GroupOperation Core and Mixin Behaviours

Source code for group operations and mixin behaviours.

class padocc.operations.group.GroupOperation(groupID: str, workdir: str = None, forceful: bool = None, dryrun: bool = None, thorough: bool = None, logger: ~logging.Logger | ~padocc.core.logs.FalseLogger = None, bypass: ~padocc.core.utils.BypassSwitch = <padocc.core.utils.BypassSwitch object>, label: str = None, fh: str = None, logid: str = None, verbose: int = 0)

merge(group_B)

Merge group B into group A. 1. Migrate all projects from B to A and reset groupID values. 2. Combine datasets.csv 3. Combine project codes 4. Combine blacklists.

unmerge(group_B, dataset_list: list)

Separate elements from group_A into group_B according to the list 1. Migrate projects 2. Set the datasets 3. Set the blacklists 4. Project codes (remove group B sections)

class padocc.operations.mixins.EvaluationsMixin

Group Mixin for methods to evaluate the status of a group.

get_operation(opt)

Operation to perform - deprecated

progress(repeat_id, write=True)

Give a general overview of progress within the pipeline - How many datasets currently at each stage of the pipeline - Errors within each pipeline phase - Allows for examination of error logs - Allows saving codes matching an error type into a new repeat group

remove_projects()

Delete a set of projects which match some criteria.

summary_data()

Summarise data stored across all files

class padocc.operations.mixins.InitialisationMixin

Mixin container class for initialisation routines for groups via input files.

init_from_file(input_file: str, substitutions: dict = None)

Run initialisation by loading configurations from input sources, determine input file type and use appropriate functions to instantiate group and project directories.

Parameters:

input_file – (str) Path to an input file from which to initialise the project.

Returns:

None