def test_newstyle_mkdir (self): test_pipeline = Pipeline("test") test_pipeline.follows(task_which_makes_directories, mkdir(directories), mkdir(tempdir + 'c'), mkdir(tempdir + 'd', tempdir + 'e'), mkdir(tempdir + 'e')) test_pipeline.run(multiprocess = 10, verbose = 0) for d in 'abcde': fullpath = os.path.join(os.path.dirname(__file__), tempdir, d) self.assertTrue(os.path.exists(fullpath))
def test_newstyle_mkdir(self): test_pipeline = Pipeline("test") test_pipeline.follows(task_which_makes_directories, mkdir(directories), mkdir(tempdir + 'c'), mkdir(tempdir + 'd', tempdir + 'e'), mkdir(tempdir + 'e')) test_pipeline.run(multiprocess=10, verbose=0) for d in 'abcde': fullpath = os.path.join(os.path.dirname(__file__), tempdir, d) self.assertTrue(os.path.exists(fullpath))
def test_newstyle_mkdir (self): test_pipeline = Pipeline("test") test_pipeline.follows(task_which_makes_directories, mkdir(directories), mkdir(unicode(tempdir + "c")), mkdir(unicode(tempdir + "d"), unicode(tempdir + "e")), mkdir(unicode(tempdir + "e")))\ .posttask(touch_file(unicode(tempdir + "f"))) test_pipeline.originate(task_which_makes_files, [tempdir + "g", tempdir + "h"]) test_pipeline.run(multiprocess = 10, verbose = 0) for d in 'abcdefgh': fullpath = os.path.join(os.path.dirname(__file__), tempdir, d) self.assertTrue(os.path.exists(fullpath))
def test_newstyle_mkdir(self): test_pipeline = Pipeline("test") test_pipeline.follows(task_which_makes_directories, mkdir(directories), mkdir(unicode(tempdir + "c")), mkdir(unicode(tempdir + "d"), unicode(tempdir + "e")), mkdir(unicode(tempdir + "e")))\ .posttask(touch_file(unicode(tempdir + "f"))) test_pipeline.originate(task_which_makes_files, [tempdir + "g", tempdir + "h"]) test_pipeline.run(multiprocess=10, verbose=0) for d in 'abcdefgh': fullpath = os.path.join(os.path.dirname(__file__), tempdir, d) self.assertTrue(os.path.exists(fullpath))
def test_newstyle_ruffus (self): test_pipeline = Pipeline("test") test_pipeline.follows(setup_simulation_data, mkdir(gene_data_dir, simulation_data_dir)) test_pipeline.files(gwas_simulation, generate_simulation_params)\ .follows(setup_simulation_data)\ .follows(mkdir(working_dir, os.path.join(working_dir, "simulation_results"))) test_pipeline.collate(statistical_summary, gwas_simulation, regex(r"simulation_results/(\d+).\d+.simulation_res"), r"\1.mean")\ .posttask(lambda : sys.stdout.write("\nOK\n")) test_pipeline.run(multiprocess = 50, verbose = 0) for oo in "000.mean", "001.mean": results_file_name = os.path.join(working_dir, oo) if not os.path.exists(results_file_name): raise Exception("Missing %s" % results_file_name)
def test_newstyle_ruffus(self): test_pipeline = Pipeline("test") test_pipeline.follows(setup_simulation_data, mkdir(gene_data_dir, simulation_data_dir)) test_pipeline.files(gwas_simulation, generate_simulation_params)\ .follows(setup_simulation_data)\ .follows(mkdir(working_dir, os.path.join(working_dir, "simulation_results"))) test_pipeline.collate(statistical_summary, gwas_simulation, regex(r"simulation_results/(\d+).\d+.simulation_res"), r"\1.mean")\ .posttask(lambda: sys.stdout.write("\nOK\n")) test_pipeline.run(multiprocess=50, verbose=0) for oo in "000.mean", "001.mean": results_file_name = os.path.join(working_dir, oo) if not os.path.exists(results_file_name): raise Exception("Missing %s" % results_file_name)
def test_newstyle_graphviz_dot(self): test_pipeline = Pipeline("test") test_pipeline.check_if_uptodate (Up_to_date_task1, lambda : (False, "")) test_pipeline.follows(Up_to_date_task2, Up_to_date_task1)\ .check_if_uptodate (lambda : (False, ""))\ .graphviz(URL='"http://cnn.com"', fillcolor = '"#FFCCCC"', color = '"#FF0000"', pencolor='"#FF0000"', fontcolor='"#4B6000"', label_suffix = "???", label_prefix = "What is this?<BR/> ", label = "<What <FONT COLOR=\"red\">is</FONT>this>", shape= "component", height = 1.5, peripheries = 5, style="dashed") test_pipeline.follows(Up_to_date_task3, Up_to_date_task2)\ .check_if_uptodate (lambda : (False, "")) test_pipeline.follows(Up_to_date_final_target, Up_to_date_task3)\ .check_if_uptodate (lambda : (False, "")) test_pipeline.follows(Explicitly_specified_task, Up_to_date_task1)\ .check_if_uptodate (lambda : (False, "")) test_pipeline.follows(Task_to_run1, Explicitly_specified_task) test_pipeline.follows(Task_to_run2, Task_to_run1) test_pipeline.follows(Task_to_run3, Task_to_run2) test_pipeline.follows(Up_to_date_task_forced_to_rerun, Task_to_run2)\ .check_if_uptodate (lambda : (False, "")) test_pipeline.follows(Final_target, Up_to_date_task_forced_to_rerun, Task_to_run3) test_pipeline.follows(Downstream_task1_ignored, Final_target) test_pipeline.follows(Downstream_task2_ignored, Final_target) if sys.hexversion >= 0x03000000: # everything is unicode in python3 s = BytesIO() else: s = StringIO() test_pipeline.printout_graph ( s, # use flowchart file name extension to decide flowchart format # e.g. svg, jpg etc. "dot", [Final_target, Up_to_date_final_target]) self.assertTrue('[URL="http://cnn.com", color="#FF0000", fillcolor="#FFCCCC", fontcolor="#4B6000", height=1.5, label=<What is this?<BR/> What <FONT COLOR="red">is</FONT>this???>, pencolor="#FF0000", peripheries=5, shape=component, style=dashed]' in s.getvalue().decode())