checker module¶

module responsible for checking MAVIS output. Determines if jobs completed correctly and what the status of the pipeline is

class mavis.checker.LibraryRun(name, output_dir)[source]¶

stores run information for pipeline steps that are run on individual libraries

class mavis.checker.LogDetails(filename)[source]¶

stores information about the log status

class mavis.checker.PipelineStageRun(name, output_dir)[source]¶

collect_log(job_task_id=None)[source]¶: finds and stores the job log file

collect_stamp(job_task_id=None)[source]¶: finds and stores the job complete stamp

estimate_run_time()[source]¶: pull the run time information from the logs/stamps

report(indent=' ', indent_level=0, time_stamp=False)[source]¶

parses log files and checks for complete stamps. Reports any errors observed

Returns:	success True: no errors or incomplete files were found False: some errors or incomplete files
Return type:	bool

mavis.checker.check_completion(target_dir, skipped_stages=None)[source]¶

Parameters:	target_dir (str) – path to the main pipeline output directory

mavis.checker.convert_set_to_ranges(input_set)[source]¶

for a set of integers returns a list of consecutive ranges as strings

Example

>>> convert_set_to_ranges({1, 2, 3, 7, 9, 10, 11})
['1-3', '7', '10-11']