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