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@@ -1,115 +1,117 b'' | |||||
1 | """Module containing a preprocessor that removes the outputs from code cells""" |
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1 | """Module containing a preprocessor that removes the outputs from code cells""" | |
2 |
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2 | |||
3 | # Copyright (c) IPython Development Team. |
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3 | # Copyright (c) IPython Development Team. | |
4 | # Distributed under the terms of the Modified BSD License. |
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4 | # Distributed under the terms of the Modified BSD License. | |
5 |
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5 | |||
6 | import os |
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6 | import os | |
7 |
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7 | |||
8 | try: |
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8 | try: | |
9 | from queue import Empty # Py 3 |
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9 | from queue import Empty # Py 3 | |
10 | except ImportError: |
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10 | except ImportError: | |
11 | from Queue import Empty # Py 2 |
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11 | from Queue import Empty # Py 2 | |
12 |
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12 | |||
13 | from IPython.utils.traitlets import List, Unicode |
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13 | from IPython.utils.traitlets import List, Unicode | |
14 |
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14 | |||
15 | from IPython.nbformat.v4 import output_from_msg |
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15 | from IPython.nbformat.v4 import output_from_msg | |
16 | from .base import Preprocessor |
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16 | from .base import Preprocessor | |
17 | from IPython.utils.traitlets import Integer |
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17 | from IPython.utils.traitlets import Integer | |
18 |
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18 | |||
19 |
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19 | |||
20 | class ExecutePreprocessor(Preprocessor): |
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20 | class ExecutePreprocessor(Preprocessor): | |
21 | """ |
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21 | """ | |
22 | Executes all the cells in a notebook |
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22 | Executes all the cells in a notebook | |
23 | """ |
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23 | """ | |
24 |
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24 | |||
25 | timeout = Integer(30, config=True, |
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25 | timeout = Integer(30, config=True, | |
26 | help="The time to wait (in seconds) for output from executions." |
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26 | help="The time to wait (in seconds) for output from executions." | |
27 | ) |
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27 | ) | |
28 |
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28 | |||
29 | extra_arguments = List(Unicode) |
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29 | extra_arguments = List(Unicode) | |
30 |
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30 | |||
31 | def preprocess(self, nb, resources): |
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31 | def preprocess(self, nb, resources): | |
32 |
path = resources.get('metadata', {}).get('path', |
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32 | path = resources.get('metadata', {}).get('path', '') | |
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33 | if path == '': | |||
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34 | path = None | |||
33 |
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35 | |||
34 | from IPython.kernel import run_kernel |
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36 | from IPython.kernel import run_kernel | |
35 | kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python') |
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37 | kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python') | |
36 | self.log.info("Executing notebook with kernel: %s" % kernel_name) |
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38 | self.log.info("Executing notebook with kernel: %s" % kernel_name) | |
37 | with run_kernel(kernel_name=kernel_name, |
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39 | with run_kernel(kernel_name=kernel_name, | |
38 | extra_arguments=self.extra_arguments, |
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40 | extra_arguments=self.extra_arguments, | |
39 | stderr=open(os.devnull, 'w'), |
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41 | stderr=open(os.devnull, 'w'), | |
40 | cwd=path) as kc: |
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42 | cwd=path) as kc: | |
41 | self.kc = kc |
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43 | self.kc = kc | |
42 | self.kc.allow_stdin = False |
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44 | self.kc.allow_stdin = False | |
43 | nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) |
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45 | nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) | |
44 | return nb, resources |
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46 | return nb, resources | |
45 |
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47 | |||
46 | def preprocess_cell(self, cell, resources, cell_index): |
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48 | def preprocess_cell(self, cell, resources, cell_index): | |
47 | """ |
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49 | """ | |
48 | Apply a transformation on each code cell. See base.py for details. |
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50 | Apply a transformation on each code cell. See base.py for details. | |
49 | """ |
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51 | """ | |
50 | if cell.cell_type != 'code': |
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52 | if cell.cell_type != 'code': | |
51 | return cell, resources |
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53 | return cell, resources | |
52 | try: |
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54 | try: | |
53 | outputs = self.run_cell(cell) |
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55 | outputs = self.run_cell(cell) | |
54 | except Exception as e: |
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56 | except Exception as e: | |
55 | self.log.error("failed to run cell: " + repr(e)) |
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57 | self.log.error("failed to run cell: " + repr(e)) | |
56 | self.log.error(str(cell.source)) |
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58 | self.log.error(str(cell.source)) | |
57 | raise |
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59 | raise | |
58 | cell.outputs = outputs |
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60 | cell.outputs = outputs | |
59 | return cell, resources |
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61 | return cell, resources | |
60 |
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62 | |||
61 | def run_cell(self, cell): |
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63 | def run_cell(self, cell): | |
62 | msg_id = self.kc.execute(cell.source) |
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64 | msg_id = self.kc.execute(cell.source) | |
63 | self.log.debug("Executing cell:\n%s", cell.source) |
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65 | self.log.debug("Executing cell:\n%s", cell.source) | |
64 | # wait for finish, with timeout |
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66 | # wait for finish, with timeout | |
65 | while True: |
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67 | while True: | |
66 | try: |
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68 | try: | |
67 | msg = self.kc.shell_channel.get_msg(timeout=self.timeout) |
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69 | msg = self.kc.shell_channel.get_msg(timeout=self.timeout) | |
68 | except Empty: |
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70 | except Empty: | |
69 | self.log.error("Timeout waiting for execute reply") |
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71 | self.log.error("Timeout waiting for execute reply") | |
70 | raise |
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72 | raise | |
71 | if msg['parent_header'].get('msg_id') == msg_id: |
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73 | if msg['parent_header'].get('msg_id') == msg_id: | |
72 | break |
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74 | break | |
73 | else: |
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75 | else: | |
74 | # not our reply |
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76 | # not our reply | |
75 | continue |
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77 | continue | |
76 |
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78 | |||
77 | outs = [] |
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79 | outs = [] | |
78 |
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80 | |||
79 | while True: |
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81 | while True: | |
80 | try: |
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82 | try: | |
81 | msg = self.kc.iopub_channel.get_msg(timeout=self.timeout) |
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83 | msg = self.kc.iopub_channel.get_msg(timeout=self.timeout) | |
82 | except Empty: |
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84 | except Empty: | |
83 | self.log.warn("Timeout waiting for IOPub output") |
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85 | self.log.warn("Timeout waiting for IOPub output") | |
84 | break |
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86 | break | |
85 | if msg['parent_header'].get('msg_id') != msg_id: |
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87 | if msg['parent_header'].get('msg_id') != msg_id: | |
86 | # not an output from our execution |
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88 | # not an output from our execution | |
87 | continue |
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89 | continue | |
88 |
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90 | |||
89 | msg_type = msg['msg_type'] |
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91 | msg_type = msg['msg_type'] | |
90 | self.log.debug("output: %s", msg_type) |
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92 | self.log.debug("output: %s", msg_type) | |
91 | content = msg['content'] |
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93 | content = msg['content'] | |
92 |
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94 | |||
93 | # set the prompt number for the input and the output |
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95 | # set the prompt number for the input and the output | |
94 | if 'execution_count' in content: |
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96 | if 'execution_count' in content: | |
95 | cell['execution_count'] = content['execution_count'] |
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97 | cell['execution_count'] = content['execution_count'] | |
96 |
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98 | |||
97 | if msg_type == 'status': |
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99 | if msg_type == 'status': | |
98 | if content['execution_state'] == 'idle': |
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100 | if content['execution_state'] == 'idle': | |
99 | break |
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101 | break | |
100 | else: |
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102 | else: | |
101 | continue |
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103 | continue | |
102 | elif msg_type == 'execute_input': |
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104 | elif msg_type == 'execute_input': | |
103 | continue |
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105 | continue | |
104 | elif msg_type == 'clear_output': |
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106 | elif msg_type == 'clear_output': | |
105 | outs = [] |
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107 | outs = [] | |
106 | continue |
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108 | continue | |
107 |
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109 | |||
108 | try: |
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110 | try: | |
109 | out = output_from_msg(msg) |
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111 | out = output_from_msg(msg) | |
110 | except ValueError: |
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112 | except ValueError: | |
111 | self.log.error("unhandled iopub msg: " + msg_type) |
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113 | self.log.error("unhandled iopub msg: " + msg_type) | |
112 | else: |
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114 | else: | |
113 | outs.append(out) |
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115 | outs.append(out) | |
114 |
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116 | |||
115 | return outs |
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117 | return outs |
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