assemblerflow.generator.pipeline_parser module

assemblerflow.generator.pipeline_parser.remove_inner_forks(text)

Recursively removes nested brackets

This function is used to remove nested brackets from fork strings using regular expressions

Parameters:

text: str

The string that contains brackets with inner forks to be removed

Returns:

text: str

the string with only the processes that are not in inner forks, thus the processes that belong to a given fork.

assemblerflow.generator.pipeline_parser.empty_tasks(p_string)

Function to check if pipeline string is empty or has an empty string

Parameters:

p_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.brackets_but_no_lanes(p_string)

Function to check if a LANE_TOKEN is provided but no fork is initiated. Parameters ———- p_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.brackets_insanity_check(p_string)

This function performs a check for different number of ‘(‘ and ‘)’ characters, which indicates that some forks are poorly constructed.

Parameters:

p_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.lane_char_insanity_check(p_string)

This function performs a sanity check for multiple ‘|’ character between two processes.

Parameters:

p_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.final_char_insanity_check(p_string)

This function checks if lane token is the last element of the pipeline string.

Parameters:

p_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.fork_procs_insanity_check(p_string)

This function checks if the pipeline string contains a process between the fork start token or end token and the separator (lane) token. Checks for the absence of processes in one of the branches of the fork [‘|)' and '(|’] and for the existence of a process before starting a fork (in an inner fork) [‘|(‘].

Parameters:

p_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.start_proc_insanity_check(p_string)

This function checks if there is a starting process after the beginning of each fork. It checks for duplicated start tokens [‘((‘].

Parameters:

p_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.late_proc_insanity_check(p_string)

This function checks if there are processes after the close token. It searches for everything that isn’t “|” or “)” after a “)” token.

Parameters:

p_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.inner_fork_insanity_checks(pipeline_string)

This function performs two sanity checks in the pipeline string. The first check, assures that each fork contains a lane token ‘|’, while the second check looks for duplicated processes within the same fork.

Parameters:

pipeline_string: str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

assemblerflow.generator.pipeline_parser.insanity_checks(pipeline_str)

Wrapper that performs all sanity checks on the pipeline string

Parameters:

pipeline_str : str

String with the pipeline definition

assemblerflow.generator.pipeline_parser.parse_pipeline(pipeline_str)

Parses a pipeline string into a dictionary with the connections between process

Parameters:

pipeline_str : str

String with the definition of the pipeline, e.g.::

‘processA processB processC(ProcessD | ProcessE)’

Returns:

pipeline_links : list

assemblerflow.generator.pipeline_parser.get_source_lane(fork_process, pipeline_list)

Returns the lane of the last process that matches fork_process

Parameters:

fork_process : list

List of processes before the fork.

pipeline_list : list

List with the pipeline connection dictionaries.

Returns:

int

Lane of the last process that matches fork_process

assemblerflow.generator.pipeline_parser.get_lanes(lanes_str)

From a raw pipeline string, get a list of lanes from the start of the current fork.

When the pipeline is being parsed, it will be split at every fork position. The string at the right of the fork position will be provided to this function. It’s job is to retrieve the lanes that result from that fork, ignoring any nested forks.

Parameters:

lanes_str : str

Pipeline string after a fork split

Returns:

lanes : list

List of lists, with the list of processes for each lane

assemblerflow.generator.pipeline_parser.linear_connection(plist, lane)

Connects a linear list of processes into a list of dictionaries

Parameters:

plist : list

List with process names. This list should contain at least two entries.

lane : int

Corresponding lane of the processes

Returns:

res : list

List of dictionaries with the links between processes

assemblerflow.generator.pipeline_parser.fork_connection(source, sink, source_lane, lane)

Makes the connection between a process and the first processes in the lanes to wich it forks.

The lane argument should correspond to the lane of the source process. For each lane in sink, the lane counter will increase.

Parameters:

source : str

Name of the process that is forking

sink : list

List of the processes where the source will fork to. Each element corresponds to the start of a lane.

source_lane : int

Lane of the forking process

lane : int

Lane of the source process

Returns:

res : list

List of dictionaries with the links between processes

assemblerflow.generator.pipeline_parser.linear_lane_connection(lane_list, lane)

Parameters:

lane_list : list

Each element should correspond to a list of processes for a given lane

lane : int

Lane counter before the fork start

Returns:

res : list

List of dictionaries with the links between processes