How to use test_single_run method in Molotov

Best Python code snippet using molotov_python

workflow_test.py

Source:workflow_test.py

...14class Base(object):15    """Base class to test the full workflow16    """17    @pytest.mark.workflowtest18    def test_single_run(self, extension, bilby=False):19        """Test the full workflow for a single result file case20        Parameters21        ----------22        result_file: str23            path to result file you wish to run with24        """25        opts, inputs = make_argparse(outdir=self.tmpdir, 26            gw=False, extension=extension, bilby=bilby)27        func = functions(opts)28        PlotGeneration(inputs)29        WebpageGeneration(inputs)30        func["MetaFile"](inputs)31        func["FinishingTouches"](inputs)32        plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))33        files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))34        assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, gw=False)))35        assert all(i in plots for i in get_list_of_plots(outdir=self.tmpdir, gw=False))36        assert all(i in get_list_of_plots(outdir=self.tmpdir, gw=False) for i in plots)37        assert all(i == j for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, gw=False)))38        assert all(i in files for i in get_list_of_files(outdir=self.tmpdir, gw=False))39        assert all(i in get_list_of_files(outdir=self.tmpdir, gw=False) for i in files)40        self.check_samples(extension, bilby=bilby)41    def check_samples(self, extension, bilby=False):42        """Check that the samples in the result file are consistent with the43        inputs44        """45        from pesummary.core.file.read import read46        initial_samples = read_result_file(extension=extension, bilby=bilby, outdir=self.tmpdir)47        data = read("{}/samples/posterior_samples.h5".format(self.tmpdir))48        samples = data.samples_dict49        label = data.labels[0]50        for param in initial_samples.keys():51            for i, j in zip(initial_samples[param], samples[label][param]):52                assert np.round(i, 8) == np.round(j, 8)53        54class GWBase(Base):55    """Base class to test the full workflow including gw specific options56    """57    @pytest.mark.workflowtest58    def test_single_run(self, extension, bilby=False, lalinference=False):59        """Test the full workflow for a single result file case60        Parameters61        ----------62        result_file: str63            path to result file you wish to run with64        """65        opts, inputs = make_argparse(outdir=self.tmpdir, 66            gw=True, extension=extension, bilby=bilby, lalinference=lalinference)67        print(opts)68        func = functions(opts)69        PlotGeneration(inputs, gw=True)70        WebpageGeneration(inputs, gw=True)71        func["MetaFile"](inputs)72        func["FinishingTouches"](inputs)73        plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))74        files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))75        assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, gw=True)))76        assert all(i in plots for i in get_list_of_plots(outdir=self.tmpdir, gw=True))77        assert all(i in get_list_of_plots(outdir=self.tmpdir, gw=True) for i in plots)78        for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, gw=True)):79            print(i, j)80        assert all(i == j for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, gw=True)))81        assert all(i in files for i in get_list_of_files(outdir=self.tmpdir, gw=True))82        assert all(i in get_list_of_files(outdir=self.tmpdir, gw=True) for i in files)83        self.check_samples(extension, bilby=bilby, lalinference=lalinference)84    def check_samples(self, extension, bilby=False, lalinference=False):85        """Check that the samples in the result file are consistent with the86        inputs87        """88        from pesummary.core.file.read import read89        initial_samples = read_result_file(90            extension=extension, bilby=bilby, lalinference=lalinference,91            outdir=self.tmpdir92        )93        data = read("{}/samples/posterior_samples.h5".format(self.tmpdir))94        samples = data.samples_dict95        label = data.labels[0]96        for param in initial_samples.keys():97            for i, j in zip(initial_samples[param], samples[label][param]):98                assert np.round(i, 8) == np.round(j, 8)99class TestCoreDat(Base):100    """Test the full workflow with a core dat file101    """102    def setup(self):103        """Setup the TestCoreDat class104        """105        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name106        if not os.path.isdir(self.tmpdir):107            os.mkdir(self.tmpdir)108    def teardown(self):109        """Remove the files and directories created from this class110        """111        if os.path.isdir(self.tmpdir):112            shutil.rmtree(self.tmpdir)113    @pytest.mark.workflowtest114    def test_single_run(self):115        """Test the full workflow with a core dat result file116        """117        extension = "dat"118        super(TestCoreDat, self).test_single_run(extension)119class TestCoreJson(Base):120    """Test the full workflow with a core json file121    """122    def setup(self):123        """Setup the TestCoreJson class124        """125        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name126        if not os.path.isdir(self.tmpdir):127            os.mkdir(self.tmpdir)128    def teardown(self):129        """Remove the files and directories created from this class130        """131        if os.path.isdir(self.tmpdir):132            shutil.rmtree(self.tmpdir)133    @pytest.mark.workflowtest134    def test_single_run(self):135        """Test the full workflow with a core json result file136        """137        extension = "json"138        super(TestCoreJson, self).test_single_run(extension)139class TestCoreHDF5(Base):140    """Test the full workflow with a core hdf5 file141    """142    def setup(self):143        """Setup the TestCoreHDF5 class144        """145        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name146        if not os.path.isdir(self.tmpdir):147            os.mkdir(self.tmpdir)148    def teardown(self):149        """Remove the files and directories created from this class150        """151        if os.path.isdir(self.tmpdir):152            shutil.rmtree(self.tmpdir)153    @pytest.mark.workflowtest154    def test_single_run(self):155        """Test the full workflow with a core hdf5 result file156        """157        extension = "h5"158        super(TestCoreHDF5, self).test_single_run(extension)159class TestCoreBilbyJson(Base):160    """Test the full workflow with a core json bilby file161    """162    def setup(self):163        """Setup the TestCoreBilby class164        """165        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name166        if not os.path.isdir(self.tmpdir):167            os.mkdir(self.tmpdir)168    def teardown(self):169        """Remove the files and directories created from this class170        """171        if os.path.isdir(self.tmpdir):172            shutil.rmtree(self.tmpdir)173        if os.path.isdir("{}_pesummary".format(self.tmpdir)):174            shutil.rmtree("{}_pesummary".format(self.tmpdir))175    @pytest.mark.workflowtest176    def test_single_run(self):177        """Test the full workflow with a core bilby result file178        """179        extension = "json"180        super(TestCoreBilbyJson, self).test_single_run(extension, bilby=True)181    @pytest.mark.workflowtest182    def test_double_run(self):183        """Test the full workflow for 2 lalinference result files184        """185        opts, inputs = make_argparse(outdir=self.tmpdir, 186            gw=False, extension="json", bilby=True, number=2)187        func = functions(opts)188        PlotGeneration(inputs)189        WebpageGeneration(inputs)190        func["MetaFile"](inputs)191        func["FinishingTouches"](inputs)192        plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))193        files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))194        assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, 195                       gw=False, number=2)))196        assert all(i in plots for i in get_list_of_plots(outdir=self.tmpdir, gw=False, number=2))197        assert all(i in get_list_of_plots(outdir=self.tmpdir, gw=False, number=2) for i in plots)198        assert all(i == j for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, 199                       gw=False, number=2)))200        assert all(i in files for i in get_list_of_files(outdir=self.tmpdir, gw=False, number=2))201        assert all(i in get_list_of_files(outdir=self.tmpdir, gw=False, number=2) for i in files)202    @pytest.mark.workflowtest203    def test_existing_run(self):204        """Test the fill workflow for when you add to an existing webpage205        """206        opts, inputs = make_argparse(outdir=self.tmpdir, 207            gw=False, extension="json", bilby=True)208        func = functions(opts)209        PlotGeneration(inputs)210        WebpageGeneration(inputs)211        func["MetaFile"](inputs)212        func["FinishingTouches"](inputs)213        opts, inputs = make_argparse(outdir=self.tmpdir, 214            gw=False, extension="json", bilby=True, existing=True)215        func = functions(opts)216        PlotGeneration(inputs)217        WebpageGeneration(inputs)218        func["MetaFile"](inputs)219        func["FinishingTouches"](inputs)220        plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))221        files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))222        assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, 223                       gw=False, number=2)))224        assert all(i in plots for i in get_list_of_plots(outdir=self.tmpdir, gw=False, number=2))225        assert all(i in get_list_of_plots(outdir=self.tmpdir, gw=False, number=2) for i in plots)226        assert all(i == j for i, j in zip(files, get_list_of_files(outdir=self.tmpdir, 227                       gw=False, number=2)))228        assert all(i in files for i in get_list_of_files(outdir=self.tmpdir, gw=False, number=2))229        assert all(i in get_list_of_files(outdir=self.tmpdir, gw=False, number=2) for i in files)230    @pytest.mark.workflowtest231    def test_pesummary_input(self):232        """Test the full workflow for a pesummary input file233        """234        opts, inputs = make_argparse(outdir=self.tmpdir, 235            gw=False, extension="json", bilby=True, number=2)236        func = functions(opts)237        PlotGeneration(inputs)238        WebpageGeneration(inputs)239        func["MetaFile"](inputs)240        func["FinishingTouches"](inputs)241        plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))242        files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))243        from pesummary.core.cli.command_line import command_line244        parser = command_line()245        default_args = ["--webdir", "{}_pesummary".format(self.tmpdir),246                        "--samples", "{}/samples/posterior_samples.h5".format(self.tmpdir),247                        "--disable_expert"]248        opts = parser.parse_args(default_args)249        func = functions(opts)250        inputs = func["input"](opts)251        PlotGeneration(inputs)252        WebpageGeneration(inputs)253        func["MetaFile"](inputs)254        func["FinishingTouches"](inputs)255        plots_pesummary = sorted(glob.glob("{}_pesummary/plots/*.png".format(self.tmpdir)))256        files_pesummary = sorted(glob.glob("{}_pesummary/html/*.html".format(self.tmpdir)))257        assert all(i.split("/")[-1] == j.split("/")[-1] for i, j in zip(258                   plots, plots_pesummary))259        assert all(i.split("/")[-1] == j.split("/")[-1] for i, j in zip(260                   files, files_pesummary))261class TestCoreBilbyHDF5(Base):262    """Test the full workflow with a core hdf5 bilby file263    """264    def setup(self):265        """Setup the TestCoreBilby class266        """267        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name268        if not os.path.isdir(self.tmpdir):269            os.mkdir(self.tmpdir)270    def teardown(self):271        """Remove the files and directories created from this class272        """273        if os.path.isdir(self.tmpdir):274            shutil.rmtree(self.tmpdir)275    @pytest.mark.workflowtest276    def test_single_run(self):277        """Test the full workflow with a core bilby result file278        """279        extension = "h5"280        super(TestCoreBilbyHDF5, self).test_single_run(extension, bilby=True)281class TestGWDat(GWBase):282    """Test the full workflow with a gw dat file283    """284    def setup(self):285        """Setup the TestCoreDat class286        """287        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name288        if not os.path.isdir(self.tmpdir):289            os.mkdir(self.tmpdir)290    def teardown(self):291        """Remove the files and directories created from this class292        """293        if os.path.isdir(self.tmpdir):294            shutil.rmtree(self.tmpdir)295    @pytest.mark.workflowtest296    def test_single_run(self):297        """Test the full workflow with a gw dat result file298        """299        extension = "dat"300        super(TestGWDat, self).test_single_run(extension)301class TestGWJson(GWBase):302    """Test the full workflow with a json dat file303    """304    def setup(self):305        """Setup the TestGWJson class306        """307        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name308        if not os.path.isdir(self.tmpdir):309            os.mkdir(self.tmpdir)310    def teardown(self):311        """Remove the files and directories created from this class312        """313        if os.path.isdir(self.tmpdir):314            shutil.rmtree(self.tmpdir)315    @pytest.mark.workflowtest316    def test_single_run(self):317        """Test the full workflow with a gw json result file318        """319        extension = "json"320        super(TestGWJson, self).test_single_run(extension)321class TestGWBilbyJson(GWBase):322    """Test the full workflow with a gw bilby json file323    """324    def setup(self):325        """Setup the TestGWJson class326        """327        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name328        if not os.path.isdir(self.tmpdir):329            os.mkdir(self.tmpdir)330    def teardown(self):331        """Remove the files and directories created from this class332        """333        if os.path.isdir(self.tmpdir):334            shutil.rmtree(self.tmpdir)335    @pytest.mark.workflowtest336    def test_single_run(self):337        """Test the full workflow with a gw bilby json result file338        """339        extension = "json"340        super(TestGWBilbyJson, self).test_single_run(extension, bilby=True)341class TestGWBilbyHDF5(GWBase):342    """Test the full workflow with a gw bilby HDF5 file343    """344    def setup(self):345        """Setup the TestGWJson class346        """347        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name348        if not os.path.isdir(self.tmpdir):349            os.mkdir(self.tmpdir)350    def teardown(self):351        """Remove the files and directories created from this class352        """353        if os.path.isdir(self.tmpdir):354            shutil.rmtree(self.tmpdir)355    @pytest.mark.workflowtest356    def test_single_run(self):357        """Test the full workflow with a gw bilby HDF5 result file358        """359        extension = "h5"360        super(TestGWBilbyHDF5, self).test_single_run(extension, bilby=True)361class TestGWLALInference(GWBase):362    """Test the full workflow with a lalinference file363    """364    def setup(self):365        """Setup the TestGWJson class366        """367        self.tmpdir = tempfile.TemporaryDirectory(prefix=".", dir=".").name368        if not os.path.isdir(self.tmpdir):369            os.mkdir(self.tmpdir)370    def teardown(self):371        """Remove the files and directories created from this class372        """373        if os.path.isdir(self.tmpdir):374            shutil.rmtree(self.tmpdir)375        if os.path.isdir("{}_pesummary".format(self.tmpdir)):376            shutil.rmtree("{}_pesummary".format(self.tmpdir))377    @pytest.mark.workflowtest378    def test_single_run(self):379        """Test the full workflow with a lalinference result file380        """381        extension = "hdf5"382        super(TestGWLALInference, self).test_single_run(extension, lalinference=True)383    @pytest.mark.workflowtest384    def test_double_run(self):385        """Test the full workflow for 2 lalinference result files386        """387        opts, inputs = make_argparse(outdir=self.tmpdir, 388            gw=True, extension="hdf5", lalinference=True, number=2)389        func = functions(opts)390        PlotGeneration(inputs, gw=True)391        WebpageGeneration(inputs, gw=True)392        func["MetaFile"](inputs)393        func["FinishingTouches"](inputs)394        plots = sorted(glob.glob("{}/plots/*.png".format(self.tmpdir)))395        files = sorted(glob.glob("{}/html/*.html".format(self.tmpdir)))396        assert all(i == j for i, j in zip(plots, get_list_of_plots(outdir=self.tmpdir, ...

simulator_test.py

Source:simulator_test.py

...37    plt.legend(loc="upper right")38    plt.xlabel('staff num')39    plt.ylabel('y axis')4041def test_single_run(simulator, round):42    (average_staff_used, average_time_waited) = simulator.run(round)43    print(average_staff_used)44    print(average_time_waited)4546def test_staff_num(simulator, round):47    total_staff_used_list = []48    total_time_waited_list = []49    staff_num_list = [i for i in range(1, GROUP_SIZE + 1)]5051    for staff_num in range(1, GROUP_SIZE + 1):52        print("this is time %d" % staff_num)53        simulator.set_staff_num(staff_num)54        (average_staff_used, average_time_waited) = simulator.run(round)55        total_staff_used_list.append(average_staff_used)56        total_time_waited_list.append(average_time_waited)5758    return total_staff_used_list, total_time_waited_list5960def test_influence_of_distance(simulator, round, range_start, range_end):61    rec_total_staff_used_list = []62    rec_total_time_waited_list = []63    rec_staff_num_list = []64    for distance in range(range_start, range_end):65        simulator.set_distance(distance)66        print("\n\n\n\n\nthis is distance %d\n\n\n\n\n" % distance)67        (total_staff_used_list, total_time_waited_list) = test_staff_num(simulator, round)68        rec_total_staff_used_list.append(total_staff_used_list)69        rec_total_time_waited_list.append(total_time_waited_list)70        rec_staff_num_list.append([i for i in range(1, GROUP_SIZE + 1)])7172    draw_graph_staff_num(rec_staff_num_list, rec_total_staff_used_list)73    draw_graph_time_waited(rec_staff_num_list, rec_total_time_waited_list)74    plt.show()757677if __name__ == '__main__':78    test_round = 1000079    simulator = Simulator(FAILURE_RATE, GROUP_SIZE, GROUP_NUM, STAFF_NUM, GROUP_INTERVAL, MACHINE_INTERVAL, SPEED, FIX_TIME, X_DIVIDE)80    # test_influence_of_distance(simulator, test_round, 0, 1)81    time_start = time.time()82    test_single_run(simulator, test_round)83    time_end = time.time()84    print("time for this run is:")85    print(time_end - time_start)8687    # (total_staff_used_list, total_time_waited_list) = test_staff_num(simulator, test_round)88    # draw_graph_time_waited([[i for i in range(1, GROUP_SIZE + 1)]], [total_time_waited_list])89    # plt.show()909192    # result_staff = []93    # result_waited_time = []94    # staff_num_list = []95    # for i in range(1, GROUP_SIZE + 1):96    #     simulator.set_staff_num(i)
...

test_enrichr.py

Source:test_enrichr.py

...4from magine.enrichment.enrichr import Enrichr, clean_drug_dbs, clean_tf_names, \5    get_background_list, get_libraries, run_enrichment_for_project6from magine.tests.sample_experimental_data import exp_data7e = Enrichr()8def test_single_run():9    e.print_valid_libs()10    list_2 = ['CASP3', 'CASP6', 'FAS', 'FADD', 'CASP8', 'CFLAR', 'BFAR', 'BAD',11              'BID', 'PMAIP1', 'MCL1', 'BCL2', 'BCL2L1', 'BAX', 'BAK1',12              'DIABLO', 'CYCS', 'PARP1', 'APAF1', 'XIAP']13    df = e.run(list_2, 'GO_Biological_Process_2017')14    terms = df['term_name']15    ok_(len(terms) == 185)16def test_libaries():17    get_libraries()18def test_project():19    slimmed = exp_data.species.copy()20    slimmed = slimmed.loc[slimmed.source.isin(['label_free', 'silac'])]21    slimmed = slimmed.loc[slimmed.sample_id.isin(['Time_1', 'Time_2', ])]22    slimmed = ExperimentalData(slimmed)23    run_enrichment_for_project(slimmed, 'test',24                               databases=['KEGG_2016'])25    slimmed = exp_data.species.copy()26    slimmed = slimmed.loc[slimmed.source.isin(['label_free'])]27    slimmed = slimmed.loc[slimmed.sample_id.isin(['Time_1', 'Time_2', ])]28    slimmed = ExperimentalData(slimmed)29    run_enrichment_for_project(slimmed, 'test',30                               databases=['KEGG_2016'])31def test_get_gene_set_lib():32    get_background_list('Phosphatase_Substrates_from_DEPOD')33def test_clean_drug_dbs():34    list_2 = ['CASP3', 'CASP6', 'FAS', 'FADD', 'CASP8', 'CFLAR', 'BFAR', 'BAD',35              'BID', 'PMAIP1', 'MCL1', 'BCL2', 'BCL2L1', 'BAX', 'BAK1',36              'DIABLO', 'CYCS', 'PARP1', 'APAF1', 'XIAP']37    df = e.run(list_2, ['Drug_Perturbations_from_GEO_2014',38                        'LINCS_L1000_Chem_Pert_up'39                        ])40    df = clean_drug_dbs(df)41    ok_(len(df['term_name']) == 6243)42    ok_(len(df.sig['term_name']) == 249)43def test_multi_sample():44    lists = [['BAX', 'BCL2', 'CASP3'],45             ['CASP10', 'CASP8', 'BAK'],46             ['BIM', 'CASP3']]47    df2 = e.run_samples(lists, ['1', '2', '3'], save_name='enrichr_test')48    ok_(df2.shape == (111, 11))49def test_multi_sample_plotting():50    up = exp_data.genes.sig.up_by_sample51    out_dir = tempfile.mkdtemp()52    e.run_samples(up, ['1', '2', '3'],53                  gene_set_lib=['Human_Phenotype_Ontology',54                                'MGI_Mammalian_Phenotype_2017'],55                  save_name='enrichr_test',56                  exp_data=exp_data,57                  create_html=True,58                  pivot=True,59                  out_dir=out_dir)60def test_set_of_dbs():61    lists = [['BAX', 'BCL2', 'CASP3'],62             ['CASP10', 'CASP8', 'BAK'],63             ['BIM', 'CASP3']]64    df2 = e.run_samples(lists, ['1', '2', '3'],65                        gene_set_lib=['KEGG_2016', 'NCI-Nature_2016']66                        )67    ok_(df2.shape == (128, 11))68def test_tf_names():69    df = e.run(['BAX', 'BCL2', 'MCL1'], ['ARCHS4_TFs_Coexp', 'ChEA_2016'])70    tfs = clean_tf_names(df)71    for i in tfs['term_name']:72        ok_('_' not in i)73if __name__ == '__main__':...

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