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@@ -1,165 +1,142 b'' | |||
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1 | 1 | """Module containing a preprocessor that removes the outputs from code cells""" |
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2 | 2 | |
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3 | 3 | # Copyright (c) IPython Development Team. |
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4 | 4 | # Distributed under the terms of the Modified BSD License. |
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5 | 5 | |
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6 | 6 | import os |
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7 | 7 | import sys |
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8 | 8 | |
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9 | 9 | try: |
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10 | 10 | from queue import Empty # Py 3 |
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11 | 11 | except ImportError: |
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12 | 12 | from Queue import Empty # Py 2 |
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13 | 13 | |
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14 | 14 | from IPython.utils.traitlets import List, Unicode |
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15 | 15 | |
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16 | 16 | from IPython.nbformat.current import reads, NotebookNode, writes |
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17 | 17 | from .base import Preprocessor |
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18 | 18 | from IPython.utils.traitlets import Integer |
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19 | 19 | |
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20 | 20 | class ExecutePreprocessor(Preprocessor): |
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21 | 21 | """ |
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22 | 22 | Executes all the cells in a notebook |
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23 | 23 | """ |
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24 | 24 | |
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25 | 25 | timeout = Integer(30, config=True, |
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26 | 26 | help="The time to wait (in seconds) for output from executions." |
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27 | 27 | ) |
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28 | 28 | # FIXME: to be removed with nbformat v4 |
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29 | 29 | # map msg_type to v3 output_type |
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30 | 30 | msg_type_map = { |
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31 | 31 | "error" : "pyerr", |
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32 | 32 | "execute_result" : "pyout", |
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33 | 33 | } |
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34 | 34 | |
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35 | 35 | # FIXME: to be removed with nbformat v4 |
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36 | 36 | # map mime-type to v3 mime-type keys |
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37 | 37 | mime_map = { |
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38 | 38 | "text/plain" : "text", |
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39 | 39 | "text/html" : "html", |
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40 | 40 | "image/svg+xml" : "svg", |
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41 | 41 | "image/png" : "png", |
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42 | 42 | "image/jpeg" : "jpeg", |
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43 | 43 | "text/latex" : "latex", |
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44 | 44 | "application/json" : "json", |
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45 | 45 | "application/javascript" : "javascript", |
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46 | 46 | } |
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47 | 47 | |
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48 | 48 | extra_arguments = List(Unicode) |
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49 | ||
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50 | def _create_client(self): | |
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51 | from IPython.kernel import KernelManager | |
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52 | self.km = KernelManager() | |
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53 | self.km.write_connection_file() | |
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54 | self.kc = self.km.client() | |
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55 | self.kc.start_channels() | |
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56 | self.km.start_kernel(extra_arguments=self.extra_arguments, stderr=open(os.devnull, 'w')) | |
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57 | self.iopub = self.kc.iopub_channel | |
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58 | self.shell = self.kc.shell_channel | |
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59 | self.shell.kernel_info() | |
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60 | try: | |
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61 | self.shell.get_msg(timeout=self.timeout) | |
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62 | except Empty: | |
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63 | self.log.error("Timeout waiting for kernel_info reply") | |
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64 | raise | |
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65 | # flush IOPub | |
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66 | while True: | |
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67 | try: | |
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68 | self.iopub.get_msg(block=True, timeout=0.25) | |
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69 | except Empty: | |
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70 | break | |
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71 | ||
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72 | def _shutdown_client(self): | |
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73 | self.kc.stop_channels() | |
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74 | self.km.shutdown_kernel() | |
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75 | del self.km | |
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76 | 49 | |
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77 | 50 | def preprocess(self, nb, resources): |
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78 | self._create_client() | |
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79 | nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) | |
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80 | self._shutdown_client() | |
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51 | from IPython.kernel import run_kernel | |
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52 | kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python') | |
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53 | with run_kernel(kernel_name=kernel_name, | |
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54 | extra_arguments=self.extra_arguments, | |
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55 | stderr=open(os.devnull, 'w')) as kc: | |
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56 | self.kc = kc | |
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57 | nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) | |
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81 | 58 | return nb, resources |
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82 | 59 | |
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83 | 60 | def preprocess_cell(self, cell, resources, cell_index): |
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84 | 61 | """ |
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85 | 62 | Apply a transformation on each code cell. See base.py for details. |
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86 | 63 | """ |
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87 | 64 | if cell.cell_type != 'code': |
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88 | 65 | return cell, resources |
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89 | 66 | try: |
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90 | outputs = self.run_cell(self.shell, self.iopub, cell) | |
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67 | outputs = self.run_cell(self.kc.shell_channel, self.kc.iopub_channel, cell) | |
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91 | 68 | except Exception as e: |
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92 | 69 | self.log.error("failed to run cell: " + repr(e)) |
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93 | 70 | self.log.error(str(cell.input)) |
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94 | 71 | raise |
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95 | 72 | cell.outputs = outputs |
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96 | 73 | return cell, resources |
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97 | 74 | |
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98 | 75 | def run_cell(self, shell, iopub, cell): |
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99 | 76 | msg_id = shell.execute(cell.input) |
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100 | 77 | self.log.debug("Executing cell:\n%s", cell.input) |
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101 | 78 | # wait for finish, with timeout |
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102 | 79 | while True: |
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103 | 80 | try: |
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104 | 81 | msg = shell.get_msg(timeout=self.timeout) |
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105 | 82 | except Empty: |
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106 | 83 | self.log.error("Timeout waiting for execute reply") |
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107 | 84 | raise |
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108 | 85 | if msg['parent_header'].get('msg_id') == msg_id: |
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109 | 86 | break |
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110 | 87 | else: |
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111 | 88 | # not our reply |
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112 | 89 | continue |
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113 | 90 | |
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114 | 91 | outs = [] |
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115 | 92 | |
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116 | 93 | while True: |
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117 | 94 | try: |
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118 | 95 | msg = iopub.get_msg(timeout=self.timeout) |
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119 | 96 | except Empty: |
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120 | 97 | self.log.warn("Timeout waiting for IOPub output") |
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121 | 98 | break |
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122 | 99 | if msg['parent_header'].get('msg_id') != msg_id: |
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123 | 100 | # not an output from our execution |
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124 | 101 | continue |
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125 | 102 | |
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126 | 103 | msg_type = msg['msg_type'] |
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127 | 104 | self.log.debug("output: %s", msg_type) |
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128 | 105 | content = msg['content'] |
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129 | 106 | if msg_type == 'status': |
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130 | 107 | if content['execution_state'] == 'idle': |
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131 | 108 | break |
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132 | 109 | else: |
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133 | 110 | continue |
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134 | 111 | elif msg_type in {'execute_input', 'pyin'}: |
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135 | 112 | continue |
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136 | 113 | elif msg_type == 'clear_output': |
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137 | 114 | outs = [] |
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138 | 115 | continue |
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139 | 116 | |
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140 | 117 | out = NotebookNode(output_type=self.msg_type_map.get(msg_type, msg_type)) |
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141 | 118 | |
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142 | 119 | # set the prompt number for the input and the output |
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143 | 120 | if 'execution_count' in content: |
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144 | 121 | cell['prompt_number'] = content['execution_count'] |
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145 | 122 | out.prompt_number = content['execution_count'] |
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146 | 123 | |
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147 | 124 | if msg_type == 'stream': |
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148 | 125 | out.stream = content['name'] |
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149 | 126 | out.text = content['data'] |
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150 | 127 | elif msg_type in ('display_data', 'execute_result'): |
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151 | 128 | out['metadata'] = content['metadata'] |
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152 | 129 | for mime, data in content['data'].items(): |
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153 | 130 | # map mime-type keys to nbformat v3 keys |
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154 | 131 | # this will be unnecessary in nbformat v4 |
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155 | 132 | key = self.mime_map.get(mime, mime) |
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156 | 133 | out[key] = data |
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157 | 134 | elif msg_type == 'error': |
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158 | 135 | out.ename = content['ename'] |
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159 | 136 | out.evalue = content['evalue'] |
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160 | 137 | out.traceback = content['traceback'] |
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161 | 138 | else: |
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162 | 139 | self.log.error("unhandled iopub msg: " + msg_type) |
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163 | 140 | |
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164 | 141 | outs.append(out) |
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165 | 142 | return outs |
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