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def validate_netmask(s):
"""Validate that a dotted-quad ip address is a valid netmask.
>>> validate_netmask('0.0.0.0')
True
>>> validate_netmask('128.0.0.0')
True
>>> validate_netmask('255.0.0.0')
True
>>> validate_netmask('255.255.255.255')
True
>>> validate_netmask(BROADCAST)... |
def validate_subnet(s):
"""Validate a dotted-quad ip address including a netmask.
The string is considered a valid dotted-quad address with netmask if it
consists of one to four octets (0-255) seperated by periods (.) followed
by a forward slash (/) and a subnet bitmask which is expressed in
dotted... |
def ip2long(ip):
"""Convert a dotted-quad ip address to a network byte order 32-bit
integer.
>>> ip2long('127.0.0.1')
2130706433
>>> ip2long('127.1')
2130706433
>>> ip2long('127')
2130706432
>>> ip2long('127.0.0.256') is None
True
:param ip: Dotted-quad ip address (eg. '1... |
def ip2network(ip):
"""Convert a dotted-quad ip to base network number.
This differs from :func:`ip2long` in that partial addresses as treated as
all network instead of network plus host (eg. '127.1' expands to
'127.1.0.0')
:param ip: dotted-quad ip address (eg. ‘127.0.0.1’).
:type ip: str
... |
def long2ip(l):
"""Convert a network byte order 32-bit integer to a dotted quad ip
address.
>>> long2ip(2130706433)
'127.0.0.1'
>>> long2ip(MIN_IP)
'0.0.0.0'
>>> long2ip(MAX_IP)
'255.255.255.255'
>>> long2ip(None) #doctest: +IGNORE_EXCEPTION_DETAIL
Traceback (most recent call l... |
def cidr2block(cidr):
"""Convert a CIDR notation ip address into a tuple containing the network
block start and end addresses.
>>> cidr2block('127.0.0.1/32')
('127.0.0.1', '127.0.0.1')
>>> cidr2block('127/8')
('127.0.0.0', '127.255.255.255')
>>> cidr2block('127.0.1/16')
('127.0.0.0', '... |
def subnet2block(subnet):
"""Convert a dotted-quad ip address including a netmask into a tuple
containing the network block start and end addresses.
>>> subnet2block('127.0.0.1/255.255.255.255')
('127.0.0.1', '127.0.0.1')
>>> subnet2block('127/255')
('127.0.0.0', '127.255.255.255')
>>> sub... |
def _block_from_ip_and_prefix(ip, prefix):
"""Create a tuple of (start, end) dotted-quad addresses from the given
ip address and prefix length.
:param ip: Ip address in block
:type ip: long
:param prefix: Prefix size for block
:type prefix: int
:returns: Tuple of block (start, end)
"""
... |
def download_shared_files(job, samples, config):
"""
Downloads files shared by all samples in the pipeline
:param JobFunctionWrappingJob job: passed automatically by Toil
:param Namespace config: Argparse Namespace object containing argument inputs
:param list[list] samples: A nested list of sample... |
def reference_preprocessing(job, samples, config):
"""
Spawn the jobs that create index and dict file for reference
:param JobFunctionWrappingJob job: passed automatically by Toil
:param Namespace config: Argparse Namespace object containing argument inputs
:param list[list] samples: A nested list ... |
def download_sample(job, sample, config):
"""
Download sample and store sample specific attributes
:param JobFunctionWrappingJob job: passed automatically by Toil
:param list sample: Contains uuid, normal URL, and tumor URL
:param Namespace config: Argparse Namespace object containing argument inpu... |
def index_bams(job, config):
"""
Convenience job for handling bam indexing to make the workflow declaration cleaner
:param JobFunctionWrappingJob job: passed automatically by Toil
:param Namespace config: Argparse Namespace object containing argument inputs
"""
job.fileStore.logToMaster('Indexe... |
def preprocessing_declaration(job, config):
"""
Declare jobs related to preprocessing
:param JobFunctionWrappingJob job: passed automatically by Toil
:param Namespace config: Argparse Namespace object containing argument inputs
"""
if config.preprocessing:
job.fileStore.logToMaster('Ran... |
def static_workflow_declaration(job, config, normal_bam, normal_bai, tumor_bam, tumor_bai):
"""
Statically declare workflow so sections can be modularly repurposed
:param JobFunctionWrappingJob job: passed automatically by Toil
:param Namespace config: Argparse Namespace object containing argument inpu... |
def consolidate_output(job, config, mutect, pindel, muse):
"""
Combine the contents of separate tarball outputs into one via streaming
:param JobFunctionWrappingJob job: passed automatically by Toil
:param Namespace config: Argparse Namespace object containing argument inputs
:param str mutect: MuT... |
def parse_manifest(path_to_manifest):
"""
Parses samples, specified in either a manifest or listed with --samples
:param str path_to_manifest: Path to configuration file
:return: Samples and their attributes as defined in the manifest
:rtype: list[list]
"""
samples = []
with open(path_t... |
def main():
"""
Computational Genomics Lab, Genomics Institute, UC Santa Cruz
Toil exome pipeline
Perform variant / indel analysis given a pair of tumor/normal BAM files.
Samples are optionally preprocessed (indel realignment and base quality score recalibration)
The output of this pipeline is ... |
def download_reference_files(job, inputs, samples):
"""
Downloads shared files that are used by all samples for alignment, or generates them if they were not provided.
:param JobFunctionWrappingJob job: passed automatically by Toil
:param Namespace inputs: Input arguments (see main)
:param list[lis... |
def download_sample_and_align(job, sample, inputs, ids):
"""
Downloads the sample and runs BWA-kit
:param JobFunctionWrappingJob job: Passed by Toil automatically
:param tuple(str, list) sample: UUID and URLS for sample
:param Namespace inputs: Contains input arguments
:param dict ids: FileStor... |
def parse_manifest(manifest_path):
"""
Parse manifest file
:param str manifest_path: Path to manifest file
:return: samples
:rtype: list[str, list]
"""
samples = []
with open(manifest_path, 'r') as f:
for line in f:
if not line.isspace() and not line.startswith('#'):... |
def main():
"""
Computational Genomics Lab, Genomics Institute, UC Santa Cruz
Toil BWA pipeline
Alignment of fastq reads via BWA-kit
General usage:
1. Type "toil-bwa generate" to create an editable manifest and config in the current working directory.
2. Parameterize the pipeline by editin... |
def _address2long(address):
"""
Convert an address string to a long.
"""
parsed = ipv4.ip2long(address)
if parsed is None:
parsed = ipv6.ip2long(address)
return parsed |
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 ca... |
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 ... |
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 tim... |
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
ret... |
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.... |
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)
... |
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... |
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 e... |
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
... |
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 `... |
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 unt... |
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 li... |
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 rese... |
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 Addres... |
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 = Fa... |
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',... |
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()),
... |
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,
) |
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],
envi... |
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", "-... |
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
-------
... |
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 sample... |
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 fi... |
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
eno... |
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.
... |
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 dtyp... |
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.
... |
def class_balancing_sampler(y, indices):
"""
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
... |
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 = time... |
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(file... |
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
-------... |
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 chun... |
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 f... |
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 filesyst... |
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
sou... |
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... |
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]
ENVIRON... |
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 env... |
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_se... |
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... |
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/ref... |
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 ... |
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... |
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)))
... |
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_b... |
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:... |
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'],
)
... |
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: '/pr... |
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... |
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... |
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'][... |
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 |
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, s... |
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) |
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 ... |
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
... |
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) |
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))
... |
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) |
def create_virtualenv(self):
"""
Populate venv from preloaded image
"""
return task.create_virtualenv(self.target, self.datadir,
self._preload_image(), self._get_container_name) |
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,
) |
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) |
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 ... |
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={s... |
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',
'/pr... |
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') |
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 ch... |
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 ... |
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 = SafeConfig... |
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')
... |
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(),
... |
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',
... |
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 |
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) |
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']:
... |
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_exist... |
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 an... |
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',
'password': password,
... |
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