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@@ -1,112 +1,112 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 | |
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8 | 8 | try: |
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9 | 9 | from queue import Empty # Py 3 |
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10 | 10 | except ImportError: |
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11 | 11 | from Queue import Empty # Py 2 |
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12 | 12 | |
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13 |
from IPython.utils.traitlets import List, Unicode |
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13 | from IPython.utils.traitlets import List, Unicode | |
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14 | 14 | |
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15 | 15 | from IPython.nbformat.v4 import output_from_msg |
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16 | 16 | from .base import Preprocessor |
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17 | 17 | from IPython.utils.traitlets import Integer |
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18 | 18 | |
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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 | ||
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28 | ||
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29 | 29 | extra_arguments = List(Unicode) |
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30 | 30 | |
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31 | 31 | def preprocess(self, nb, resources): |
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32 | 32 | from IPython.kernel import run_kernel |
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33 | 33 | kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python') |
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34 | 34 | self.log.info("Executing notebook with kernel: %s" % kernel_name) |
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35 | 35 | with run_kernel(kernel_name=kernel_name, |
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36 | 36 | extra_arguments=self.extra_arguments, |
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37 | 37 | stderr=open(os.devnull, 'w')) as kc: |
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38 | 38 | self.kc = kc |
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39 | 39 | self.kc.allow_stdin = False |
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40 | 40 | nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) |
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41 | 41 | return nb, resources |
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42 | 42 | |
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43 | 43 | def preprocess_cell(self, cell, resources, cell_index): |
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44 | 44 | """ |
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45 | 45 | Apply a transformation on each code cell. See base.py for details. |
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46 | 46 | """ |
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47 | 47 | if cell.cell_type != 'code': |
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48 | 48 | return cell, resources |
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49 | 49 | try: |
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50 | 50 | outputs = self.run_cell(cell) |
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51 | 51 | except Exception as e: |
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52 | 52 | self.log.error("failed to run cell: " + repr(e)) |
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53 | 53 | self.log.error(str(cell.source)) |
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54 | 54 | raise |
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55 | 55 | cell.outputs = outputs |
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56 | 56 | return cell, resources |
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57 | 57 | |
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58 | 58 | def run_cell(self, cell): |
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59 | 59 | msg_id = self.kc.execute(cell.source) |
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60 | 60 | self.log.debug("Executing cell:\n%s", cell.source) |
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61 | 61 | # wait for finish, with timeout |
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62 | 62 | while True: |
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63 | 63 | try: |
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64 | 64 | msg = self.kc.shell_channel.get_msg(timeout=self.timeout) |
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65 | 65 | except Empty: |
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66 | 66 | self.log.error("Timeout waiting for execute reply") |
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67 | 67 | raise |
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68 | 68 | if msg['parent_header'].get('msg_id') == msg_id: |
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69 | 69 | break |
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70 | 70 | else: |
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71 | 71 | # not our reply |
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72 | 72 | continue |
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73 | 73 | |
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74 | 74 | outs = [] |
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75 | 75 | |
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76 | 76 | while True: |
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77 | 77 | try: |
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78 | 78 | msg = self.kc.iopub_channel.get_msg(timeout=self.timeout) |
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79 | 79 | except Empty: |
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80 | 80 | self.log.warn("Timeout waiting for IOPub output") |
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81 | 81 | break |
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82 | 82 | if msg['parent_header'].get('msg_id') != msg_id: |
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83 | 83 | # not an output from our execution |
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84 | 84 | continue |
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85 | 85 | |
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86 | 86 | msg_type = msg['msg_type'] |
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87 | 87 | self.log.debug("output: %s", msg_type) |
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88 | 88 | content = msg['content'] |
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89 | 89 | |
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90 | 90 | # set the prompt number for the input and the output |
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91 | 91 | if 'execution_count' in content: |
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92 | 92 | cell['execution_count'] = content['execution_count'] |
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93 | 93 | |
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94 | 94 | if msg_type == 'status': |
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95 | 95 | if content['execution_state'] == 'idle': |
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96 | 96 | break |
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97 | 97 | else: |
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98 | 98 | continue |
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99 | 99 | elif msg_type == 'execute_input': |
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100 | 100 | continue |
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101 | 101 | elif msg_type == 'clear_output': |
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102 | 102 | outs = [] |
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103 | 103 | continue |
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104 | 104 | |
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105 | 105 | try: |
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106 | 106 | out = output_from_msg(msg) |
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107 | 107 | except ValueError: |
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108 | 108 | self.log.error("unhandled iopub msg: " + msg_type) |
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109 | 109 | else: |
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110 | 110 | outs.append(out) |
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111 | 111 | |
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112 | 112 | return outs |
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