#!/usr/bin/env python2.5 """ test_tasks.py """ #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # options #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 from optparse import OptionParser import sys, os import os.path import StringIO # add self to search path for testing exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0] if __name__ == '__main__': module_name = os.path.split(sys.argv[0])[1] module_name = os.path.splitext(module_name)[0]; else: module_name = __name__ parser = OptionParser(version="%prog 1.0") parser.add_option("-t", "--target_tasks", dest="target_tasks", action="append", default = list(), metavar="JOBNAME", type="string", help="Target task(s) of pipeline.") parser.add_option("-f", "--forced_tasks", dest="forced_tasks", action="append", default = list(), metavar="JOBNAME", type="string", help="Pipeline task(s) which will be included even if they are up to date.") parser.add_option("-j", "--jobs", dest="jobs", default=5, metavar="jobs", type="int", help="Specifies the number of jobs (commands) to run simultaneously.") parser.add_option("-v", "--verbose", dest = "verbose", action="store_true", default=False, help="Do not echo to shell but only print to log.") parser.add_option("-d", "--dependency", dest="dependency_file", default="simple.svg", metavar="FILE", type="string", help="Print a dependency graph of the pipeline that would be executed " "to FILE, but do not execute it.") parser.add_option("-F", "--dependency_graph_format", dest="dependency_graph_format", metavar="FORMAT", type="string", default = 'svg', help="format of dependency graph file. Can be 'ps' (PostScript), "+ "'svg' 'svgz' (Structured Vector Graphics), " + "'png' 'gif' (bitmap graphics) etc ") parser.add_option("-n", "--just_print", dest="just_print", action="store_true", default=False, help="Print a description of the jobs that would be executed, " "but do not execute them.") parser.add_option("-M", "--minimal_rebuild_mode", dest="minimal_rebuild_mode", action="store_true", default=False, help="Rebuild a minimum of tasks necessary for the target. " "Ignore upstream out of date tasks if intervening tasks are fine.") parser.add_option("-K", "--no_key_legend_in_graph", dest="no_key_legend_in_graph", action="store_true", default=False, help="Do not print out legend and key for dependency graph.") parser.add_option("-H", "--draw_graph_horizontally", dest="draw_horizontally", action="store_true", default=False, help="Draw horizontal dependency graph.") parameters = [ ] #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # imports #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 import StringIO import re import operator import sys from collections import defaultdict sys.path.append(os.path.abspath(os.path.join(exe_path,"..", ".."))) from ruffus import * import json #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # Functions #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 def create_custom_file_func(params): """ creates function which can be used as input to @files_func """ def cust_func (): for job_param in params: yield job_param return cust_func def is_job_uptodate (infiles, outfiles, *extra_params): """ assumes first two parameters are files, checks if they are up to date """ return task.needs_update_check_modify_time (infiles, outfiles, *extra_params) def test_post_task_function (): print "Hooray" import time def test_job_io(infiles, outfiles, extra_params): """ cat input files content to output files after writing out job parameters """ # dump parameters params = (infiles, outfiles) + extra_params sys.stdout.write(' job = %s\n' % json.dumps(params)) if isinstance(infiles, str): infiles = [infiles] elif infiles is None: infiles = [] if isinstance(outfiles, str): outfiles = [outfiles] output_text = list() for f in infiles: output_text.append(open(f).read()) output_text = "".join(sorted(output_text)) output_text += json.dumps(infiles) + " -> " + json.dumps(outfiles) + "\n" for f in outfiles: open(f, "w").write(output_text) time.sleep(1) #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # Main logic #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # get help string f =StringIO.StringIO() parser.print_help(f) helpstr = f.getvalue() (options, remaining_args) = parser.parse_args() #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # Tasks #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # # task1 # @files(None, 'a.1') def task1(infiles, outfiles, *extra_params): """ First task """ test_job_io(infiles, outfiles, extra_params) # # task2 # @files_re('*.1', '(.*).1', r'\1.1', r'\1.2') @follows(task1) def task2(infiles, outfiles, *extra_params): """ Second task """ test_job_io(infiles, outfiles, extra_params) # # task3 # @files_re('*.1', '(.*).1', r'\1.2', r'\1.3') @follows(task2) def task3(infiles, outfiles, *extra_params): """ Third task """ test_job_io(infiles, outfiles, extra_params) # # task4 # @files_re('*.1', '(.*).1', r'\1.3', r'\1.4') @follows(task3) def task4(infiles, outfiles, *extra_params): """ Fourth task """ test_job_io(infiles, outfiles, extra_params) if options.just_print: pipeline_printout(sys.stdout, options.target_tasks, options.forced_tasks, long_winded=True, gnu_make_maximal_rebuild_mode = not options.minimal_rebuild_mode) elif options.dependency_file: pipeline_printout_graph ( open(options.dependency_file, "w"), options.dependency_graph_format, options.target_tasks, options.forced_tasks, draw_vertically = not options.draw_horizontally, gnu_make_maximal_rebuild_mode = not options.minimal_rebuild_mode, no_key_legend = options.no_key_legend_in_graph) else: pipeline_run(options.target_tasks, options.forced_tasks, multiprocess = options.jobs, gnu_make_maximal_rebuild_mode = not options.minimal_rebuild_mode)