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def create_zip_dir(zipfile_path, *file_list): """ This function creates a zipfile located in zipFilePath with the files in the file list # fileList can be both a comma separated list or an array """ try: if isinstance(file_list, (list, tuple)): #unfolding list of list or tuple if len(file_...
def file_zipper(root_dir): """ This function will zip the files created in the runroot directory and subdirectories """ # FINDING AND ZIPPING UNZIPPED FILES for root, dirs, files in os.walk(root_dir, topdown=False): if root != "": if root[-1] != '/': root += '/' for current_file in f...
def file_unzipper(directory): """ This function will unzip all files in the runroot directory and subdirectories """ debug.log("Unzipping directory (%s)..."%directory) #FINDING AND UNZIPPING ZIPPED FILES for root, dirs, files in os.walk(directory, topdown=False): if root != "": orig_dir...
def move_file(src, dst): """ this function will simply move the file from the source path to the dest path given as input """ # Sanity checkpoint src = re.sub('[^\w/\-\.\*]', '', src) dst = re.sub('[^\w/\-\.\*]', '', dst) if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5: ...
def copy_file(src, dst, ignore=None): """ this function will simply copy the file from the source path to the dest path given as input """ # Sanity checkpoint src = re.sub('[^\w/\-\.\*]', '', src) dst = re.sub('[^\w/\-\.\*]', '', dst) if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', ds...
def copy_dir(src, dst): """ this function will simply copy the file from the source path to the dest path given as input """ try: debug.log("copy dir from "+ src, "to "+ dst) shutil.copytree(src, dst) except Exception as e: debug.log("Error: happened while copying!\n%s\n"%e)
def print_out(self, *lst): """ Print list of strings to the predefined stdout. """ self.print2file(self.stdout, True, True, *lst)
def print_err(self, *lst): """ Print list of strings to the predefined stdout. """ self.print2file(self.stderr, False, True, *lst)
def print2file(self, logfile, print2screen, addLineFeed, *lst): """ This function prints to the screen and logs to a file, all the strings given. # print2screen eg. True, *lst is a commaseparated list of strings """ if addLineFeed: linefeed = '\n' else: linefeed = '' i...
def log(self, *lst): """ Print list of strings to the predefined logfile if debug is set. and sets the caught_error message if an error is found """ self.print2file(self.logfile, self.debug, True, *lst) if 'Error' in '\n'.join([str(x) for x in lst]): self.caught_error = '\n'.join(...
def log_no_newline(self, msg): """ print the message to the predefined log file without newline """ self.print2file(self.logfile, False, False, msg)
def graceful_exit(self, msg): """ This function Tries to update the MSQL database before exiting. """ # Print stored errors to stderr if self.caught_error: self.print2file(self.stderr, False, False, self.caught_error) # Kill process with error message self.log(msg) sys.exit(...
def get_tree(self, list_of_keys): """ gettree will extract the value from a nested tree INPUT list_of_keys: a list of keys ie. ['key1', 'key2'] USAGE >>> # Access the value for key2 within the nested dictionary >>> adv_dict({'key1': {'key2': 'value'}}).gettree(['key1', 'key...
def invert(self): ''' Return inverse mapping of dictionary with sorted values. USAGE >>> # Switch the keys and values >>> adv_dict({ ... 'A': [1, 2, 3], ... 'B': [4, 2], ... 'C': [1, 4], ... }).invert() {1: ['A', 'C'], 2: ['A', 'B'],...
def sub(self, replace, string, count=0): """ returns new string where the matching cases (limited by the count) in the string is replaced. """ return self.re.sub(replace, string, count)
def match(self, s): """ Matches the string to the stored regular expression, and stores all groups in mathches. Returns False on negative match. """ self.matches = self.re.search(s) return self.matches
def match(self, s): """ Matching the pattern to the input string, returns True/False and saves the matched string in the internal list """ if self.re.match(s): self.list.append(s) return True else: return False
def reporter(self): """ Create the MASH report """ logging.info('Creating {} report'.format(self.analysistype)) make_path(self.reportpath) header = 'Strain,ReferenceGenus,ReferenceFile,ReferenceGenomeMashDistance,Pvalue,NumMatchingHashes\n' data = '' for s...
def get_function(pkgpath): """Take a full path to a python method or class, for example mypkg.subpkg.method and return the method or class (after importing the required packages) """ # Extract the module and function name from pkgpath elems = pkgpath.split('.') if len(elems) <= 1: ra...
def runner(self): """ Run the necessary methods in the correct order """ printtime('Starting {} analysis pipeline'.format(self.analysistype), self.starttime) # Create the objects to be used in the analyses objects = Objectprep(self) objects.objectprep() se...
def syllabify(word): '''Syllabify the given word, whether simplex or complex.''' word = split(word) # detect any non-delimited compounds compound = True if re.search(r'-| |\.', word) else False syllabify = _syllabify_compound if compound else _syllabify syll, rules = syllabify(word) yield syll...
def edges(self): """ Return the edge characters of this node. """ edge_str = ctypes.create_string_buffer(MAX_CHARS) cgaddag.gdg_edges(self.gdg, self.node, edge_str) return [char for char in edge_str.value.decode("ascii")]
def letter_set(self): """ Return the letter set of this node. """ end_str = ctypes.create_string_buffer(MAX_CHARS) cgaddag.gdg_letter_set(self.gdg, self.node, end_str) return [char for char in end_str.value.decode("ascii")]
def is_end(self, char): """ Return `True` if this `char` is part of this node's letter set, `False` otherwise. """ char = char.lower() return bool(cgaddag.gdg_is_end(self.gdg, self.node, char.encode("ascii")))
def follow(self, chars): """ Traverse the GADDAG to the node at the end of the given characters. Args: chars: An string of characters to traverse in the GADDAG. Returns: The Node which is found by traversing the tree. """ chars = chars.lower() ...
def _split_docker_link(alias_name): """ Splits a docker link string into a list of 3 items (protocol, host, port). - Assumes IPv4 Docker links ex: _split_docker_link('DB') -> ['tcp', '172.17.0.82', '8080'] """ sanitized_name = alias_name.strip().upper() split_list = re.split(r':|//', core.s...
def read(alias_name, allow_none=False): """Get the raw docker link value. Get the raw environment variable for the docker link Args: alias_name: The environment variable name default: The default value if the link isn't available allow_none: If the return value can be `None` (i.e. ...
def isset(alias_name): """Return a boolean if the docker link is set or not and is a valid looking docker link value. Args: alias_name: The link alias name """ warnings.warn('Will be removed in v1.0', DeprecationWarning, stacklevel=2) raw_value = read(alias_name, allow_none=True) if raw...
def protocol(alias_name, default=None, allow_none=False): """Get the protocol from the docker link alias or return the default. Args: alias_name: The docker link alias default: The default value if the link isn't available allow_none: If the return value can be `None` (i.e. optional) ...
def port(alias_name, default=None, allow_none=False): """Get the port from the docker link alias or return the default. Args: alias_name: The docker link alias default: The default value if the link isn't available allow_none: If the return value can be `None` (i.e. optional) Examp...
def runner(self): """ Run the necessary methods in the correct order """ printtime('Starting {} analysis pipeline'.format(self.analysistype), self.starttime) if not self.pipeline: # If the metadata has been passed from the method script, self.pipeline must still be fa...
def attributer(self): """ Parses the 16S target files to link accession numbers stored in the .fai and metadata files to the genera stored in the target file """ from Bio import SeqIO import operator for sample in self.runmetadata.samples: # Load the r...
def reporter(self): """ Creates a report of the results """ # Create the path in which the reports are stored make_path(self.reportpath) header = 'Strain,Gene,PercentIdentity,Genus,FoldCoverage\n' data = '' with open(os.path.join(self.reportpath, self.anal...
def spawn_server_api(api_name, app, api_spec, error_callback, decorator): """Take a a Flask app and a swagger file in YAML format describing a REST API, and populate the app with routes handling all the paths and methods declared in the swagger file. Also handle marshaling and unmarshaling between json...
def _responsify(api_spec, error, status): """Take a bravado-core model representing an error, and return a Flask Response with the given error code and error instance as body""" result_json = api_spec.model_to_json(error) r = jsonify(result_json) r.status_code = status return r
def _generate_handler_wrapper(api_name, api_spec, endpoint, handler_func, error_callback, global_decorator): """Generate a handler method for the given url method+path and operation""" # Decorate the handler function, if Swagger spec tells us to if endpoint.decorate_server: endpoint_decorator = get...
def format_escape( foreground=None, background=None, bold=False, faint=False, italic=False, underline=False, blink=False, inverted=False ): """Returns the ANSI escape sequence to set character formatting. foreground Foreground colour to use. Accepted types: None, int (xterm palette ID), tup...
def format_string( string, foreground=None, background=None, reset=True, bold=False, faint=False, italic=False, underline=False, blink=False, inverted=False ): """Returns a Unicode string formatted with an ANSI escape sequence. string String to format foreground Foreground colour to us...
def format_pixels( top, bottom, reset=True, repeat=1 ): """Return the ANSI escape sequence to render two vertically-stacked pixels as a single monospace character. top Top colour to use. Accepted types: None, int (xterm palette ID), tuple (RGB, RGBA), Colour bottom Bottom colou...
def format_image_iter( data_fetch, x_start=0, y_start=0, width=32, height=32, frame=0, columns=1, downsample=1 ): """Return the ANSI escape sequence to render a bitmap image. data_fetch Function that takes three arguments (x position, y position, and frame) and returns a Colour corresponding to...
def update_buffer_with_value( self, value, buffer, parent=None ): """Write a Python object into a byte array, using the field definition. value Input Python object to process. buffer Output byte array to encode value into. parent Parent block object...
def get_end_offset( self, value, parent=None, index=None ): """Return the end offset of the Field's data. Useful for chainloading. value Input Python object to process. parent Parent block object where this Field is defined. Used for e.g. evaluating Refs. ...
def nonalpha_split(string): '''Split 'string' along any punctuation or whitespace.''' return re.findall(r'[%s]+|[^%s]+' % (A, A), string, flags=FLAGS)
def syllable_split(string): '''Split 'string' into (stressed) syllables and punctuation/whitespace.''' p = r'\'[%s]+|`[%s]+|[%s]+|[^%s\'`\.]+|[^\.]{1}' % (A, A, A, A) return re.findall(p, string, flags=FLAGS)
def extract_words(string): '''Extract all alphabetic syllabified forms from 'string'.''' return re.findall(r'[%s]+[%s\.]*[%s]+' % (A, A, A), string, flags=FLAGS)
def init_threads(t=None, s=None): """Should define dummyThread class and dummySignal class""" global THREAD, SIGNAL THREAD = t or dummyThread SIGNAL = s or dummySignal
def thread_with_callback(on_error, on_done, requete_with_callback): """ Return a thread emiting `state_changed` between each sub-requests. :param on_error: callback str -> None :param on_done: callback object -> None :param requete_with_callback: Job to execute. monitor_callable -> None :return...
def protege_data(datas_str, sens): """ Used to crypt/decrypt data before saving locally. Override if securit is needed. bytes -> str when decrypting str -> bytes when crypting :param datas_str: When crypting, str. when decrypting bytes :param sens: True to crypt, False to decrypt """ ...
def build_parser(parser: argparse.ArgumentParser) -> None: """Build a parser for CLI arguments and options.""" parser.add_argument( '--delimiter', help='a delimiter for the samples (teeth) in the key', default=' ', ) parser.add_argument( '--encoding', help='the en...
def default_parser() -> argparse.ArgumentParser: """Create a parser for CLI arguments and options.""" parser = argparse.ArgumentParser( prog=CONSOLE_SCRIPT, formatter_class=argparse.ArgumentDefaultsHelpFormatter, ) build_parser(parser) return parser
def key( seq: Sequence, tooth: Callable[[Sequence], str] = ( lambda seq: str(random.SystemRandom().choice(seq)).strip() ), nteeth: int = 6, delimiter: str = ' ', ) -> str: """Concatenate strings generated by the tooth function.""" return delimiter.join(tooth(s...
def main(argv: Sequence[str] = SYS_ARGV) -> int: """Execute CLI commands.""" args = default_parser().parse_args(argv) try: seq = POPULATIONS[args.population] # type: Sequence except KeyError: try: with open(args.population, 'r', encoding=args.encoding) as file_: ...
def add_firewalld_service(service, permanent=True): """ adds a firewall rule """ yum_install(packages=['firewalld']) with settings(hide('warnings', 'running', 'stdout', 'stderr'), warn_only=True, capture=True): p = '' if permanent: p = '--permanent' sud...
def add_firewalld_port(port, permanent=True): """ adds a firewall rule """ yum_install(packages=['firewalld']) log_green('adding a new fw rule: %s' % port) with settings(hide('warnings', 'running', 'stdout', 'stderr'), warn_only=True, capture=True): p = '' if permanen...
def apt_add_repository_from_apt_string(apt_string, apt_file): """ adds a new repository file for apt """ apt_file_path = '/etc/apt/sources.list.d/%s' % apt_file if not file_contains(apt_file_path, apt_string.lower(), use_sudo=True): file_append(apt_file_path, apt_string.lower(), use_sudo=True) ...
def arch(): """ returns the current cpu archictecture """ with settings(hide('warnings', 'running', 'stdout', 'stderr'), warn_only=True, capture=True): result = sudo('rpm -E %dist').strip() return result
def disable_openssh_rdns(distribution): """ Set 'UseDNS no' in openssh config to disable rDNS lookups On each request for a new channel openssh defaults to an rDNS lookup on the client IP. This can be slow, if it fails for instance, adding 10s of overhead to every request for a new channel (not...
def connect_to_ec2(region, access_key_id, secret_access_key): """ returns a connection object to AWS EC2 """ conn = boto.ec2.connect_to_region(region, aws_access_key_id=access_key_id, aws_secret_access_key=secret_access_key) return...
def connect_to_rackspace(region, access_key_id, secret_access_key): """ returns a connection object to Rackspace """ pyrax.set_setting('identity_type', 'rackspace') pyrax.set_default_region(region) pyrax.set_credentials(access_key_id, secret_access_key)...
def create_gce_image(zone, project, instance_name, name, description): """ Shuts down the instance and creates and image from the disk. Assumes that the disk name is the same as the instance_name (this is the default be...
def create_image(cloud, **kwargs): """ proxy call for ec2, rackspace create ami backend functions """ if cloud == 'ec2': return create_ami(**kwargs) if cloud == 'rackspace': return create_rackspace_image(**kwargs) if cloud == 'gce': return create_gce_image(**kwargs)
def create_server(cloud, **kwargs): """ Create a new instance """ if cloud == 'ec2': _create_server_ec2(**kwargs) elif cloud == 'rackspace': _create_server_rackspace(**kwargs) elif cloud == 'gce': _create_server_gce(**kwargs) else: raise ValueError("Unknow...
def gce_wait_until_done(operation): """ Perform a GCE operation, blocking until the operation completes. This function will then poll the operation until it reaches state 'DONE' or times out, and then returns the final operation resource dict. :param operation: A dict representing a pending GC...
def startup_gce_instance(instance_name, project, zone, username, machine_type, image, public_key, disk_name=None): """ For now, jclouds is broken for GCE and we will have static slaves in Jenkins. Use this to boot them. """ log_green("Started...") log_yellow("...Creatin...
def _create_server_ec2(region, access_key_id, secret_access_key, disk_name, disk_size, ami, key_pair, instance_type, username, ...
def _create_server_rackspace(region, access_key_id, secret_access_key, disk_name, disk_size, ami, key_pair, instance_...
def dir_attribs(location, mode=None, owner=None, group=None, recursive=False, use_sudo=False): """ cuisine dir_attribs doesn't do sudo, so we implement our own Updates the mode/owner/group for the given remote directory.""" recursive = recursive and "-R " or "" if mode: if us...
def disable_selinux(): """ disables selinux """ if contains(filename='/etc/selinux/config', text='SELINUX=enforcing'): sed('/etc/selinux/config', 'SELINUX=enforcing', 'SELINUX=disabled', use_sudo=True) if contains(filename='/etc/selinux/config', text='SE...
def destroy_ebs_volume(region, volume_id, access_key_id, secret_access_key): """ destroys an ebs volume """ conn = connect_to_ec2(region, access_key_id, secret_access_key) if ebs_volume_exists(region, volume_id, access_key_id, secret_access_key): log_yellow('destroying EBS volume ...') conn...
def destroy_ec2(region, instance_id, access_key_id, secret_access_key): """ terminates the instance """ conn = connect_to_ec2(region, access_key_id, secret_access_key) data = get_ec2_info(instance_id=instance_id, region=region, access_key_id=access_key_id, ...
def destroy_rackspace(region, instance_id, access_key_id, secret_access_key): """ terminates the instance """ nova = connect_to_rackspace(region, access_key_id, secret_access_key) server = nova.servers.get(instance_id) log_yellow('deleting...
def down_ec2(instance_id, region, access_key_id, secret_access_key): """ shutdown of an existing EC2 instance """ conn = connect_to_ec2(region, access_key_id, secret_access_key) # get the instance_id from the state file, and stop the instance instance = conn.stop_instances(instance_ids=instance_id)[0] ...
def ebs_volume_exists(region, volume_id, access_key_id, secret_access_key): """ finds out if a ebs volume exists """ conn = connect_to_ec2(region, access_key_id, secret_access_key) for vol in conn.get_all_volumes(): if vol.id == volume_id: return True
def enable_marathon_basic_authentication(principal, password): """ configures marathon to start with authentication """ upstart_file = '/etc/init/marathon.conf' with hide('running', 'stdout'): sudo('echo -n "{}" > /etc/marathon-mesos.credentials'.format(password)) boot_args = ' '.join(['exec', ...
def enable_mesos_basic_authentication(principal, password): """ enables and adds a new authorized principal """ restart = False secrets_file = '/etc/mesos/secrets' secrets_entry = '%s %s' % (principal, password) if not file_contains(filename=secrets_file, text=secrets_entry,...
def file_attribs(location, mode=None, owner=None, group=None, sudo=False): """Updates the mode/owner/group for the remote file at the given location.""" return dir_attribs(location, mode, owner, group, False, sudo)
def get_ec2_info(instance_id, region, access_key_id, secret_access_key, username): """ queries EC2 for details about a particular instance_id """ conn = connect_to_ec2(region, access_key_id, secret_access_key) instance = conn.get_only_i...
def get_ip_address_from_rackspace_server(server_id): """ returns an ipaddress for a rackspace instance """ nova = connect_to_rackspace() server = nova.servers.get(server_id) # the server was assigned IPv4 and IPv6 addresses, locate the IPv4 address ip_address = None for network in server...
def get_rackspace_info(server_id, region, access_key_id, secret_access_key, username): """ queries Rackspace for details about a particular server id """ nova = connect_to_rackspace(region, access_key_id, secret_acce...
def install_oracle_java(distribution, java_version): """ installs oracle java """ if 'ubuntu' in distribution: accept_oracle_license = ('echo ' 'oracle-java' + java_version + 'installer ' 'shared/accepted-oracle-license-v1-1 ' ...
def install_mesos_single_box_mode(distribution): """ install mesos (all of it) on a single node""" if 'ubuntu' in distribution: log_green('adding mesosphere apt-key') apt_add_key(keyid='E56151BF') os = lsb_release() apt_string = 'deb http://repos.mesosphere.io/%s %s main' % ( ...
def insert_line_in_file_after_regex(path, line, after_regex, use_sudo=False): """ inserts a line in the middle of a file """ tmpfile = str(uuid.uuid4()) get_file(path, tmpfile, use_sudo=use_sudo) with open(tmpfile) as f: original = f.read() if line not in original: outfile = str(uu...
def install_python_module(name): """ instals a python module using pip """ with settings(hide('warnings', 'running', 'stdout', 'stderr'), warn_only=False, capture=True): run('pip --quiet install %s' % name)
def install_python_module_locally(name): """ instals a python module using pip """ with settings(hide('warnings', 'running', 'stdout', 'stderr'), warn_only=False, capture=True): local('pip --quiet install %s' % name)
def install_system_gem(gem): """ install a particular gem """ with settings(hide('warnings', 'running', 'stdout', 'stderr'), warn_only=False, capture=True): sudo("gem install %s --no-rdoc --no-ri" % gem)
def is_vagrant_plugin_installed(plugin, use_sudo=False): """ checks if vagrant plugin is installed """ cmd = 'vagrant plugin list' if use_sudo: results = sudo(cmd) else: results = run(cmd) installed_plugins = [] for line in results: plugin = re.search('^(\S.*) \((.*)\)...
def is_deb_package_installed(pkg): """ checks if a particular deb package is installed """ with settings(hide('warnings', 'running', 'stdout', 'stderr'), warn_only=True, capture=True): result = sudo('dpkg-query -l "%s" | grep -q ^.i' % pkg) return not bool(result.return_code)
def is_ssh_available(host, port=22): """ checks if ssh port is open """ s = socket.socket() try: s.connect((host, port)) return True except: return False
def os_release(username, ip_address): """ returns /etc/os-release in a dictionary """ with settings(hide('warnings', 'running', 'stdout', 'stderr'), warn_only=True, capture=True): _os_release = {} with settings(host_string=username + '@' + ip_address): data = run('...
def load_state_from_disk(): """ loads the state from a local data.json file """ if is_there_state(): with open('data.json', 'r') as f: data = json.load(f) return data else: return False
def print_ec2_info(region, instance_id, access_key_id, secret_access_key, username): """ outputs information about our EC2 instance """ data = get_ec2_info(instance_id=instance_id, region=region, ...
def print_gce_info(zone, project, instance_name, data): """ outputs information about our Rackspace instance """ try: instance_info = _get_gce_compute().instances().get( project=project, zone=zone, instance=instance_name ).execute() log_yellow(pformat(...
def print_rackspace_info(region, instance_id, access_key_id, secret_access_key, username): """ outputs information about our Rackspace instance """ data = get_rackspace_info(server_id=instance_id, ...
def restart_service(service): """ restarts a service """ with settings(hide('running', 'stdout'), warn_only=True): log_yellow('stoping service %s' % service) sudo('service %s stop' % service) log_yellow('starting service %s' % service) sudo('service %s start' % service)
def rsync(): """ syncs the src code to the remote box """ log_green('syncing code to remote box...') data = load_state_from_disk() if 'SOURCE_PATH' in os.environ: with lcd(os.environ['SOURCE_PATH']): local("rsync -a " "--info=progress2 " "--exclud...
def save_ec2_state_locally(instance_id, region, username, access_key_id, secret_access_key): """ queries EC2 for details about a particular instance_id and stores those details locally """ # r...
def ssh_session(key_filename, username, ip_address, *cli): """ opens a ssh shell to the host """ local('ssh -t -i %s %s@%s %s' % (key_filename, username, ip_address, ...
def up_ec2(region, access_key_id, secret_access_key, instance_id, username): """ boots an existing ec2_instance """ conn = connect_to_ec2(region, access_key_id, secret_access_key) # boot the ec2 instance instance = conn.start_instances(instance_ids=instance_i...
def wait_for_ssh(host, port=22, timeout=600): """ probes the ssh port and waits until it is available """ log_yellow('waiting for ssh...') for iteration in xrange(1, timeout): #noqa sleep(1) if is_ssh_available(host, port): return True else: log_yellow('waitin...
def _get_visuals(user): """ Renvoi les éléments graphiques d'un utilisateur. :param user: Dictionnaire d'infos de l'utilisateur :return QPixmap,QLabel: Image et nom """ pixmap = SuperUserAvatar() if user["status"] == "admin" else UserAvatar() label = user["label"] return pixmap, QLabel(...