Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/verify/__init__.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Module of utilities for verifying test results.""" |
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2 |
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3 import difflib |
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4 import filecmp |
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5 import hashlib |
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6 import json |
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7 import logging |
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8 import os |
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9 import os.path |
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10 import re |
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11 import shutil |
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12 import tempfile |
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13 |
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14 try: |
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15 import pysam |
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16 except ImportError: |
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17 pysam = None |
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18 |
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19 from galaxy.tool_util.parser.util import ( |
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20 DEFAULT_DELTA, |
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21 DEFAULT_DELTA_FRAC |
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22 ) |
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23 from galaxy.util import unicodify |
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24 from galaxy.util.compression_utils import get_fileobj |
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25 from .asserts import verify_assertions |
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26 from .test_data import TestDataResolver |
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27 |
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28 log = logging.getLogger(__name__) |
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29 |
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30 DEFAULT_TEST_DATA_RESOLVER = TestDataResolver() |
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31 |
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32 |
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33 def verify( |
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34 item_label, |
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35 output_content, |
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36 attributes, |
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37 filename=None, |
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38 get_filecontent=None, |
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39 get_filename=None, |
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40 keep_outputs_dir=None, |
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41 verify_extra_files=None, |
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42 mode='file', |
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43 ): |
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44 """Verify the content of a test output using test definitions described by attributes. |
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45 |
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46 Throw an informative assertion error if any of these tests fail. |
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47 """ |
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48 if get_filename is None: |
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49 if get_filecontent is None: |
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50 get_filecontent = DEFAULT_TEST_DATA_RESOLVER.get_filecontent |
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51 |
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52 def get_filename(filename): |
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53 file_content = get_filecontent(filename) |
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54 local_name = make_temp_fname(fname=filename) |
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55 with open(local_name, 'wb') as f: |
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56 f.write(file_content) |
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57 return local_name |
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58 |
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59 # Check assertions... |
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60 assertions = attributes.get("assert_list", None) |
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61 if attributes is not None and assertions is not None: |
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62 try: |
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63 verify_assertions(output_content, attributes["assert_list"]) |
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64 except AssertionError as err: |
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65 errmsg = '%s different than expected\n' % (item_label) |
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66 errmsg += unicodify(err) |
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67 raise AssertionError(errmsg) |
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68 |
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69 # Verify checksum attributes... |
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70 # works with older Galaxy style md5=<expected_sum> or cwltest |
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71 # style checksum=<hash_type>$<hash>. |
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72 expected_checksum_type = None |
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73 expected_checksum = None |
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74 if attributes is not None and attributes.get("md5", None) is not None: |
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75 expected_checksum_type = "md5" |
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76 expected_checksum = attributes.get("md5") |
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77 elif attributes is not None and attributes.get("checksum", None) is not None: |
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78 checksum_value = attributes.get("checksum", None) |
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79 expected_checksum_type, expected_checksum = checksum_value.split("$", 1) |
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80 |
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81 if expected_checksum_type: |
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82 try: |
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83 _verify_checksum(output_content, expected_checksum_type, expected_checksum) |
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84 except AssertionError as err: |
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85 errmsg = '%s different than expected\n' % (item_label) |
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86 errmsg += unicodify(err) |
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87 raise AssertionError(errmsg) |
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88 |
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89 if attributes is None: |
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90 attributes = {} |
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91 |
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92 # expected object might be None, so don't pull unless available |
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93 has_expected_object = 'object' in attributes |
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94 if has_expected_object: |
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95 assert filename is None |
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96 expected_object = attributes.get('object') |
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97 actual_object = json.loads(output_content) |
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98 |
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99 expected_object_type = type(expected_object) |
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100 actual_object_type = type(actual_object) |
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101 |
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102 if expected_object_type != actual_object_type: |
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103 message = f"Type mismatch between expected object ({expected_object_type}) and actual object ({actual_object_type})" |
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104 raise AssertionError(message) |
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105 |
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106 if expected_object != actual_object: |
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107 message = f"Expected object ({expected_object}) does not match actual object ({actual_object})" |
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108 raise AssertionError(message) |
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109 |
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110 elif filename is not None: |
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111 temp_name = make_temp_fname(fname=filename) |
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112 with open(temp_name, 'wb') as f: |
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113 f.write(output_content) |
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114 |
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115 # If the server's env has GALAXY_TEST_SAVE, save the output file to that |
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116 # directory. |
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117 # This needs to be done before the call to `get_filename()` because that |
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118 # may raise an exception if `filename` does not exist (e.g. when |
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119 # generating a tool output file from scratch with |
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120 # `planemo test --update_test_data`). |
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121 if keep_outputs_dir: |
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122 ofn = os.path.join(keep_outputs_dir, filename) |
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123 out_dir = os.path.dirname(ofn) |
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124 if not os.path.exists(out_dir): |
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125 os.makedirs(out_dir) |
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126 log.debug('keep_outputs_dir: %s, ofn: %s', keep_outputs_dir, ofn) |
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127 try: |
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128 shutil.copy(temp_name, ofn) |
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129 except Exception: |
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130 log.exception('Could not save output file %s to %s', temp_name, ofn) |
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131 else: |
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132 log.debug('## GALAXY_TEST_SAVE=%s. saved %s', keep_outputs_dir, ofn) |
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133 |
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134 if mode == 'directory': |
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135 # if verifying a file inside a extra_files_path directory |
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136 # filename already point to a file that exists on disk |
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137 local_name = filename |
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138 else: |
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139 local_name = get_filename(filename) |
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140 |
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141 compare = attributes.get('compare', 'diff') |
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142 try: |
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143 if attributes.get('ftype', None) in ['bam', 'qname_sorted.bam', 'qname_input_sorted.bam', 'unsorted.bam', 'cram']: |
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144 try: |
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145 local_fh, temp_name = _bam_to_sam(local_name, temp_name) |
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146 local_name = local_fh.name |
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147 except Exception as e: |
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148 log.warning("%s. Will compare BAM files", unicodify(e)) |
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149 if compare == 'diff': |
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150 files_diff(local_name, temp_name, attributes=attributes) |
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151 elif compare == 're_match': |
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152 files_re_match(local_name, temp_name, attributes=attributes) |
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153 elif compare == 're_match_multiline': |
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154 files_re_match_multiline(local_name, temp_name, attributes=attributes) |
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155 elif compare == 'sim_size': |
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156 files_delta(local_name, temp_name, attributes=attributes) |
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157 elif compare == "contains": |
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158 files_contains(local_name, temp_name, attributes=attributes) |
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159 else: |
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160 raise Exception('Unimplemented Compare type: %s' % compare) |
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161 except AssertionError as err: |
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162 errmsg = f'{item_label} different than expected, difference (using {compare}):\n' |
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163 errmsg += f"( {local_name} v. {temp_name} )\n" |
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164 errmsg += unicodify(err) |
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165 raise AssertionError(errmsg) |
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166 finally: |
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167 if 'GALAXY_TEST_NO_CLEANUP' not in os.environ: |
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168 os.remove(temp_name) |
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169 |
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170 if verify_extra_files: |
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171 extra_files = attributes.get('extra_files', None) |
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172 if extra_files: |
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173 verify_extra_files(extra_files) |
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174 |
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175 |
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176 def make_temp_fname(fname=None): |
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177 """Safe temp name - preserve the file extension for tools that interpret it.""" |
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178 suffix = os.path.split(fname)[-1] # ignore full path |
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179 with tempfile.NamedTemporaryFile(prefix='tmp', suffix=suffix, delete=False) as temp: |
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180 return temp.name |
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181 |
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182 |
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183 def _bam_to_sam(local_name, temp_name): |
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184 temp_local = tempfile.NamedTemporaryFile(suffix='.sam', prefix='local_bam_converted_to_sam_') |
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185 with tempfile.NamedTemporaryFile(suffix='.sam', prefix='history_bam_converted_to_sam_', delete=False) as temp: |
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186 try: |
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187 pysam.view('-h', '-o%s' % temp_local.name, local_name) |
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188 except Exception as e: |
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189 msg = "Converting local (test-data) BAM to SAM failed: %s" % unicodify(e) |
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190 raise Exception(msg) |
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191 try: |
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192 pysam.view('-h', '-o%s' % temp.name, temp_name) |
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193 except Exception as e: |
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194 msg = "Converting history BAM to SAM failed: %s" % unicodify(e) |
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195 raise Exception(msg) |
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196 os.remove(temp_name) |
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197 return temp_local, temp.name |
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198 |
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199 |
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200 def _verify_checksum(data, checksum_type, expected_checksum_value): |
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201 if checksum_type not in ["md5", "sha1", "sha256", "sha512"]: |
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202 raise Exception("Unimplemented hash algorithm [%s] encountered." % checksum_type) |
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203 |
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204 h = hashlib.new(checksum_type) |
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205 h.update(data) |
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206 actual_checksum_value = h.hexdigest() |
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207 if expected_checksum_value != actual_checksum_value: |
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208 template = "Output checksum [%s] does not match expected [%s] (using hash algorithm %s)." |
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209 message = template % (actual_checksum_value, expected_checksum_value, checksum_type) |
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210 raise AssertionError(message) |
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211 |
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212 |
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213 def files_delta(file1, file2, attributes=None): |
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214 """Check the contents of 2 files for size differences.""" |
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215 if attributes is None: |
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216 attributes = {} |
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217 delta = attributes.get('delta', DEFAULT_DELTA) |
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218 delta_frac = attributes.get('delta_frac', DEFAULT_DELTA_FRAC) |
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219 s1 = os.path.getsize(file1) |
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220 s2 = os.path.getsize(file2) |
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221 if abs(s1 - s2) > delta: |
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222 raise AssertionError('Files %s=%db but %s=%db - compare by size (delta=%s) failed' % (file1, s1, file2, s2, delta)) |
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223 if delta_frac is not None and not (s1 - (s1 * delta_frac) <= s2 <= s1 + (s1 * delta_frac)): |
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224 raise AssertionError('Files %s=%db but %s=%db - compare by size (delta_frac=%s) failed' % (file1, s1, file2, s2, delta_frac)) |
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225 |
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226 |
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227 def files_diff(file1, file2, attributes=None): |
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228 """Check the contents of 2 files for differences.""" |
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229 def get_lines_diff(diff): |
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230 count = 0 |
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231 for line in diff: |
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232 if (line.startswith('+') and not line.startswith('+++')) or (line.startswith('-') and not line.startswith('---')): |
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233 count += 1 |
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234 return count |
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235 |
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236 if not filecmp.cmp(file1, file2, shallow=False): |
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237 if attributes is None: |
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238 attributes = {} |
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239 decompress = attributes.get("decompress", None) |
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240 if decompress: |
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241 # None means all compressed formats are allowed |
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242 compressed_formats = None |
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243 else: |
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244 compressed_formats = [] |
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245 is_pdf = False |
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246 try: |
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247 with get_fileobj(file2, compressed_formats=compressed_formats) as fh: |
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248 history_data = fh.readlines() |
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249 with get_fileobj(file1, compressed_formats=compressed_formats) as fh: |
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250 local_file = fh.readlines() |
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251 except UnicodeDecodeError: |
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252 if file1.endswith('.pdf') or file2.endswith('.pdf'): |
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253 is_pdf = True |
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254 # Replace non-Unicode characters using unicodify(), |
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255 # difflib.unified_diff doesn't work on list of bytes |
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256 history_data = [unicodify(l) for l in get_fileobj(file2, mode='rb', compressed_formats=compressed_formats)] |
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257 local_file = [unicodify(l) for l in get_fileobj(file1, mode='rb', compressed_formats=compressed_formats)] |
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258 else: |
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259 raise AssertionError("Binary data detected, not displaying diff") |
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260 if attributes.get('sort', False): |
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261 local_file.sort() |
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262 history_data.sort() |
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263 allowed_diff_count = int(attributes.get('lines_diff', 0)) |
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264 diff = list(difflib.unified_diff(local_file, history_data, "local_file", "history_data")) |
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265 diff_lines = get_lines_diff(diff) |
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266 if diff_lines > allowed_diff_count: |
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267 if 'GALAXY_TEST_RAW_DIFF' in os.environ: |
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268 diff_slice = diff |
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269 else: |
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270 if len(diff) < 60: |
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271 diff_slice = diff[0:40] |
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272 else: |
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273 diff_slice = diff[:25] + ["********\n", "*SNIP *\n", "********\n"] + diff[-25:] |
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274 # FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff |
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275 # due to unknown desired behavior when used in conjunction with a non-zero lines_diff |
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276 # PDF forgiveness can probably be handled better by not special casing by __extension__ here |
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277 # and instead using lines_diff or a regular expression matching |
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278 # or by creating and using a specialized pdf comparison function |
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279 if is_pdf: |
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280 # PDF files contain creation dates, modification dates, ids and descriptions that change with each |
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281 # new file, so we need to handle these differences. As long as the rest of the PDF file does |
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282 # not differ we're ok. |
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283 valid_diff_strs = ['description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator'] |
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284 valid_diff = False |
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285 invalid_diff_lines = 0 |
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286 for line in diff_slice: |
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287 # Make sure to lower case strings before checking. |
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288 line = line.lower() |
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289 # Diff lines will always start with a + or - character, but handle special cases: '--- local_file \n', '+++ history_data \n' |
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290 if (line.startswith('+') or line.startswith('-')) and line.find('local_file') < 0 and line.find('history_data') < 0: |
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291 for vdf in valid_diff_strs: |
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292 if line.find(vdf) < 0: |
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293 valid_diff = False |
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294 else: |
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295 valid_diff = True |
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296 # Stop checking as soon as we know we have a valid difference |
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297 break |
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298 if not valid_diff: |
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299 invalid_diff_lines += 1 |
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300 log.info("## files diff on '%s' and '%s': lines_diff = %d, found diff = %d, found pdf invalid diff = %d" % (file1, file2, allowed_diff_count, diff_lines, invalid_diff_lines)) |
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301 if invalid_diff_lines > allowed_diff_count: |
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302 # Print out diff_slice so we can see what failed |
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303 log.info("###### diff_slice ######") |
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304 raise AssertionError("".join(diff_slice)) |
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305 else: |
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306 log.info("## files diff on '%s' and '%s': lines_diff = %d, found diff = %d" % (file1, file2, allowed_diff_count, diff_lines)) |
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307 raise AssertionError("".join(diff_slice)) |
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308 |
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309 |
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310 def files_re_match(file1, file2, attributes=None): |
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311 """Check the contents of 2 files for differences using re.match.""" |
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312 join_char = '' |
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313 to_strip = os.linesep |
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314 try: |
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315 with open(file2, encoding='utf-8') as fh: |
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316 history_data = fh.readlines() |
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317 with open(file1, encoding='utf-8') as fh: |
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318 local_file = fh.readlines() |
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319 except UnicodeDecodeError: |
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320 join_char = b'' |
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321 to_strip = os.linesep.encode('utf-8') |
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322 with open(file2, 'rb') as fh: |
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323 history_data = fh.readlines() |
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324 with open(file1, 'rb') as fh: |
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325 local_file = fh.readlines() |
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326 assert len(local_file) == len(history_data), 'Data File and Regular Expression File contain a different number of lines (%d != %d)\nHistory Data (first 40 lines):\n%s' % (len(local_file), len(history_data), join_char.join(history_data[:40])) |
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327 if attributes is None: |
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328 attributes = {} |
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329 if attributes.get('sort', False): |
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330 history_data.sort() |
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331 lines_diff = int(attributes.get('lines_diff', 0)) |
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332 line_diff_count = 0 |
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333 diffs = [] |
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334 for regex_line, data_line in zip(local_file, history_data): |
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335 regex_line = regex_line.rstrip(to_strip) |
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336 data_line = data_line.rstrip(to_strip) |
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337 if not re.match(regex_line, data_line): |
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338 line_diff_count += 1 |
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339 diffs.append(f'Regular Expression: {regex_line}, Data file: {data_line}\n') |
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340 if line_diff_count > lines_diff: |
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341 raise AssertionError("Regular expression did not match data file (allowed variants=%i):\n%s" % (lines_diff, "".join(diffs))) |
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342 |
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343 |
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344 def files_re_match_multiline(file1, file2, attributes=None): |
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345 """Check the contents of 2 files for differences using re.match in multiline mode.""" |
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346 join_char = '' |
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347 try: |
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348 with open(file2, encoding='utf-8') as fh: |
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349 history_data = fh.readlines() |
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350 with open(file1, encoding='utf-8') as fh: |
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351 local_file = fh.read() |
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352 except UnicodeDecodeError: |
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353 join_char = b'' |
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354 with open(file2, 'rb') as fh: |
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355 history_data = fh.readlines() |
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356 with open(file1, 'rb') as fh: |
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357 local_file = fh.read() |
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358 if attributes is None: |
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359 attributes = {} |
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360 if attributes.get('sort', False): |
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361 history_data.sort() |
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362 history_data = join_char.join(history_data) |
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363 # lines_diff not applicable to multiline matching |
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364 assert re.match(local_file, history_data, re.MULTILINE), "Multiline Regular expression did not match data file" |
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365 |
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366 |
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367 def files_contains(file1, file2, attributes=None): |
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368 """Check the contents of file2 for substrings found in file1, on a per-line basis.""" |
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369 # TODO: allow forcing ordering of contains |
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370 to_strip = os.linesep |
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371 try: |
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372 with open(file2, encoding='utf-8') as fh: |
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373 history_data = fh.read() |
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374 with open(file1, encoding='utf-8') as fh: |
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375 local_file = fh.readlines() |
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376 except UnicodeDecodeError: |
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377 to_strip = os.linesep.encode('utf-8') |
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378 with open(file2, 'rb') as fh: |
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379 history_data = fh.read() |
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380 with open(file1, 'rb') as fh: |
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381 local_file = fh.readlines() |
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382 if attributes is None: |
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383 attributes = {} |
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384 lines_diff = int(attributes.get('lines_diff', 0)) |
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385 line_diff_count = 0 |
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386 for contains in local_file: |
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387 contains = contains.rstrip(to_strip) |
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388 if contains not in history_data: |
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389 line_diff_count += 1 |
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390 if line_diff_count > lines_diff: |
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391 raise AssertionError("Failed to find '%s' in history data. (lines_diff=%i)" % (contains, lines_diff)) |