How to use compare_files method in toolium

Best Python code snippet using toolium_python

xml_compare_test.py

Source:xml_compare_test.py

...35        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'36        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'37        f1 = file_obj_from_string(doc_1)38        f2 = file_obj_from_string(doc_2)39        self.assertIsNone(xml_compare.compare_files(f1, f2))40    def test_doctype_version_mismatch(self):41        # Basic document42        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'43        doc_2 = get_xml_declaration('1.1', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'44        f1 = file_obj_from_string(doc_1)45        f2 = file_obj_from_string(doc_2)46        self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))47    def test_doctype_encoding_mismatch(self):48        # Basic document49        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'50        doc_2 = get_xml_declaration('1.0', 'utf-16') + (get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>').encode('utf-16')51        f1 = file_obj_from_string(doc_1)52        f2 = file_obj_from_string(doc_2)53        self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))54    def test_doctype_system_url_mismatch(self):55        # Basic document56        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test1.dtd') + '<foo><bar /></foo>'57        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test2.dtd') + '<foo><bar /></foo>'58        f1 = file_obj_from_string(doc_1)59        f2 = file_obj_from_string(doc_2)60        self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))61    def test_doctype_root_tag_mismatch(self):62        # Basic document63        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'64        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('baz', 'SYSTEM', 'test.dtd') + '<baz><bar /></baz>'65        f1 = file_obj_from_string(doc_1)66        f2 = file_obj_from_string(doc_2)67        self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))68        69    def test_successful_comapre_with_param(self):70        # Basic document71        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="1" b="c"><bar /></foo>'72        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="1" b="c"><bar /></foo>'73        f1 = file_obj_from_string(doc_1)74        f2 = file_obj_from_string(doc_2)75        self.assertIsNone(xml_compare.compare_files(f1, f2))76    def test_param_mismatch(self):77        # Basic document78        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="1"><bar /></foo>'79        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo b="c"><bar /></foo>'80        f1 = file_obj_from_string(doc_1)81        f2 = file_obj_from_string(doc_2)82        self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))83    def test_child_num_mismatch(self):84        # Basic document85        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'86        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /><bar /></foo>'87        f1 = file_obj_from_string(doc_1)88        f2 = file_obj_from_string(doc_2)89        self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))90        91    def test_child_tag_mismatch(self):92        # Basic document93        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /><car /></foo>'94        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /><bar /></foo>'95        f1 = file_obj_from_string(doc_1)96        f2 = file_obj_from_string(doc_2)97        self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))98        99    def test_text_compare(self):100        # Basic document101        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo>bar</foo>'102        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo>bar</foo>'103        f1 = file_obj_from_string(doc_1)104        f2 = file_obj_from_string(doc_2)105        self.assertIsNone(xml_compare.compare_files(f1, f2))106        107    def test_text_compare_with_whitespace(self):108        """109        Ensure that whitespace is ignored if ignore_whitespace is set to True.110        """111        # Basic document112        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo>bar</foo>'113        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + """<foo>114        115bar116</foo>"""117        f1 = file_obj_from_string(doc_1)118        f2 = file_obj_from_string(doc_2)119        self.assertIsNone(xml_compare.compare_files(f1, f2))120        121    def test_text_no_ignore_whitespace(self):122        """123        Ensure that whitespace is not ignored if ignore_whitespace is set to false.124        """125        126        # Basic document127        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo>bar</foo>'128        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + """<foo>129        130bar131</foo>"""132        f1 = file_obj_from_string(doc_1)133        f2 = file_obj_from_string(doc_2)134        with self.assertRaises(Exception):135            xml_compare.compare_files(f1, f2, ignore_whitespace = False)136    def test_ignore_empty(self):137        """138        Ensure that empty tags are ignored if ignore_empty_tags is set to True.139        140        """141        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo></foo>'142        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'143        f1 = file_obj_from_string(doc_1)144        f2 = file_obj_from_string(doc_2)145        self.assertIsNone(xml_compare.compare_files(f1, f2))146               147    def test_no_ignore_empty(self):148        """149        Ensure that empty tags are not ignored if ignore_empty_tags is set to False.150        """151        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo></foo>'152        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'153        f1 = file_obj_from_string(doc_1)154        f2 = file_obj_from_string(doc_2)155        with self.assertRaises(Exception):156            xml_compare.compare_files(f1, f2, ignore_empty_tags = False)157            158    def test_custom_compare_function(self):159        def lower_case_compare(s1, s2):160            return s1.lower() == s2.lower()161    162        doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="HeLlO"></foo>'163        doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="hElLo"></foo>'164        f1 = file_obj_from_string(doc_1)165        f2 = file_obj_from_string(doc_2)166        167        with self.assertRaises(Exception):168            # Compare using the default compare function, which should fail169            xml_compare.compare_files(f1, f2)170    171        # Compare using the custom, lower-case compare function172        self.assertIsNone(xml_compare.compare_files(f1, f2, compare_function = lower_case_compare))...

run_eval_all.py

Source:run_eval_all.py

1import argparse2import sys3import numpy as np4np.random.seed(1)5import os, time6import math7import re8import tempfile9from tempfile import mkdtemp10from subprocess import Popen, check_output11import pandas as pd12import gzip13from os.path import splitext, basename, exists, abspath, isfile, getsize14def filesize(filename):15    if os.path.isfile(filename):16        return getsize(filename)17    else:18        return -119def test_sub_finished(filename, keyword):20    while not isfile(filename):21        time.sleep(60)22    while True:23        with open(filename) as f:24            all_lines = f.readlines()25            if len(all_lines) > 0:26                last = all_lines[-1]27                if keyword in last:28                    break29        time.sleep(60)30def main(argv=sys.argv):31    parser = argparse.ArgumentParser(description='iVariant v0.01.')32    parser.add_argument("-m", dest='run_mode', default="all",33                        help="annotation input")34    parser.add_argument("-i", dest='input', default="",35                        help="annotation input")36    args = parser.parse_args()37    old_path = abspath("./")38    env_path = './'39    gpu_path = './'40    eval_path = './'41    if args.input == '':42        fea_input = '%s/input/input.list' % (env_path)43    else:44        fea_input = args.input45    log_file = './tvar.log'46    cmd = 'rm -f %s' % (log_file)47    check_output(cmd, shell=True)48    #49    # if args.run_mode == 'pca' or args.run_mode == 'all':50    #     background_list = '/fs0/yangh8/DVAR/input/train.input'51    #     cmd1 = 'python TVar_cpu.py -m fea_train -i %s -t 8' % (background_list)52    #     print(cmd1)53    #     check_output(cmd1, shell=True)54    if args.run_mode == 'fea' or args.run_mode == 'all':55        for line in open(fea_input):56            cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())57            # check_output(cmd, shell=True)58    # if args.run_mode == 'cv' or args.run_mode == 'all':59    #     cmds = []60    #     train_input = './input/train.list'61    #     for line in open(train_input):62    #         cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())63    #         check_output(cmd, shell=True)64    #     cmd1 = "python TVar_gpu.py -m cv"65    #     cmds.append(cmd1)66    #     for cmd in cmds:67    #         check_output(cmd, shell=True)68    #     cmd = 'python TVar_cpu.py -m cv'69    #     check_output(cmd, shell=True)70    #     print("CV OK!")71    #     return72    if args.run_mode == 'train' or args.run_mode == 'all' or args.run_mode == 'train_score':73        cmds = []74        train_input = './input/train.list'75        for line in open(train_input):76            cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())77            # check_output(cmd, shell=True)78        cmd1 = "python TVar_gpu.py -m train"79        # check_output(cmd1, shell=True)80    if args.run_mode == 'score' or args.run_mode == 'all' or args.run_mode == 'train_score':81        cmds = []82        for line in open(fea_input):83            cmd = "python TVar_gpu.py -m score -i %s" % (line.rstrip())84            cmds.append(cmd)85        # for cmd in cmds:86        #     check_output(cmd, shell=True)87    # if args.run_mode == 'rare' or args.run_mode == 'all' or args.run_mode == 'train_score':88    #     clinvar_input = './input/rare.input'89    #     for line in open(clinvar_input):90    #         cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())91    #         #check_output(cmd, shell=True)92    #     cmds = []93    #     for line in open(clinvar_input):94    #         tissue = basename(line.rstrip()).replace("_rare_neg.gz", "")95    #         tissue = tissue.replace("_rare_pos.gz", "")96    #         cmd = "python TVar_gpu.py -m rare -n %s -i %s" % (tissue, line.rstrip())97    #         cmds.append(cmd)98    #     for cmd in cmds:99    #         check_output(cmd, shell=True)100    #     compare_files = []101    #     cmd = "rm -f ./eval/rare.log"102    #     check_output(cmd, shell=True)103    #     for line in open(clinvar_input):104    #         base_file = splitext(basename(line.rstrip()))[0]105    #         score_file = './score/' + base_file + '.tvar'106    #         compare_files.append(score_file)107    #         if len(compare_files) == 2:108    #             cmd = 'Rscript TVAR_gwas_test.R -p %s -q %s >> ./eval/rare.log' % (compare_files[0], compare_files[1])109    #             check_output(cmd, shell=True)110    #             compare_files.clear()111    #112    # if args.run_mode == 'gwas' or args.run_mode == 'all' or args.run_mode == 'train_score':113    #     clinvar_input = './input/gwas.input'114    #     for line in open(clinvar_input):115    #         cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())116    #         #check_output(cmd, shell=True)117    #     cmds = []118    #     for line in open(clinvar_input):119    #         tissue = basename(line.rstrip()).replace("_gwas_neg.gz", "")120    #         tissue = tissue.replace("_gwas_pos.gz", "")121    #         cmd = "python TVar_gpu.py -m gwas -n %s -i %s" % (tissue, line.rstrip())122    #         cmds.append(cmd)123    #     for cmd in cmds:124    #         check_output(cmd, shell=True)125    #     compare_files = []126    #     cmd = ''127    #     check_output(cmd, shell=True)128    #     cmd = "rm -f ./eval/gwas.log"129    #     check_output(cmd, shell=True)130    #     for line in open(clinvar_input):131    #         base_file = splitext(basename(line.rstrip()))[0]132    #         score_file = './score/' + base_file + '.tvar'133    #         compare_files.append(score_file)134    #         if len(compare_files) == 2:135    #             cmd = 'Rscript TVAR_gwas_test.R -p %s -q %s >> ./eval/gwas.log' % (compare_files[0], compare_files[1])136    #             check_output(cmd, shell=True)137    #             compare_files.clear()138    # if args.run_mode == 'eval' or args.run_mode == 'all' or args.run_mode == 'merge':139    #     cmd = 'python remove_set.py'140    #     check_output(cmd, shell=True)141    #     cmd0 = 'python compare.py -m eval > four_sets.log'142    #     check_output(cmd0, shell=True)143    if args.run_mode == 'comp' or args.run_mode == 'all' or args.run_mode == 'train_score':144        clinvar_input = './input/rare.input'145        compare_files = []146        log_file = './eval/rare.log'147        cmd = 'rm -f %s' % (log_file)148        check_output(cmd, shell=True)149        for line in open(clinvar_input):150            base_file = splitext(basename(line.rstrip()))[0]151            score_file = './score/' + base_file + '.deepsea'152            compare_files.append(score_file)153            if len(compare_files) == 2:154                cmd = 'Rscript TVAR_gwas_test.R -p %s -q %s >> %s' % (compare_files[0], compare_files[1], log_file)155                check_output(cmd, shell=True)156                compare_files.clear()157if __name__ == "__main__":...

test_filesys.py

Source:test_filesys.py

...33            - Test two text files and verify the contents are different.34        """35        f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__diff1.txt')36        f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__diff1.txt')37        test = filesys.compare_files(file1=f1, file2=f2)38        utilities.assert_true(expected=False, test=test, msg=self._MSG1)39    def test01__compare_files__diff2(self):40        """Test the ``compare_files`` method, for different files.41        :Test:42            - Test two text files and verify the contents are different,43              although the file signatures are the same.44        """45        f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__diff2.txt')46        f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__diff2.txt')47        test = filesys.compare_files(file1=f1, file2=f2)48        utilities.assert_true(expected=False, test=test, msg=self._MSG1)49    def test01__compare_files__file_dir(self):50        """Test the ``compare_files`` method, for a file and a directory.51        :Test:52            - Pass a file and a directory into the testing method and verify53              the regular file signature test returns False.54        """55        f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__same.txt')56        f2 = self._DIR_RESRC57        test = filesys.compare_files(file1=f1, file2=f2)58        utilities.assert_true(expected=False, test=test, msg=self._MSG1)59    def test01__compare_files__line_endings(self):60        """Test the ``compare_files`` method, for the same file with different61        line engines.62        :Test:63            - Test two text files and verify the contents are same, although64              having different line endings.65        """66        f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__dos.txt')67        f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__unix.txt')68        test = filesys.compare_files(file1=f1, file2=f2, contents_only=True)69        utilities.assert_true(expected=True, test=test, msg=self._MSG1)70    def test01__compare_files__same(self):71        """Test the ``compare_files`` method, for the same files.72        :Test:73            - Test two text files and verify the contents are the same.74        """75        f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__same.txt')76        f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__same.txt')77        test = filesys.compare_files(file1=f1, file2=f2)78        utilities.assert_true(expected=True, test=test, msg=self._MSG1)79    def test01__compare_files__sig_only__true(self):80        """Test the ``compare_files`` method, testing the signature only, for81        a True result.82        :Test:83            - Test the signature only for two files, expecting a True response.84        """85        f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__same.txt')86        f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__same.txt')87        test = filesys.compare_files(file1=f1, file2=f2, sig_only=True)88        utilities.assert_true(expected=True, test=test, msg=self._MSG1)89    def test01__compare_files__sig_only__false(self):90        """Test the ``compare_files`` method, testing the signature only, for91        a False result.92        :Test:93            - Test the signature only for two files, expecting a False response.94        """95        f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__diff1.txt')96        f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__diff1.txt')97        test = filesys.compare_files(file1=f1, file2=f2, sig_only=True)98        utilities.assert_true(expected=False, test=test, msg=self._MSG1)99    def test02__sig(self):100        """Test the ``_sig`` method, to verify the returned file signature.101        :Test:102            - Test a series of files, and verify the returned signatures are103              as expected.104        """105        f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__same.txt')106        f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__diff1.txt')107        f3 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__dos.txt')108        files = [f1, f2, f3]109        exp = ((734, 32768, 33204), (734, 32768, 33204), (744, 32768, 33204))110        for f, e in zip(files, exp):111            with self.subTest(msg=f'{f=} {e=}'):...

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