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__':...

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