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How to use skip_test method in Lemoncheesecake

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test_ncbi.py

Source:test_ncbi.py

1#!/usr/bin/python2__author__ = "tomkinsc@broadinstitute.org"3# built-ins4import unittest5import os6import argparse7import pickle8import shutil9import tempfile10from collections import OrderedDict11import logging12# module-specific13from test import TestCaseWithTmp14import ncbi15import util.file16log = logging.getLogger(__name__)17skip_test = True18@unittest.skipIf(skip_test, "test is marked to be skipped")19class TestNcbiFetch(TestCaseWithTmp):20    def setUp(self):21        super(TestNcbiFetch, self).setUp()22        # these are Orungo accessions23        self.accessions = ["JQ610675.1", "JQ610676.1", "JQ610677.1", "JQ610678.1", "JQ610679.1", "JQ610680.1",24                           "JQ610681.1", "JQ610682.1", "JQ610683.1", "JQ610684.1"]25        self.myInputDir = util.file.get_test_input_path(self)26    def perform_download_and_check(self, parser_func, additional_args, expected_files, null_files):27        temp_dir = tempfile.gettempdir()28        args = ["viral-ngs-test@example.com", temp_dir]29        args.extend(self.accessions)30        args.extend(additional_args)31        args = parser_func(argparse.ArgumentParser()).parse_args(args)32        args.func_main(args)33        # check that each file that each expected file was downloaded34        # and that the contents match what they should be35        for fileName in expected_files:36            createdFilePath = os.path.join(temp_dir, fileName)37            log.info("createdFilePath: {}".format(createdFilePath))38            assert os.path.exists(39                createdFilePath), "File that should have been created does not exist: %s" % createdFilePath40            self.assertEqualContents(createdFilePath, os.path.join(self.myInputDir, fileName))41        for fileName in null_files:42            shouldNotExistFilePath = os.path.join(temp_dir, fileName)43            assert not os.path.exists(44                shouldNotExistFilePath), "File exists but it should not: %s" % shouldNotExistFilePath45class TestFastaFetch(TestNcbiFetch):46    def setUp(self):47        super(TestFastaFetch, self).setUp()48    @unittest.skipIf(skip_test, "test is marked to be skipped")49    def test_download(self):50        args = []51        expectedFiles = [a + ".fasta" for a in self.accessions]52        null_files = []53        self.perform_download_and_check(ncbi.parser_fetch_fastas,54                                        additional_args=args,55                                        expected_files=expectedFiles,56                                        null_files=null_files)57    @unittest.skipIf(skip_test, "test is marked to be skipped")58    def test_concat(self):59        args = ["--combinedFilePrefix", "orungo"]60        expectedFiles = ["orungo.fasta"]61        null_files = []62        self.perform_download_and_check(ncbi.parser_fetch_fastas,63                                        additional_args=args,64                                        expected_files=expectedFiles,65                                        null_files=null_files)66    @unittest.skipIf(skip_test, "test is marked to be skipped")67    def test_removal_of_intermediates(self):68        args = ["--combinedFilePrefix", "orungo", "--removeSeparateFiles"]69        expectedFiles = ["orungo.fasta"]70        null_files = [a + ".fasta" for a in self.accessions]71        self.perform_download_and_check(ncbi.parser_fetch_fastas,72                                        additional_args=args,73                                        expected_files=expectedFiles,74                                        null_files=null_files)75    @unittest.skipIf(skip_test, "test is marked to be skipped")76    def test_individual_preexistance(self):77        # since the arguments are positional, including an accession here makes a duplicate that should78        # raise an Error79        args = [self.accessions[0]]80        args.extend(["--combinedFilePrefix", "orungo"])81        expectedFiles = ["orungo.fasta"]82        null_files = []83        with self.assertRaises(AssertionError):84            self.perform_download_and_check(ncbi.parser_fetch_fastas,85                                            additional_args=args,86                                            expected_files=expectedFiles,87                                            null_files=null_files)88    @unittest.skipIf(skip_test, "test is marked to be skipped")89    def test_combined_preexistance(self):90        args = ["--combinedFilePrefix", "orungo"]91        expectedFiles = ["orungo.fasta"]92        null_files = []93        # call once to create the combined file94        self.perform_download_and_check(ncbi.parser_fetch_fastas,95                                        additional_args=args,96                                        expected_files=expectedFiles,97                                        null_files=null_files)98        # an error should be raised the second time the call is made99        with self.assertRaises(AssertionError):100            self.perform_download_and_check(ncbi.parser_fetch_fastas,101                                            additional_args=args,102                                            expected_files=expectedFiles,103                                            null_files=null_files)104    @unittest.skipIf(skip_test, "test is marked to be skipped")105    def test_overwrite(self):106        args = ["--combinedFilePrefix", "orungo", "--forceOverwrite"]107        expectedFiles = ["orungo.fasta"]108        null_files = []109        # call once to create the combined file110        self.perform_download_and_check(ncbi.parser_fetch_fastas,111                                        additional_args=args,112                                        expected_files=expectedFiles,113                                        null_files=null_files)114        # no error should be raised the second time the call is made115        self.perform_download_and_check(ncbi.parser_fetch_fastas,116                                        additional_args=args,117                                        expected_files=expectedFiles,118                                        null_files=null_files)119    @unittest.skipIf(skip_test, "test is marked to be skipped")120    def test_different_file_extension(self):121        args = ["--fileExt", "fa", "--combinedFilePrefix", "orungo"]122        expectedFiles = [a + ".fa" for a in self.accessions]123        expectedFiles.append("orungo.fa")124        null_files = []125        self.perform_download_and_check(ncbi.parser_fetch_fastas,126                                        additional_args=args,127                                        expected_files=expectedFiles,128                                        null_files=null_files)129class TestFeatureTableFetch(TestNcbiFetch):130    def setUp(self):131        super(TestFeatureTableFetch, self).setUp()132    @unittest.skipIf(skip_test, "test is marked to be skipped")133    def test_download(self):134        args = []135        expectedFiles = [a + ".tbl" for a in self.accessions]136        null_files = []137        self.perform_download_and_check(ncbi.parser_fetch_feature_tables,138                                        additional_args=args,139                                        expected_files=expectedFiles,140                                        null_files=null_files)141    @unittest.skipIf(skip_test, "test is marked to be skipped")142    def test_concat(self):143        args = ["--combinedFilePrefix", "orungo"]144        expectedFiles = ["orungo.tbl"]145        null_files = []146        self.perform_download_and_check(ncbi.parser_fetch_feature_tables,147                                        additional_args=args,148                                        expected_files=expectedFiles,149                                        null_files=null_files)150    @unittest.skipIf(skip_test, "test is marked to be skipped")151    def test_removal_of_intermediates(self):152        args = ["--combinedFilePrefix", "orungo", "--removeSeparateFiles"]153        expectedFiles = ["orungo.tbl"]154        null_files = [a + ".tbl" for a in self.accessions]155        self.perform_download_and_check(ncbi.parser_fetch_feature_tables,156                                        additional_args=args,157                                        expected_files=expectedFiles,158                                        null_files=null_files)159    @unittest.skipIf(skip_test, "test is marked to be skipped")160    def test_individual_preexistance(self):161        # since the arguments are positional, including an accession here makes a duplicate that should162        # raise an Error163        args = [self.accessions[0]]164        args.extend(["--combinedFilePrefix", "orungo"])165        expectedFiles = ["orungo.tbl"]166        null_files = []167        with self.assertRaises(AssertionError):168            self.perform_download_and_check(ncbi.parser_fetch_feature_tables,169                                            additional_args=args,170                                            expected_files=expectedFiles,171                                            null_files=null_files)172    @unittest.skipIf(skip_test, "test is marked to be skipped")173    def test_combined_preexistance(self):174        args = ["--combinedFilePrefix", "orungo"]175        expectedFiles = ["orungo.tbl"]176        null_files = []177        # call once to create the combined file178        self.perform_download_and_check(ncbi.parser_fetch_feature_tables,179                                        additional_args=args,180                                        expected_files=expectedFiles,181                                        null_files=null_files)182        # an error should be raised the second time the call is made183        with self.assertRaises(AssertionError):184            self.perform_download_and_check(ncbi.parser_fetch_feature_tables,185                                            additional_args=args,186                                            expected_files=expectedFiles,187                                            null_files=null_files)188    @unittest.skipIf(skip_test, "test is marked to be skipped")189    def test_overwrite(self):190        args = ["--combinedFilePrefix", "orungo", "--forceOverwrite"]191        expectedFiles = ["orungo.tbl"]192        null_files = []193        # call once to create the combined file194        self.perform_download_and_check(ncbi.parser_fetch_feature_tables,195                                        additional_args=args,196                                        expected_files=expectedFiles,197                                        null_files=null_files)198        # no error should be raised the second time the call is made199        self.perform_download_and_check(ncbi.parser_fetch_feature_tables,200                                        additional_args=args,201                                        expected_files=expectedFiles,202                                        null_files=null_files)203    @unittest.skipIf(skip_test, "test is marked to be skipped")204    def test_different_file_extension(self):205        args = ["--fileExt", "table", "--combinedFilePrefix", "orungo"]206        expectedFiles = [a + ".table" for a in self.accessions]207        expectedFiles.append("orungo.table")208        null_files = []209        self.perform_download_and_check(ncbi.parser_fetch_feature_tables,210                                        additional_args=args,211                                        expected_files=expectedFiles,212                                        null_files=null_files)213class TestGenbankRecordFetch(TestNcbiFetch):214    def setUp(self):215        super(TestGenbankRecordFetch, self).setUp()216    @unittest.skipIf(skip_test, "test is marked to be skipped")217    def test_download(self):218        args = []219        expectedFiles = [a + ".gbk" for a in self.accessions]220        null_files = []221        self.perform_download_and_check(ncbi.parser_fetch_genbank_records,222                                        additional_args=args,223                                        expected_files=expectedFiles,224                                        null_files=null_files)225    @unittest.skipIf(skip_test, "test is marked to be skipped")226    def test_concat(self):227        args = ["--combinedFilePrefix", "orungo"]228        expectedFiles = ["orungo.gbk"]229        null_files = []230        self.perform_download_and_check(ncbi.parser_fetch_genbank_records,231                                        additional_args=args,232                                        expected_files=expectedFiles,233                                        null_files=null_files)234    @unittest.skipIf(skip_test, "test is marked to be skipped")235    def test_removal_of_intermediates(self):236        args = ["--combinedFilePrefix", "orungo", "--removeSeparateFiles"]237        expectedFiles = ["orungo.gbk"]238        null_files = [a + ".gbk" for a in self.accessions]239        self.perform_download_and_check(ncbi.parser_fetch_genbank_records,240                                        additional_args=args,241                                        expected_files=expectedFiles,242                                        null_files=null_files)243    @unittest.skipIf(skip_test, "test is marked to be skipped")244    def test_individual_preexistance(self):245        # since the arguments are positional, including an accession here makes a duplicate that should246        # raise an Error247        args = [self.accessions[0]]248        args.extend(["--combinedFilePrefix", "orungo"])249        expectedFiles = ["orungo.gbk"]250        null_files = []251        with self.assertRaises(AssertionError):252            self.perform_download_and_check(ncbi.parser_fetch_genbank_records,253                                            additional_args=args,254                                            expected_files=expectedFiles,255                                            null_files=null_files)256    @unittest.skipIf(skip_test, "test is marked to be skipped")257    def test_combined_preexistance(self):258        args = ["--combinedFilePrefix", "orungo"]259        expectedFiles = ["orungo.gbk"]260        null_files = []261        # call once to create the combined file262        self.perform_download_and_check(ncbi.parser_fetch_genbank_records,263                                        additional_args=args,264                                        expected_files=expectedFiles,265                                        null_files=null_files)266        # an error should be raised the second time the call is made267        with self.assertRaises(AssertionError):268            self.perform_download_and_check(ncbi.parser_fetch_genbank_records,269                                            additional_args=args,270                                            expected_files=expectedFiles,271                                            null_files=null_files)272    @unittest.skipIf(skip_test, "test is marked to be skipped")273    def test_overwrite(self):274        args = ["--combinedFilePrefix", "orungo", "--forceOverwrite"]275        expectedFiles = ["orungo.gbk"]276        null_files = []277        # call once to create the combined file278        self.perform_download_and_check(ncbi.parser_fetch_genbank_records,279                                        additional_args=args,280                                        expected_files=expectedFiles,281                                        null_files=null_files)282        # no error should be raised the second time the call is made283        self.perform_download_and_check(ncbi.parser_fetch_genbank_records,284                                        additional_args=args,285                                        expected_files=expectedFiles,286                                        null_files=null_files)287    @unittest.skipIf(skip_test, "test is marked to be skipped")288    def test_different_file_extension(self):289        args = ["--fileExt", "gb", "--combinedFilePrefix", "orungo"]290        expectedFiles = [a + ".gb" for a in self.accessions]291        expectedFiles.append("orungo.gb")292        null_files = []293        self.perform_download_and_check(ncbi.parser_fetch_genbank_records,294                                        additional_args=args,295                                        expected_files=expectedFiles,...

validate_api.py

Source:validate_api.py

1#!/usr/bin/env python32"""3   @author TELEMAC-MASCARET Consortium4   @brief Function for validation of the Python API5"""6from os import path, chdir, remove, listdir, sep7from filecmp import cmp8import shutil9from argparse import ArgumentParser10from vvytel import copy_file_to_tmp11from vvytel import get_result_file_name12from vvytel import run_telemac_api13from vvytel import run_telemac_normal14from config import add_config_argument, update_config, CFGS15MODULE_HANDLED = ['telemac2d', 'telemac3d', 'artemis', 'tomawac']16def main(modules, example, nncsize, clean):17    """18    Main function19    """20    # Running main function21    root_dir = CFGS.get_root()22    if path.exists('ValidationTelApy.log'):23        remove('ValidationTelApy.log')24    fichier = open('ValidationTelApy.log', 'a')25    fichier.write("-----Listing Validation telapy-------\n")26    seq_only = {}27    skip_test = {}28    # Specifcation for each module29    for module in MODULE_HANDLED:30        seq_only[module] = []31        skip_test[module] = []32    # Sequential only test cases33    seq_only['telemac2d'].append('t2d_hydraulic_jump_v1p0.cas')34    seq_only['telemac2d'].append('t2d_hydraulic_jump_v2p0.cas')35    seq_only['telemac2d'].append('t2d_wesel.cas')36    seq_only['telemac2d'].append('t2d_wesel_pos.cas')37    seq_only['telemac2d'].append('t2d_delwaq.cas')38    seq_only['telemac2d'].append('t2d_ruptmoui.cas')39    seq_only['telemac2d'].append('t2d_triangular_shelf.cas')40    seq_only['telemac2d'].append('t2d_island.cas')41    seq_only['telemac2d'].append('t2d_tide-jmj_real_gen.cas')42    seq_only['telemac2d'].append('t2d_tide-jmj_type_gen.cas')43    seq_only['telemac2d'].append('t2d_dambreak_v1p0.cas')44    seq_only['telemac3d'].append('t3d_delwaq.cas')45    seq_only['telemac3d'].append('t3d_pluie.cas')46    seq_only['telemac3d'].append('t3d_tide-jmj_real_gen.cas')47    seq_only['artemis'].append('none')48    seq_only['tomawac'].append('tom_turning_wind.cas')49    seq_only['tomawac'].append('tom_manche.cas')50    seq_only['tomawac'].append('tom_manchelim.cas')51    # Test case that can not work with api52    # Using homere_adj not handle by api53    skip_test['telemac2d'].append('estimation')54    # Reruning telemac from homere not handled by api55    skip_test['telemac2d'].append('convergence')56    # Case that are not run by validation57    skip_test['telemac2d'].append('t2d_tide-jmj_type_med.cas')58    skip_test['telemac2d'].append('t2d_tide-ES_real.cas')59    # Non telemac3d case in folder60    skip_test['telemac3d'].append('t2d_canal.cas')61    skip_test['telemac3d'].append('p3d_amr.cas')62    skip_test['telemac3d'].append('p3d_bump.cas')63    skip_test['telemac3d'].append('p3d_canal.cas')64    skip_test['telemac3d'].append('p3d_cooper.cas')65    skip_test['telemac3d'].append('p3d_depot.cas')66    skip_test['telemac3d'].append('p3d_flume_slope.cas')67    skip_test['telemac3d'].append('p3d_gouttedo.cas')68    skip_test['telemac3d'].append('p3d_lock-hydro.cas')69    skip_test['telemac3d'].append('p3d_lock-nonhydro.cas')70    skip_test['telemac3d'].append('p3d_nonlinearwave.cas')71    skip_test['telemac3d'].append('p3d_piledepon.cas')72    skip_test['telemac3d'].append('p3d_piledepon-nonhydro.cas')73    skip_test['telemac3d'].append('p3d_pluie.cas')74    skip_test['telemac3d'].append('p3d_rouse.cas')75    skip_test['telemac3d'].append('p3d_stratification.cas')76    skip_test['telemac3d'].append('p3d_tetra.cas')77    skip_test['telemac3d'].append('p3d_vent.cas')78    skip_test['telemac3d'].append('p3d_V.cas')79    # Coupling test case80    skip_test['telemac3d'].append('depot')81    skip_test['telemac3d'].append('heat_exchange')82    # Artemis animated test case83    skip_test['artemis'].append('art_bj78_animated.cas')84    skip_test['artemis'].append('art_creocean_animated.cas')85    skip_test['artemis'].append('art_creocean_2.cas')86    skip_test['artemis'].append('art_creocean.cas')87    # Tomawac coupled test cases88    skip_test['tomawac'].append('3Dcoupling')89    for module in modules:90        fichier.write("-- For module " + module + "\n")91        module_dir = path.join(root_dir, 'examples', module)92        list_test_case = []93        if example != '':94            list_test_case.append(example)95        else:96            list_test_case = sorted(listdir(module_dir))97        # Sequential only test_case98        for i, test_case in enumerate(list_test_case):99            if test_case in skip_test[module]:100                continue101            case_dir = path.join(module_dir, test_case)102            tmp_dir = path.join(case_dir, 'tmp')103            print("<"+str(i+1)+"/"+str(len(list_test_case))+'> '+str(test_case))104            fichier.write('Running test case '+test_case+'\n')105            list_file = copy_file_to_tmp.copy_file_to_tmp(\106                    case_dir, tmp_dir, \107                    module, root_dir, skip_test[module])108            chdir(tmp_dir)109            for cas, fortran in list_file:110                #111                # Running Telemac based on telapy112                #113                if cas in skip_test[module]:114                    continue115                # Get results names116                res_file = get_result_file_name.get_result_file_name(module,117                                                                     cas)118                api_res_file = res_file+'_api'119                # Running in sequential mode120                # if the case does not run in parallel121                if cas in seq_only[module]:122                    ncsize = 1123                else:124                    ncsize = nncsize125                passed_api = run_telemac_api.run_telemac_api(module, cas,126                                                             ncsize, fortran)127                if passed_api:128                    shutil.move(res_file, api_res_file)129                # Running Telemac classical way130                #131                passed_normal = run_telemac_normal.run_telemac_normal(module,132                                                                      cas,133                                                                      ncsize)134                #135                # Result comparison between api and136                #  classical Telemac computation137                #138                if not passed_normal:139                    fichier.write('   Normal run crashed\n')140                if not passed_api:141                    fichier.write('   Api run crashed\n')142                if not passed_api or not passed_normal:143                    fichier.write(str(cas)+'                       FAILED'+'\n')144                    continue145                if not path.exists(res_file):146                    fichier.write('   Missing '+res_file+"\n")147                    fichier.write(str(cas)+'                       FAILED'+'\n')148                    continue149                if not path.exists(api_res_file):150                    fichier.write('   Missing '+api_res_file+"\n")151                    fichier.write(str(cas)+'                       FAILED'+'\n')152                    continue153                compare = cmp(res_file, api_res_file)154                if compare:155                    fichier.write(str(cas)+'                       PASSED'+'\n')156                else:157                    fichier.write(str(cas)+'                       FAILED'+'\n')158            if clean:159                chdir(module_dir+sep+test_case)160                shutil.rmtree(module_dir+sep+test_case+sep+'tmp')161        fichier.write('my work is done '+'\n')162if __name__ == "__main__":163# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<164# ~~ Reads config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~165    print('\n\nLoading Options and Configurations\n'+72*'~'+'\n')166    PARSER = ArgumentParser(\167        description='Make the validation of Telemac-Mascaret API '\168            'and/or executable using the API')169    PARSER = add_config_argument(PARSER)170    PARSER.add_argument(\171        "-m", "--module",172        dest='modules',173        default="telemac2d",174        help="specify the list of folder to validate seprated by ,")175    PARSER.add_argument(\176        "--clean",177        action="store_true",178        dest="clean",179        default=False,180        help="Remove tmp folders")181    PARSER.add_argument(\182        "-n", "--cnsize",183        dest='ncsize',184        default=4,185        help="specify the number of processor the test case will be run with")186    PARSER.add_argument(\187        "-e", "--example",188        dest='example',189        default="",190        help="specify the name of the test case to compute")191    ARGS = PARSER.parse_args()192    update_config(ARGS)193    main(ARGS.modules.split(','), \...

ensembler.py

Source:ensembler.py

1import sys, gzip, json, os, math, pickle, re, copy2import numpy as np3import multiprocessing as mp4pool_size = int(mp.cpu_count())5from datetime import datetime6from math import exp, log, sqrt7root_path = '/home/marsan/workspace/tnative'8sys.path.append(root_path)9from lib import dgen as dgen10from lib import top as top11#==========================================12#   machein learning flow wrapper13#==========================================  14# [container of model unit]15class ml_unit(object):16  def __init__(self, alg, D, data, tmin, tmax, en_plot, en_fast_data, skip_test, debug):17    self.ml = top.ml(alg=alg, D=D, en_plot=en_plot, en_fast_data=en_fast_data, debug=debug)18    self.data = data19    self.tmin = tmin20    self.tmax = tmax21    self.vrng = abs(tmax - tmin)22    self.vmin = 1 - self.vrng if self.vrng < 0.5 else self.vrng23    self.vmax = 124    self.y2p = []25    self.pnorm = -126    self.skip_test = skip_test27    # self.q = mp.Queue()28    # update data filter29    for fea, val in self.data.items():30      self.ml.dgen.tbl = eval("self.ml.dgen.tbl.filter(%s=val)" % (fea))31    32  # for multiprocess33  def train_unit(self):34    self.ml.train(self.tmin, self.tmax, self.vmin, self.vmax, skip_test=self.skip_test)35    # q.put([self.ml.learner])36    return self.ml.learner37class ensembler(object):38  def __init__(self, segments, vrate, D=2**24, en_fast_data=None, en_plot=False, en_pnorm=False, skip_test=False, debug=False):39    # samples40    self.D = D41    self.vmin = 1 - vrate42    self.vmax = 143    44    # ctrl45    self.en_plot = en_plot46    self.en_pnorm = en_pnorm47    self.skip_test = skip_test48    self.en_fast_data = en_fast_data49    self.debug = debug50    51    # initialize models 52    self.dgen = dgen.data_gen(D=self.D, en_fast_data=self.en_fast_data, debug=self.debug) # samples for final test53    self.ml_group = []54    for s in segments:55      item = ml_unit(alg=s['alg'], D=self.D, data=s['data'], tmin=s['tmin'], tmax=s['tmax'], en_plot=self.en_plot, en_fast_data=self.en_fast_data, skip_test=self.skip_test, debug=self.debug)56      self.ml_group.append(item)57      58  #-------------------------59  #   convension60  #-------------------------61  def finitize(self, n, e=35):62    return max(min(n, e), -e)   # make -e <= n <= e63  def merge_sigmoid(self, nlist, e=35):64    nlist = [-log(max((1/max(n, 1e-35) - 1), 1e-35)) for n in nlist]65    nmean = np.mean(nlist)66    nsig = 1. / (1. + exp(-self.finitize(nmean, e)))67    return nsig68  #-------------------------69  #   train & test70  #-------------------------71  def train_and_test(self, en_multi_threads=False):72    self.train_all(en_multi_threads)73    roc_auc, yr_ens, yp_ens = self.test()74    self.save(roc_auc)75    return roc_auc, yr_ens, yp_ens76  def train_all(self, en_multi_threads=True):77    processes = []78    mp_pool = mp.Pool(pool_size)79    for l in self.ml_group:80      if not en_multi_threads:81        l.ml.train(l.tmin, l.tmax, l.vmin, l.vmax, skip_test=self.skip_test)  # [single process for debug]82      else:83        p = mp_pool.apply_async(l.train_unit, ())84        processes.append((l, p))85        # p = mp.Process(target=l.train_unit, args=(l.q,))86        # processes.append(p)87        # p.start()88    if en_multi_threads:89      for l, p in processes:90        l.ml.learner = p.get()91      # for l in self.ml_group:92      #   l.ml.learner = l.q.get()[0]93      # for p in processes: p.join()94    print("[Ensembler] models training done @ %s" % datetime.now())95    return self.ml_group96  def test(self):97    print("\n%s\n#  [Ensembler] start grader %.2f - %.2f @ %s\n%s" % ("-"*60, 100*self.vmin, 100*self.vmax, datetime.now(), "-"*60))98    yr_ens = {}99    yp_ens = {}100    for s in self.ml_group:101      sdgen = copy.copy(self.dgen)102      for fea, val in s.data.items():103        sdgen.tbl = eval("sdgen.tbl.filter(%s=val)" % (fea))104      ids = [str(r.id) for r in sdgen.raw_range(self.vmin, self.vmax).only('id')]105      raw = sdgen.gen_data(self.vmin, self.vmax)106      # get y2p107      s.y2p = s.ml.learner.train(raw, training=False, info={'all_cnt': -1})108      if self.en_pnorm:109        s.pnorm = s.ml.grader.find_pnorm(s.y2p)110        s.y2p = [[y, min(1, p/s.pnorm)] for y, p in s.y2p]111      # map to ensembled y2p112      for i in range(len(ids)):113        key = ids[i]114        if key not in yp_ens: 115          yr_ens[key] = []116          yp_ens[key] = []117        yr_ens[key].append(s.y2p[i][0])118        yp_ens[key].append(s.y2p[i][1])119    y2p_ens = [(np.mean(yrs), self.merge_sigmoid(yp_ens[rid])) for rid, yrs in yr_ens.items()]120    grader = self.ml_group[0].ml.grader121    roc_auc = grader.auc_curve(y2p_ens)122    scan = grader.scan_all_threshold(y2p_ens)123    print("[Ensembler] ensembled ROC: %.3f%% @ %s" % (roc_auc*100, datetime.now()))124    return roc_auc, yr_ens, yp_ens125  #-------------------------126  #   layer-2127  #-------------------------128  def train_layer2(self):129    # collect samples130    Xt = []131    Yt = []132    sdgen = copy.copy(self.dgen)133    pass134  def test_layer2(self):135    pass136  #-------------------------137  #   model reuse138  #-------------------------139  def save(self, auc):140    filepath = "%s/models/m%i_v%i_auc_%i_%s" % (root_path, len(self.ml_group), (self.vmax-self.vmin)*100, auc*1000, datetime.now().strftime("%Y%m%d_%H%M"))141    trained_models = [mlu.ml.learner for mlu in self.ml_group]142    pickle.dump(trained_models, open(filepath, 'wb'))143    print("ensemble model saved in %s @ %s" % (filepath, datetime.now()))144    return filepath145#==========================================146#   experiments147#==========================================148def k_fold_ensemble(alg, k, vrate=0.1, en_plot=False, en_fast_data=None, skip_compare=True):149  if not skip_compare:150    print("="*5, '[train by single thread]', '='*40)151    top.ml(alg=alg, en_plot=en_plot).train(0, 1-vrate)152  print("[%i_fold_%s_ensemble] start @ %s" % (k, alg, datetime.now()))153  segments = []154  step = (1.0 - vrate)/k155  for i in range(k):156    segments.append({157      'alg': alg,158      'tmin': step*(i+1),159      'tmax': step*i,160      'data': {161        'isad__ne': None,162        # 'label__ne': None,163      }164    })165  ens = ensembler(segments, vrate=vrate, en_plot=en_plot, en_fast_data=en_fast_data, skip_test=True)  # k-fold MUST skip_test=True!! since we block ens.vmin166  for item in ens.ml_group: # prevent models from getting test samples167    item.ml.dgen.tbl = item.ml.dgen.tbl.filter(rand__lt=ens.vmin) 168  return ens.train_and_test()169def xgboost_sklr(vrate=0.1, en_plot=False):170  segments = [171    {172      'alg': alg, 173      'tmin': 0, 174      'tmax': 1-vrate,175      'data': {176        'isad__ne': None,177        # 'label__ne': None,178      },179    } for alg in ['sklr', 'xgboost']180  ]181  return ensembler(segments, vrate=vrate, en_plot=en_plot).train_and_test()182#==========================================183#   dnq ensemble (divide-and-conquer)184#==========================================185dnq_segments = {186  'status'  : [('status', 'bad'), ('status', 'normal')],187  'lang'    : [('meta_lang__icontains', 'en'), ('meta_lang', '')],188  'domain'  : [('domain__icontains', '.net'), ('domain__icontains', '.com'), ('domain__icontains', '.org'), ('domain__icontains', '.uk')],189}190def dnq_ensemble(alg, segname, vrate=0.1, en_plot=False, skip_compare=True):191  srate = 1-vrate if vrate > 0.5 else vrate192  if not skip_compare:193    print("="*5, '[train by single thread]', '='*40)194    auc_single = top.ml(alg='sklr', en_plot=en_plot).train(0, srate)195  print("="*5, '[train by ensemble]', '='*40)196  if segname == 'all':197    segs = ([('fid__ne', -1)] + [j for k in dnq_segments.values() for j in k])198  else:199    segs = ([('fid__ne', -1)] + dnq_segments[segname])200  segments = [{201    'alg': alg, 202    'tmin': 0, 203    'tmax': srate,204    'data': {205      'isad__ne': None,206      s: v,207    },208  } for s,v in segs]209  print("[dnq_ensemble] condition: ", segments)210  ens = ensembler(segments, vrate=vrate, en_plot=en_plot)211  return ens.train_and_test()212#==========================================213#   verify214#==========================================215if __name__ == '__main__':216  cmd = str(sys.argv[1])217  vrate = float(sys.argv[2])218  if (len(sys.argv) >= 4): cmd2 = str(sys.argv[3])219  #220  if cmd == '5_fold_xgboost':221    k_fold_ensemble('xgboost', k=5, vrate=vrate, en_plot=False)222  elif cmd == '5_fold_sklr':223    k_fold_ensemble('sklr', k=5, vrate=vrate, en_plot=False, en_fast_data='D_20_tfidf_cnts')224  elif cmd == 'xgboost_sklr':225    xgboost_sklr(vrate=vrate, en_plot=False)226  elif cmd == 'dnq_ensemble':227    dnq_ensemble('sklr', cmd2, vrate=vrate, en_plot=False)    228  elif cmd == 'dnq_all':...

test_carrito_compras.py

Source:test_carrito_compras.py

1import pytest2skip_test = pytest.mark.skipif(False, reason="skip")3#34@skip_test5def test_create_carrito_quantity_is_cero():6    from module.producto import Producto7    from module.detalleproducto import DetalleProducto8    from module.carrito import Carrito9    name = "producto 1"10    stock= 511    description= "description"12    producto_valido = Producto.create_product(13        name=name, 14        stock=stock, 15        description=description)16            17    assert producto_valido["name"] == name18    assert producto_valido["stock"] == stock19    assert producto_valido["description"] == description20    cantidad = 021    with pytest.raises(ValueError, match="cantidad can not be 0"):22        detalle_producto = DetalleProducto.crear_detalle(23            cantidad=cantidad,24            producto= producto_valido25        )26#527@skip_test28def test_create_carrito():29    from module.producto import Producto30    from module.detalleproducto import DetalleProducto31    from module.carrito import Carrito32    name = "producto 1"33    stock=1034    description= "description"35    producto_valido = Producto.create_product(36        name=name, 37        stock=stock, 38        description=description)39    40    assert producto_valido["name"] == name41    assert producto_valido["stock"] == stock42    assert producto_valido["description"] == description43    producto_valido_2 = Producto.create_product(44        name=name, 45        stock=stock, 46        description=description)47    48    assert producto_valido_2["name"] == name49    assert producto_valido_2["stock"] == stock50    assert producto_valido_2["description"] == description51    cantidad = 152    detalle_producto = DetalleProducto.crear_detalle(53        cantidad=cantidad,54        producto= producto_valido55    )56    assert detalle_producto["cantidad"] == cantidad57    detalle_producto_2 = DetalleProducto.crear_detalle(58        cantidad=cantidad,59        producto= producto_valido60    )61    assert detalle_producto_2["cantidad"] == cantidad62    lista_detalles =[detalle_producto, detalle_producto_2]63    carrito = Carrito.agregar_producto(lista_productos=lista_detalles)64    assert len(carrito) > 065#666@skip_test67def test_nombre_producto_distinto_null():68    from module.producto import Producto69    with pytest.raises(ValueError, match="none is not an allowed value"):70        crear_producto = Producto.create_product(71            name=None, 72            stock=1, 73            description="descripcion")74#775@skip_test76def test_nombre_producto_numerico():77    from module.producto import Producto78    with pytest.raises(ValueError, match="name can not be an integer"):79        crear_producto = Producto.create_product(80            name=11111, 81            stock=1, 82            description="descripcion")83#984@skip_test85def test_descripcion_producto_distinto_null():86    from module.producto import Producto87    with pytest.raises(ValueError, match="none is not an allowed value"):88        crear_producto = Producto.create_product(89            name="Juan", 90            stock=1, 91            description=None)92#1293@skip_test94def test_stock_producto_no_negativo():95    from module.producto import Producto96    with pytest.raises(ValueError, match="ensure this value is greater than -1"):97        crear_producto = Producto.create_product(98            name="juan", 99            stock=-1, 100            description="descripcion")101#8102@skip_test103def test_nombre_producto_name_too_long():104    from module.producto import Producto105    from random import choice106    from string import ascii_uppercase107    name = ''.join(choice(ascii_uppercase) for i in range(11))108    with pytest.raises(ValueError, match="ensure this value has at most 10 characters"):109        crear_producto = Producto.create_product(110            name=name, 111            stock=1, 112            description="descripcion")113#11114@skip_test115def test_create_product():116    from module.producto import Producto117    name = "juan"118    stock=10119    description= "description"120    crear_producto = Producto.create_product(121        name=name, 122        stock=stock, 123        description=description)124    125    assert crear_producto["name"] == name126    assert crear_producto["stock"] == stock127    assert crear_producto["description"] == description128#13129@skip_test130def test_stock_producto_puede_ser_cero():131    from module.producto import Producto132    crear_producto = Producto.create_product(133        name="juan", 134        stock=0, 135        description="descripcion")136    137    assert crear_producto["stock"] == 0138#15139@skip_test140def test_stock_producto_distinto_null():141    from module.producto import Producto142    with pytest.raises(ValueError, match="none is not an allowed value"):143        crear_producto = Producto.create_product(144            name="juan", 145            stock=None, 146            description="descripcion")147#17148@skip_test149def test_stock_valido_name_nulo_descripcion_nula():150    from module.producto import Producto151    with pytest.raises(ValueError, match="none is not an allowed value"):152        crear_producto = Producto.create_product(153            name=None, 154            stock=0, 155            description=None)156#18157@skip_test158def test_descripcion_valido_name_nulo_stock_nulo():159    from module.producto import Producto160    with pytest.raises(ValueError, match="none is not an allowed value"):161        crear_producto = Producto.create_product(162            name=None, 163            stock=None, 164            description="descripcion")165#19166@skip_test167def test_create_detalle_producto():168    from module.producto import Producto169    from module.detalleproducto import DetalleProducto170    name = "producto 1"171    stock=10172    description= "description"173    producto_valido = Producto.create_product(174        name=name, 175        stock=stock, 176        description=description)177    178    assert producto_valido["name"] == name179    assert producto_valido["stock"] == stock180    assert producto_valido["description"] == description181    cantidad = 1182    detalle_producto = DetalleProducto.crear_detalle(183        cantidad=cantidad,184        producto= producto_valido185    )186    assert detalle_producto["cantidad"] == cantidad187    assert detalle_producto["producto"]["stock"] == stock-cantidad188#20189@skip_test190def test_create_detalle_producto_cantidad_negativa():191    from module.producto import Producto192    from module.detalleproducto import DetalleProducto193    name = "producto 1"194    stock=10195    description= "description"196    producto_valido = Producto.create_product(197        name=name, 198        stock=stock, 199        description=description)200    201    assert producto_valido["name"] == name202    assert producto_valido["stock"] == stock203    assert producto_valido["description"] == description204    cantidad = 0205    with pytest.raises(ValueError, match="cantidad can not be 0"):206        detalle_producto = DetalleProducto.crear_detalle(207            cantidad=cantidad,208            producto=producto_valido...

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