KaneAI - World’s First E2E Software Testing Agent.Book a Demo Join TestMu Conference

How to use test_result_json method in tox

Best Python code snippet using tox_python

test_first_test.py

Source:test_first_test.py

1# -*- coding: utf-8 -*-2################################################################################3# MacSyFinder - Detection of macromolecular systems in protein datasets        #4#               using systems modelling and similarity search.                 #5# Authors: Sophie Abby, Bertrand NÃ©ron                                         #6# Copyright Â© 2014  Institut Pasteur, Paris.                                   #7# See the COPYRIGHT file for details                                           #8#                                                                              #9# MacsyFinder is distributed under the terms of the GNU General Public License #10# (GPLv3). See the COPYING file for details.                                   #11################################################################################12import shutil13import tempfile14import os15from subprocess import Popen16import json17from tests import MacsyTest18from macsypy.utils import which19class Test(MacsyTest):20    def setUp(self):21        if 'MACSY_HOME' in os.environ:22            self.macsy_home = os.environ['MACSY_HOME']23            self.local_install = True24        else:25            self.local_install = False26            self.macsy_home = os.path.normpath(os.path.abspath(os.path.join(os.path.dirname(__file__), '..' '..')))27        self.tmp_dir = tempfile.gettempdir()28    def tearDown(self):29        try:30            shutil.rmtree(self.out_dir)31        except:32            pass33    def test_basic_run(self):34        """35        test if returncode of macsyfinder is 0 and36        test each element of the json37        macsyfinder is launched to search T9SS T3SS T4SS_typeI systems38        with test_aesu.fa sequence db in gembase format39        """40        self.out_dir = os.path.join(self.tmp_dir, 'macsyfinder_test_basic_run')41        os.makedirs(self.out_dir)42        macsy_bin = os.path.join(self.macsy_home, 'bin', 'macsyfinder') if self.local_install else which('macsyfinder')43        command = "{bin} --def={def_dir} --profile-dir={profiles} --out-dir={out_dir} --sequence-db={seq_db} --db-type=gembase {systems}".format(44                    bin=macsy_bin,45                    out_dir=self.out_dir,46                    def_dir=os.path.join(self._data_dir, 'data_set_1', 'def'),47                    profiles=os.path.join(self._data_dir, 'data_set_1', 'profiles'),48                    seq_db=os.path.join(self._data_dir, 'base', 'test_aesu.fa'),49                    systems="T9SS T3SS T4SS_typeI",50                    )51        if not bin:52            raise RuntimeError('macsyfinder not found, macsyfinder must be either in your path or MACSY_HOME must be defined')53        # I redirect stdout and stderr in dev null I don't want them on screen54        # I cannot redirect them in output directory as --out-dir expect a non existing directory or an empty one55        # but Popen need to have a file as argument of stdout/err56        # I need to prepend the command by setsid because macsyfinder use killpg with group_id to terminated all57        # threads and subprocess when an error occurred in one hmmsearch. It's work fine but when58        # macsyfinder is launched by the tests.py srcipt the kill group kill also the tests.py script59        # so we must run macsyfinder in a new process group60        try:61            macsy_process = Popen("setsid " + command,62                                  shell=True,63                                  stdin=None,64                                  stdout=open(os.devnull, 'w'),65                                  stderr=open(os.devnull, 'w'),66                                  close_fds=False67                                  )68        except Exception as err:69            msg = "macsyfinder execution failed: command = {0} : {1}".format(command, err)70            print71            print msg72            raise err73        macsy_process.wait()74        self.assertEqual(macsy_process.returncode, 0,75                         "macsyfinder finished with non zero exit code: {0} command launched=\n{1}".format(76                          macsy_process.returncode,77                          command))78        expected_result_path = os.path.join(self._data_dir, 'data_set_1', 'basic_run_results',79                                            'results.macsyfinder.json')80        with open(expected_result_path) as expected_result_file:81            expected_result_json = json.load(expected_result_file)82        test_result_path = os.path.join(self.out_dir, 'results.macsyfinder.json')83        with open(test_result_path) as test_result_file:84            test_result_json = json.load(test_result_file)85        # it should have only one occurrence of T9SS86        self.assertEqual(len(test_result_json), 1,87                         "different type of systems expected: 1  retrieved: {0}".format(len(test_result_json)))88        expected_result_json = expected_result_json[0]89        test_result_json = test_result_json[0]90        self.assertEqual(expected_result_json['name'],91                         test_result_json['name'],92                         "type of system name expected: {0}   retrieved: {1}".format(expected_result_json['name'],93                                                                                     test_result_json['name']))94        self.assertEqual(expected_result_json['occurrence_number'],95                         test_result_json['occurrence_number'],96                         "occurrence number expected {0}   retrieved: {1}".format(expected_result_json['occurrence_number'],97                                                                                  test_result_json['occurrence_number']))98        self.assertDictEqual(expected_result_json['replicon'],99                             test_result_json['replicon'],100                             "replicon expected {0}   retrieved: {1}".format(expected_result_json['occurrence_number'],101                                                                             test_result_json['occurrence_number']))102        self.assertEqual(expected_result_json['id'],103                         test_result_json['id'],104                         "system occurrence id expected {0}   retrieved: {1}".format(expected_result_json['id'],105                                                                                     test_result_json['id']))106        self.assertDictEqual(expected_result_json['summary']['mandatory'],107                             test_result_json['summary']['mandatory'],108                             "mandatory genes expected {0}   retrieved: {1}".format(expected_result_json['summary']['mandatory'],109                                                                                    test_result_json['summary']['mandatory']))110        self.assertDictEqual(expected_result_json['summary']['accessory'],111                             test_result_json['summary']['accessory'],112                             "accessory genes expected {0}   retrieved: {1}".format(expected_result_json['summary']['accessory'],113                                                                                    test_result_json['summary']['accessory']))114        self.assertDictEqual(expected_result_json['summary']['forbidden'],115                             test_result_json['summary']['forbidden'],116                             "forbidden genes expected {0}   retrieved: {1}".format(expected_result_json['summary']['forbidden'],117                                                                                    test_result_json['summary']['forbidden']))118        self.assertListEqual(expected_result_json['genes'], test_result_json['genes'],119                             "genes expected {0}   retrieved: {1}".format(expected_result_json['genes'],...

transform_tests.py

Source:transform_tests.py

1# -*- coding: utf-8 -*-2import json3import unittest4from www.api.transform import ESResultTransformer5class TestCPDStringMethods(unittest.TestCase):6    """7    Test class for the ESResultTransformer class.  The static methods are called on a representative8    dataset.  The four static methods are called and a basic smoke test is run on the results.9    The datasets were extracted from a debugging screen query, results were pruned down to one entry10    and results were manually validated.11    """12    test_result_json = """{"took":5,"timed_out":false,"_shards":{"total":10,"successful":10,"failed":0},"hits":{"total":3173,"max_score":1.0,"hits":[{"_index":"human_ppi_current","_type":"human_ppi","_id":"AV7tgtgwsEC71Kh3t5_-","_score":1.0,"_source":{"interaction_participants": "TRIO_HUMAN,BLMH_HUMAN", "source_databases": "PhosphoPOINT,Spike,IntAct,HPRD,MINT,Biogrid", "interaction_publications": "16169070", "interaction_confidence": "0.82"}}]}}"""13    test_hit_json = """{"_index":"human_ppi_current","_type":"human_ppi","_id":"AV7tgtgwsEC71Kh3t5_-","_score":1.0,"_source":{"interaction_participants": "TRIO_HUMAN,BLMH_HUMAN", "source_databases": "PhosphoPOINT,Spike,IntAct,HPRD,MINT,Biogrid", "interaction_publications": "16169070", "interaction_confidence": "0.82"}}"""14    i_hit = 015    def test_CPD_parse_confidence(self):16        test_data = json.loads(self.test_result_json)17        test_hit = json.loads(self.test_hit_json)18        result_data = ESResultTransformer.parse_confidence(test_data, self.i_hit, test_hit)19        self.assertEqual(result_data['hits']['hits'][0]['_source'][ESResultTransformer.PpiFields.CONF], .82)20    def test_CPD_parse_participants(self):21        test_data = json.loads(self.test_result_json)22        test_hit = json.loads(self.test_hit_json)23        result_data = ESResultTransformer.parse_participants(test_data, self.i_hit, test_hit)24        self.assertEqual(len(result_data['hits']['hits'][0]['_source'][ESResultTransformer.PpiFields.PART]), 2)25    def test_CPD_parse_publications(self):26        test_data = json.loads(self.test_result_json)27        test_hit = json.loads(self.test_hit_json)28        result_data = ESResultTransformer.parse_publications(test_data, self.i_hit, test_hit)29        self.assertEqual(result_data['hits']['hits'][0]['_source'][ESResultTransformer.PpiFields.PUBS][0], 16169070)30    def test_CPD_parse_databases(self):31        test_data = json.loads(self.test_result_json)32        test_hit = json.loads(self.test_hit_json)33        result_data = ESResultTransformer.parse_databases(test_data, self.i_hit, test_hit)34        self.assertEqual(len(result_data['hits']['hits'][0]['_source'][ESResultTransformer.PpiFields.DBS]), 6)35if __name__ == '__main__':...

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.