_iterator(self, batch_size, shuffle_rng):
"""
Create an iterator that generates randomly shuffled mini-batches of
sample indices. The batches will have `batch_size` elements.
The generated mini-batches indices take the form of 1D NumPy integer
arrays.
Parameters
----------
batch_size: int
Mini-batch size
shuffle_rng: a `numpy.random.RandomState` that will be used to
randomise element order.
Returns
-------
iterator
An iterator that generates mini-batches in the form of 1D NumPy
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"""
while True:
yield shuffle_rng.choice(len(self.weights), size=(batch_size,),
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Britefury/batchup | batchup/sampling.py | WeightedSampler.class_balancing_sample_weights | def class_balancing_sample_weights(y):
"""
Compute sample weight given an array of sample classes. The weights
are assigned on a per-class basis and the per-class weights are
inversely proportional to their frequency.
Parameters
----------
y: NumPy array, 1D dtype=int
sample classes, values must be 0 or positive
Returns
-------
NumPy array, 1D dtype=float
per sample weight array
"""
h = np.bincount(y)
cls_weight = 1.0 / (h.astype(float) * len(np.nonzero(h)[0]))
cls_weight[np.isnan(cls_weight)] = 0.0
sample_weight = cls_weight[y]
return sample_weight | python | def class_balancing_sample_weights(y):
"""
Compute sample weight given an array of sample classes. The weights
are assigned on a per-class basis and the per-class weights are
inversely proportional to their frequency.
Parameters
----------
y: NumPy array, 1D dtype=int
sample classes, values must be 0 or positive
Returns
-------
NumPy array, 1D dtype=float
per sample weight array
"""
h = np.bincount(y)
cls_weight = 1.0 / (h.astype(float) * len(np.nonzero(h)[0]))
cls_weight[np.isnan(cls_weight)] = 0.0
sample_weight = cls_weight[y]
return sample_weight | [
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Britefury/batchup | batchup/sampling.py | WeightedSubsetSampler.shuffled_indices_batch_iterator | def shuffled_indices_batch_iterator(self, batch_size, shuffle_rng):
"""
Create an iterator that generates randomly shuffled mini-batches of
sample indices. The batches will have `batch_size` elements.
The generated mini-batches indices take the form of 1D NumPy integer
arrays.
Parameters
----------
batch_size: int
Mini-batch size
shuffle_rng: a `numpy.random.RandomState` that will be used to
randomise element order.
Returns
-------
iterator
An iterator that generates mini-batches in the form of 1D NumPy
integer arrays.
"""
while True:
yield shuffle_rng.choice(self.indices, size=(batch_size,),
p=self.sub_weights) | python | def shuffled_indices_batch_iterator(self, batch_size, shuffle_rng):
"""
Create an iterator that generates randomly shuffled mini-batches of
sample indices. The batches will have `batch_size` elements.
The generated mini-batches indices take the form of 1D NumPy integer
arrays.
Parameters
----------
batch_size: int
Mini-batch size
shuffle_rng: a `numpy.random.RandomState` that will be used to
randomise element order.
Returns
-------
iterator
An iterator that generates mini-batches in the form of 1D NumPy
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"""
while True:
yield shuffle_rng.choice(self.indices, size=(batch_size,),
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Britefury/batchup | batchup/sampling.py | WeightedSubsetSampler.class_balancing_sampler | def class_balancing_sampler(y, indices):
"""
Construct a `WeightedSubsetSampler` that compensates for class
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Parameters
----------
y: NumPy array, 1D dtype=int
sample classes, values must be 0 or positive
indices: NumPy array, 1D dtype=int
An array of indices that identify the subset of samples drawn
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WeightedSubsetSampler instance
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weights = WeightedSampler.class_balancing_sample_weights(y[indices])
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"""
Construct a `WeightedSubsetSampler` that compensates for class
imbalance.
Parameters
----------
y: NumPy array, 1D dtype=int
sample classes, values must be 0 or positive
indices: NumPy array, 1D dtype=int
An array of indices that identify the subset of samples drawn
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Returns
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WeightedSubsetSampler instance
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weights = WeightedSampler.class_balancing_sample_weights(y[indices])
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datacats/datacats | datacats/network.py | wait_for_service_available | def wait_for_service_available(container, url, timeout):
"""
Wait up to timeout seconds for service at host:port
to start.
Returns True if service becomes available, False if the
container stops or raises ServiceTimeout if timeout is
reached.
"""
start = time.time()
remaining = timeout
while True:
remaining = start + timeout - time.time()
if remaining < 0:
raise ServiceTimeout
try:
response = get(url,
timeout=min(remaining, REQUEST_TIMEOUT_SECONDS))
if 500 <= response.status_code < 600:
return False
return True
except (ConnectionError, Timeout):
pass
if not inspect_container(container)['State']['Running']:
return False
remaining = start + timeout - time.time()
delay = max(0, min(RETRY_DELAY_SECONDS, remaining))
time.sleep(delay)
raise ServiceTimeout | python | def wait_for_service_available(container, url, timeout):
"""
Wait up to timeout seconds for service at host:port
to start.
Returns True if service becomes available, False if the
container stops or raises ServiceTimeout if timeout is
reached.
"""
start = time.time()
remaining = timeout
while True:
remaining = start + timeout - time.time()
if remaining < 0:
raise ServiceTimeout
try:
response = get(url,
timeout=min(remaining, REQUEST_TIMEOUT_SECONDS))
if 500 <= response.status_code < 600:
return False
return True
except (ConnectionError, Timeout):
pass
if not inspect_container(container)['State']['Running']:
return False
remaining = start + timeout - time.time()
delay = max(0, min(RETRY_DELAY_SECONDS, remaining))
time.sleep(delay)
raise ServiceTimeout | [
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Britefury/batchup | batchup/config.py | get_data_path | def get_data_path(filename):
"""
Get the path of the given file within the batchup data directory
Parameters
----------
filename: str
The filename to locate within the batchup data directory
Returns
-------
str
The full path of the file
"""
if os.path.isabs(filename):
return filename
else:
return os.path.join(get_data_dir(), filename) | python | def get_data_path(filename):
"""
Get the path of the given file within the batchup data directory
Parameters
----------
filename: str
The filename to locate within the batchup data directory
Returns
-------
str
The full path of the file
"""
if os.path.isabs(filename):
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else:
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Britefury/batchup | batchup/config.py | download | def download(path, source_url):
"""
Download a file to a given path from a given URL, if it does not exist.
Parameters
----------
path: str
The (destination) path of the file on the local filesystem
source_url: str
The URL from which to download the file
Returns
-------
str
The path of the file
"""
dir_path = os.path.dirname(path)
if not os.path.exists(dir_path):
os.makedirs(dir_path)
if not os.path.exists(path):
print('Downloading {} to {}'.format(source_url, path))
filename = source_url.split('/')[-1]
def _progress(count, block_size, total_size):
sys.stdout.write('\rDownloading {} {:.2%}'.format(
filename, float(count * block_size) / float(total_size)))
sys.stdout.flush()
try:
urlretrieve(source_url, path, reporthook=_progress)
except:
sys.stdout.write('\r')
# Exception; remove any partially downloaded file and re-raise
if os.path.exists(path):
os.remove(path)
raise
sys.stdout.write('\r')
return path | python | def download(path, source_url):
"""
Download a file to a given path from a given URL, if it does not exist.
Parameters
----------
path: str
The (destination) path of the file on the local filesystem
source_url: str
The URL from which to download the file
Returns
-------
str
The path of the file
"""
dir_path = os.path.dirname(path)
if not os.path.exists(dir_path):
os.makedirs(dir_path)
if not os.path.exists(path):
print('Downloading {} to {}'.format(source_url, path))
filename = source_url.split('/')[-1]
def _progress(count, block_size, total_size):
sys.stdout.write('\rDownloading {} {:.2%}'.format(
filename, float(count * block_size) / float(total_size)))
sys.stdout.flush()
try:
urlretrieve(source_url, path, reporthook=_progress)
except:
sys.stdout.write('\r')
# Exception; remove any partially downloaded file and re-raise
if os.path.exists(path):
os.remove(path)
raise
sys.stdout.write('\r')
return path | [
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Parameters
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path: str
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source_url: str
The URL from which to download the file
Returns
-------
str
The path of the file | [
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Britefury/batchup | batchup/config.py | compute_sha256 | def compute_sha256(path):
"""
Compute the SHA-256 hash of the file at the given path
Parameters
----------
path: str
The path of the file
Returns
-------
str
The SHA-256 HEX digest
"""
hasher = hashlib.sha256()
with open(path, 'rb') as f:
# 10MB chunks
for chunk in iter(lambda: f.read(10 * 1024 * 1024), b''):
hasher.update(chunk)
return hasher.hexdigest() | python | def compute_sha256(path):
"""
Compute the SHA-256 hash of the file at the given path
Parameters
----------
path: str
The path of the file
Returns
-------
str
The SHA-256 HEX digest
"""
hasher = hashlib.sha256()
with open(path, 'rb') as f:
# 10MB chunks
for chunk in iter(lambda: f.read(10 * 1024 * 1024), b''):
hasher.update(chunk)
return hasher.hexdigest() | [
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path: str
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Britefury/batchup | batchup/config.py | verify_file | def verify_file(path, sha256):
"""
Verify the integrity of a file by checking its SHA-256 hash.
If no digest is supplied, the digest is printed to the console.
Closely follows the code in `torchvision.datasets.utils.check_integrity`
Parameters
----------
path: str
The path of the file to check
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
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Returns
-------
bool
Indicates if the file passes the integrity check or not
"""
if not os.path.isfile(path):
return False
digest = compute_sha256(path)
if sha256 is None:
# No digest supplied; report it to the console so a develop can fill
# it in
print('SHA-256 of {}:'.format(path))
print(' "{}"'.format(digest))
else:
if digest != sha256:
return False
return True | python | def verify_file(path, sha256):
"""
Verify the integrity of a file by checking its SHA-256 hash.
If no digest is supplied, the digest is printed to the console.
Closely follows the code in `torchvision.datasets.utils.check_integrity`
Parameters
----------
path: str
The path of the file to check
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
digest of the file to the console
Returns
-------
bool
Indicates if the file passes the integrity check or not
"""
if not os.path.isfile(path):
return False
digest = compute_sha256(path)
if sha256 is None:
# No digest supplied; report it to the console so a develop can fill
# it in
print('SHA-256 of {}:'.format(path))
print(' "{}"'.format(digest))
else:
if digest != sha256:
return False
return True | [
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----------
path: str
The path of the file to check
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
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Britefury/batchup | batchup/config.py | download_and_verify | def download_and_verify(path, source_url, sha256):
"""
Download a file to a given path from a given URL, if it does not exist.
After downloading it, verify it integrity by checking the SHA-256 hash.
Parameters
----------
path: str
The (destination) path of the file on the local filesystem
source_url: str
The URL from which to download the file
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
digest of the file to the console
Returns
-------
str or None
The path of the file if successfully downloaded otherwise `None`
"""
if os.path.exists(path):
# Already exists?
# Nothing to do, except print the SHA-256 if necessary
if sha256 is None:
print('The SHA-256 of {} is "{}"'.format(
path, compute_sha256(path)))
return path
# Compute the path of the unverified file
unverified_path = path + '.unverified'
for i in range(_MAX_DOWNLOAD_TRIES):
# Download it
try:
unverified_path = download(unverified_path, source_url)
except Exception as e:
# Report failure
print(
'Download of {} unsuccessful; error {}; '
'deleting and re-trying...'.format(source_url, e))
# Delete so that we can retry
if os.path.exists(unverified_path):
os.remove(unverified_path)
else:
if os.path.exists(unverified_path):
# Got something...
if verify_file(unverified_path, sha256):
# Success: rename the unverified file to the destination
# filename
os.rename(unverified_path, path)
return path
else:
# Report failure
print(
'Download of {} unsuccessful; verification failed; '
'deleting and re-trying...'.format(source_url))
# Delete so that we can retry
os.remove(unverified_path)
print('Did not succeed in downloading {} (tried {} times)'.format(
source_url, _MAX_DOWNLOAD_TRIES
))
return None | python | def download_and_verify(path, source_url, sha256):
"""
Download a file to a given path from a given URL, if it does not exist.
After downloading it, verify it integrity by checking the SHA-256 hash.
Parameters
----------
path: str
The (destination) path of the file on the local filesystem
source_url: str
The URL from which to download the file
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
digest of the file to the console
Returns
-------
str or None
The path of the file if successfully downloaded otherwise `None`
"""
if os.path.exists(path):
# Already exists?
# Nothing to do, except print the SHA-256 if necessary
if sha256 is None:
print('The SHA-256 of {} is "{}"'.format(
path, compute_sha256(path)))
return path
# Compute the path of the unverified file
unverified_path = path + '.unverified'
for i in range(_MAX_DOWNLOAD_TRIES):
# Download it
try:
unverified_path = download(unverified_path, source_url)
except Exception as e:
# Report failure
print(
'Download of {} unsuccessful; error {}; '
'deleting and re-trying...'.format(source_url, e))
# Delete so that we can retry
if os.path.exists(unverified_path):
os.remove(unverified_path)
else:
if os.path.exists(unverified_path):
# Got something...
if verify_file(unverified_path, sha256):
# Success: rename the unverified file to the destination
# filename
os.rename(unverified_path, path)
return path
else:
# Report failure
print(
'Download of {} unsuccessful; verification failed; '
'deleting and re-trying...'.format(source_url))
# Delete so that we can retry
os.remove(unverified_path)
print('Did not succeed in downloading {} (tried {} times)'.format(
source_url, _MAX_DOWNLOAD_TRIES
))
return None | [
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The (destination) path of the file on the local filesystem
source_url: str
The URL from which to download the file
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
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Returns
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Britefury/batchup | batchup/config.py | copy_and_verify | def copy_and_verify(path, source_path, sha256):
"""
Copy a file to a given path from a given path, if it does not exist.
After copying it, verify it integrity by checking the SHA-256 hash.
Parameters
----------
path: str
The (destination) path of the file on the local filesystem
source_path: str
The path from which to copy the file
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
digest of the file to the console
Returns
-------
str or None
The path of the file if successfully downloaded otherwise `None`
"""
if os.path.exists(path):
# Already exists?
# Nothing to do, except print the SHA-256 if necessary
if sha256 is None:
print('The SHA-256 of {} is "{}"'.format(
path, compute_sha256(path)))
return path
if not os.path.exists(source_path):
return None
# Compute the path of the unverified file
unverified_path = path + '.unverified'
# Copy it
dir_path = os.path.dirname(path)
if not os.path.exists(dir_path):
os.makedirs(dir_path)
shutil.copy(source_path, unverified_path)
if os.path.exists(unverified_path):
# Got something...
if verify_file(unverified_path, sha256):
# Success: rename the unverified file to the destination
# filename
os.rename(unverified_path, path)
return path
else:
# Report failure
print('SHA verification of file {} failed'.format(source_path))
# Delete
os.remove(unverified_path)
return None | python | def copy_and_verify(path, source_path, sha256):
"""
Copy a file to a given path from a given path, if it does not exist.
After copying it, verify it integrity by checking the SHA-256 hash.
Parameters
----------
path: str
The (destination) path of the file on the local filesystem
source_path: str
The path from which to copy the file
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
digest of the file to the console
Returns
-------
str or None
The path of the file if successfully downloaded otherwise `None`
"""
if os.path.exists(path):
# Already exists?
# Nothing to do, except print the SHA-256 if necessary
if sha256 is None:
print('The SHA-256 of {} is "{}"'.format(
path, compute_sha256(path)))
return path
if not os.path.exists(source_path):
return None
# Compute the path of the unverified file
unverified_path = path + '.unverified'
# Copy it
dir_path = os.path.dirname(path)
if not os.path.exists(dir_path):
os.makedirs(dir_path)
shutil.copy(source_path, unverified_path)
if os.path.exists(unverified_path):
# Got something...
if verify_file(unverified_path, sha256):
# Success: rename the unverified file to the destination
# filename
os.rename(unverified_path, path)
return path
else:
# Report failure
print('SHA verification of file {} failed'.format(source_path))
# Delete
os.remove(unverified_path)
return None | [
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The (destination) path of the file on the local filesystem
source_path: str
The path from which to copy the file
sha256: str
The expected SHA-256 hex digest of the file, or `None` to print the
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Returns
-------
str or None
The path of the file if successfully downloaded otherwise `None` | [
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datacats/datacats | datacats/template.py | ckan_extension_template | def ckan_extension_template(name, target):
"""
Create ckanext-(name) in target directory.
"""
setupdir = '{0}/ckanext-{1}theme'.format(target, name)
extdir = setupdir + '/ckanext/{0}theme'.format(name)
templatedir = extdir + '/templates/'
staticdir = extdir + '/static/datacats'
makedirs(templatedir + '/home/snippets')
makedirs(staticdir)
here = dirname(__file__)
copyfile(here + '/images/chart.png', staticdir + '/chart.png')
copyfile(here + '/images/datacats-footer.png',
staticdir + '/datacats-footer.png')
filecontents = [
(setupdir + '/setup.py', SETUP_PY),
(setupdir + '/.gitignore', DOT_GITIGNORE),
(setupdir + '/ckanext/__init__.py', NAMESPACE_PACKAGE),
(extdir + '/__init__.py', ''),
(extdir + '/plugins.py', PLUGINS_PY),
(templatedir + '/home/snippets/promoted.html', PROMOTED_SNIPPET),
(templatedir + '/footer.html', FOOTER_HTML),
]
for filename, content in filecontents:
with open(filename, 'w') as f:
f.write(content.replace('##name##', name)) | python | def ckan_extension_template(name, target):
"""
Create ckanext-(name) in target directory.
"""
setupdir = '{0}/ckanext-{1}theme'.format(target, name)
extdir = setupdir + '/ckanext/{0}theme'.format(name)
templatedir = extdir + '/templates/'
staticdir = extdir + '/static/datacats'
makedirs(templatedir + '/home/snippets')
makedirs(staticdir)
here = dirname(__file__)
copyfile(here + '/images/chart.png', staticdir + '/chart.png')
copyfile(here + '/images/datacats-footer.png',
staticdir + '/datacats-footer.png')
filecontents = [
(setupdir + '/setup.py', SETUP_PY),
(setupdir + '/.gitignore', DOT_GITIGNORE),
(setupdir + '/ckanext/__init__.py', NAMESPACE_PACKAGE),
(extdir + '/__init__.py', ''),
(extdir + '/plugins.py', PLUGINS_PY),
(templatedir + '/home/snippets/promoted.html', PROMOTED_SNIPPET),
(templatedir + '/footer.html', FOOTER_HTML),
]
for filename, content in filecontents:
with open(filename, 'w') as f:
f.write(content.replace('##name##', name)) | [
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datacats/datacats | datacats/cli/shell.py | shell | def shell(environment, opts):
"""Run a command or interactive shell within this environment
Usage:
datacats [-d] [-s NAME] shell [ENVIRONMENT [COMMAND...]]
Options:
-d --detach Run the resulting container in the background
-s --site=NAME Specify a site to run the shell on [default: primary]
ENVIRONMENT may be an environment name or a path to an environment directory.
Default: '.'
"""
environment.require_data()
environment.start_supporting_containers()
return environment.interactive_shell(
opts['COMMAND'],
detach=opts['--detach']
) | python | def shell(environment, opts):
"""Run a command or interactive shell within this environment
Usage:
datacats [-d] [-s NAME] shell [ENVIRONMENT [COMMAND...]]
Options:
-d --detach Run the resulting container in the background
-s --site=NAME Specify a site to run the shell on [default: primary]
ENVIRONMENT may be an environment name or a path to an environment directory.
Default: '.'
"""
environment.require_data()
environment.start_supporting_containers()
return environment.interactive_shell(
opts['COMMAND'],
detach=opts['--detach']
) | [
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datacats/datacats | datacats/cli/shell.py | paster | def paster(opts):
"""Run a paster command from the current directory
Usage:
datacats paster [-d] [-s NAME] [COMMAND...]
Options:
-s --site=NAME Specify a site to run this paster command on [default: primary]
-d --detach Run the resulting container in the background
You must be inside a datacats environment to run this. The paster command will
run within your current directory inside the environment. You don't need to
specify the --plugin option. The --config option also need not be specified.
"""
environment = Environment.load('.')
environment.require_data()
environment.start_supporting_containers()
if not opts['COMMAND']:
opts['COMMAND'] = ['--', 'help']
assert opts['COMMAND'][0] == '--'
return environment.interactive_shell(
opts['COMMAND'][1:],
paster=True,
detach=opts['--detach']
) | python | def paster(opts):
"""Run a paster command from the current directory
Usage:
datacats paster [-d] [-s NAME] [COMMAND...]
Options:
-s --site=NAME Specify a site to run this paster command on [default: primary]
-d --detach Run the resulting container in the background
You must be inside a datacats environment to run this. The paster command will
run within your current directory inside the environment. You don't need to
specify the --plugin option. The --config option also need not be specified.
"""
environment = Environment.load('.')
environment.require_data()
environment.start_supporting_containers()
if not opts['COMMAND']:
opts['COMMAND'] = ['--', 'help']
assert opts['COMMAND'][0] == '--'
return environment.interactive_shell(
opts['COMMAND'][1:],
paster=True,
detach=opts['--detach']
) | [
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-d --detach Run the resulting container in the background
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datacats/datacats | datacats/task.py | save_new_site | def save_new_site(site_name, sitedir, srcdir, port, address, site_url,
passwords):
"""
Add a site's configuration to the source dir and site dir
"""
cp = ConfigParser.SafeConfigParser()
cp.read([srcdir + '/.datacats-environment'])
section_name = 'site_' + site_name
if not cp.has_section(section_name):
cp.add_section(section_name)
cp.set(section_name, 'port', str(port))
if address:
cp.set(section_name, 'address', address)
if site_url:
cp.set(section_name, 'site_url', site_url)
with open(srcdir + '/.datacats-environment', 'w') as config:
cp.write(config)
# save passwords to datadir
cp = ConfigParser.SafeConfigParser()
cp.add_section('passwords')
for n in sorted(passwords):
cp.set('passwords', n.lower(), passwords[n])
# Write to the sitedir so we maintain separate passwords.
with open(sitedir + '/passwords.ini', 'w') as config:
cp.write(config) | python | def save_new_site(site_name, sitedir, srcdir, port, address, site_url,
passwords):
"""
Add a site's configuration to the source dir and site dir
"""
cp = ConfigParser.SafeConfigParser()
cp.read([srcdir + '/.datacats-environment'])
section_name = 'site_' + site_name
if not cp.has_section(section_name):
cp.add_section(section_name)
cp.set(section_name, 'port', str(port))
if address:
cp.set(section_name, 'address', address)
if site_url:
cp.set(section_name, 'site_url', site_url)
with open(srcdir + '/.datacats-environment', 'w') as config:
cp.write(config)
# save passwords to datadir
cp = ConfigParser.SafeConfigParser()
cp.add_section('passwords')
for n in sorted(passwords):
cp.set('passwords', n.lower(), passwords[n])
# Write to the sitedir so we maintain separate passwords.
with open(sitedir + '/passwords.ini', 'w') as config:
cp.write(config) | [
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datacats/datacats | datacats/task.py | save_new_environment | def save_new_environment(name, datadir, srcdir, ckan_version,
deploy_target=None, always_prod=False):
"""
Save an environment's configuration to the source dir and data dir
"""
with open(datadir + '/.version', 'w') as f:
f.write('2')
cp = ConfigParser.SafeConfigParser()
cp.read(srcdir + '/.datacats-environment')
if not cp.has_section('datacats'):
cp.add_section('datacats')
cp.set('datacats', 'name', name)
cp.set('datacats', 'ckan_version', ckan_version)
if deploy_target:
if not cp.has_section('deploy'):
cp.add_section('deploy')
cp.set('deploy', 'target', deploy_target)
if always_prod:
cp.set('datacats', 'always_prod', 'true')
with open(srcdir + '/.datacats-environment', 'w') as config:
cp.write(config)
save_srcdir_location(datadir, srcdir) | python | def save_new_environment(name, datadir, srcdir, ckan_version,
deploy_target=None, always_prod=False):
"""
Save an environment's configuration to the source dir and data dir
"""
with open(datadir + '/.version', 'w') as f:
f.write('2')
cp = ConfigParser.SafeConfigParser()
cp.read(srcdir + '/.datacats-environment')
if not cp.has_section('datacats'):
cp.add_section('datacats')
cp.set('datacats', 'name', name)
cp.set('datacats', 'ckan_version', ckan_version)
if deploy_target:
if not cp.has_section('deploy'):
cp.add_section('deploy')
cp.set('deploy', 'target', deploy_target)
if always_prod:
cp.set('datacats', 'always_prod', 'true')
with open(srcdir + '/.datacats-environment', 'w') as config:
cp.write(config)
save_srcdir_location(datadir, srcdir) | [
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datacats/datacats | datacats/task.py | find_environment_dirs | def find_environment_dirs(environment_name=None, data_only=False):
"""
:param environment_name: exising environment name, path or None to
look in current or parent directories for project
returns (srcdir, extension_dir, datadir)
extension_dir is the name of extension directory user was in/referenced,
default: 'ckan'. This value is used by the paster cli command.
datadir will be None if environment_name was a path or None (not a name)
"""
docker.require_images()
if environment_name is None:
environment_name = '.'
extension_dir = 'ckan'
if validate.valid_name(environment_name) and path.isdir(
path.expanduser('~/.datacats/' + environment_name)):
# loading from a name
datadir = path.expanduser('~/.datacats/' + environment_name)
with open(datadir + '/project-dir') as pd:
srcdir = pd.read()
if not data_only and not path.exists(srcdir + '/.datacats-environment'):
raise DatacatsError(
'Environment data found but environment directory is'
' missing. Try again from the new environment directory'
' location or remove the environment data with'
' "datacats purge"')
return srcdir, extension_dir, datadir
# loading from a path
srcdir = path.abspath(environment_name)
if not path.isdir(srcdir):
raise DatacatsError('No environment found with that name')
wd = srcdir
oldwd = None
while not path.exists(wd + '/.datacats-environment'):
oldwd = wd
wd, _ = path.split(wd)
if wd == oldwd:
raise DatacatsError(
'Environment not found in {0} or above'.format(srcdir))
srcdir = wd
if oldwd:
_, extension_dir = path.split(oldwd)
return srcdir, extension_dir, None | python | def find_environment_dirs(environment_name=None, data_only=False):
"""
:param environment_name: exising environment name, path or None to
look in current or parent directories for project
returns (srcdir, extension_dir, datadir)
extension_dir is the name of extension directory user was in/referenced,
default: 'ckan'. This value is used by the paster cli command.
datadir will be None if environment_name was a path or None (not a name)
"""
docker.require_images()
if environment_name is None:
environment_name = '.'
extension_dir = 'ckan'
if validate.valid_name(environment_name) and path.isdir(
path.expanduser('~/.datacats/' + environment_name)):
# loading from a name
datadir = path.expanduser('~/.datacats/' + environment_name)
with open(datadir + '/project-dir') as pd:
srcdir = pd.read()
if not data_only and not path.exists(srcdir + '/.datacats-environment'):
raise DatacatsError(
'Environment data found but environment directory is'
' missing. Try again from the new environment directory'
' location or remove the environment data with'
' "datacats purge"')
return srcdir, extension_dir, datadir
# loading from a path
srcdir = path.abspath(environment_name)
if not path.isdir(srcdir):
raise DatacatsError('No environment found with that name')
wd = srcdir
oldwd = None
while not path.exists(wd + '/.datacats-environment'):
oldwd = wd
wd, _ = path.split(wd)
if wd == oldwd:
raise DatacatsError(
'Environment not found in {0} or above'.format(srcdir))
srcdir = wd
if oldwd:
_, extension_dir = path.split(oldwd)
return srcdir, extension_dir, None | [
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look in current or parent directories for project
returns (srcdir, extension_dir, datadir)
extension_dir is the name of extension directory user was in/referenced,
default: 'ckan'. This value is used by the paster cli command.
datadir will be None if environment_name was a path or None (not a name) | [
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datacats/datacats | datacats/task.py | load_environment | def load_environment(srcdir, datadir=None, allow_old=False):
"""
Load configuration values for an environment
:param srcdir: environment source directory
:param datadir: environment data direcory, if None will be discovered
from srcdir
:param allow_old: Don't throw an exception if this is an old site
This is only valid for sites that you are purging.
if datadir is None it will be discovered from srcdir
Returns (datadir, name, ckan_version, always_prod, deploy_target,
remote_server_key)
"""
cp = ConfigParser.SafeConfigParser()
try:
cp.read([srcdir + '/.datacats-environment'])
except ConfigParser.Error:
raise DatacatsError('Error reading environment information')
name = cp.get('datacats', 'name')
if datadir:
# update the link in case user moved their srcdir
save_srcdir_location(datadir, srcdir)
else:
datadir = path.expanduser('~/.datacats/' + name)
# FIXME: check if datadir is sane, project-dir points back to srcdir
if migrate.needs_format_conversion(datadir) and not allow_old:
raise DatacatsError('This environment uses an old format. You must'
' migrate to the new format. To do so, use the'
' "datacats migrate" command.')
if migrate.is_locked(datadir):
raise DatacatsError('Migration in progress, cannot continue.\n'
'If you interrupted a migration, you should'
' attempt manual recovery or contact us by'
' filing an issue at http://github.com/datacats/'
'datacats.\nAs a last resort, you could delete'
' all your stored data and create a new environment'
' by running "datacats purge" followed by'
' "datacats init".')
# FIXME: consider doing data_complete check here
ckan_version = cp.get('datacats', 'ckan_version')
try:
always_prod = cp.getboolean('datacats', 'always_prod')
except ConfigParser.NoOptionError:
always_prod = False
try:
extra_containers = cp.get('datacats', 'extra_containers').split(' ')
except ConfigParser.NoOptionError:
extra_containers = ()
# if remote_server's custom ssh connection
# address is defined,
# we overwrite the default datacats.com one
try:
deploy_target = cp.get('deploy', 'remote_server_user') \
+ "@" + cp.get('deploy', 'remote_server')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
deploy_target = DEFAULT_REMOTE_SERVER_TARGET
# if remote_server's ssh public key is given,
# we overwrite the default datacats.com one
try:
remote_server_key = cp.get('deploy', 'remote_server_key')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
remote_server_key = None
return (datadir, name, ckan_version, always_prod, deploy_target,
remote_server_key, extra_containers) | python | def load_environment(srcdir, datadir=None, allow_old=False):
"""
Load configuration values for an environment
:param srcdir: environment source directory
:param datadir: environment data direcory, if None will be discovered
from srcdir
:param allow_old: Don't throw an exception if this is an old site
This is only valid for sites that you are purging.
if datadir is None it will be discovered from srcdir
Returns (datadir, name, ckan_version, always_prod, deploy_target,
remote_server_key)
"""
cp = ConfigParser.SafeConfigParser()
try:
cp.read([srcdir + '/.datacats-environment'])
except ConfigParser.Error:
raise DatacatsError('Error reading environment information')
name = cp.get('datacats', 'name')
if datadir:
# update the link in case user moved their srcdir
save_srcdir_location(datadir, srcdir)
else:
datadir = path.expanduser('~/.datacats/' + name)
# FIXME: check if datadir is sane, project-dir points back to srcdir
if migrate.needs_format_conversion(datadir) and not allow_old:
raise DatacatsError('This environment uses an old format. You must'
' migrate to the new format. To do so, use the'
' "datacats migrate" command.')
if migrate.is_locked(datadir):
raise DatacatsError('Migration in progress, cannot continue.\n'
'If you interrupted a migration, you should'
' attempt manual recovery or contact us by'
' filing an issue at http://github.com/datacats/'
'datacats.\nAs a last resort, you could delete'
' all your stored data and create a new environment'
' by running "datacats purge" followed by'
' "datacats init".')
# FIXME: consider doing data_complete check here
ckan_version = cp.get('datacats', 'ckan_version')
try:
always_prod = cp.getboolean('datacats', 'always_prod')
except ConfigParser.NoOptionError:
always_prod = False
try:
extra_containers = cp.get('datacats', 'extra_containers').split(' ')
except ConfigParser.NoOptionError:
extra_containers = ()
# if remote_server's custom ssh connection
# address is defined,
# we overwrite the default datacats.com one
try:
deploy_target = cp.get('deploy', 'remote_server_user') \
+ "@" + cp.get('deploy', 'remote_server')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
deploy_target = DEFAULT_REMOTE_SERVER_TARGET
# if remote_server's ssh public key is given,
# we overwrite the default datacats.com one
try:
remote_server_key = cp.get('deploy', 'remote_server_key')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
remote_server_key = None
return (datadir, name, ckan_version, always_prod, deploy_target,
remote_server_key, extra_containers) | [
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:param allow_old: Don't throw an exception if this is an old site
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datacats/datacats | datacats/task.py | load_site | def load_site(srcdir, datadir, site_name=None):
"""
Load configuration values for a site.
Returns (port, address, site_url, passwords)
"""
if site_name is None:
site_name = 'primary'
if not validate.valid_name(site_name):
raise DatacatsError('{} is not a valid site name.'.format(site_name))
cp = ConfigParser.SafeConfigParser()
try:
cp.read([srcdir + '/.datacats-environment'])
except ConfigParser.Error:
raise DatacatsError('Error reading environment information')
site_section = 'site_' + site_name
try:
port = cp.getint(site_section, 'port')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
port = None
try:
address = cp.get(site_section, 'address')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
address = None
try:
site_url = cp.get(site_section, 'site_url')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
site_url = None
passwords = {}
cp = ConfigParser.SafeConfigParser()
cp.read(datadir + '/sites/' + site_name + '/passwords.ini')
try:
pw_options = cp.options('passwords')
except ConfigParser.NoSectionError:
pw_options = []
for n in pw_options:
passwords[n.upper()] = cp.get('passwords', n)
return port, address, site_url, passwords | python | def load_site(srcdir, datadir, site_name=None):
"""
Load configuration values for a site.
Returns (port, address, site_url, passwords)
"""
if site_name is None:
site_name = 'primary'
if not validate.valid_name(site_name):
raise DatacatsError('{} is not a valid site name.'.format(site_name))
cp = ConfigParser.SafeConfigParser()
try:
cp.read([srcdir + '/.datacats-environment'])
except ConfigParser.Error:
raise DatacatsError('Error reading environment information')
site_section = 'site_' + site_name
try:
port = cp.getint(site_section, 'port')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
port = None
try:
address = cp.get(site_section, 'address')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
address = None
try:
site_url = cp.get(site_section, 'site_url')
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
site_url = None
passwords = {}
cp = ConfigParser.SafeConfigParser()
cp.read(datadir + '/sites/' + site_name + '/passwords.ini')
try:
pw_options = cp.options('passwords')
except ConfigParser.NoSectionError:
pw_options = []
for n in pw_options:
passwords[n.upper()] = cp.get('passwords', n)
return port, address, site_url, passwords | [
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datacats/datacats | datacats/task.py | new_environment_check | def new_environment_check(srcpath, site_name, ckan_version):
"""
Check if a new environment or site can be created at the given path.
Returns (name, datadir, sitedir, srcdir) or raises DatacatsError
"""
docker.require_images()
workdir, name = path.split(path.abspath(path.expanduser(srcpath)))
if not validate.valid_name(name):
raise DatacatsError('Please choose an environment name starting'
' with a letter and including only lowercase letters'
' and digits')
if not path.isdir(workdir):
raise DatacatsError('Parent directory for environment'
' does not exist')
datadir = path.expanduser('~/.datacats/' + name)
sitedir = datadir + '/sites/' + site_name
# We track through the datadir to the target if we are just making a
# site
if path.isdir(datadir):
with open(datadir + '/project-dir') as pd:
srcdir = pd.read()
else:
srcdir = workdir + '/' + name
if ckan_version not in SUPPORTED_PRELOADS:
raise DatacatsError('''Datacats does not currently support CKAN version {}.
Versions that are currently supported are: {}'''.format(ckan_version,
', '.join(SUPPORTED_PRELOADS)))
preload_name = str(ckan_version)
# Get all the versions from the tags
downloaded_versions = [tag for tag in docker.get_tags('datacats/ckan')]
if ckan_version not in downloaded_versions:
retrying_pull_image('datacats/ckan:{}'.format(preload_name))
if path.isdir(sitedir):
raise DatacatsError('Site data directory {0} already exists'.format(
sitedir))
# This is the case where the data dir has been removed,
if path.isdir(srcdir) and not path.isdir(datadir):
raise DatacatsError('Environment directory exists, but data directory does not.\n'
'If you simply want to recreate the data directory, run '
'"datacats init" in the environment directory.')
return name, datadir, srcdir | python | def new_environment_check(srcpath, site_name, ckan_version):
"""
Check if a new environment or site can be created at the given path.
Returns (name, datadir, sitedir, srcdir) or raises DatacatsError
"""
docker.require_images()
workdir, name = path.split(path.abspath(path.expanduser(srcpath)))
if not validate.valid_name(name):
raise DatacatsError('Please choose an environment name starting'
' with a letter and including only lowercase letters'
' and digits')
if not path.isdir(workdir):
raise DatacatsError('Parent directory for environment'
' does not exist')
datadir = path.expanduser('~/.datacats/' + name)
sitedir = datadir + '/sites/' + site_name
# We track through the datadir to the target if we are just making a
# site
if path.isdir(datadir):
with open(datadir + '/project-dir') as pd:
srcdir = pd.read()
else:
srcdir = workdir + '/' + name
if ckan_version not in SUPPORTED_PRELOADS:
raise DatacatsError('''Datacats does not currently support CKAN version {}.
Versions that are currently supported are: {}'''.format(ckan_version,
', '.join(SUPPORTED_PRELOADS)))
preload_name = str(ckan_version)
# Get all the versions from the tags
downloaded_versions = [tag for tag in docker.get_tags('datacats/ckan')]
if ckan_version not in downloaded_versions:
retrying_pull_image('datacats/ckan:{}'.format(preload_name))
if path.isdir(sitedir):
raise DatacatsError('Site data directory {0} already exists'.format(
sitedir))
# This is the case where the data dir has been removed,
if path.isdir(srcdir) and not path.isdir(datadir):
raise DatacatsError('Environment directory exists, but data directory does not.\n'
'If you simply want to recreate the data directory, run '
'"datacats init" in the environment directory.')
return name, datadir, srcdir | [
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datacats/datacats | datacats/task.py | data_complete | def data_complete(datadir, sitedir, get_container_name):
"""
Return True if the directories and containers we're expecting
are present in datadir, sitedir and containers
"""
if any(not path.isdir(sitedir + x)
for x in ('/files', '/run', '/solr')):
return False
if docker.is_boot2docker():
# Inspect returns None if the container doesn't exist.
return all(docker.inspect_container(get_container_name(x))
for x in ('pgdata', 'venv'))
return path.isdir(datadir + '/venv') and path.isdir(sitedir + '/postgres') | python | def data_complete(datadir, sitedir, get_container_name):
"""
Return True if the directories and containers we're expecting
are present in datadir, sitedir and containers
"""
if any(not path.isdir(sitedir + x)
for x in ('/files', '/run', '/solr')):
return False
if docker.is_boot2docker():
# Inspect returns None if the container doesn't exist.
return all(docker.inspect_container(get_container_name(x))
for x in ('pgdata', 'venv'))
return path.isdir(datadir + '/venv') and path.isdir(sitedir + '/postgres') | [
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datacats/datacats | datacats/task.py | create_directories | def create_directories(datadir, sitedir, srcdir=None):
"""
Create expected directories in datadir, sitedir
and optionally srcdir
"""
# It's possible that the datadir already exists
# (we're making a secondary site)
if not path.isdir(datadir):
os.makedirs(datadir, mode=0o700)
try:
# This should take care if the 'site' subdir if needed
os.makedirs(sitedir, mode=0o700)
except OSError:
raise DatacatsError("Site already exists.")
# venv isn't site-specific, the rest are.
if not docker.is_boot2docker():
if not path.isdir(datadir + '/venv'):
os.makedirs(datadir + '/venv')
os.makedirs(sitedir + '/postgres')
os.makedirs(sitedir + '/solr')
os.makedirs(sitedir + '/files')
os.makedirs(sitedir + '/run')
if srcdir:
os.makedirs(srcdir) | python | def create_directories(datadir, sitedir, srcdir=None):
"""
Create expected directories in datadir, sitedir
and optionally srcdir
"""
# It's possible that the datadir already exists
# (we're making a secondary site)
if not path.isdir(datadir):
os.makedirs(datadir, mode=0o700)
try:
# This should take care if the 'site' subdir if needed
os.makedirs(sitedir, mode=0o700)
except OSError:
raise DatacatsError("Site already exists.")
# venv isn't site-specific, the rest are.
if not docker.is_boot2docker():
if not path.isdir(datadir + '/venv'):
os.makedirs(datadir + '/venv')
os.makedirs(sitedir + '/postgres')
os.makedirs(sitedir + '/solr')
os.makedirs(sitedir + '/files')
os.makedirs(sitedir + '/run')
if srcdir:
os.makedirs(srcdir) | [
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datacats/datacats | datacats/task.py | create_virtualenv | def create_virtualenv(srcdir, datadir, preload_image, get_container_name):
"""
Populate venv from preloaded image
"""
try:
if docker.is_boot2docker():
docker.data_only_container(
get_container_name('venv'),
['/usr/lib/ckan'],
)
img_id = docker.web_command(
'/bin/mv /usr/lib/ckan/ /usr/lib/ckan_original',
image=preload_image,
commit=True,
)
docker.web_command(
command='/bin/cp -a /usr/lib/ckan_original/. /usr/lib/ckan/.',
volumes_from=get_container_name('venv'),
image=img_id,
)
docker.remove_image(img_id)
return
docker.web_command(
command='/bin/cp -a /usr/lib/ckan/. /usr/lib/ckan_target/.',
rw={datadir + '/venv': '/usr/lib/ckan_target'},
image=preload_image,
)
finally:
rw = {datadir + '/venv': '/usr/lib/ckan'} if not docker.is_boot2docker() else {}
volumes_from = get_container_name('venv') if docker.is_boot2docker() else None
# fix venv permissions
docker.web_command(
command='/bin/chown -R --reference=/project /usr/lib/ckan',
rw=rw,
volumes_from=volumes_from,
ro={srcdir: '/project'},
) | python | def create_virtualenv(srcdir, datadir, preload_image, get_container_name):
"""
Populate venv from preloaded image
"""
try:
if docker.is_boot2docker():
docker.data_only_container(
get_container_name('venv'),
['/usr/lib/ckan'],
)
img_id = docker.web_command(
'/bin/mv /usr/lib/ckan/ /usr/lib/ckan_original',
image=preload_image,
commit=True,
)
docker.web_command(
command='/bin/cp -a /usr/lib/ckan_original/. /usr/lib/ckan/.',
volumes_from=get_container_name('venv'),
image=img_id,
)
docker.remove_image(img_id)
return
docker.web_command(
command='/bin/cp -a /usr/lib/ckan/. /usr/lib/ckan_target/.',
rw={datadir + '/venv': '/usr/lib/ckan_target'},
image=preload_image,
)
finally:
rw = {datadir + '/venv': '/usr/lib/ckan'} if not docker.is_boot2docker() else {}
volumes_from = get_container_name('venv') if docker.is_boot2docker() else None
# fix venv permissions
docker.web_command(
command='/bin/chown -R --reference=/project /usr/lib/ckan',
rw=rw,
volumes_from=volumes_from,
ro={srcdir: '/project'},
) | [
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datacats/datacats | datacats/task.py | create_source | def create_source(srcdir, preload_image, datapusher=False):
"""
Copy ckan source, datapusher source (optional), who.ini and schema.xml
from preload image into srcdir
"""
try:
docker.web_command(
command='/bin/cp -a /project/ckan /project_target/ckan',
rw={srcdir: '/project_target'},
image=preload_image)
if datapusher:
docker.web_command(
command='/bin/cp -a /project/datapusher /project_target/datapusher',
rw={srcdir: '/project_target'},
image=preload_image)
shutil.copy(
srcdir + '/ckan/ckan/config/who.ini',
srcdir)
shutil.copy(
srcdir + '/ckan/ckan/config/solr/schema.xml',
srcdir)
finally:
# fix srcdir permissions
docker.web_command(
command='/bin/chown -R --reference=/project /project',
rw={srcdir: '/project'},
) | python | def create_source(srcdir, preload_image, datapusher=False):
"""
Copy ckan source, datapusher source (optional), who.ini and schema.xml
from preload image into srcdir
"""
try:
docker.web_command(
command='/bin/cp -a /project/ckan /project_target/ckan',
rw={srcdir: '/project_target'},
image=preload_image)
if datapusher:
docker.web_command(
command='/bin/cp -a /project/datapusher /project_target/datapusher',
rw={srcdir: '/project_target'},
image=preload_image)
shutil.copy(
srcdir + '/ckan/ckan/config/who.ini',
srcdir)
shutil.copy(
srcdir + '/ckan/ckan/config/solr/schema.xml',
srcdir)
finally:
# fix srcdir permissions
docker.web_command(
command='/bin/chown -R --reference=/project /project',
rw={srcdir: '/project'},
) | [
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datacats/datacats | datacats/task.py | start_supporting_containers | def start_supporting_containers(sitedir, srcdir, passwords,
get_container_name, extra_containers, log_syslog=False):
"""
Start all supporting containers (containers required for CKAN to
operate) if they aren't already running, along with some extra
containers specified by the user
"""
if docker.is_boot2docker():
docker.data_only_container(get_container_name('pgdata'),
['/var/lib/postgresql/data'])
rw = {}
volumes_from = get_container_name('pgdata')
else:
rw = {sitedir + '/postgres': '/var/lib/postgresql/data'}
volumes_from = None
running = set(containers_running(get_container_name))
needed = set(extra_containers).union({'postgres', 'solr'})
if not needed.issubset(running):
stop_supporting_containers(get_container_name, extra_containers)
# users are created when data dir is blank so we must pass
# all the user passwords as environment vars
# XXX: postgres entrypoint magic
docker.run_container(
name=get_container_name('postgres'),
image='datacats/postgres',
environment=passwords,
rw=rw,
volumes_from=volumes_from,
log_syslog=log_syslog)
docker.run_container(
name=get_container_name('solr'),
image='datacats/solr',
rw={sitedir + '/solr': '/var/lib/solr'},
ro={srcdir + '/schema.xml': '/etc/solr/conf/schema.xml'},
log_syslog=log_syslog)
for container in extra_containers:
# We don't know a whole lot about the extra containers so we're just gonna have to
# mount /project and /datadir r/o even if they're not needed for ease of
# implementation.
docker.run_container(
name=get_container_name(container),
image=EXTRA_IMAGE_MAPPING[container],
ro={
sitedir: '/datadir',
srcdir: '/project'
},
log_syslog=log_syslog
) | python | def start_supporting_containers(sitedir, srcdir, passwords,
get_container_name, extra_containers, log_syslog=False):
"""
Start all supporting containers (containers required for CKAN to
operate) if they aren't already running, along with some extra
containers specified by the user
"""
if docker.is_boot2docker():
docker.data_only_container(get_container_name('pgdata'),
['/var/lib/postgresql/data'])
rw = {}
volumes_from = get_container_name('pgdata')
else:
rw = {sitedir + '/postgres': '/var/lib/postgresql/data'}
volumes_from = None
running = set(containers_running(get_container_name))
needed = set(extra_containers).union({'postgres', 'solr'})
if not needed.issubset(running):
stop_supporting_containers(get_container_name, extra_containers)
# users are created when data dir is blank so we must pass
# all the user passwords as environment vars
# XXX: postgres entrypoint magic
docker.run_container(
name=get_container_name('postgres'),
image='datacats/postgres',
environment=passwords,
rw=rw,
volumes_from=volumes_from,
log_syslog=log_syslog)
docker.run_container(
name=get_container_name('solr'),
image='datacats/solr',
rw={sitedir + '/solr': '/var/lib/solr'},
ro={srcdir + '/schema.xml': '/etc/solr/conf/schema.xml'},
log_syslog=log_syslog)
for container in extra_containers:
# We don't know a whole lot about the extra containers so we're just gonna have to
# mount /project and /datadir r/o even if they're not needed for ease of
# implementation.
docker.run_container(
name=get_container_name(container),
image=EXTRA_IMAGE_MAPPING[container],
ro={
sitedir: '/datadir',
srcdir: '/project'
},
log_syslog=log_syslog
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datacats/datacats | datacats/task.py | stop_supporting_containers | def stop_supporting_containers(get_container_name, extra_containers):
"""
Stop postgres and solr containers, along with any specified extra containers
"""
docker.remove_container(get_container_name('postgres'))
docker.remove_container(get_container_name('solr'))
for container in extra_containers:
docker.remove_container(get_container_name(container)) | python | def stop_supporting_containers(get_container_name, extra_containers):
"""
Stop postgres and solr containers, along with any specified extra containers
"""
docker.remove_container(get_container_name('postgres'))
docker.remove_container(get_container_name('solr'))
for container in extra_containers:
docker.remove_container(get_container_name(container)) | [
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datacats/datacats | datacats/task.py | containers_running | def containers_running(get_container_name):
"""
Return a list of containers tracked by this environment that are running
"""
running = []
for n in ['web', 'postgres', 'solr', 'datapusher', 'redis']:
info = docker.inspect_container(get_container_name(n))
if info and not info['State']['Running']:
running.append(n + '(halted)')
elif info:
running.append(n)
return running | python | def containers_running(get_container_name):
"""
Return a list of containers tracked by this environment that are running
"""
running = []
for n in ['web', 'postgres', 'solr', 'datapusher', 'redis']:
info = docker.inspect_container(get_container_name(n))
if info and not info['State']['Running']:
running.append(n + '(halted)')
elif info:
running.append(n)
return running | [
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datacats/datacats | datacats/environment.py | Environment._load_sites | def _load_sites(self):
"""
Gets the names of all of the sites from the datadir and stores them
in self.sites. Also returns this list.
"""
if not self.sites:
self.sites = task.list_sites(self.datadir)
return self.sites | python | def _load_sites(self):
"""
Gets the names of all of the sites from the datadir and stores them
in self.sites. Also returns this list.
"""
if not self.sites:
self.sites = task.list_sites(self.datadir)
return self.sites | [
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datacats/datacats | datacats/environment.py | Environment.save_site | def save_site(self, create=True):
"""
Save environment settings in the directory that need to be saved
even when creating only a new sub-site env.
"""
self._load_sites()
if create:
self.sites.append(self.site_name)
task.save_new_site(self.site_name, self.sitedir, self.target, self.port,
self.address, self.site_url, self.passwords) | python | def save_site(self, create=True):
"""
Save environment settings in the directory that need to be saved
even when creating only a new sub-site env.
"""
self._load_sites()
if create:
self.sites.append(self.site_name)
task.save_new_site(self.site_name, self.sitedir, self.target, self.port,
self.address, self.site_url, self.passwords) | [
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datacats/datacats | datacats/environment.py | Environment.save | def save(self):
"""
Save environment settings into environment directory, overwriting
any existing configuration and discarding site config
"""
task.save_new_environment(self.name, self.datadir, self.target,
self.ckan_version, self.deploy_target, self.always_prod) | python | def save(self):
"""
Save environment settings into environment directory, overwriting
any existing configuration and discarding site config
"""
task.save_new_environment(self.name, self.datadir, self.target,
self.ckan_version, self.deploy_target, self.always_prod) | [
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datacats/datacats | datacats/environment.py | Environment.new | def new(cls, path, ckan_version, site_name, **kwargs):
"""
Return a Environment object with settings for a new project.
No directories or containers are created by this call.
:params path: location for new project directory, may be relative
:params ckan_version: release of CKAN to install
:params site_name: The name of the site to install database and solr \
eventually.
For additional keyword arguments see the __init__ method.
Raises DatcatsError if directories or project with same
name already exits.
"""
if ckan_version == 'master':
ckan_version = 'latest'
name, datadir, srcdir = task.new_environment_check(path, site_name, ckan_version)
environment = cls(name, srcdir, datadir, site_name, ckan_version, **kwargs)
environment._generate_passwords()
return environment | python | def new(cls, path, ckan_version, site_name, **kwargs):
"""
Return a Environment object with settings for a new project.
No directories or containers are created by this call.
:params path: location for new project directory, may be relative
:params ckan_version: release of CKAN to install
:params site_name: The name of the site to install database and solr \
eventually.
For additional keyword arguments see the __init__ method.
Raises DatcatsError if directories or project with same
name already exits.
"""
if ckan_version == 'master':
ckan_version = 'latest'
name, datadir, srcdir = task.new_environment_check(path, site_name, ckan_version)
environment = cls(name, srcdir, datadir, site_name, ckan_version, **kwargs)
environment._generate_passwords()
return environment | [
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datacats/datacats | datacats/environment.py | Environment.load | def load(cls, environment_name=None, site_name='primary', data_only=False, allow_old=False):
"""
Return an Environment object based on an existing environnment+site.
:param environment_name: exising environment name, path or None to
look in current or parent directories for project
:param data_only: set to True to only load from data dir, not
the project dir; Used for purging environment data.
:param allow_old: load a very minimal subset of what we usually
load. This will only work for purging environment data on an old site.
Raises DatacatsError if environment can't be found or if there is an
error parsing the environment information.
"""
srcdir, extension_dir, datadir = task.find_environment_dirs(
environment_name, data_only)
if datadir and data_only:
return cls(environment_name, None, datadir, site_name)
(datadir, name, ckan_version, always_prod, deploy_target,
remote_server_key, extra_containers) = task.load_environment(srcdir, datadir, allow_old)
if not allow_old:
(port, address, site_url, passwords) = task.load_site(srcdir, datadir, site_name)
else:
(port, address, site_url, passwords) = (None, None, None, None)
environment = cls(name, srcdir, datadir, site_name, ckan_version=ckan_version,
port=port, deploy_target=deploy_target, site_url=site_url,
always_prod=always_prod, address=address,
extension_dir=extension_dir,
remote_server_key=remote_server_key,
extra_containers=extra_containers)
if passwords:
environment.passwords = passwords
else:
environment._generate_passwords()
if not allow_old:
environment._load_sites()
return environment | python | def load(cls, environment_name=None, site_name='primary', data_only=False, allow_old=False):
"""
Return an Environment object based on an existing environnment+site.
:param environment_name: exising environment name, path or None to
look in current or parent directories for project
:param data_only: set to True to only load from data dir, not
the project dir; Used for purging environment data.
:param allow_old: load a very minimal subset of what we usually
load. This will only work for purging environment data on an old site.
Raises DatacatsError if environment can't be found or if there is an
error parsing the environment information.
"""
srcdir, extension_dir, datadir = task.find_environment_dirs(
environment_name, data_only)
if datadir and data_only:
return cls(environment_name, None, datadir, site_name)
(datadir, name, ckan_version, always_prod, deploy_target,
remote_server_key, extra_containers) = task.load_environment(srcdir, datadir, allow_old)
if not allow_old:
(port, address, site_url, passwords) = task.load_site(srcdir, datadir, site_name)
else:
(port, address, site_url, passwords) = (None, None, None, None)
environment = cls(name, srcdir, datadir, site_name, ckan_version=ckan_version,
port=port, deploy_target=deploy_target, site_url=site_url,
always_prod=always_prod, address=address,
extension_dir=extension_dir,
remote_server_key=remote_server_key,
extra_containers=extra_containers)
if passwords:
environment.passwords = passwords
else:
environment._generate_passwords()
if not allow_old:
environment._load_sites()
return environment | [
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:param environment_name: exising environment name, path or None to
look in current or parent directories for project
:param data_only: set to True to only load from data dir, not
the project dir; Used for purging environment data.
:param allow_old: load a very minimal subset of what we usually
load. This will only work for purging environment data on an old site.
Raises DatacatsError if environment can't be found or if there is an
error parsing the environment information. | [
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datacats/datacats | datacats/environment.py | Environment.data_complete | def data_complete(self):
"""
Return True if all the expected datadir files are present
"""
return task.data_complete(self.datadir, self.sitedir,
self._get_container_name) | python | def data_complete(self):
"""
Return True if all the expected datadir files are present
"""
return task.data_complete(self.datadir, self.sitedir,
self._get_container_name) | [
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datacats/datacats | datacats/environment.py | Environment.require_data | def require_data(self):
"""
raise a DatacatsError if the datadir or volumes are missing or damaged
"""
files = task.source_missing(self.target)
if files:
raise DatacatsError('Missing files in source directory:\n' +
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if not self.data_exists():
raise DatacatsError('Environment datadir missing. '
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if not self.data_complete():
raise DatacatsError('Environment datadir damaged or volumes '
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'To reset and discard all data use '
'"datacats reset"') | python | def require_data(self):
"""
raise a DatacatsError if the datadir or volumes are missing or damaged
"""
files = task.source_missing(self.target)
if files:
raise DatacatsError('Missing files in source directory:\n' +
'\n'.join(files))
if not self.data_exists():
raise DatacatsError('Environment datadir missing. '
'Try "datacats init".')
if not self.data_complete():
raise DatacatsError('Environment datadir damaged or volumes '
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datacats/datacats | datacats/environment.py | Environment.create_directories | def create_directories(self, create_project_dir=True):
"""
Call once for new projects to create the initial project directories.
"""
return task.create_directories(self.datadir, self.sitedir,
self.target if create_project_dir else None) | python | def create_directories(self, create_project_dir=True):
"""
Call once for new projects to create the initial project directories.
"""
return task.create_directories(self.datadir, self.sitedir,
self.target if create_project_dir else None) | [
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datacats/datacats | datacats/environment.py | Environment.create_virtualenv | def create_virtualenv(self):
"""
Populate venv from preloaded image
"""
return task.create_virtualenv(self.target, self.datadir,
self._preload_image(), self._get_container_name) | python | def create_virtualenv(self):
"""
Populate venv from preloaded image
"""
return task.create_virtualenv(self.target, self.datadir,
self._preload_image(), self._get_container_name) | [
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datacats/datacats | datacats/environment.py | Environment.clean_virtualenv | def clean_virtualenv(self):
"""
Empty our virtualenv so that new (or older) dependencies may be
installed
"""
self.user_run_script(
script=scripts.get_script_path('clean_virtualenv.sh'),
args=[],
rw_venv=True,
) | python | def clean_virtualenv(self):
"""
Empty our virtualenv so that new (or older) dependencies may be
installed
"""
self.user_run_script(
script=scripts.get_script_path('clean_virtualenv.sh'),
args=[],
rw_venv=True,
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datacats/datacats | datacats/environment.py | Environment.create_source | def create_source(self, datapusher=True):
"""
Populate ckan directory from preloaded image and copy
who.ini and schema.xml info conf directory
"""
task.create_source(self.target, self._preload_image(), datapusher) | python | def create_source(self, datapusher=True):
"""
Populate ckan directory from preloaded image and copy
who.ini and schema.xml info conf directory
"""
task.create_source(self.target, self._preload_image(), datapusher) | [
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datacats/datacats | datacats/environment.py | Environment.start_supporting_containers | def start_supporting_containers(self, log_syslog=False):
"""
Start all supporting containers (containers required for CKAN to
operate) if they aren't already running.
:param log_syslog: A flag to redirect all container logs to host's syslog
"""
log_syslog = True if self.always_prod else log_syslog
# in production we always use log_syslog driver (to aggregate all the logs)
task.start_supporting_containers(
self.sitedir,
self.target,
self.passwords,
self._get_container_name,
self.extra_containers,
log_syslog=log_syslog
) | python | def start_supporting_containers(self, log_syslog=False):
"""
Start all supporting containers (containers required for CKAN to
operate) if they aren't already running.
:param log_syslog: A flag to redirect all container logs to host's syslog
"""
log_syslog = True if self.always_prod else log_syslog
# in production we always use log_syslog driver (to aggregate all the logs)
task.start_supporting_containers(
self.sitedir,
self.target,
self.passwords,
self._get_container_name,
self.extra_containers,
log_syslog=log_syslog
) | [
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datacats/datacats | datacats/environment.py | Environment.create_ckan_ini | def create_ckan_ini(self):
"""
Use make-config to generate an initial development.ini file
"""
self.run_command(
command='/scripts/run_as_user.sh /usr/lib/ckan/bin/paster make-config'
' ckan /project/development.ini',
rw_project=True,
ro={scripts.get_script_path('run_as_user.sh'): '/scripts/run_as_user.sh'},
) | python | def create_ckan_ini(self):
"""
Use make-config to generate an initial development.ini file
"""
self.run_command(
command='/scripts/run_as_user.sh /usr/lib/ckan/bin/paster make-config'
' ckan /project/development.ini',
rw_project=True,
ro={scripts.get_script_path('run_as_user.sh'): '/scripts/run_as_user.sh'},
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datacats/datacats | datacats/environment.py | Environment.update_ckan_ini | def update_ckan_ini(self, skin=True):
"""
Use config-tool to update development.ini with our environment settings
:param skin: use environment template skin plugin True/False
"""
command = [
'/usr/lib/ckan/bin/paster', '--plugin=ckan', 'config-tool',
'/project/development.ini', '-e',
'sqlalchemy.url = postgresql://<hidden>',
'ckan.datastore.read_url = postgresql://<hidden>',
'ckan.datastore.write_url = postgresql://<hidden>',
'ckan.datapusher.url = http://datapusher:8800',
'solr_url = http://solr:8080/solr',
'ckan.storage_path = /var/www/storage',
'ckan.plugins = datastore resource_proxy text_view ' +
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+ 'recline_grid_view recline_graph_view'
+ (' {0}_theme'.format(self.name) if skin else ''),
'ckan.site_title = ' + self.name,
'ckan.site_logo =',
'ckan.auth.create_user_via_web = false',
]
self.run_command(command=command, rw_project=True) | python | def update_ckan_ini(self, skin=True):
"""
Use config-tool to update development.ini with our environment settings
:param skin: use environment template skin plugin True/False
"""
command = [
'/usr/lib/ckan/bin/paster', '--plugin=ckan', 'config-tool',
'/project/development.ini', '-e',
'sqlalchemy.url = postgresql://<hidden>',
'ckan.datastore.read_url = postgresql://<hidden>',
'ckan.datastore.write_url = postgresql://<hidden>',
'ckan.datapusher.url = http://datapusher:8800',
'solr_url = http://solr:8080/solr',
'ckan.storage_path = /var/www/storage',
'ckan.plugins = datastore resource_proxy text_view ' +
('datapusher ' if exists(self.target + '/datapusher') else '')
+ 'recline_grid_view recline_graph_view'
+ (' {0}_theme'.format(self.name) if skin else ''),
'ckan.site_title = ' + self.name,
'ckan.site_logo =',
'ckan.auth.create_user_via_web = false',
]
self.run_command(command=command, rw_project=True) | [
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datacats/datacats | datacats/environment.py | Environment.create_install_template_skin | def create_install_template_skin(self):
"""
Create an example ckan extension for this environment and install it
"""
ckan_extension_template(self.name, self.target)
self.install_package_develop('ckanext-' + self.name + 'theme') | python | def create_install_template_skin(self):
"""
Create an example ckan extension for this environment and install it
"""
ckan_extension_template(self.name, self.target)
self.install_package_develop('ckanext-' + self.name + 'theme') | [
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datacats/datacats | datacats/environment.py | Environment.ckan_db_init | def ckan_db_init(self, retry_seconds=DB_INIT_RETRY_SECONDS):
"""
Run db init to create all ckan tables
:param retry_seconds: how long to retry waiting for db to start
"""
# XXX workaround for not knowing how long we need to wait
# for postgres to be ready. fix this by changing the postgres
# entrypoint, or possibly running once with command=/bin/true
started = time.time()
while True:
try:
self.run_command(
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db_links=True,
clean_up=True,
)
break
except WebCommandError:
if started + retry_seconds > time.time():
raise
time.sleep(DB_INIT_RETRY_DELAY) | python | def ckan_db_init(self, retry_seconds=DB_INIT_RETRY_SECONDS):
"""
Run db init to create all ckan tables
:param retry_seconds: how long to retry waiting for db to start
"""
# XXX workaround for not knowing how long we need to wait
# for postgres to be ready. fix this by changing the postgres
# entrypoint, or possibly running once with command=/bin/true
started = time.time()
while True:
try:
self.run_command(
'/usr/lib/ckan/bin/paster --plugin=ckan db init '
'-c /project/development.ini',
db_links=True,
clean_up=True,
)
break
except WebCommandError:
if started + retry_seconds > time.time():
raise
time.sleep(DB_INIT_RETRY_DELAY) | [
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datacats/datacats | datacats/environment.py | Environment.start_ckan | def start_ckan(self, production=False, log_syslog=False, paster_reload=True,
interactive=False):
"""
Start the apache server or paster serve
:param log_syslog: A flag to redirect all container logs to host's syslog
:param production: True for apache, False for paster serve + debug on
:param paster_reload: Instruct paster to watch for file changes
"""
self.stop_ckan()
address = self.address or '127.0.0.1'
port = self.port
# in prod we always use log_syslog driver
log_syslog = True if self.always_prod else log_syslog
production = production or self.always_prod
# We only override the site URL with the docker URL on three conditions
override_site_url = (self.address is None
and not is_boot2docker()
and not self.site_url)
command = ['/scripts/web.sh', str(production), str(override_site_url), str(paster_reload)]
# XXX nasty hack, remove this once we have a lessc command
# for users (not just for building our preload image)
if not production:
css = self.target + '/ckan/ckan/public/base/css'
if not exists(css + '/main.debug.css'):
from shutil import copyfile
copyfile(css + '/main.css', css + '/main.debug.css')
ro = {
self.target: '/project',
scripts.get_script_path('datapusher.sh'): '/scripts/datapusher.sh'
}
if not is_boot2docker():
ro[self.datadir + '/venv'] = '/usr/lib/ckan'
datapusher = self.needs_datapusher()
if datapusher:
run_container(
self._get_container_name('datapusher'),
'datacats/web',
'/scripts/datapusher.sh',
ro=ro,
volumes_from=(self._get_container_name('venv') if is_boot2docker() else None),
log_syslog=log_syslog)
while True:
self._create_run_ini(port, production)
try:
self._run_web_container(port, command, address, log_syslog=log_syslog,
datapusher=datapusher, interactive=interactive)
if not is_boot2docker():
self.address = address
except PortAllocatedError:
port = self._next_port(port)
continue
break | python | def start_ckan(self, production=False, log_syslog=False, paster_reload=True,
interactive=False):
"""
Start the apache server or paster serve
:param log_syslog: A flag to redirect all container logs to host's syslog
:param production: True for apache, False for paster serve + debug on
:param paster_reload: Instruct paster to watch for file changes
"""
self.stop_ckan()
address = self.address or '127.0.0.1'
port = self.port
# in prod we always use log_syslog driver
log_syslog = True if self.always_prod else log_syslog
production = production or self.always_prod
# We only override the site URL with the docker URL on three conditions
override_site_url = (self.address is None
and not is_boot2docker()
and not self.site_url)
command = ['/scripts/web.sh', str(production), str(override_site_url), str(paster_reload)]
# XXX nasty hack, remove this once we have a lessc command
# for users (not just for building our preload image)
if not production:
css = self.target + '/ckan/ckan/public/base/css'
if not exists(css + '/main.debug.css'):
from shutil import copyfile
copyfile(css + '/main.css', css + '/main.debug.css')
ro = {
self.target: '/project',
scripts.get_script_path('datapusher.sh'): '/scripts/datapusher.sh'
}
if not is_boot2docker():
ro[self.datadir + '/venv'] = '/usr/lib/ckan'
datapusher = self.needs_datapusher()
if datapusher:
run_container(
self._get_container_name('datapusher'),
'datacats/web',
'/scripts/datapusher.sh',
ro=ro,
volumes_from=(self._get_container_name('venv') if is_boot2docker() else None),
log_syslog=log_syslog)
while True:
self._create_run_ini(port, production)
try:
self._run_web_container(port, command, address, log_syslog=log_syslog,
datapusher=datapusher, interactive=interactive)
if not is_boot2docker():
self.address = address
except PortAllocatedError:
port = self._next_port(port)
continue
break | [
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:param log_syslog: A flag to redirect all container logs to host's syslog
:param production: True for apache, False for paster serve + debug on
:param paster_reload: Instruct paster to watch for file changes | [
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] | e4bae503efa997660fb3f34fe166699569653157 | https://github.com/datacats/datacats/blob/e4bae503efa997660fb3f34fe166699569653157/datacats/environment.py#L391-L450 | train |
datacats/datacats | datacats/environment.py | Environment._create_run_ini | def _create_run_ini(self, port, production, output='development.ini',
source='development.ini', override_site_url=True):
"""
Create run/development.ini in datadir with debug and site_url overridden
and with correct db passwords inserted
"""
cp = SafeConfigParser()
try:
cp.read([self.target + '/' + source])
except ConfigParserError:
raise DatacatsError('Error reading development.ini')
cp.set('DEFAULT', 'debug', 'false' if production else 'true')
if self.site_url:
site_url = self.site_url
else:
if is_boot2docker():
web_address = socket.gethostbyname(docker_host())
else:
web_address = self.address
site_url = 'http://{}:{}'.format(web_address, port)
if override_site_url:
cp.set('app:main', 'ckan.site_url', site_url)
cp.set('app:main', 'sqlalchemy.url',
'postgresql://ckan:{0}@db:5432/ckan'
.format(self.passwords['CKAN_PASSWORD']))
cp.set('app:main', 'ckan.datastore.read_url',
'postgresql://ckan_datastore_readonly:{0}@db:5432/ckan_datastore'
.format(self.passwords['DATASTORE_RO_PASSWORD']))
cp.set('app:main', 'ckan.datastore.write_url',
'postgresql://ckan_datastore_readwrite:{0}@db:5432/ckan_datastore'
.format(self.passwords['DATASTORE_RW_PASSWORD']))
cp.set('app:main', 'solr_url', 'http://solr:8080/solr')
cp.set('app:main', 'ckan.redis.url', 'http://redis:6379')
cp.set('app:main', 'beaker.session.secret', self.passwords['BEAKER_SESSION_SECRET'])
if not isdir(self.sitedir + '/run'):
makedirs(self.sitedir + '/run') # upgrade old datadir
with open(self.sitedir + '/run/' + output, 'w') as runini:
cp.write(runini) | python | def _create_run_ini(self, port, production, output='development.ini',
source='development.ini', override_site_url=True):
"""
Create run/development.ini in datadir with debug and site_url overridden
and with correct db passwords inserted
"""
cp = SafeConfigParser()
try:
cp.read([self.target + '/' + source])
except ConfigParserError:
raise DatacatsError('Error reading development.ini')
cp.set('DEFAULT', 'debug', 'false' if production else 'true')
if self.site_url:
site_url = self.site_url
else:
if is_boot2docker():
web_address = socket.gethostbyname(docker_host())
else:
web_address = self.address
site_url = 'http://{}:{}'.format(web_address, port)
if override_site_url:
cp.set('app:main', 'ckan.site_url', site_url)
cp.set('app:main', 'sqlalchemy.url',
'postgresql://ckan:{0}@db:5432/ckan'
.format(self.passwords['CKAN_PASSWORD']))
cp.set('app:main', 'ckan.datastore.read_url',
'postgresql://ckan_datastore_readonly:{0}@db:5432/ckan_datastore'
.format(self.passwords['DATASTORE_RO_PASSWORD']))
cp.set('app:main', 'ckan.datastore.write_url',
'postgresql://ckan_datastore_readwrite:{0}@db:5432/ckan_datastore'
.format(self.passwords['DATASTORE_RW_PASSWORD']))
cp.set('app:main', 'solr_url', 'http://solr:8080/solr')
cp.set('app:main', 'ckan.redis.url', 'http://redis:6379')
cp.set('app:main', 'beaker.session.secret', self.passwords['BEAKER_SESSION_SECRET'])
if not isdir(self.sitedir + '/run'):
makedirs(self.sitedir + '/run') # upgrade old datadir
with open(self.sitedir + '/run/' + output, 'w') as runini:
cp.write(runini) | [
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and with correct db passwords inserted | [
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datacats/datacats | datacats/environment.py | Environment._run_web_container | def _run_web_container(self, port, command, address, log_syslog=False,
datapusher=True, interactive=False):
"""
Start web container on port with command
"""
if is_boot2docker():
ro = {}
volumes_from = self._get_container_name('venv')
else:
ro = {self.datadir + '/venv': '/usr/lib/ckan'}
volumes_from = None
links = {
self._get_container_name('solr'): 'solr',
self._get_container_name('postgres'): 'db'
}
links.update({self._get_container_name(container): container
for container in self.extra_containers})
if datapusher:
if 'datapusher' not in self.containers_running():
raise DatacatsError(container_logs(self._get_container_name('datapusher'), "all",
False, False))
links[self._get_container_name('datapusher')] = 'datapusher'
ro = dict({
self.target: '/project/',
scripts.get_script_path('web.sh'): '/scripts/web.sh',
scripts.get_script_path('adjust_devini.py'): '/scripts/adjust_devini.py'},
**ro)
rw = {
self.sitedir + '/files': '/var/www/storage',
self.sitedir + '/run/development.ini': '/project/development.ini'
}
try:
if not interactive:
run_container(
name=self._get_container_name('web'),
image='datacats/web',
rw=rw,
ro=ro,
links=links,
volumes_from=volumes_from,
command=command,
port_bindings={
5000: port if is_boot2docker() else (address, port)},
log_syslog=log_syslog
)
else:
# FIXME: share more code with interactive_shell
if is_boot2docker():
switches = ['--volumes-from',
self._get_container_name('pgdata'), '--volumes-from',
self._get_container_name('venv')]
else:
switches = []
switches += ['--volume={}:{}:ro'.format(vol, ro[vol]) for vol in ro]
switches += ['--volume={}:{}'.format(vol, rw[vol]) for vol in rw]
links = ['--link={}:{}'.format(link, links[link]) for link in links]
args = ['docker', 'run', '-it', '--name', self._get_container_name('web'),
'-p', '{}:5000'.format(port) if is_boot2docker()
else '{}:{}:5000'.format(address, port)] + \
switches + links + ['datacats/web', ] + command
subprocess.call(args)
except APIError as e:
if '409' in str(e):
raise DatacatsError('Web container already running. '
'Please stop_web before running.')
else:
raise | python | def _run_web_container(self, port, command, address, log_syslog=False,
datapusher=True, interactive=False):
"""
Start web container on port with command
"""
if is_boot2docker():
ro = {}
volumes_from = self._get_container_name('venv')
else:
ro = {self.datadir + '/venv': '/usr/lib/ckan'}
volumes_from = None
links = {
self._get_container_name('solr'): 'solr',
self._get_container_name('postgres'): 'db'
}
links.update({self._get_container_name(container): container
for container in self.extra_containers})
if datapusher:
if 'datapusher' not in self.containers_running():
raise DatacatsError(container_logs(self._get_container_name('datapusher'), "all",
False, False))
links[self._get_container_name('datapusher')] = 'datapusher'
ro = dict({
self.target: '/project/',
scripts.get_script_path('web.sh'): '/scripts/web.sh',
scripts.get_script_path('adjust_devini.py'): '/scripts/adjust_devini.py'},
**ro)
rw = {
self.sitedir + '/files': '/var/www/storage',
self.sitedir + '/run/development.ini': '/project/development.ini'
}
try:
if not interactive:
run_container(
name=self._get_container_name('web'),
image='datacats/web',
rw=rw,
ro=ro,
links=links,
volumes_from=volumes_from,
command=command,
port_bindings={
5000: port if is_boot2docker() else (address, port)},
log_syslog=log_syslog
)
else:
# FIXME: share more code with interactive_shell
if is_boot2docker():
switches = ['--volumes-from',
self._get_container_name('pgdata'), '--volumes-from',
self._get_container_name('venv')]
else:
switches = []
switches += ['--volume={}:{}:ro'.format(vol, ro[vol]) for vol in ro]
switches += ['--volume={}:{}'.format(vol, rw[vol]) for vol in rw]
links = ['--link={}:{}'.format(link, links[link]) for link in links]
args = ['docker', 'run', '-it', '--name', self._get_container_name('web'),
'-p', '{}:5000'.format(port) if is_boot2docker()
else '{}:{}:5000'.format(address, port)] + \
switches + links + ['datacats/web', ] + command
subprocess.call(args)
except APIError as e:
if '409' in str(e):
raise DatacatsError('Web container already running. '
'Please stop_web before running.')
else:
raise | [
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datacats/datacats | datacats/environment.py | Environment.wait_for_web_available | def wait_for_web_available(self):
"""
Wait for the web server to become available or raise DatacatsError
if it fails to start.
"""
try:
if not wait_for_service_available(
self._get_container_name('web'),
self.web_address(),
WEB_START_TIMEOUT_SECONDS):
raise DatacatsError('Error while starting web container:\n' +
container_logs(self._get_container_name('web'), "all",
False, None))
except ServiceTimeout:
raise DatacatsError('Timeout while starting web container. Logs:' +
container_logs(self._get_container_name('web'), "all", False, None)) | python | def wait_for_web_available(self):
"""
Wait for the web server to become available or raise DatacatsError
if it fails to start.
"""
try:
if not wait_for_service_available(
self._get_container_name('web'),
self.web_address(),
WEB_START_TIMEOUT_SECONDS):
raise DatacatsError('Error while starting web container:\n' +
container_logs(self._get_container_name('web'), "all",
False, None))
except ServiceTimeout:
raise DatacatsError('Timeout while starting web container. Logs:' +
container_logs(self._get_container_name('web'), "all", False, None)) | [
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datacats/datacats | datacats/environment.py | Environment._choose_port | def _choose_port(self):
"""
Return a port number from 5000-5999 based on the environment name
to be used as a default when the user hasn't selected one.
"""
# instead of random let's base it on the name chosen (and the site name)
return 5000 + unpack('Q',
sha((self.name + self.site_name)
.decode('ascii')).digest()[:8])[0] % 1000 | python | def _choose_port(self):
"""
Return a port number from 5000-5999 based on the environment name
to be used as a default when the user hasn't selected one.
"""
# instead of random let's base it on the name chosen (and the site name)
return 5000 + unpack('Q',
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datacats/datacats | datacats/environment.py | Environment._next_port | def _next_port(self, port):
"""
Return another port from the 5000-5999 range
"""
port = 5000 + (port + 1) % 1000
if port == self.port:
raise DatacatsError('Too many instances running')
return port | python | def _next_port(self, port):
"""
Return another port from the 5000-5999 range
"""
port = 5000 + (port + 1) % 1000
if port == self.port:
raise DatacatsError('Too many instances running')
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datacats/datacats | datacats/environment.py | Environment.stop_ckan | def stop_ckan(self):
"""
Stop and remove the web container
"""
remove_container(self._get_container_name('web'), force=True)
remove_container(self._get_container_name('datapusher'), force=True) | python | def stop_ckan(self):
"""
Stop and remove the web container
"""
remove_container(self._get_container_name('web'), force=True)
remove_container(self._get_container_name('datapusher'), force=True) | [
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datacats/datacats | datacats/environment.py | Environment._current_web_port | def _current_web_port(self):
"""
return just the port number for the web container, or None if
not running
"""
info = inspect_container(self._get_container_name('web'))
if info is None:
return None
try:
if not info['State']['Running']:
return None
return info['NetworkSettings']['Ports']['5000/tcp'][0]['HostPort']
except TypeError:
return None | python | def _current_web_port(self):
"""
return just the port number for the web container, or None if
not running
"""
info = inspect_container(self._get_container_name('web'))
if info is None:
return None
try:
if not info['State']['Running']:
return None
return info['NetworkSettings']['Ports']['5000/tcp'][0]['HostPort']
except TypeError:
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datacats/datacats | datacats/environment.py | Environment.add_extra_container | def add_extra_container(self, container, error_on_exists=False):
"""
Add a container as a 'extra'. These are running containers which are not necessary for
running default CKAN but are useful for certain extensions
:param container: The container name to add
:param error_on_exists: Raise a DatacatsError if the extra container already exists.
"""
if container in self.extra_containers:
if error_on_exists:
raise DatacatsError('{} is already added as an extra container.'.format(container))
else:
return
self.extra_containers.append(container)
cp = SafeConfigParser()
cp.read(self.target + '/.datacats-environment')
cp.set('datacats', 'extra_containers', ' '.join(self.extra_containers))
with open(self.target + '/.datacats-environment', 'w') as f:
cp.write(f) | python | def add_extra_container(self, container, error_on_exists=False):
"""
Add a container as a 'extra'. These are running containers which are not necessary for
running default CKAN but are useful for certain extensions
:param container: The container name to add
:param error_on_exists: Raise a DatacatsError if the extra container already exists.
"""
if container in self.extra_containers:
if error_on_exists:
raise DatacatsError('{} is already added as an extra container.'.format(container))
else:
return
self.extra_containers.append(container)
cp = SafeConfigParser()
cp.read(self.target + '/.datacats-environment')
cp.set('datacats', 'extra_containers', ' '.join(self.extra_containers))
with open(self.target + '/.datacats-environment', 'w') as f:
cp.write(f) | [
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datacats/datacats | datacats/environment.py | Environment.web_address | def web_address(self):
"""
Return the url of the web server or None if not running
"""
port = self._current_web_port()
address = self.address or '127.0.0.1'
if port is None:
return None
return 'http://{0}:{1}/'.format(
address if address and not is_boot2docker() else docker_host(),
port) | python | def web_address(self):
"""
Return the url of the web server or None if not running
"""
port = self._current_web_port()
address = self.address or '127.0.0.1'
if port is None:
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datacats/datacats | datacats/environment.py | Environment.create_admin_set_password | def create_admin_set_password(self, password):
"""
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"""
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remove(self.sitedir + '/run/admin.json') | python | def create_admin_set_password(self, password):
"""
create 'admin' account with given password
"""
with open(self.sitedir + '/run/admin.json', 'w') as out:
json.dump({
'name': 'admin',
'email': 'none',
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db_links=True,
ro={
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remove(self.sitedir + '/run/admin.json') | [
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datacats/datacats | datacats/environment.py | Environment.interactive_shell | def interactive_shell(self, command=None, paster=False, detach=False):
"""
launch interactive shell session with all writable volumes
:param: list of strings to execute instead of bash
"""
if not exists(self.target + '/.bash_profile'):
# this file is required for activating the virtualenv
self.create_bash_profile()
if not command:
command = []
use_tty = sys.stdin.isatty() and sys.stdout.isatty()
background = environ.get('CIRCLECI', False) or detach
if is_boot2docker():
venv_volumes = ['--volumes-from', self._get_container_name('venv')]
else:
venv_volumes = ['-v', self.datadir + '/venv:/usr/lib/ckan:rw']
self._create_run_ini(self.port, production=False, output='run.ini')
self._create_run_ini(self.port, production=True, output='test.ini',
source='ckan/test-core.ini', override_site_url=False)
script = scripts.get_script_path('shell.sh')
if paster:
script = scripts.get_script_path('paster.sh')
if command and command != ['help'] and command != ['--help']:
command += ['--config=/project/development.ini']
command = [self.extension_dir] + command
proxy_settings = self._proxy_settings()
if proxy_settings:
venv_volumes += ['-v',
self.sitedir + '/run/proxy-environment:/etc/environment:ro']
links = {self._get_container_name('solr'): 'solr',
self._get_container_name('postgres'): 'db'}
links.update({self._get_container_name(container): container for container
in self.extra_containers})
link_params = []
for link in links:
link_params.append('--link')
link_params.append(link + ':' + links[link])
if 'datapusher' in self.containers_running():
link_params.append('--link')
link_params.append(self._get_container_name('datapusher') + ':datapusher')
# FIXME: consider switching this to dockerpty
# using subprocess for docker client's interactive session
return subprocess.call([
DOCKER_EXE, 'run',
] + (['--rm'] if not background else []) + [
'-t' if use_tty else '',
'-d' if detach else '-i',
] + venv_volumes + [
'-v', self.target + ':/project:rw',
'-v', self.sitedir + '/files:/var/www/storage:rw',
'-v', script + ':/scripts/shell.sh:ro',
'-v', scripts.get_script_path('paster_cd.sh') + ':/scripts/paster_cd.sh:ro',
'-v', self.sitedir + '/run/run.ini:/project/development.ini:ro',
'-v', self.sitedir +
'/run/test.ini:/project/ckan/test-core.ini:ro'] +
link_params +
['--hostname', self.name,
'datacats/web', '/scripts/shell.sh'] + command) | python | def interactive_shell(self, command=None, paster=False, detach=False):
"""
launch interactive shell session with all writable volumes
:param: list of strings to execute instead of bash
"""
if not exists(self.target + '/.bash_profile'):
# this file is required for activating the virtualenv
self.create_bash_profile()
if not command:
command = []
use_tty = sys.stdin.isatty() and sys.stdout.isatty()
background = environ.get('CIRCLECI', False) or detach
if is_boot2docker():
venv_volumes = ['--volumes-from', self._get_container_name('venv')]
else:
venv_volumes = ['-v', self.datadir + '/venv:/usr/lib/ckan:rw']
self._create_run_ini(self.port, production=False, output='run.ini')
self._create_run_ini(self.port, production=True, output='test.ini',
source='ckan/test-core.ini', override_site_url=False)
script = scripts.get_script_path('shell.sh')
if paster:
script = scripts.get_script_path('paster.sh')
if command and command != ['help'] and command != ['--help']:
command += ['--config=/project/development.ini']
command = [self.extension_dir] + command
proxy_settings = self._proxy_settings()
if proxy_settings:
venv_volumes += ['-v',
self.sitedir + '/run/proxy-environment:/etc/environment:ro']
links = {self._get_container_name('solr'): 'solr',
self._get_container_name('postgres'): 'db'}
links.update({self._get_container_name(container): container for container
in self.extra_containers})
link_params = []
for link in links:
link_params.append('--link')
link_params.append(link + ':' + links[link])
if 'datapusher' in self.containers_running():
link_params.append('--link')
link_params.append(self._get_container_name('datapusher') + ':datapusher')
# FIXME: consider switching this to dockerpty
# using subprocess for docker client's interactive session
return subprocess.call([
DOCKER_EXE, 'run',
] + (['--rm'] if not background else []) + [
'-t' if use_tty else '',
'-d' if detach else '-i',
] + venv_volumes + [
'-v', self.target + ':/project:rw',
'-v', self.sitedir + '/files:/var/www/storage:rw',
'-v', script + ':/scripts/shell.sh:ro',
'-v', scripts.get_script_path('paster_cd.sh') + ':/scripts/paster_cd.sh:ro',
'-v', self.sitedir + '/run/run.ini:/project/development.ini:ro',
'-v', self.sitedir +
'/run/test.ini:/project/ckan/test-core.ini:ro'] +
link_params +
['--hostname', self.name,
'datacats/web', '/scripts/shell.sh'] + command) | [
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:param: list of strings to execute instead of bash | [
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datacats/datacats | datacats/environment.py | Environment.install_package_requirements | def install_package_requirements(self, psrc, stream_output=None):
"""
Install from requirements.txt file found in psrc
:param psrc: name of directory in environment directory
"""
package = self.target + '/' + psrc
assert isdir(package), package
reqname = '/requirements.txt'
if not exists(package + reqname):
reqname = '/pip-requirements.txt'
if not exists(package + reqname):
return
return self.user_run_script(
script=scripts.get_script_path('install_reqs.sh'),
args=['/project/' + psrc + reqname],
rw_venv=True,
rw_project=True,
stream_output=stream_output
) | python | def install_package_requirements(self, psrc, stream_output=None):
"""
Install from requirements.txt file found in psrc
:param psrc: name of directory in environment directory
"""
package = self.target + '/' + psrc
assert isdir(package), package
reqname = '/requirements.txt'
if not exists(package + reqname):
reqname = '/pip-requirements.txt'
if not exists(package + reqname):
return
return self.user_run_script(
script=scripts.get_script_path('install_reqs.sh'),
args=['/project/' + psrc + reqname],
rw_venv=True,
rw_project=True,
stream_output=stream_output
) | [
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datacats/datacats | datacats/environment.py | Environment.purge_data | def purge_data(self, which_sites=None, never_delete=False):
"""
Remove uploaded files, postgres db, solr index, venv
"""
# Default to the set of all sites
if not exists(self.datadir + '/.version'):
format_version = 1
else:
with open(self.datadir + '/.version') as f:
format_version = int(f.read().strip())
if format_version == 1:
print 'WARNING: Defaulting to old purge for version 1.'
datadirs = ['files', 'solr']
if is_boot2docker():
remove_container('datacats_pgdata_{}'.format(self.name))
remove_container('datacats_venv_{}'.format(self.name))
else:
datadirs += ['postgres', 'venv']
web_command(
command=['/scripts/purge.sh']
+ ['/project/data/' + d for d in datadirs],
ro={scripts.get_script_path('purge.sh'): '/scripts/purge.sh'},
rw={self.datadir: '/project/data'},
)
shutil.rmtree(self.datadir)
elif format_version == 2:
if not which_sites:
which_sites = self.sites
datadirs = []
boot2docker = is_boot2docker()
if which_sites:
if self.target:
cp = SafeConfigParser()
cp.read([self.target + '/.datacats-environment'])
for site in which_sites:
if boot2docker:
remove_container(self._get_container_name('pgdata'))
else:
datadirs += [site + '/postgres']
# Always rm the site dir & solr & files
datadirs += [site, site + '/files', site + '/solr']
if self.target:
cp.remove_section('site_' + site)
self.sites.remove(site)
if self.target:
with open(self.target + '/.datacats-environment', 'w') as conf:
cp.write(conf)
datadirs = ['sites/' + datadir for datadir in datadirs]
if not self.sites and not never_delete:
datadirs.append('venv')
web_command(
command=['/scripts/purge.sh']
+ ['/project/data/' + d for d in datadirs],
ro={scripts.get_script_path('purge.sh'): '/scripts/purge.sh'},
rw={self.datadir: '/project/data'},
)
if not self.sites and not never_delete:
shutil.rmtree(self.datadir)
else:
raise DatacatsError('Unknown format version {}'.format(format_version)) | python | def purge_data(self, which_sites=None, never_delete=False):
"""
Remove uploaded files, postgres db, solr index, venv
"""
# Default to the set of all sites
if not exists(self.datadir + '/.version'):
format_version = 1
else:
with open(self.datadir + '/.version') as f:
format_version = int(f.read().strip())
if format_version == 1:
print 'WARNING: Defaulting to old purge for version 1.'
datadirs = ['files', 'solr']
if is_boot2docker():
remove_container('datacats_pgdata_{}'.format(self.name))
remove_container('datacats_venv_{}'.format(self.name))
else:
datadirs += ['postgres', 'venv']
web_command(
command=['/scripts/purge.sh']
+ ['/project/data/' + d for d in datadirs],
ro={scripts.get_script_path('purge.sh'): '/scripts/purge.sh'},
rw={self.datadir: '/project/data'},
)
shutil.rmtree(self.datadir)
elif format_version == 2:
if not which_sites:
which_sites = self.sites
datadirs = []
boot2docker = is_boot2docker()
if which_sites:
if self.target:
cp = SafeConfigParser()
cp.read([self.target + '/.datacats-environment'])
for site in which_sites:
if boot2docker:
remove_container(self._get_container_name('pgdata'))
else:
datadirs += [site + '/postgres']
# Always rm the site dir & solr & files
datadirs += [site, site + '/files', site + '/solr']
if self.target:
cp.remove_section('site_' + site)
self.sites.remove(site)
if self.target:
with open(self.target + '/.datacats-environment', 'w') as conf:
cp.write(conf)
datadirs = ['sites/' + datadir for datadir in datadirs]
if not self.sites and not never_delete:
datadirs.append('venv')
web_command(
command=['/scripts/purge.sh']
+ ['/project/data/' + d for d in datadirs],
ro={scripts.get_script_path('purge.sh'): '/scripts/purge.sh'},
rw={self.datadir: '/project/data'},
)
if not self.sites and not never_delete:
shutil.rmtree(self.datadir)
else:
raise DatacatsError('Unknown format version {}'.format(format_version)) | [
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datacats/datacats | datacats/environment.py | Environment.logs | def logs(self, container, tail='all', follow=False, timestamps=False):
"""
:param container: 'web', 'solr' or 'postgres'
:param tail: number of lines to show
:param follow: True to return generator instead of list
:param timestamps: True to include timestamps
"""
return container_logs(
self._get_container_name(container),
tail,
follow,
timestamps) | python | def logs(self, container, tail='all', follow=False, timestamps=False):
"""
:param container: 'web', 'solr' or 'postgres'
:param tail: number of lines to show
:param follow: True to return generator instead of list
:param timestamps: True to include timestamps
"""
return container_logs(
self._get_container_name(container),
tail,
follow,
timestamps) | [
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datacats/datacats | datacats/environment.py | Environment._proxy_settings | def _proxy_settings(self):
"""
Create/replace ~/.datacats/run/proxy-environment and return
entry for ro mount for containers
"""
if not ('https_proxy' in environ or 'HTTPS_PROXY' in environ
or 'http_proxy' in environ or 'HTTP_PROXY' in environ):
return {}
https_proxy = environ.get('https_proxy')
if https_proxy is None:
https_proxy = environ.get('HTTPS_PROXY')
http_proxy = environ.get('http_proxy')
if http_proxy is None:
http_proxy = environ.get('HTTP_PROXY')
no_proxy = environ.get('no_proxy')
if no_proxy is None:
no_proxy = environ.get('NO_PROXY', '')
no_proxy = no_proxy + ',solr,db'
out = [
'PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:'
'/bin:/usr/games:/usr/local/games"\n']
if https_proxy is not None:
out.append('https_proxy=' + posix_quote(https_proxy) + '\n')
out.append('HTTPS_PROXY=' + posix_quote(https_proxy) + '\n')
if http_proxy is not None:
out.append('http_proxy=' + posix_quote(http_proxy) + '\n')
out.append('HTTP_PROXY=' + posix_quote(http_proxy) + '\n')
if no_proxy is not None:
out.append('no_proxy=' + posix_quote(no_proxy) + '\n')
out.append('NO_PROXY=' + posix_quote(no_proxy) + '\n')
with open(self.sitedir + '/run/proxy-environment', 'w') as f:
f.write("".join(out))
return {self.sitedir + '/run/proxy-environment': '/etc/environment'} | python | def _proxy_settings(self):
"""
Create/replace ~/.datacats/run/proxy-environment and return
entry for ro mount for containers
"""
if not ('https_proxy' in environ or 'HTTPS_PROXY' in environ
or 'http_proxy' in environ or 'HTTP_PROXY' in environ):
return {}
https_proxy = environ.get('https_proxy')
if https_proxy is None:
https_proxy = environ.get('HTTPS_PROXY')
http_proxy = environ.get('http_proxy')
if http_proxy is None:
http_proxy = environ.get('HTTP_PROXY')
no_proxy = environ.get('no_proxy')
if no_proxy is None:
no_proxy = environ.get('NO_PROXY', '')
no_proxy = no_proxy + ',solr,db'
out = [
'PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:'
'/bin:/usr/games:/usr/local/games"\n']
if https_proxy is not None:
out.append('https_proxy=' + posix_quote(https_proxy) + '\n')
out.append('HTTPS_PROXY=' + posix_quote(https_proxy) + '\n')
if http_proxy is not None:
out.append('http_proxy=' + posix_quote(http_proxy) + '\n')
out.append('HTTP_PROXY=' + posix_quote(http_proxy) + '\n')
if no_proxy is not None:
out.append('no_proxy=' + posix_quote(no_proxy) + '\n')
out.append('NO_PROXY=' + posix_quote(no_proxy) + '\n')
with open(self.sitedir + '/run/proxy-environment', 'w') as f:
f.write("".join(out))
return {self.sitedir + '/run/proxy-environment': '/etc/environment'} | [
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datacats/datacats | datacats/environment.py | Environment._get_container_name | def _get_container_name(self, container_type):
"""
Gets the full name of a container of the type specified.
Currently the supported types are:
- 'venv'
- 'postgres'
- 'solr'
- 'web'
- 'pgdata'
- 'lessc'
- 'datapusher'
- 'redis'
The name will be formatted appropriately with any prefixes and postfixes
needed.
:param container_type: The type of container name to generate (see above).
"""
if container_type in ['venv']:
return 'datacats_{}_{}'.format(container_type, self.name)
else:
return 'datacats_{}_{}_{}'.format(container_type, self.name, self.site_name) | python | def _get_container_name(self, container_type):
"""
Gets the full name of a container of the type specified.
Currently the supported types are:
- 'venv'
- 'postgres'
- 'solr'
- 'web'
- 'pgdata'
- 'lessc'
- 'datapusher'
- 'redis'
The name will be formatted appropriately with any prefixes and postfixes
needed.
:param container_type: The type of container name to generate (see above).
"""
if container_type in ['venv']:
return 'datacats_{}_{}'.format(container_type, self.name)
else:
return 'datacats_{}_{}_{}'.format(container_type, self.name, self.site_name) | [
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datacats/datacats | datacats/cli/less.py | less | def less(environment, opts):
# pylint: disable=unused-argument
"""Recompiles less files in an environment.
Usage:
datacats less [ENVIRONMENT]
ENVIRONMENT may be an environment name or a path to an environment directory.
Default: '.'
"""
require_extra_image(LESSC_IMAGE)
print 'Converting .less files to .css...'
for log in environment.compile_less():
print log | python | def less(environment, opts):
# pylint: disable=unused-argument
"""Recompiles less files in an environment.
Usage:
datacats less [ENVIRONMENT]
ENVIRONMENT may be an environment name or a path to an environment directory.
Default: '.'
"""
require_extra_image(LESSC_IMAGE)
print 'Converting .less files to .css...'
for log in environment.compile_less():
print log | [
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Usage:
datacats less [ENVIRONMENT]
ENVIRONMENT may be an environment name or a path to an environment directory.
Default: '.' | [
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Britefury/batchup | batchup/datasets/dataset.py | fetch_and_convert_dataset | def fetch_and_convert_dataset(source_files, target_filename):
"""
Decorator applied to a dataset conversion function that converts acquired
source files into a dataset file that BatchUp can use.
Parameters
----------
source_file: list of `AbstractSourceFile` instances
A list of files to be acquired
target_filename: str or callable
The name of the target file in which to store the converted data
either as a string or as a function of the form `fn() -> str`
that returns it.
The conversion function is of the form `fn(source_paths, target_path)`.
It should return `target_path` if successful, `None` otherwise.
After the conversion function is successfully applied, the temporary
source files that were downloaded or copied into BatchUp's temporary
directory are deleted, unless the conversion function moved or deleted
them in which case no action is taken.
Example
-------
In this example, we will show how to acquire the USPS dataset from an
online source. USPS is provided as an HDF5 file anyway, so the
conversion function simply moves it to the target path:
>>> import shutil
>>>
>>> _USPS_SRC_ONLINE = DownloadSourceFile(
... filename='usps.h5',
... url='https://github.com/Britefury/usps_dataset/raw/master/'
... 'usps.h5',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_ONLINE], 'usps.h5')
... def usps_data_online(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it:
>>> usps_path = usps_data_online() #doctest: +SKIP
In this example, the USPS dataset will be acquired from a file on the
filesystem. Note that the source path is fixed; the next example
shows how we can determine the source path dynamically:
>>> _USPS_SRC_OFFLINE_FIXED = CopySourceFile(
... filename='usps.h5',
... source_path='some/path/to/usps.h5',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_OFFLINE_FIXED], 'usps.h5')
... def usps_data_offline_fixed(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it:
>>> usps_path = usps_data_offline_fixed() #doctest: +SKIP
The source path is provided as an argument to the decorated fetch
function:
>>> _USPS_SRC_OFFLINE_DYNAMIC = CopySourceFile(
... filename='usps.h5',
... arg_name='usps_path',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_OFFLINE_DYNAMIC], 'usps.h5')
... def usps_data_offline_dynamic(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it (note that the KW-arg `usps_path` is the same
>>> # as the `arg_name` parameter given to `CopySourceFile` above:
>>> usps_path = usps_data_offline_dynamic(
... usps_path=get_config('mypath')) #doctest: +SKIP
"""
if not isinstance(target_filename, six.string_types) and \
not callable(target_filename):
raise TypeError(
'target_filename must either be a string or be callable (it is '
'a {})'.format(type(target_filename)))
for src in source_files:
if not isinstance(src, AbstractSourceFile):
raise TypeError('source_files should contain'
'`AbstractSourceFile` instances, '
'not {}'.format(type(src)))
def decorate_fetcher(convert_function):
def fetch(**kwargs):
target_fn = path_string(target_filename)
target_path = config.get_data_path(target_fn)
# If the target file does not exist, we need to acquire the
# source files and convert them
if not os.path.exists(target_path):
# Acquire the source files
source_paths = []
for src in source_files:
p = src.acquire(**kwargs)
if p is not None:
if p in source_paths:
raise ValueError(
'Duplicate source file {}'.format(p))
source_paths.append(p)
else:
print('Failed to acquire {}'.format(src))
return None
# Got the source files
# Convert
converted_path = convert_function(source_paths, target_path)
# If successful, delete the source files
if converted_path is not None:
for src in source_files:
src.clean_up()
return converted_path
else:
# Target file already exists
return target_path
fetch.__name__ = convert_function.__name__
return fetch
return decorate_fetcher | python | def fetch_and_convert_dataset(source_files, target_filename):
"""
Decorator applied to a dataset conversion function that converts acquired
source files into a dataset file that BatchUp can use.
Parameters
----------
source_file: list of `AbstractSourceFile` instances
A list of files to be acquired
target_filename: str or callable
The name of the target file in which to store the converted data
either as a string or as a function of the form `fn() -> str`
that returns it.
The conversion function is of the form `fn(source_paths, target_path)`.
It should return `target_path` if successful, `None` otherwise.
After the conversion function is successfully applied, the temporary
source files that were downloaded or copied into BatchUp's temporary
directory are deleted, unless the conversion function moved or deleted
them in which case no action is taken.
Example
-------
In this example, we will show how to acquire the USPS dataset from an
online source. USPS is provided as an HDF5 file anyway, so the
conversion function simply moves it to the target path:
>>> import shutil
>>>
>>> _USPS_SRC_ONLINE = DownloadSourceFile(
... filename='usps.h5',
... url='https://github.com/Britefury/usps_dataset/raw/master/'
... 'usps.h5',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_ONLINE], 'usps.h5')
... def usps_data_online(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it:
>>> usps_path = usps_data_online() #doctest: +SKIP
In this example, the USPS dataset will be acquired from a file on the
filesystem. Note that the source path is fixed; the next example
shows how we can determine the source path dynamically:
>>> _USPS_SRC_OFFLINE_FIXED = CopySourceFile(
... filename='usps.h5',
... source_path='some/path/to/usps.h5',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_OFFLINE_FIXED], 'usps.h5')
... def usps_data_offline_fixed(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it:
>>> usps_path = usps_data_offline_fixed() #doctest: +SKIP
The source path is provided as an argument to the decorated fetch
function:
>>> _USPS_SRC_OFFLINE_DYNAMIC = CopySourceFile(
... filename='usps.h5',
... arg_name='usps_path',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_OFFLINE_DYNAMIC], 'usps.h5')
... def usps_data_offline_dynamic(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it (note that the KW-arg `usps_path` is the same
>>> # as the `arg_name` parameter given to `CopySourceFile` above:
>>> usps_path = usps_data_offline_dynamic(
... usps_path=get_config('mypath')) #doctest: +SKIP
"""
if not isinstance(target_filename, six.string_types) and \
not callable(target_filename):
raise TypeError(
'target_filename must either be a string or be callable (it is '
'a {})'.format(type(target_filename)))
for src in source_files:
if not isinstance(src, AbstractSourceFile):
raise TypeError('source_files should contain'
'`AbstractSourceFile` instances, '
'not {}'.format(type(src)))
def decorate_fetcher(convert_function):
def fetch(**kwargs):
target_fn = path_string(target_filename)
target_path = config.get_data_path(target_fn)
# If the target file does not exist, we need to acquire the
# source files and convert them
if not os.path.exists(target_path):
# Acquire the source files
source_paths = []
for src in source_files:
p = src.acquire(**kwargs)
if p is not None:
if p in source_paths:
raise ValueError(
'Duplicate source file {}'.format(p))
source_paths.append(p)
else:
print('Failed to acquire {}'.format(src))
return None
# Got the source files
# Convert
converted_path = convert_function(source_paths, target_path)
# If successful, delete the source files
if converted_path is not None:
for src in source_files:
src.clean_up()
return converted_path
else:
# Target file already exists
return target_path
fetch.__name__ = convert_function.__name__
return fetch
return decorate_fetcher | [
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source files into a dataset file that BatchUp can use.
Parameters
----------
source_file: list of `AbstractSourceFile` instances
A list of files to be acquired
target_filename: str or callable
The name of the target file in which to store the converted data
either as a string or as a function of the form `fn() -> str`
that returns it.
The conversion function is of the form `fn(source_paths, target_path)`.
It should return `target_path` if successful, `None` otherwise.
After the conversion function is successfully applied, the temporary
source files that were downloaded or copied into BatchUp's temporary
directory are deleted, unless the conversion function moved or deleted
them in which case no action is taken.
Example
-------
In this example, we will show how to acquire the USPS dataset from an
online source. USPS is provided as an HDF5 file anyway, so the
conversion function simply moves it to the target path:
>>> import shutil
>>>
>>> _USPS_SRC_ONLINE = DownloadSourceFile(
... filename='usps.h5',
... url='https://github.com/Britefury/usps_dataset/raw/master/'
... 'usps.h5',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_ONLINE], 'usps.h5')
... def usps_data_online(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it:
>>> usps_path = usps_data_online() #doctest: +SKIP
In this example, the USPS dataset will be acquired from a file on the
filesystem. Note that the source path is fixed; the next example
shows how we can determine the source path dynamically:
>>> _USPS_SRC_OFFLINE_FIXED = CopySourceFile(
... filename='usps.h5',
... source_path='some/path/to/usps.h5',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_OFFLINE_FIXED], 'usps.h5')
... def usps_data_offline_fixed(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it:
>>> usps_path = usps_data_offline_fixed() #doctest: +SKIP
The source path is provided as an argument to the decorated fetch
function:
>>> _USPS_SRC_OFFLINE_DYNAMIC = CopySourceFile(
... filename='usps.h5',
... arg_name='usps_path',
... sha256='ba768d9a9b11e79b31c1e40130647c4fc04e6afc1fb41a0d4b9f11'
... '76065482b4'
... )
>>>
>>> @fetch_and_convert_dataset([_USPS_SRC_OFFLINE_DYNAMIC], 'usps.h5')
... def usps_data_offline_dynamic(source_paths, target_path):
... usps_path = source_paths[0]
... # For other datasets, you would convert the data here
... # In this case, we move the file
... shutil.move(usps_path, target_path)
... # Return the target path indicating success
... return target_path
>>>
>>> # Now use it (note that the KW-arg `usps_path` is the same
>>> # as the `arg_name` parameter given to `CopySourceFile` above:
>>> usps_path = usps_data_offline_dynamic(
... usps_path=get_config('mypath')) #doctest: +SKIP | [
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Britefury/batchup | batchup/datasets/dataset.py | delete_dataset_cache | def delete_dataset_cache(*filenames):
"""
Delete the cache (converted files) for a dataset.
Parameters
----------
filenames: str
Filenames of files to delete
"""
for filename in filenames:
filename = path_string(filename)
path = config.get_data_path(filename)
if os.path.exists(path):
os.remove(path) | python | def delete_dataset_cache(*filenames):
"""
Delete the cache (converted files) for a dataset.
Parameters
----------
filenames: str
Filenames of files to delete
"""
for filename in filenames:
filename = path_string(filename)
path = config.get_data_path(filename)
if os.path.exists(path):
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Britefury/batchup | batchup/datasets/dataset.py | DownloadSourceFile.acquire | def acquire(self, **kwargs):
"""
Download the file and return its path
Returns
-------
str or None
The path of the file in BatchUp's temporary directory or None if
the download failed.
"""
return config.download_data(self.temp_filename, self.url,
self.sha256) | python | def acquire(self, **kwargs):
"""
Download the file and return its path
Returns
-------
str or None
The path of the file in BatchUp's temporary directory or None if
the download failed.
"""
return config.download_data(self.temp_filename, self.url,
self.sha256) | [
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Britefury/batchup | batchup/datasets/dataset.py | CopySourceFile.acquire | def acquire(self, **kwargs):
"""
Copy the file and return its path
Returns
-------
str or None
The path of the file in BatchUp's temporary directory or None if
the copy failed.
"""
if self.source_path is None:
source_path = kwargs[self.arg_name]
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source_path = self.source_path
return config.copy_data(self.temp_filename, source_path, self.sha256) | python | def acquire(self, **kwargs):
"""
Copy the file and return its path
Returns
-------
str or None
The path of the file in BatchUp's temporary directory or None if
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"""
if self.source_path is None:
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Britefury/batchup | batchup/datasets/dataset.py | ExistingSourceFile.acquire | def acquire(self, **kwargs):
"""
Copy the file and return its path
Returns
-------
str or None
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"""
path = path_string(self.path)
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return None | python | def acquire(self, **kwargs):
"""
Copy the file and return its path
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datacats/datacats | datacats/cli/pull.py | _retry_func | def _retry_func(func, param, num, retry_notif, error_msg):
"""
A function which retries a given function num times and calls retry_notif each
time the function is retried.
:param func: The function to retry num times.
:param num: The number of times to try before giving up.
:param retry_notif: Will be called with the same parameter as func if we have to retry the
function. Will also receive the number of retries so far as a second
parameter.
:param: error_msg: The message
Throws DatacatsError if we run out of retries. Returns otherwise.
"""
for retry_num in range(num):
if retry_num:
retry_notif(param, retry_num)
try:
func(param)
return
except DatacatsError:
pass
raise DatacatsError(error_msg) | python | def _retry_func(func, param, num, retry_notif, error_msg):
"""
A function which retries a given function num times and calls retry_notif each
time the function is retried.
:param func: The function to retry num times.
:param num: The number of times to try before giving up.
:param retry_notif: Will be called with the same parameter as func if we have to retry the
function. Will also receive the number of retries so far as a second
parameter.
:param: error_msg: The message
Throws DatacatsError if we run out of retries. Returns otherwise.
"""
for retry_num in range(num):
if retry_num:
retry_notif(param, retry_num)
try:
func(param)
return
except DatacatsError:
pass
raise DatacatsError(error_msg) | [
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Britefury/batchup | batchup/work_pool.py | WorkStream.retrieve | def retrieve(self):
"""
Retrieve a result from executing a task. Note that tasks are executed
in order and that if the next task has not yet completed, this call
will block until the result is available.
Returns
-------
A result from the result buffer.
"""
if len(self.__result_buffer) > 0:
res = self.__result_buffer.popleft()
value = res.get()
else:
return None
self.__populate_buffer()
return value | python | def retrieve(self):
"""
Retrieve a result from executing a task. Note that tasks are executed
in order and that if the next task has not yet completed, this call
will block until the result is available.
Returns
-------
A result from the result buffer.
"""
if len(self.__result_buffer) > 0:
res = self.__result_buffer.popleft()
value = res.get()
else:
return None
self.__populate_buffer()
return value | [
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datacats/datacats | datacats/cli/install.py | install | def install(environment, opts):
"""Install or reinstall Python packages within this environment
Usage:
datacats install [-q] [--address=IP] [ENVIRONMENT [PACKAGE ...]]
datacats install -c [q] [--address=IP] [ENVIRONMENT]
Options:
--address=IP The address to bind to when reloading after install
-c --clean Reinstall packages into a clean virtualenv
-q --quiet Do not show output from installing packages and requirements.
ENVIRONMENT may be an environment name or a path to an environment directory.
Default: '.'
"""
environment.require_data()
install_all(environment, opts['--clean'], verbose=not opts['--quiet'],
packages=opts['PACKAGE'])
for site in environment.sites:
environment = Environment.load(environment.name, site)
if 'web' in environment.containers_running():
# FIXME: reload without changing debug setting?
manage.reload_(environment, {
'--address': opts['--address'],
'--background': False,
'--no-watch': False,
'--production': False,
'PORT': None,
'--syslog': False,
'--site-url': None,
'--interactive': False
}) | python | def install(environment, opts):
"""Install or reinstall Python packages within this environment
Usage:
datacats install [-q] [--address=IP] [ENVIRONMENT [PACKAGE ...]]
datacats install -c [q] [--address=IP] [ENVIRONMENT]
Options:
--address=IP The address to bind to when reloading after install
-c --clean Reinstall packages into a clean virtualenv
-q --quiet Do not show output from installing packages and requirements.
ENVIRONMENT may be an environment name or a path to an environment directory.
Default: '.'
"""
environment.require_data()
install_all(environment, opts['--clean'], verbose=not opts['--quiet'],
packages=opts['PACKAGE'])
for site in environment.sites:
environment = Environment.load(environment.name, site)
if 'web' in environment.containers_running():
# FIXME: reload without changing debug setting?
manage.reload_(environment, {
'--address': opts['--address'],
'--background': False,
'--no-watch': False,
'--production': False,
'PORT': None,
'--syslog': False,
'--site-url': None,
'--interactive': False
}) | [
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Usage:
datacats install [-q] [--address=IP] [ENVIRONMENT [PACKAGE ...]]
datacats install -c [q] [--address=IP] [ENVIRONMENT]
Options:
--address=IP The address to bind to when reloading after install
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datacats/datacats | datacats/cli/migrate.py | migrate | def migrate(opts):
"""Migrate an environment to a given revision of the datadir format.
Usage:
datacats migrate [-y] [-r VERSION] [ENVIRONMENT_DIR]
Options:
-r --revision=VERSION The version of the datadir format you want
to convert to [default: 2]
-y --yes Answer yes to all questions.
Defaults to '.' if ENVIRONMENT_DIR isn't specified.
"""
try:
version = int(opts['--revision'])
except:
raise DatacatsError('--revision parameter must be an integer.')
always_yes = opts['--yes']
if 'ENVIRONMENT_DIR' not in opts or not opts['ENVIRONMENT_DIR']:
cwd = getcwd()
# Get the dirname
opts['ENVIRONMENT_DIR'] = split(cwd if cwd[-1] != '/' else cwd[:-1])[1]
datadir = expanduser('~/.datacats/' + opts['ENVIRONMENT_DIR'])
if needs_format_conversion(datadir, version):
convert_environment(datadir, version, always_yes)
print 'Successfully converted datadir {} to format version {}'.format(datadir, version)
else:
print 'datadir {} is already at version {}.'.format(datadir, version) | python | def migrate(opts):
"""Migrate an environment to a given revision of the datadir format.
Usage:
datacats migrate [-y] [-r VERSION] [ENVIRONMENT_DIR]
Options:
-r --revision=VERSION The version of the datadir format you want
to convert to [default: 2]
-y --yes Answer yes to all questions.
Defaults to '.' if ENVIRONMENT_DIR isn't specified.
"""
try:
version = int(opts['--revision'])
except:
raise DatacatsError('--revision parameter must be an integer.')
always_yes = opts['--yes']
if 'ENVIRONMENT_DIR' not in opts or not opts['ENVIRONMENT_DIR']:
cwd = getcwd()
# Get the dirname
opts['ENVIRONMENT_DIR'] = split(cwd if cwd[-1] != '/' else cwd[:-1])[1]
datadir = expanduser('~/.datacats/' + opts['ENVIRONMENT_DIR'])
if needs_format_conversion(datadir, version):
convert_environment(datadir, version, always_yes)
print 'Successfully converted datadir {} to format version {}'.format(datadir, version)
else:
print 'datadir {} is already at version {}.'.format(datadir, version) | [
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datacats migrate [-y] [-r VERSION] [ENVIRONMENT_DIR]
Options:
-r --revision=VERSION The version of the datadir format you want
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-y --yes Answer yes to all questions.
Defaults to '.' if ENVIRONMENT_DIR isn't specified. | [
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datacats/datacats | datacats/cli/deploy.py | deploy | def deploy(environment, opts, profile):
"""Deploy environment to production DataCats.com cloud service
Usage:
datacats deploy [--create] [ENVIRONMENT [TARGET_NAME]]
Options:
--create Create a new environment on DataCats.com instead
of updating an existing environment
ENVIRONMENT may be an environment name or a path to a environment directory.
Default: '.'
TARGET_NAME is the name of the environment on DataCats.com. Defaults to
the environment name.
"""
target_name = opts['TARGET_NAME']
if target_name is None:
target_name = environment.name
if not valid_deploy_name(target_name):
raise DatacatsError(" `{target_name}` target name for deployment can't be accepted.\n"
"Can't have http://{target_name}.datacats.io for your datcat URL\n"
"Please choose a target name at least 5 characters long,\n"
"and containing only lowercase letters and numbers\n"
.format(target_name=target_name))
if opts['--create']:
profile.create(environment, target_name)
profile.deploy(environment, target_name, stdout)
print "Deployed source to http://{0}.datacats.io".format(target_name)
if opts['--create']:
try:
pw = confirm_password()
profile.admin_password(environment, target_name, pw)
except KeyboardInterrupt:
pass | python | def deploy(environment, opts, profile):
"""Deploy environment to production DataCats.com cloud service
Usage:
datacats deploy [--create] [ENVIRONMENT [TARGET_NAME]]
Options:
--create Create a new environment on DataCats.com instead
of updating an existing environment
ENVIRONMENT may be an environment name or a path to a environment directory.
Default: '.'
TARGET_NAME is the name of the environment on DataCats.com. Defaults to
the environment name.
"""
target_name = opts['TARGET_NAME']
if target_name is None:
target_name = environment.name
if not valid_deploy_name(target_name):
raise DatacatsError(" `{target_name}` target name for deployment can't be accepted.\n"
"Can't have http://{target_name}.datacats.io for your datcat URL\n"
"Please choose a target name at least 5 characters long,\n"
"and containing only lowercase letters and numbers\n"
.format(target_name=target_name))
if opts['--create']:
profile.create(environment, target_name)
profile.deploy(environment, target_name, stdout)
print "Deployed source to http://{0}.datacats.io".format(target_name)
if opts['--create']:
try:
pw = confirm_password()
profile.admin_password(environment, target_name, pw)
except KeyboardInterrupt:
pass | [
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Usage:
datacats deploy [--create] [ENVIRONMENT [TARGET_NAME]]
Options:
--create Create a new environment on DataCats.com instead
of updating an existing environment
ENVIRONMENT may be an environment name or a path to a environment directory.
Default: '.'
TARGET_NAME is the name of the environment on DataCats.com. Defaults to
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Britefury/batchup | batchup/data_source.py | _trim_batch | def _trim_batch(batch, length):
"""Trim the mini-batch `batch` to the size `length`.
`batch` can be:
- a NumPy array, in which case it's first axis will be trimmed to size
`length`
- a tuple, in which case `_trim_batch` applied recursively to
each element and the resulting tuple returned
As a consequence, mini-batches can be structured; lists and tuples can
be nested arbitrarily deep.
Parameters
----------
batch: tuple or NumPy array
the mini-batch to trim
length: int
the size to which `batch` is to be trimmed
Returns
-------
tuple or NumPy array of same structure as `batch`
The trimmed mini-batch
"""
if isinstance(batch, tuple):
return tuple([_trim_batch(b, length) for b in batch])
else:
return batch[:length] | python | def _trim_batch(batch, length):
"""Trim the mini-batch `batch` to the size `length`.
`batch` can be:
- a NumPy array, in which case it's first axis will be trimmed to size
`length`
- a tuple, in which case `_trim_batch` applied recursively to
each element and the resulting tuple returned
As a consequence, mini-batches can be structured; lists and tuples can
be nested arbitrarily deep.
Parameters
----------
batch: tuple or NumPy array
the mini-batch to trim
length: int
the size to which `batch` is to be trimmed
Returns
-------
tuple or NumPy array of same structure as `batch`
The trimmed mini-batch
"""
if isinstance(batch, tuple):
return tuple([_trim_batch(b, length) for b in batch])
else:
return batch[:length] | [
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`batch` can be:
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`length`
- a tuple, in which case `_trim_batch` applied recursively to
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the mini-batch to trim
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the size to which `batch` is to be trimmed
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tuple or NumPy array of same structure as `batch`
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Britefury/batchup | batchup/data_source.py | batch_map_concat | def batch_map_concat(func, batch_iter, progress_iter_func=None,
n_batches=None, prepend_args=None):
"""
Apply a function to all the samples that are accessed as mini-batches
obtained from an iterator.
Returns the per-sample results.
The function `func` should return the result for each sample in the
mini-batch as an array. To return multiple results (e.g. loss and errors)
return a tuple of arrays (e.g. `(loss_array, error_array)`)
`batch_iter` must be an iterator that generates mini-batches that
contain samples
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_iter: data set iterator
Iterator that generates mini-batches of data
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
n_batches: [optional] integer
Process at most this number of batches before returning.
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The per-sample sum of the results of the function `func` e.g.
`(batch_A, batch_B, ...)`
Returns an empty tuple if there were 0 samples in the data set.
Examples
--------
In these examples we will demonstrate the use of `batch_map` to apply
a function (e.g. a Theano function that runs on the GPU) to samples
in a data set. We construct an iterator that generates mini-batches from
the data set and pass it to `batch_map` along with the function that
we wish to apply. The function will receive the batches and process them.
Define a function to apply to samples:
>>> def sqr_sum(x):
... # Ensure that we receive batches of the expected size:
... assert len(x) in {5, 2}
... return (x ** 2).sum(axis=1)
Construct data to process and create a data source:
>>> X = np.random.normal(size=(7, 10))
>>> ds = ArrayDataSource([X])
Apply the function defined above:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> X_sqr_sum = batch_map_concat(sqr_sum, batch_iter)
>>> assert np.allclose(X_sqr_sum[0], (X ** 2).sum(axis=1))
There are also cases where we wish to limit the number of batches that
will be processed:
- when the iterator generates an infinite number of samples
- when the data set is huge and we wish to show results as we go
Use the `n_batches` argument to limit the number of batches to process:
>>> X_large = np.random.normal(size=(100, 10))
>>> ds_large = ArrayDataSource([X_large])
>>> iter_large = ds_large.batch_iterator(batch_size=5)
>>> for i in range(10):
... partial_result = batch_map_concat(sqr_sum, iter_large, n_batches=2)
... # Should have 10 samples per partial result
... assert len(partial_result[0]) == 10
... j = i * 10
... assert np.allclose(partial_result[0],
... (X_large[j:j + 10]**2).sum(axis=1))
"""
# Accumulator for results and number of samples
results = []
# If `progress_iter_func` is not `None`, apply it
if progress_iter_func is not None:
batch_iter = progress_iter_func(batch_iter, total=n_batches,
leave=False)
# Apply `func` to each batch
n_processed = 0
for batch in batch_iter:
# Apply on batch and check the type of the results
if prepend_args is not None:
batch_results = func(*(prepend_args + tuple(batch)))
else:
batch_results = func(*batch)
if batch_results is None:
pass
elif isinstance(batch_results, np.ndarray):
batch_results = (batch_results,)
elif isinstance(batch_results, tuple):
pass
else:
raise TypeError(
'Batch function should return a tuple of results, a '
'single result as a NumPy array, or None, '
'not {}'.format(type(batch_results)))
# Accumulate training results
if batch_results is not None:
results.append(batch_results)
n_processed += 1
if n_batches is not None and n_processed >= n_batches:
break
# Concatenate result arrays
if len(results) > 0:
results = zip(*results)
results = tuple([np.concatenate(list(r), axis=0) for r in results])
return results
else:
return None | python | def batch_map_concat(func, batch_iter, progress_iter_func=None,
n_batches=None, prepend_args=None):
"""
Apply a function to all the samples that are accessed as mini-batches
obtained from an iterator.
Returns the per-sample results.
The function `func` should return the result for each sample in the
mini-batch as an array. To return multiple results (e.g. loss and errors)
return a tuple of arrays (e.g. `(loss_array, error_array)`)
`batch_iter` must be an iterator that generates mini-batches that
contain samples
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_iter: data set iterator
Iterator that generates mini-batches of data
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
n_batches: [optional] integer
Process at most this number of batches before returning.
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The per-sample sum of the results of the function `func` e.g.
`(batch_A, batch_B, ...)`
Returns an empty tuple if there were 0 samples in the data set.
Examples
--------
In these examples we will demonstrate the use of `batch_map` to apply
a function (e.g. a Theano function that runs on the GPU) to samples
in a data set. We construct an iterator that generates mini-batches from
the data set and pass it to `batch_map` along with the function that
we wish to apply. The function will receive the batches and process them.
Define a function to apply to samples:
>>> def sqr_sum(x):
... # Ensure that we receive batches of the expected size:
... assert len(x) in {5, 2}
... return (x ** 2).sum(axis=1)
Construct data to process and create a data source:
>>> X = np.random.normal(size=(7, 10))
>>> ds = ArrayDataSource([X])
Apply the function defined above:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> X_sqr_sum = batch_map_concat(sqr_sum, batch_iter)
>>> assert np.allclose(X_sqr_sum[0], (X ** 2).sum(axis=1))
There are also cases where we wish to limit the number of batches that
will be processed:
- when the iterator generates an infinite number of samples
- when the data set is huge and we wish to show results as we go
Use the `n_batches` argument to limit the number of batches to process:
>>> X_large = np.random.normal(size=(100, 10))
>>> ds_large = ArrayDataSource([X_large])
>>> iter_large = ds_large.batch_iterator(batch_size=5)
>>> for i in range(10):
... partial_result = batch_map_concat(sqr_sum, iter_large, n_batches=2)
... # Should have 10 samples per partial result
... assert len(partial_result[0]) == 10
... j = i * 10
... assert np.allclose(partial_result[0],
... (X_large[j:j + 10]**2).sum(axis=1))
"""
# Accumulator for results and number of samples
results = []
# If `progress_iter_func` is not `None`, apply it
if progress_iter_func is not None:
batch_iter = progress_iter_func(batch_iter, total=n_batches,
leave=False)
# Apply `func` to each batch
n_processed = 0
for batch in batch_iter:
# Apply on batch and check the type of the results
if prepend_args is not None:
batch_results = func(*(prepend_args + tuple(batch)))
else:
batch_results = func(*batch)
if batch_results is None:
pass
elif isinstance(batch_results, np.ndarray):
batch_results = (batch_results,)
elif isinstance(batch_results, tuple):
pass
else:
raise TypeError(
'Batch function should return a tuple of results, a '
'single result as a NumPy array, or None, '
'not {}'.format(type(batch_results)))
# Accumulate training results
if batch_results is not None:
results.append(batch_results)
n_processed += 1
if n_batches is not None and n_processed >= n_batches:
break
# Concatenate result arrays
if len(results) > 0:
results = zip(*results)
results = tuple([np.concatenate(list(r), axis=0) for r in results])
return results
else:
return None | [
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] | Apply a function to all the samples that are accessed as mini-batches
obtained from an iterator.
Returns the per-sample results.
The function `func` should return the result for each sample in the
mini-batch as an array. To return multiple results (e.g. loss and errors)
return a tuple of arrays (e.g. `(loss_array, error_array)`)
`batch_iter` must be an iterator that generates mini-batches that
contain samples
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_iter: data set iterator
Iterator that generates mini-batches of data
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
n_batches: [optional] integer
Process at most this number of batches before returning.
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The per-sample sum of the results of the function `func` e.g.
`(batch_A, batch_B, ...)`
Returns an empty tuple if there were 0 samples in the data set.
Examples
--------
In these examples we will demonstrate the use of `batch_map` to apply
a function (e.g. a Theano function that runs on the GPU) to samples
in a data set. We construct an iterator that generates mini-batches from
the data set and pass it to `batch_map` along with the function that
we wish to apply. The function will receive the batches and process them.
Define a function to apply to samples:
>>> def sqr_sum(x):
... # Ensure that we receive batches of the expected size:
... assert len(x) in {5, 2}
... return (x ** 2).sum(axis=1)
Construct data to process and create a data source:
>>> X = np.random.normal(size=(7, 10))
>>> ds = ArrayDataSource([X])
Apply the function defined above:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> X_sqr_sum = batch_map_concat(sqr_sum, batch_iter)
>>> assert np.allclose(X_sqr_sum[0], (X ** 2).sum(axis=1))
There are also cases where we wish to limit the number of batches that
will be processed:
- when the iterator generates an infinite number of samples
- when the data set is huge and we wish to show results as we go
Use the `n_batches` argument to limit the number of batches to process:
>>> X_large = np.random.normal(size=(100, 10))
>>> ds_large = ArrayDataSource([X_large])
>>> iter_large = ds_large.batch_iterator(batch_size=5)
>>> for i in range(10):
... partial_result = batch_map_concat(sqr_sum, iter_large, n_batches=2)
... # Should have 10 samples per partial result
... assert len(partial_result[0]) == 10
... j = i * 10
... assert np.allclose(partial_result[0],
... (X_large[j:j + 10]**2).sum(axis=1)) | [
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] | 3fc2304e629f813c05f9e7a85a18acef3581a536 | https://github.com/Britefury/batchup/blob/3fc2304e629f813c05f9e7a85a18acef3581a536/batchup/data_source.py#L1478-L1599 | train |
Britefury/batchup | batchup/data_source.py | batch_map_mean | def batch_map_mean(func, batch_iter, progress_iter_func=None, sum_axis=None,
n_batches=None, prepend_args=None):
"""
Apply a function to all the samples that are accessed as mini-batches
obtained from an iterator.
Returns the across-samples mean of the results returned by `func`
The `sum_axis` arguments tells `mean_batch_map` how to process the
results of `func` before accumulating them:
- If `sum_axis` is `None`, `func` should return the
across-samples SUM of the results of operating on the mini-batch the
sum of the values for the samples, e.g. for loss and error it should
return `(sum([loss0, loss1, ... lossN]), sum([err0, err1, ... errN]))`
- Otherwise, `sum_axis` should specify the axis or axes over which
the the batch results should be summed, e.g. if `func` returns a
per-sample loss and error in two arrays
`[[loss0, loss1, ... lossN], [err0, err1, ... errN]`, give `sum_axis`
a value of `0` to sum over axis 0 to get the per-batch loss and error.
These results will be accumulated and divided by the number of samples
at the end to get the mean.
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_iter: data set iterator
Iterator that generates mini-batches of data
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
sum_axis: (default=`None`) int, tuple of ints or None
If an integer or a tuple of integers, the results returned by `func`
will be summed across this axis / these axes before being accumulated;
e.g. if `func` returns an array of per-sample losses, with axis 0
being the sample dimension, passing a value of `0` as `sum_axis`
will cause these results to be summed along axis 0 to get the
per-batch sum before accumulating the losses. The total summed loss
will be divided by the number of samples at the end in order to
compute the mean loss.
n_batches: [optional] integer that specifies the number of mini-batches
to process before returning
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The sum of the results of the function `fn` divided by the number of
samples processed, e.g.
`(sum(outA_per_batch) / n_samples,
sum(outB_per_batch) / n_samples,
...)`
Examples
--------
The following examples will demonstrate the use of `mean_batch_map`
to compute binary cross entropy loss over a data set.
A few variants will be demonstrated:
- the default behaviour in which the function being applied should
return the sum over the batch sample axis
- having the function return per sample results and maving
`mean_batch_map` perform the sum operation. This is easier to
understand but less efficient as a Theano function would have to
move more data back from the GPU.
- limiting the number of batches that will be processed in order to get
partial results when dealing with a large data set
Define a function to compute the per-sample binary cross entropy
loss:
>>> def binary_crossentropy_loss(pred, target):
... e = -target * np.log(pred) - (1 - target) * np.log(1 - pred)
... return e.mean(axis=1)
Now define a function that computes the *SUM* of the binary cross
entropy losses over the sample axis (axis 0), as the default
behaviour of `mean_batch_map` will sum them up and divide by the
number of samples at the end:
>>> def binary_crossentropy_loss_sum(pred, target):
... return binary_crossentropy_loss(pred, target).sum()
Construct prediction and target data
>>> pred = np.random.uniform(0.1, 0.9, size=(7, 10))
>>> tgt = np.random.uniform(0.1, 0.9, size=(7, 10))
>>> ds = ArrayDataSource([pred, tgt])
Apply the loss sum function defined above:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> loss = batch_map_mean(binary_crossentropy_loss_sum, batch_iter)
>>> assert np.allclose(
... loss, binary_crossentropy_loss(pred, tgt).mean())
Have `mean_batch_map` sum over axis 0:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> loss = batch_map_mean(binary_crossentropy_loss, batch_iter,
... sum_axis=0)
>>> assert np.allclose(
... loss, binary_crossentropy_loss(pred, tgt).mean())
Construct a large data set and use `batch
>>> pred_large = np.random.uniform(0.1, 0.9, size=(100, 10))
>>> tgt_large = np.random.uniform(0.1, 0.9, size=(100, 10))
>>> ds_large = ArrayDataSource([pred_large, tgt_large])
>>> iter_large = ds_large.batch_iterator(batch_size=5)
>>> for i in range(10):
... partial_loss = batch_map_mean(binary_crossentropy_loss_sum,
... iter_large, n_batches=2)
... j = i * 10
... assert np.allclose(
... partial_loss, binary_crossentropy_loss(
... pred_large[j:j + 10], tgt_large[j:j + 10]).mean())
"""
# Accumulator for results and number of samples
results_accum = None
n_samples_accum = 0
# If `progress_iter_func` is not `None`, apply it
if progress_iter_func is not None:
batch_iter = progress_iter_func(batch_iter, total=n_batches,
leave=False)
# Train on each batch
n_processed = 0
for batch in batch_iter:
# Get number of samples in batch; can vary
batch_n = _length_of_batch(batch)
# Apply on batch and check the type of the results
if prepend_args is not None:
batch_results = func(*(prepend_args + tuple(batch)))
else:
batch_results = func(*batch)
if batch_results is None:
pass
elif isinstance(batch_results, (np.ndarray, float)):
batch_results = (batch_results,)
elif isinstance(batch_results, tuple):
pass
else:
raise TypeError(
'Batch function should return a tuple of results, a '
'single result as a NumPy array or float, or None, '
'not {}'.format(type(batch_results)))
# Accumulate results and number of samples
if results_accum is None:
# Initialise the accumulator to the batch results if `func`
# returns summed results or if it returned None;
# don't attempt to iterate over None and sum each item
if batch_results is None:
pass
elif sum_axis is None:
results_accum = list(batch_results)
else:
results_accum = [br.sum(axis=sum_axis) for br in batch_results]
else:
if batch_results is not None:
for i in range(len(results_accum)):
br = batch_results[i]
if sum_axis is not None:
br = br.sum(axis=sum_axis)
results_accum[i] += br
n_samples_accum += batch_n
n_processed += 1
if n_batches is not None and n_processed >= n_batches:
break
# Divide by the number of training examples used to compute mean
if results_accum is not None:
results_accum = tuple([np.array(r).astype(float) / n_samples_accum
for r in results_accum])
return results_accum | python | def batch_map_mean(func, batch_iter, progress_iter_func=None, sum_axis=None,
n_batches=None, prepend_args=None):
"""
Apply a function to all the samples that are accessed as mini-batches
obtained from an iterator.
Returns the across-samples mean of the results returned by `func`
The `sum_axis` arguments tells `mean_batch_map` how to process the
results of `func` before accumulating them:
- If `sum_axis` is `None`, `func` should return the
across-samples SUM of the results of operating on the mini-batch the
sum of the values for the samples, e.g. for loss and error it should
return `(sum([loss0, loss1, ... lossN]), sum([err0, err1, ... errN]))`
- Otherwise, `sum_axis` should specify the axis or axes over which
the the batch results should be summed, e.g. if `func` returns a
per-sample loss and error in two arrays
`[[loss0, loss1, ... lossN], [err0, err1, ... errN]`, give `sum_axis`
a value of `0` to sum over axis 0 to get the per-batch loss and error.
These results will be accumulated and divided by the number of samples
at the end to get the mean.
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_iter: data set iterator
Iterator that generates mini-batches of data
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
sum_axis: (default=`None`) int, tuple of ints or None
If an integer or a tuple of integers, the results returned by `func`
will be summed across this axis / these axes before being accumulated;
e.g. if `func` returns an array of per-sample losses, with axis 0
being the sample dimension, passing a value of `0` as `sum_axis`
will cause these results to be summed along axis 0 to get the
per-batch sum before accumulating the losses. The total summed loss
will be divided by the number of samples at the end in order to
compute the mean loss.
n_batches: [optional] integer that specifies the number of mini-batches
to process before returning
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The sum of the results of the function `fn` divided by the number of
samples processed, e.g.
`(sum(outA_per_batch) / n_samples,
sum(outB_per_batch) / n_samples,
...)`
Examples
--------
The following examples will demonstrate the use of `mean_batch_map`
to compute binary cross entropy loss over a data set.
A few variants will be demonstrated:
- the default behaviour in which the function being applied should
return the sum over the batch sample axis
- having the function return per sample results and maving
`mean_batch_map` perform the sum operation. This is easier to
understand but less efficient as a Theano function would have to
move more data back from the GPU.
- limiting the number of batches that will be processed in order to get
partial results when dealing with a large data set
Define a function to compute the per-sample binary cross entropy
loss:
>>> def binary_crossentropy_loss(pred, target):
... e = -target * np.log(pred) - (1 - target) * np.log(1 - pred)
... return e.mean(axis=1)
Now define a function that computes the *SUM* of the binary cross
entropy losses over the sample axis (axis 0), as the default
behaviour of `mean_batch_map` will sum them up and divide by the
number of samples at the end:
>>> def binary_crossentropy_loss_sum(pred, target):
... return binary_crossentropy_loss(pred, target).sum()
Construct prediction and target data
>>> pred = np.random.uniform(0.1, 0.9, size=(7, 10))
>>> tgt = np.random.uniform(0.1, 0.9, size=(7, 10))
>>> ds = ArrayDataSource([pred, tgt])
Apply the loss sum function defined above:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> loss = batch_map_mean(binary_crossentropy_loss_sum, batch_iter)
>>> assert np.allclose(
... loss, binary_crossentropy_loss(pred, tgt).mean())
Have `mean_batch_map` sum over axis 0:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> loss = batch_map_mean(binary_crossentropy_loss, batch_iter,
... sum_axis=0)
>>> assert np.allclose(
... loss, binary_crossentropy_loss(pred, tgt).mean())
Construct a large data set and use `batch
>>> pred_large = np.random.uniform(0.1, 0.9, size=(100, 10))
>>> tgt_large = np.random.uniform(0.1, 0.9, size=(100, 10))
>>> ds_large = ArrayDataSource([pred_large, tgt_large])
>>> iter_large = ds_large.batch_iterator(batch_size=5)
>>> for i in range(10):
... partial_loss = batch_map_mean(binary_crossentropy_loss_sum,
... iter_large, n_batches=2)
... j = i * 10
... assert np.allclose(
... partial_loss, binary_crossentropy_loss(
... pred_large[j:j + 10], tgt_large[j:j + 10]).mean())
"""
# Accumulator for results and number of samples
results_accum = None
n_samples_accum = 0
# If `progress_iter_func` is not `None`, apply it
if progress_iter_func is not None:
batch_iter = progress_iter_func(batch_iter, total=n_batches,
leave=False)
# Train on each batch
n_processed = 0
for batch in batch_iter:
# Get number of samples in batch; can vary
batch_n = _length_of_batch(batch)
# Apply on batch and check the type of the results
if prepend_args is not None:
batch_results = func(*(prepend_args + tuple(batch)))
else:
batch_results = func(*batch)
if batch_results is None:
pass
elif isinstance(batch_results, (np.ndarray, float)):
batch_results = (batch_results,)
elif isinstance(batch_results, tuple):
pass
else:
raise TypeError(
'Batch function should return a tuple of results, a '
'single result as a NumPy array or float, or None, '
'not {}'.format(type(batch_results)))
# Accumulate results and number of samples
if results_accum is None:
# Initialise the accumulator to the batch results if `func`
# returns summed results or if it returned None;
# don't attempt to iterate over None and sum each item
if batch_results is None:
pass
elif sum_axis is None:
results_accum = list(batch_results)
else:
results_accum = [br.sum(axis=sum_axis) for br in batch_results]
else:
if batch_results is not None:
for i in range(len(results_accum)):
br = batch_results[i]
if sum_axis is not None:
br = br.sum(axis=sum_axis)
results_accum[i] += br
n_samples_accum += batch_n
n_processed += 1
if n_batches is not None and n_processed >= n_batches:
break
# Divide by the number of training examples used to compute mean
if results_accum is not None:
results_accum = tuple([np.array(r).astype(float) / n_samples_accum
for r in results_accum])
return results_accum | [
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] | Apply a function to all the samples that are accessed as mini-batches
obtained from an iterator.
Returns the across-samples mean of the results returned by `func`
The `sum_axis` arguments tells `mean_batch_map` how to process the
results of `func` before accumulating them:
- If `sum_axis` is `None`, `func` should return the
across-samples SUM of the results of operating on the mini-batch the
sum of the values for the samples, e.g. for loss and error it should
return `(sum([loss0, loss1, ... lossN]), sum([err0, err1, ... errN]))`
- Otherwise, `sum_axis` should specify the axis or axes over which
the the batch results should be summed, e.g. if `func` returns a
per-sample loss and error in two arrays
`[[loss0, loss1, ... lossN], [err0, err1, ... errN]`, give `sum_axis`
a value of `0` to sum over axis 0 to get the per-batch loss and error.
These results will be accumulated and divided by the number of samples
at the end to get the mean.
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_iter: data set iterator
Iterator that generates mini-batches of data
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
sum_axis: (default=`None`) int, tuple of ints or None
If an integer or a tuple of integers, the results returned by `func`
will be summed across this axis / these axes before being accumulated;
e.g. if `func` returns an array of per-sample losses, with axis 0
being the sample dimension, passing a value of `0` as `sum_axis`
will cause these results to be summed along axis 0 to get the
per-batch sum before accumulating the losses. The total summed loss
will be divided by the number of samples at the end in order to
compute the mean loss.
n_batches: [optional] integer that specifies the number of mini-batches
to process before returning
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The sum of the results of the function `fn` divided by the number of
samples processed, e.g.
`(sum(outA_per_batch) / n_samples,
sum(outB_per_batch) / n_samples,
...)`
Examples
--------
The following examples will demonstrate the use of `mean_batch_map`
to compute binary cross entropy loss over a data set.
A few variants will be demonstrated:
- the default behaviour in which the function being applied should
return the sum over the batch sample axis
- having the function return per sample results and maving
`mean_batch_map` perform the sum operation. This is easier to
understand but less efficient as a Theano function would have to
move more data back from the GPU.
- limiting the number of batches that will be processed in order to get
partial results when dealing with a large data set
Define a function to compute the per-sample binary cross entropy
loss:
>>> def binary_crossentropy_loss(pred, target):
... e = -target * np.log(pred) - (1 - target) * np.log(1 - pred)
... return e.mean(axis=1)
Now define a function that computes the *SUM* of the binary cross
entropy losses over the sample axis (axis 0), as the default
behaviour of `mean_batch_map` will sum them up and divide by the
number of samples at the end:
>>> def binary_crossentropy_loss_sum(pred, target):
... return binary_crossentropy_loss(pred, target).sum()
Construct prediction and target data
>>> pred = np.random.uniform(0.1, 0.9, size=(7, 10))
>>> tgt = np.random.uniform(0.1, 0.9, size=(7, 10))
>>> ds = ArrayDataSource([pred, tgt])
Apply the loss sum function defined above:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> loss = batch_map_mean(binary_crossentropy_loss_sum, batch_iter)
>>> assert np.allclose(
... loss, binary_crossentropy_loss(pred, tgt).mean())
Have `mean_batch_map` sum over axis 0:
>>> batch_iter = ds.batch_iterator(batch_size=5)
>>> loss = batch_map_mean(binary_crossentropy_loss, batch_iter,
... sum_axis=0)
>>> assert np.allclose(
... loss, binary_crossentropy_loss(pred, tgt).mean())
Construct a large data set and use `batch
>>> pred_large = np.random.uniform(0.1, 0.9, size=(100, 10))
>>> tgt_large = np.random.uniform(0.1, 0.9, size=(100, 10))
>>> ds_large = ArrayDataSource([pred_large, tgt_large])
>>> iter_large = ds_large.batch_iterator(batch_size=5)
>>> for i in range(10):
... partial_loss = batch_map_mean(binary_crossentropy_loss_sum,
... iter_large, n_batches=2)
... j = i * 10
... assert np.allclose(
... partial_loss, binary_crossentropy_loss(
... pred_large[j:j + 10], tgt_large[j:j + 10]).mean()) | [
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] | 3fc2304e629f813c05f9e7a85a18acef3581a536 | https://github.com/Britefury/batchup/blob/3fc2304e629f813c05f9e7a85a18acef3581a536/batchup/data_source.py#L1602-L1779 | train |
Britefury/batchup | batchup/data_source.py | coerce_data_source | def coerce_data_source(x):
"""
Helper function to coerce an object into a data source, selecting the
appropriate data source class for the given object. If `x` is already
a data source it is returned as is.
Parameters
----------
x: any
The object to coerce. If `x` is a data source, it is returned as is.
If it is a list or tuple of array-like objects they will be wrapped
in an `ArrayDataSource` that will be returned. If `x` is an iterator
it will be wrapped in an `IteratorDataSource`. If it is a callable
it will be wrapped in a `CallableDataSource`.
Returns
-------
`x` coerced into a data source
Raises
------
`TypeError` if `x` is not a data souce, a list or tuple of array-like
objects, an iterator or a callable.
"""
if isinstance(x, AbstractDataSource):
return x
elif isinstance(x, (list, tuple)):
# Sequence of array-likes
items = []
for item in x:
if _is_array_like(item):
items.append(item)
else:
raise TypeError(
'Cannot convert x to a data source; x is a sequence and '
'one of the elements is not an array-like object, rather '
'a {}'.format(type(item)))
if len(items) == 0:
raise ValueError('Cannot convert x to a data source; x is an '
'empty sequence')
return ArrayDataSource(items)
elif isinstance(x, collections.Iterator):
return IteratorDataSource(x)
elif callable(x):
return CallableDataSource(x)
else:
raise TypeError('Cannot convert x to a data source; can only handle '
'iterators, callables, non-empty sequences of '
'array-like objects; cannot '
'handle {}'.format(type(x))) | python | def coerce_data_source(x):
"""
Helper function to coerce an object into a data source, selecting the
appropriate data source class for the given object. If `x` is already
a data source it is returned as is.
Parameters
----------
x: any
The object to coerce. If `x` is a data source, it is returned as is.
If it is a list or tuple of array-like objects they will be wrapped
in an `ArrayDataSource` that will be returned. If `x` is an iterator
it will be wrapped in an `IteratorDataSource`. If it is a callable
it will be wrapped in a `CallableDataSource`.
Returns
-------
`x` coerced into a data source
Raises
------
`TypeError` if `x` is not a data souce, a list or tuple of array-like
objects, an iterator or a callable.
"""
if isinstance(x, AbstractDataSource):
return x
elif isinstance(x, (list, tuple)):
# Sequence of array-likes
items = []
for item in x:
if _is_array_like(item):
items.append(item)
else:
raise TypeError(
'Cannot convert x to a data source; x is a sequence and '
'one of the elements is not an array-like object, rather '
'a {}'.format(type(item)))
if len(items) == 0:
raise ValueError('Cannot convert x to a data source; x is an '
'empty sequence')
return ArrayDataSource(items)
elif isinstance(x, collections.Iterator):
return IteratorDataSource(x)
elif callable(x):
return CallableDataSource(x)
else:
raise TypeError('Cannot convert x to a data source; can only handle '
'iterators, callables, non-empty sequences of '
'array-like objects; cannot '
'handle {}'.format(type(x))) | [
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appropriate data source class for the given object. If `x` is already
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Parameters
----------
x: any
The object to coerce. If `x` is a data source, it is returned as is.
If it is a list or tuple of array-like objects they will be wrapped
in an `ArrayDataSource` that will be returned. If `x` is an iterator
it will be wrapped in an `IteratorDataSource`. If it is a callable
it will be wrapped in a `CallableDataSource`.
Returns
-------
`x` coerced into a data source
Raises
------
`TypeError` if `x` is not a data souce, a list or tuple of array-like
objects, an iterator or a callable. | [
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] | 3fc2304e629f813c05f9e7a85a18acef3581a536 | https://github.com/Britefury/batchup/blob/3fc2304e629f813c05f9e7a85a18acef3581a536/batchup/data_source.py#L1800-L1849 | train |
Britefury/batchup | batchup/data_source.py | AbstractDataSource.batch_map_concat | def batch_map_concat(self, func, batch_size, progress_iter_func=None,
n_batches=None, prepend_args=None, **kwargs):
"""A batch oriented implementation of `map`.
Applies a function to all the samples in this data source by breaking
the data into mini-batches and applying the function to each
mini-batch.
Returns the per-sample results.
This method is a wrapper around the :func:`batch_map` function;
please see its documentation for more information and examples.
The function `func` should return the result for each sample in the
mini-batch as an array. To return multiple results (e.g. loss and
errors) return a tuple of arrays (e.g. `(loss_array, error_array)`)
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_size: int
The mini-batch size
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
n_batches: [optional] integer that specifies the number of mini-batches
to process before returning
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The per-sample sum of the results of the function `func` e.g.
`(batch_A, batch_B, ...)`
Returns an empty tuple if there were 0 samples in the data set.
Examples
--------
Define a function to apply to samples:
>>> def sqr_sum(x):
... return (x ** 2).sum(axis=1)
Construct data to process and create a data source:
>>> X = np.random.normal(size=(7, 10))
>>> ds = ArrayDataSource([X])
Apply the function defined above:
>>> X_sqr_sum = ds.batch_map_concat(sqr_sum, batch_size=5)
>>> assert (X_sqr_sum[0] == (X ** 2).sum(axis=1)).all()
"""
if n_batches is None:
n = self.num_samples(**kwargs)
if n == np.inf:
raise ValueError('Data set has infinite size or sampler will '
'generate infinite samples but no n_batches '
'limit specified')
elif n is not None:
n_batches = sampling.num_batches(n, batch_size)
batch_iter = self.batch_iterator(batch_size, **kwargs)
return batch_map_concat(func, batch_iter, progress_iter_func,
n_batches, prepend_args) | python | def batch_map_concat(self, func, batch_size, progress_iter_func=None,
n_batches=None, prepend_args=None, **kwargs):
"""A batch oriented implementation of `map`.
Applies a function to all the samples in this data source by breaking
the data into mini-batches and applying the function to each
mini-batch.
Returns the per-sample results.
This method is a wrapper around the :func:`batch_map` function;
please see its documentation for more information and examples.
The function `func` should return the result for each sample in the
mini-batch as an array. To return multiple results (e.g. loss and
errors) return a tuple of arrays (e.g. `(loss_array, error_array)`)
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_size: int
The mini-batch size
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
n_batches: [optional] integer that specifies the number of mini-batches
to process before returning
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The per-sample sum of the results of the function `func` e.g.
`(batch_A, batch_B, ...)`
Returns an empty tuple if there were 0 samples in the data set.
Examples
--------
Define a function to apply to samples:
>>> def sqr_sum(x):
... return (x ** 2).sum(axis=1)
Construct data to process and create a data source:
>>> X = np.random.normal(size=(7, 10))
>>> ds = ArrayDataSource([X])
Apply the function defined above:
>>> X_sqr_sum = ds.batch_map_concat(sqr_sum, batch_size=5)
>>> assert (X_sqr_sum[0] == (X ** 2).sum(axis=1)).all()
"""
if n_batches is None:
n = self.num_samples(**kwargs)
if n == np.inf:
raise ValueError('Data set has infinite size or sampler will '
'generate infinite samples but no n_batches '
'limit specified')
elif n is not None:
n_batches = sampling.num_batches(n, batch_size)
batch_iter = self.batch_iterator(batch_size, **kwargs)
return batch_map_concat(func, batch_iter, progress_iter_func,
n_batches, prepend_args) | [
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Applies a function to all the samples in this data source by breaking
the data into mini-batches and applying the function to each
mini-batch.
Returns the per-sample results.
This method is a wrapper around the :func:`batch_map` function;
please see its documentation for more information and examples.
The function `func` should return the result for each sample in the
mini-batch as an array. To return multiple results (e.g. loss and
errors) return a tuple of arrays (e.g. `(loss_array, error_array)`)
Parameters
----------
func: callable `func(*batch) -> results`
The function to call on each mini-batch. Note that the results
must be `None`, a tuple or a NumPy array
batch_size: int
The mini-batch size
progress_iter_func: [optional] callable
`progress_iter_func(iterator, total=total, leave=leave)`
A `tqdm` style function that will be passed the iterator that
generates training batches along with the total number of batches
and `False` for the `leave` parameter. By passing either
`tqdm.tqdm` or `tqdm.tqdm_notebook` as this argument you can have
the training loop display a progress bar.
n_batches: [optional] integer that specifies the number of mini-batches
to process before returning
prepend_args: [optional] tuple
Arguments to prepend to the arguments passed to `func`
Returns
-------
tuple
The per-sample sum of the results of the function `func` e.g.
`(batch_A, batch_B, ...)`
Returns an empty tuple if there were 0 samples in the data set.
Examples
--------
Define a function to apply to samples:
>>> def sqr_sum(x):
... return (x ** 2).sum(axis=1)
Construct data to process and create a data source:
>>> X = np.random.normal(size=(7, 10))
>>> ds = ArrayDataSource([X])
Apply the function defined above:
>>> X_sqr_sum = ds.batch_map_concat(sqr_sum, batch_size=5)
>>> assert (X_sqr_sum[0] == (X ** 2).sum(axis=1)).all() | [
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