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"""Module containing a preprocessor that removes the outputs from code cells"""
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# Copyright (c) IPython Development Team.
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# Distributed under the terms of the Modified BSD License.
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import os
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try:
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from queue import Empty # Py 3
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except ImportError:
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from Queue import Empty # Py 2
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from IPython.utils.traitlets import List, Unicode
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from IPython.nbformat.v4 import output_from_msg
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from .base import Preprocessor
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from IPython.utils.traitlets import Integer
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class ExecutePreprocessor(Preprocessor):
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"""
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Executes all the cells in a notebook
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"""
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timeout = Integer(30, config=True,
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help="The time to wait (in seconds) for output from executions."
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)
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extra_arguments = List(Unicode)
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def preprocess(self, nb, resources):
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from IPython.kernel import run_kernel
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kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python')
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self.log.info("Executing notebook with kernel: %s" % kernel_name)
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with run_kernel(kernel_name=kernel_name,
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extra_arguments=self.extra_arguments,
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stderr=open(os.devnull, 'w')) as kc:
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self.kc = kc
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nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
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return nb, resources
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def preprocess_cell(self, cell, resources, cell_index):
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"""
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Apply a transformation on each code cell. See base.py for details.
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"""
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if cell.cell_type != 'code':
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return cell, resources
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try:
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outputs = self.run_cell(self.kc.shell_channel, self.kc.iopub_channel, cell)
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except Exception as e:
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self.log.error("failed to run cell: " + repr(e))
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self.log.error(str(cell.source))
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raise
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cell.outputs = outputs
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return cell, resources
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def run_cell(self, shell, iopub, cell):
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msg_id = shell.execute(cell.source)
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self.log.debug("Executing cell:\n%s", cell.source)
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# wait for finish, with timeout
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while True:
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try:
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msg = shell.get_msg(timeout=self.timeout)
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except Empty:
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self.log.error("Timeout waiting for execute reply")
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raise
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if msg['parent_header'].get('msg_id') == msg_id:
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break
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else:
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# not our reply
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continue
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outs = []
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while True:
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try:
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msg = iopub.get_msg(timeout=self.timeout)
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except Empty:
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self.log.warn("Timeout waiting for IOPub output")
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break
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if msg['parent_header'].get('msg_id') != msg_id:
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# not an output from our execution
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continue
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msg_type = msg['msg_type']
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self.log.debug("output: %s", msg_type)
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content = msg['content']
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# set the prompt number for the input and the output
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if 'execution_count' in content:
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cell['execution_count'] = content['execution_count']
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if msg_type == 'status':
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if content['execution_state'] == 'idle':
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break
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else:
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continue
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elif msg_type == 'execute_input':
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continue
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elif msg_type == 'clear_output':
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outs = []
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continue
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try:
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out = output_from_msg(msg)
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except ValueError:
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self.log.error("unhandled iopub msg: " + msg_type)
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else:
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outs.append(out)
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return outs
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