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