def test_newstyle_ruffus(self): # alternative syntax test_pipeline = Pipeline("test") test_pipeline.mkdir(data_dir, work_dir) test_pipeline.originate(task_func=task1, output=[os.path.join(data_dir, "%s.1" % aa) for aa in "abcd"]) test_pipeline.mkdir(filter=suffix(".1"), output=".dir", output_dir=work_dir) test_pipeline.transform(task_func=task2, input=task1, filter=suffix(".1"), output=[".1", ".bak"], extras=["extra.tst", 4, r"orig_dir=\1"], output_dir=work_dir) test_pipeline.subdivide(task3, task2, suffix( ".1"), r"\1.*.2", [r"\1.a.2", r"\1.b.2"], output_dir=data_dir) test_pipeline.transform(task4, task3, suffix( ".2"), ".3", output_dir=work_dir) test_pipeline.merge(task5, task4, os.path.join(data_dir, "summary.5")) test_pipeline.run(multiprocess=50, verbose=0) with open(os.path.join(data_dir, "summary.5")) as ii: active_text = ii.read() if active_text != expected_active_text: raise Exception("Error:\n\tExpected\n%s\nInstead\n%s\n" % (expected_active_text, active_text))
def test_newstyle_mkdir_run(self): test_pipeline = Pipeline("test") test_pipeline.split(task_func=generate_initial_files1, input=1, output=[ tempdir + "/" + prefix + "_name.tmp1" for prefix in "abcd" ]) test_pipeline.transform( task_func = test_transform, input = generate_initial_files1, filter = formatter(), output = "{path[0]}/{basename[0]}.dir/{basename[0]}.tmp2")\ .mkdir(tempdir + "/test1")\ .mkdir(tempdir + "/test2")\ .mkdir(generate_initial_files1, formatter(), ["{path[0]}/{basename[0]}.dir", 3, "{path[0]}/{basename[0]}.dir2"]) test_pipeline.mkdir(test_transform2, tempdir + "/test3")\ .mkdir(generate_initial_files1, formatter(), "{path[0]}/{basename[0]}.dir2") cleanup_tmpdir() pipeline_run([test_transform, test_transform2], verbose=0, multiprocess=2, pipeline="main")
def test_newstyle_mkdir_run(self): test_pipeline = Pipeline("test") test_pipeline.split(task_func = generate_initial_files1, input = 1, output = [tempdir + "/" + prefix + "_name.tmp1" for prefix in "abcd"]) test_pipeline.transform( task_func = test_transform, input = generate_initial_files1, filter = formatter(), output = "{path[0]}/{basename[0]}.dir/{basename[0]}.tmp2")\ .mkdir(tempdir + "/test1")\ .mkdir(tempdir + "/test2")\ .mkdir(generate_initial_files1, formatter(), ["{path[0]}/{basename[0]}.dir", 3, "{path[0]}/{basename[0]}.dir2"]) test_pipeline.mkdir(test_transform2, tempdir + "/test3")\ .mkdir(generate_initial_files1, formatter(), "{path[0]}/{basename[0]}.dir2") cleanup_tmpdir() pipeline_run([test_transform, test_transform2], verbose=0, multiprocess = 2, pipeline= "main")
def test_newstyle_ruffus(self): # alternative syntax test_pipeline = Pipeline("test") test_pipeline.mkdir(data_dir, work_dir) test_pipeline.originate( task_func=task1, output=[os.path.join(data_dir, "%s.1" % aa) for aa in "abcd"]) test_pipeline.mkdir(filter=suffix(".1"), output=".dir", output_dir=work_dir) test_pipeline.transform(task_func=task2, input=task1, filter=suffix(".1"), output=[".1", ".bak"], extras=["extra.tst", 4, r"orig_dir=\1"], output_dir=work_dir) test_pipeline.subdivide(task3, task2, suffix(".1"), r"\1.*.2", [r"\1.a.2", r"\1.b.2"], output_dir=data_dir) test_pipeline.transform(task4, task3, suffix(".2"), ".3", output_dir=work_dir) test_pipeline.merge(task5, task4, os.path.join(data_dir, "summary.5")) test_pipeline.run(multiprocess=50, verbose=0) with open(os.path.join(data_dir, "summary.5")) as ii: active_text = ii.read() if active_text != expected_active_text: raise Exception("Error:\n\tExpected\n%s\nInstead\n%s\n" % (expected_active_text, active_text))