def test_add_score_output_text(self):
"""Is the score properly handled when the cell is a markdown cell?"""
cell = NotebookNode()
cell.cell_type = 'markdown'
cell.outputs = []
self.preprocessor._add_score_output(cell, 10, 15)
assert cell['outputs'] == []
def test_add_score_output(self):
"""Is the score properly formatted and added to the cell outputs?"""
cell = NotebookNode()
cell.cell_type = 'code'
cell.outputs = []
self.preprocessor._add_score_output(cell, 10, 15)
output = cell.outputs[0]
assert output.stream == "stdout"
assert output.output_type == "stream"
assert output.text == "Score: 10 / 15"
def run_cell(self, cell):
'''
Run a notebook cell and update the output of that cell in-place.
'''
logging.info('Running cell:\n%s\n', cell.input)
self.shell.execute(cell.input)
reply = self.shell.get_msg()
status = reply['content']['status']
if status == 'error':
logging.info('Cell raised uncaught exception: %s', reply['content']['ename'])
else:
logging.info('Cell returned')
outs = list()
while True:
try:
msg = self.iopub.get_msg(timeout=1)
if msg['msg_type'] == 'status':
if msg['content']['execution_state'] == 'idle':
break
except Empty:
# execution state should return to idle before the queue becomes empty,
# if it doesn't, something bad has happened
raise
content = msg['content']
msg_type = msg['msg_type']
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type in ['status', 'pyin']:
continue
elif msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].iteritems():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
setattr(out, attr, data)
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
logging.log('\n'.join(content['traceback']))
else:
raise NotImplementedError('unhandled iopub message: %s' % msg_type)
outs.append(out)
cell['outputs'] = outs
if status == 'error':
raise NotebookError()
def test_preprocess_code_cell_solution(self):
"""Is the solution version of a code cell correctly preprocessed?"""
self.preprocessor.solution = True
self.preprocessor.toc = ""
cell = self._create_code_cell()
self.preprocessor._create_client()
cell, resources = self.preprocessor.preprocess_cell(cell, {}, 1)
self.preprocessor._shutdown_client()
output = NotebookNode()
output.stream = "stdout"
output.text = "hello\n"
output.output_type = "stream"
assert cell.input == """# YOUR CODE HERE\nprint "hello\""""
assert cell.outputs == [output]
assert cell.prompt_number == 1
def run_cell(shell, iopub, cell, output=False):
shell.execute(cell.input)
#shell.get_msg() # timeout=20
outs = []
while True:
try:
msg = iopub.get_msg(timeout=0.1)
except Empty:
continue
msg_type = msg['msg_type']
if msg_type == 'pyin':
continue
elif msg_type == 'clear_output':
outs = []
continue
elif msg_type == 'status':
if msg['content']['execution_state'] == 'idle':
break
else:
outs = []
continue
content = msg['content']
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
if output:
print(out.texti)#, end="")
elif msg_type in ('display_data', 'pyout'):
out['metadata'] = content['metadata']
for mime, data in content['data'].items():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
log.error("Unhandled iopub msg : ", msg_type)
outs.append(out)
return outs
def _process_execute_error(self, msg):
""" Process a reply for an execution request that resulted in an error.
"""
content = msg['content']
# If a SystemExit is passed along, this means exit() was called - also
# all the ipython %exit magic syntax of '-k' to be used to keep
# the kernel running
if content['ename']=='SystemExit':
keepkernel = content['evalue']=='-k' or content['evalue']=='True'
self._keep_kernel_on_exit = keepkernel
self.exit_requested.emit(self)
else:
traceback = ''.join(content['traceback'])
logging.error(traceback)
out = NotebookNode(output_type='pyerr')
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
self._current_cell['outputs'].append(out)
self.run_notebook_completed(error=True, traceback=content['traceback'])
def run_cell(kc, cell):
shell = kc.shell_channel
iopub = kc.iopub_channel
outputs = []
shell.execute(cell.input)
# wait for finish, maximum 20s
try:
shell.get_msg(timeout=10)
except Empty:
return outputs
failures = 0
messages = 0
while True:
try:
reply = iopub.get_msg(timeout=0.2)
messages += 1
except Empty:
break
content = reply['content']
msg_type = reply['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outputs = []
continue
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].iteritems():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print "unhandled iopub msg:", msg_type
outputs.append(out)
return outputs
def run_cell(kc, cell):
shell = kc.shell_channel
iopub = kc.iopub_channel
outputs = []
shell.execute(cell.input)
# wait for finish, maximum 20s
try:
shell.get_msg(timeout=10)
except Empty:
return outputs
failures = 0
messages = 0
while True:
try:
reply = iopub.get_msg(timeout=0.2)
messages += 1
except Empty:
break
content = reply["content"]
msg_type = reply["msg_type"]
if msg_type in ("status", "pyin"):
continue
elif msg_type == "clear_output":
outputs = []
continue
out = NotebookNode(output_type=msg_type)
if msg_type == "stream":
out.stream = content["name"]
out.text = content["data"]
elif msg_type in ("display_data", "pyout"):
for mime, data in content["data"].iteritems():
attr = mime.split("/")[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace("+xml", "").replace("plain", "text")
setattr(out, attr, data)
if msg_type == "pyout":
out.prompt_number = content["execution_count"]
elif msg_type == "pyerr":
out.ename = content["ename"]
out.evalue = content["evalue"]
out.traceback = content["traceback"]
else:
print "unhandled iopub msg:", msg_type
outputs.append(out)
return outputs
def run_cell(shell, iopub, cell, timeout=60):
shell.execute(cell.input)
# wait for finish
shell.get_msg(timeout=timeout)
outs = []
while True:
try:
msg = iopub.get_msg(timeout=0.2)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
out['metadata'] = content['metadata']
for mime, data in content['data'].iteritems():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print "unhandled iopub msg:", msg_type
outs.append(out)
return outs
def run_cell(self, shell, iopub, cell, exec_count):
outs = []
shell.execute(cell.input)
# hard-coded timeout, problem?
shell.get_msg(timeout=20)
cell.prompt_number = exec_count # msg["content"]["execution_count"]
while True:
try:
# whats the assumption on timeout here?
# is it asynchronous?
msg = iopub.get_msg(timeout=.2)
except Empty:
break
msg_type = msg["msg_type"]
if msg_type in ["status", "pyin"]:
continue
elif msg_type == "clear_output":
outs = []
continue
content = msg["content"]
out = NotebookNode(output_type=msg_type)
if msg_type == "stream":
out.stream = content["name"]
out.text = content["data"]
elif msg_type in ["display_data", "pyout"]:
for mime, data in content["data"].iteritems():
attr = mime.split("/")[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == "pyout":
out.prompt_number = exec_count #content["execution_count"]
elif msg_type == "pyerr":
out.ename = content["ename"]
out.evalue = content["evalue"]
out.traceback = content["traceback"]
else:
print "unhandled iopub msg:", msg_type
outs.append(out)
return outs
def run_cell(km, cell, timeout=20):
shell = km.shell_channel
iopub = km.iopub_channel
shell.execute(cell.input)
shell.get_msg(timeout=timeout)
outs = []
while True:
try:
msg = iopub.get_msg(timeout=0.2)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.txt = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
attr = mime.split('/')[-1].lower()
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print("unhandled iopub msg:", msg_type)
outs.append(out)
cell.outputs = outs
return outs
def run_cell(km, cell):
shell = km.shell_channel
iopub = km.sub_channel
# print "\n\ntesting:"
# print cell.input
msg_id = shell.execute(cell.input)
# wait for finish, no maximum
msg = get_child_msg(km, msg_id)
execution_count = msg['content']['execution_count']
outs = []
while True:
try:
msg = iopub.get_msg(timeout=0.2)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
# print msg_type, content
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].iteritems():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print "unhandled iopub msg:", msg_type
outs.append(out)
return outs, execution_count
def run_notebook(self, nb, vars={}):
if len(nb['worksheets']) == 0:
nb['worksheets'] = [NotebookNode({'cells': [], 'metadata': {}})]
start = nb['worksheets'][0]['cells']
start.insert(
0,
Struct(
**{
'cell_type': 'code',
'language': 'python',
'outputs': [],
'collapsed': False,
'prompt_number': -1,
'input': 'qtipy=%s' % vars,
'metadata': {},
}))
self.runner.nb = nb
try:
self.runner.run_notebook()
except:
self.latest_run['success'] = False
raise
else:
self.latest_run['success'] = True
finally:
ext = dict(
html='html',
slides='slides',
latex='latex',
markdown='md',
python='py',
rst='rst',
)
output, resources = IPyexport(
IPyexporter_map[self.config.get('output_format')],
self.runner.nb)
output_path = vars['output_path'] + 'notebook.%s' % ext[
self.config.get('output_format')]
logging.info("Exporting updated notebook to %s" % output_path)
with open(output_path, "w") as f:
f.write(output)
def poll_for_msgs(self):
"""Polls for messages from the kernel.
Used after submitting code for execution"""
try:
msg = self.iopub.get_msg(timeout=1)
if msg['msg_type'] == 'status' and msg['content'][
'execution_state'] == 'idle':
if _debugging:
logging.info('Message -- {}:{}'.format(
msg['msg_type'], msg['content']))
self._previous_status = 'IDLE'
return NotebookNode(output_type='IDLE')
except Empty: # state should return to idle before queue becomes empty, but we ignore it now
prevstat, self._previous_status = self._previous_status, 'EMPTY'
retstat = 'END_CELL' if prevstat == 'IDLE' else 'EMPTY'
# Assuming IDLE followed by EMPTY is the end-of-cell
return NotebookNode(output_type=retstat)
self._previous_status = '' # Not idle, that's all we are concerned about for now
content, msg_type = msg['content'], msg['msg_type']
if msg_type in ['status', 'pyin']:
return NotebookNode(output_type='NoOp')
out = NotebookNode(output_type=msg_type)
if msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
tmpval = RClansiconv(data) if attr == 'text' else data
setattr(out, attr, tmpval)
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
elif msg_type == 'stream':
setattr(out, 'text', RClansiconv(content['data']))
elif msg_type == 'pyerr':
setattr(out, 'html',
RClansiconv('\n'.join(content['traceback']) + '\n'))
else:
if _debugging: logging.info('Unsupported: ' + msg_type)
raise NotImplementedError('unhandled iopub message: %s' % msg_type)
if _debugging:
logging.info(
'Sending: msg_type: [{}]; HTML: [{}]; TEXT: [{}]'.format(
msg_type, out.get('html', ''), out.get('text', '')))
return out # upstream process will handle it [e.g. send as an oob message]
def run_cell(self, shell, iopub, cell, exec_count):
outs = []
shell.execute(cell.input)
# hard-coded timeout, problem?
shell.get_msg(timeout=90)
cell.prompt_number = exec_count # msg["content"]["execution_count"]
while True:
try:
# whats the assumption on timeout here?
# is it asynchronous?
msg = iopub.get_msg(timeout=.2)
except Empty:
break
msg_type = msg["msg_type"]
if msg_type in ["status" , "pyin"]:
continue
elif msg_type == "clear_output":
outs = []
continue
content = msg["content"]
out = NotebookNode(output_type=msg_type)
if msg_type == "stream":
out.stream = content["name"]
out.text = content["data"]
elif msg_type in ["display_data", "pyout"]:
for mime, data in content["data"].iteritems():
attr = mime.split("/")[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == "pyout":
out.prompt_number = exec_count #content["execution_count"]
elif msg_type == "pyerr":
out.ename = content["ename"]
out.evalue = content["evalue"]
out.traceback = content["traceback"]
else:
print "unhandled iopub msg:", msg_type
outs.append(out)
return outs
def run(self, cell, timeout = None):
use_timeout = self.default_timeout
if timeout is not None:
use_timeout = timeout
self.shell.execute(cell.input)
self.shell.get_msg(timeout=use_timeout)
outs = []
while True:
try:
msg = self.iopub.get_msg(timeout=0.5)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
out['metadata'] = content['metadata']
for mime, data in content['data'].iteritems():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print "unhandled iopub msg:", msg_type
outs.append(out)
return outs
def run_cell(km, cell, timeout=20):
shell = km.shell_channel
iopub = km.iopub_channel
shell.execute(cell.input)
shell.get_msg(timeout=timeout)
outs = []
while True:
try:
msg = iopub.get_msg(timeout=0.2)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.txt = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
attr = mime.split('/')[-1].lower()
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print("unhandled iopub msg:", msg_type)
outs.append(out)
cell.outputs = outs
return outs
def run_cell(shell, iopub, cell):
# print cell.input
shell.execute(cell.input)
# wait for finish, maximum 20s
shell.get_msg(timeout=30)
outs = []
while True:
try:
msg = iopub.get_msg(timeout=0.2)
except queue.Empty:
break
msg_type = msg["msg_type"]
if msg_type in ("status", "pyin"):
continue
elif msg_type == "clear_output":
outs = []
continue
content = msg["content"]
# print msg_type, content
out = NotebookNode(output_type=msg_type)
if msg_type == "stream":
out.stream = content["name"]
out.text = content["data"]
elif msg_type in ("display_data", "pyout"):
out["metadata"] = content["metadata"]
for mime, data in content["data"].items():
attr = mime.split("/")[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace("+xml", "").replace("plain", "text")
setattr(out, attr, data)
if msg_type == "pyout":
out.prompt_number = content["execution_count"]
elif msg_type == "pyerr":
out.ename = content["ename"]
out.evalue = content["evalue"]
out.traceback = content["traceback"]
else:
print("unhandled iopub msg:", msg_type)
outs.append(out)
return outs
def run_cell(shell, iopub, cell):
stime = time.time()
shell.execute(cell.input)
# wait for finish or timeout (in seconds)
shell.get_msg(timeout=120)
outs = []
elapsedtime = time.time() - stime
print ' %.2f sec | cell done.\n%s' % (elapsedtime, str(cell.input)[:50])
while True:
try:
msg = iopub.get_msg(timeout=1.0)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
# print msg_type, content
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].iteritems():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
#out.prompt_number = content['execution_count']
#TODO: need to find better workaround
pass
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print "unhandled iopub msg:", msg_type
outs.append(out)
return outs
def run_cell(shell, iopub, cell):
shell.execute(cell.input)
# wait for finish, maximum 20s
shell.get_msg(timeout=20)
outs = []
while True:
try:
msg = iopub.get_msg(timeout=0.2)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
out['metadata'] = content['metadata']
for mime, data in content['data'].items():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
elif msg_type not in ('comm_msg', 'comm_open'):
print("unhandled iopub msg:", msg_type)
outs.append(out)
return outs
def poll_for_msgs(self):
"""Polls for messages from the kernel.
Used after submitting code for execution"""
try:
msg = self.iopub.get_msg(timeout=1)
if msg['msg_type'] == 'status' and msg['content']['execution_state'] == 'idle':
if _debugging: logging.info('Message -- {}:{}'.format(msg['msg_type'], msg['content']))
self._previous_status = 'IDLE'
return NotebookNode(output_type = 'IDLE')
except Empty: # state should return to idle before queue becomes empty, but we ignore it now
prevstat, self._previous_status = self._previous_status, 'EMPTY'
retstat = 'END_CELL' if prevstat == 'IDLE' else 'EMPTY'
# Assuming IDLE followed by EMPTY is the end-of-cell
return NotebookNode(output_type = retstat)
self._previous_status = '' # Not idle, that's all we are concerned about for now
content, msg_type = msg['content'], msg['msg_type']
if msg_type in ['status', 'pyin']: return NotebookNode(output_type = 'NoOp')
out = NotebookNode(output_type = msg_type)
if msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
tmpval = RClansiconv(data) if attr == 'text' else data
setattr(out, attr, tmpval)
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
elif msg_type == 'stream':
setattr(out, 'text', RClansiconv(content['data']))
elif msg_type == 'pyerr':
setattr(out, 'html', RClansiconv('\n'.join(content['traceback']) + '\n'))
else:
if _debugging: logging.info('Unsupported: ' + msg_type)
raise NotImplementedError('unhandled iopub message: %s' % msg_type)
if _debugging: logging.info('Sending: msg_type: [{}]; HTML: [{}]; TEXT: [{}]'.format(msg_type, out.get('html', ''), out.get('text', '') ))
return out # upstream process will handle it [e.g. send as an oob message]
def run_cell(shell, iopub, cell, t, tshell):
"""
Here we will figure out how the timings affect the outputs
"""
print '\n\n =========== RUNNING CELL for timeout={} ================ \n\n'.format(
t)
shell.execute(cell.input)
# This value must be significantly large to get the outputs
# According to the previous tests, it must be around 1000
# It is just needed for the outputs to be executed properly
# (when the cells are executed, it stops, so it doenst take
# 1000 secs for every cell)
shell.get_msg(timeout=tshell)
outs = []
while True:
try:
# This timing can be very small, 1 sec or so
# We still need to figure out what is different
# with the previous tshell timing variable
msg = iopub.get_msg(timeout=t)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
print '\n PRINTING THROUGH THE CELL \n'
print content
out = NotebookNode(output_type=msg_type)
def _handle_execute_result(self, msg):
""" Handle display hook output.
"""
logging.debug("execute_result: %s", msg.get('content', ''))
if not self._hidden and self._is_from_this_session(msg):
msg_id = msg['parent_header']['msg_id']
if msg_id not in self._cell_execute_ids: # Only on the in-process kernel can this happen
self._result_queue.append(msg)
return
(cell, n, pc) = self._cell_execute_ids[msg_id]
out = NotebookNode(output_type='display_data')
for mime, data in msg['content']['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
setattr(out, attr, data)
cell['outputs'].append(out)
def run_cell(self, cell, autosave):
'''
Run a notebook cell and update the output of that cell in-place.
'''
logging.info('Running cell:\n%s\n', cell.input)
self.shell.execute(cell.input)
cell['outputs'] = []
while True:
try:
msg = self.iopub.get_msg(timeout=1)
if msg['msg_type'] == 'status':
if msg['content']['execution_state'] == 'idle':
break
except Empty:
pass
content = msg['content']
msg_type = msg['msg_type']
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count'] - 1
out.prompt_number = content['execution_count'] - 1
if msg_type in ['status', 'pyin']:
continue
elif msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
#print(out.text, end='')
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
setattr(out, attr, data)
#print(data, end='')
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
#logging.error('\n'.join(content['traceback']))
else:
raise NotImplementedError('unhandled iopub message: %s' % msg_type)
cell['outputs'].append(out)
if autosave:
self.save_notebook(autosave)
reply = self.shell.get_msg()
status = reply['content']['status']
if status == 'error':
logging.info('Cell raised uncaught exception: \n%s', '\n'.join(reply['content']['traceback']))
raise NotebookError()
else:
logging.info('Cell returned')
def run_cell(self, shell, iopub, cell):
msg_id = shell.execute(cell.input)
self.log.debug("Executing cell:\n%s", cell.input)
# wait for finish, with timeout
while True:
try:
msg = shell.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 = iopub.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']
out = NotebookNode(output_type=self.msg_type_map.get(msg_type, msg_type))
# set the prompt number for the input and the output
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type == 'status':
if content['execution_state'] == 'idle':
break
else:
continue
elif msg_type in {'execute_input', 'pyin'}:
continue
elif msg_type == 'clear_output':
outs = []
continue
if msg_type == 'stream':
out.stream = content['name']
out.text = content['text']
elif msg_type in ('display_data', 'execute_result'):
out['metadata'] = content['metadata']
for mime, data in content['data'].items():
# map mime-type keys to nbformat v3 keys
# this will be unnecessary in nbformat v4
key = self.mime_map.get(mime, mime)
out[key] = data
elif msg_type == 'error':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
self.log.error("unhandled iopub msg: " + msg_type)
outs.append(out)
return outs
def run_cell(kc, cell, collect_outputs=True, timeout=10):
"""
Run contents of a cell in a kernel client.
If collect_outputs is True, return the outputs as a list.
"""
shell = kc.shell_channel
iopub = kc.iopub_channel
outputs = []
shell.execute(cell.input)
# wait for finish, maximum 20s
try:
msg = shell.get_msg(timeout=timeout)
except Empty:
return []
reply = msg['content']
if reply['status'] == 'error':
print "\nFAILURE:"
print cell.input
print '-----'
print "raised:"
print '\n'.join(reply['traceback'])
if collect_outputs:
outputs = []
while True:
try:
reply = iopub.get_msg(timeout=3)
except Empty:
break
content = reply['content']
msg_type = reply['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outputs = []
continue
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].iteritems():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = cell.prompt_number
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print "unhandled iopub msg:", msg_type
outputs.append(out)
return outputs
return []
def runtest(self):
"""
Run all the cell tests in one kernel without restarting.
It is very common for ipython notebooks to run through assuming a
single kernel.
"""
# Execute the code from the current cell and get the msg_id
# of the shell process.
msg_id = self.parent.kernel.execute_cell_input(
self.cell.input, allow_stdin=False)
# Time for the reply of the cell execution
timeout = 2000
# This list stores the output information for the entire cell
outs = []
# Wait for the execution reply (we can see this in the msg_type)
# This execution produces a dictionary where a status string can be
# obtained: 'ok' OR 'error' OR 'abort'
# We can also get how many cells have been executed
# until here, with the 'execution_count' entry
#self.parent.kernel.kc.get_shell_msg(timeout=timeout)
while True:
"""
The messages from the cell contain information such
as input code, outputs generated
and other messages. We iterate through each message
until we reach the end of the cell.
"""
try:
# Get one message at a time, per code block inside the cell
msg = self.parent.get_kernel_message(timeout=1.)
except Empty:
# This is not working: ! The code will not be checked
# if the time is out (when the cell stops to be executed?)
# raise NbCellError("Timeout of %d seconds exceeded"
# " executing cell: %s" (timeout,
# self.cell.input))
# Just break the loop when the output is empty
break
"""
Now that we have the output from a piece of code
inside the cell,
we want to compare the outputs of the messages
to a reference output (the ones that are present before
the notebook was executed)
"""
# Firstly, get the msg type from the cell to know if
# the output comes from a code
# It seems that the type 'stream' is irrelevant
msg_type = msg['msg_type']
# REF:
# execute_input: To let all frontends know what code is
# being executed at any given time, these messages contain a
# re-broadcast of the code portion of an execute_request,
# along with the execution_count.
if msg_type in ('status', 'execute_input'):
continue
# If there is no more output, continue with the executions
# (it will break if it is empty, with the previous statements)
#
# REF:
# This message type is used to clear the output that is
# visible on the frontend
# elif msg_type == 'clear_output':
# outs = []
# continue
# I added the msg_type 'idle' condition (when the cell stops)
# so we get a complete cell output
# REF:
# When the kernel starts to execute code, it will enter the 'busy'
# state and when it finishes, it will enter the 'idle' state.
# The kernel will publish state 'starting' exactly
# once at process startup.
elif (msg_type == 'clear_output'
and msg_type['execution_state'] == 'idle'):
outs = []
continue
# WE COULD ADD HERE a condition for the 'error' message type
# Making the test to fail
"""
Now we get the reply from the piece of code executed
and analyse the outputs
"""
reply = msg['content']
out = NotebookNode(output_type=msg_type)
# Now check what type of output it is
if msg_type == 'stream':
out.stream = reply['name']
out.text = reply['text']
elif msg_type in ('display_data', 'execute_result'):
# REF:
# data and metadata are identical to a display_data message.
# the object being displayed is that passed to the display
# hook, i.e. the *result* of the execution.
out['metadata'] = reply['metadata']
for mime, data in reply['data'].iteritems():
attr = mime.split('/')[-1].lower()
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'execute_result':
out.prompt_number = reply['execution_count']
else:
print("unhandled iopub msg:", msg_type)
outs.append(out)
"""
This message is the last message of the cell, which contains no output.
It only indicates whether the entire cell ran successfully or if there
was an error.
"""
reply = msg['content']
failed = False
# THIS COMPARISON IS ONLY WHEN THE OUTPUT DICTIONARIES
# ARE DIFFERENT, WHICH IS A DIFFERENT ERROR, not
# from the output in the notebook
#
# SINCE WE SANITIZE AND COMPARE, IF THERE ARE DIFFERENT
# NUMBER OF LINES, this error will be reported
#
# Compare if the outputs have the same number of lines
# and throw an error if it fails
# if len(outs) != len(self.cell.outputs):
# self.diff_number_outputs(outs, self.cell.outputs)
# failed = True
# If the outputs are the same, compare them line by line
# else:
# for out, ref in zip(outs, self.cell.outputs):
if not self.compare_outputs(outs, self.cell.outputs):
failed = True
# if reply['status'] == 'error':
# Traceback is only when an error is raised (?)
# We usually get an exception because traceback is not defined
if failed: # Use this to make the test fail
"""
The pytest exception will be raised if there are any
errors in the notebook cells. Now we check that
the outputs produced from running each cell
matches the outputs in the existing notebook.
This code is taken from [REF].
"""
raise NbCellError(self.cell_num,
# Still needs correction. We could
# add a description
"Error with cell",
self.cell.input,
# Here we must put the traceback output:
'\n'.join(self.comparisons))
def test_get_assignment_cell_type_default():
"""Is the cell type '-' when the assignment metadata is missing?"""
cell = NotebookNode()
cell.metadata = {}
cell_type = util.get_assignment_cell_type(cell)
assert cell_type == '-'
def test_get_assignment_cell_type_given():
"""Is the cell type correct when the assignment metadata is present?"""
cell = NotebookNode()
cell.metadata = dict(assignment=dict(cell_type="foo"))
cell_type = util.get_assignment_cell_type(cell)
assert cell_type == "foo"
def run_cell(self, cell):
'''
Run a notebook cell and update the output of that cell in-place.
'''
logging.info('Running cell:\n%s\n', cell.input)
self.shell.execute(cell.input)
reply = self.shell.get_msg()
status = reply['content']['status']
if status == 'error':
logging.info('Cell raised uncaught exception: %s',
reply['content']['ename'])
else:
logging.info('Cell returned')
outs = list()
while True:
try:
msg = self.iopub.get_msg(timeout=1)
if msg['msg_type'] == 'status':
if msg['content']['execution_state'] == 'idle':
break
except Empty:
# execution state should return to idle before the queue becomes empty,
# if it doesn't, something bad has happened
raise
content = msg['content']
msg_type = msg['msg_type']
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type in ['status', 'pyin']:
continue
elif msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
#print(out.text, end='')
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError('unhandled mime type: %s' %
mime)
setattr(out, attr, data)
#print(data, end='')
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
#logging.error('\n'.join(content['traceback']))
else:
raise NotImplementedError('unhandled iopub message: %s' %
msg_type)
outs.append(out)
cell['outputs'] = outs
if status == 'error':
raise NotebookError()
def run_cell(self, cell): # noqa: C901
"""Run a notebook cell and update the output of that cell in-place."""
self.shell.execute(cell.input)
reply = self.shell.get_msg()
status = reply['content']['status']
if status == 'error':
traceback_text = ("Cell raised uncaught exception: \n"
"\n".join(reply['content']['traceback']))
outs = []
while True:
msg = self.iopub.get_msg(timeout=1)
msg_type = msg['msg_type']
content = msg['content']
if msg_type == 'status' and content['execution_state'] == 'idle':
break
# IPython 3.0.0-dev writes pyerr/pyout in the notebook format
# but uses error/execute_result in the message spec. This does
# the translation needed for tests to pass with IPython 3.0.0-dev
notebook3_format_conversions = {
'error': 'pyerr',
'execute_result': 'pyout',
}
msg_type = notebook3_format_conversions.get(msg_type, msg_type)
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type in ('status', 'pyin', 'execute_input'):
continue
elif msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError(
'unhandled mime type: %s' % mime)
setattr(out, attr, data)
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
elif msg_type == 'clear_output':
outs = []
continue
else:
raise NotImplementedError(
'unhandled iopub message: %s' % msg_type)
outs.append(out)
cell['outputs'] = outs
if status == 'error':
raise Exception(traceback_text)
def run_cell(self, cell):
"""
Run a notebook cell and update the output of that cell in-place.
"""
#Changes to ensure proper order of pylab and matplotlib
if 'from pylab import *' in cell.input:
cell.input = cell.input.replace('from pylab import *', '')
cell.input = 'from pylab import *\n' + cell.input
if 'import matplotlib\n' in cell.input:
cell.input = cell.input.replace('import matplotlib\n', '\n')
if self.first_cell:
self.first_cell = False
cell.input = 'import matplotlib\nmatplotlib.use(\'pgf\')\n' + cell.input
cell.input = cell.input.replace('%matplotlib inline', '')
logging.info('Running cell:\n%s\n', cell.input)
self.kc.execute(cell.input)
reply = self.kc.get_shell_msg()
status = reply['content']['status']
traceback_text = ''
if status == 'error':
traceback_text = 'Cell raised uncaught exception: \n' + \
'\n'.join(reply['content']['traceback'])
logging.info(traceback_text)
else:
logging.info('Cell returned')
outs = list()
while True:
try:
msg = self.kc.get_iopub_msg(timeout=1)
if msg['msg_type'] == 'status':
if msg['content']['execution_state'] == 'idle':
break
except Empty:
# execution state should return to idle
# before the queue becomes empty,
# if it doesn't, something bad has happened
raise
content = msg['content']
msg_type = msg['msg_type']
# IPython 3.0.0-dev writes pyerr/pyout in the notebook format
# but uses error/execute_result in the message spec. This does the
# translation needed for tests to pass with IPython 3.0.0-dev
notebook3_format_conversions = {
'error': 'pyerr',
'execute_result': 'pyout'
}
msg_type = notebook3_format_conversions.get(msg_type, msg_type)
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type in ('status', 'pyin', 'execute_input'):
continue
elif msg_type == 'stream':
out.stream = content['name']
# in msgspec 5, this is name, text
# in msgspec 4, this is name, data
if 'text' in content:
out.text = content['text']
else:
out.text = content['data']
#print(out.text, end='')
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError(
'unhandled mime type: %s' % mime
)
setattr(out, attr, data)
#print(data, end='')
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
#logging.error('\n'.join(content['traceback']))
elif msg_type == 'clear_output':
outs = list()
continue
else:
raise NotImplementedError(
'unhandled iopub message: %s' % msg_type
)
outs.append(out)
cell['outputs'] = outs
if status == 'error':
raise NotebookError(traceback_text)
def run_cell(self, cell):
"""
Run a notebook cell and update the output of that cell in-place.
"""
logging.info("Running cell:\n%s\n", cell.input)
self.shell.execute(cell.input)
reply = self.shell.get_msg()
status = reply["content"]["status"]
if status == "error":
logging.info("Cell raised uncaught exception: \n%s", "\n".join(reply["content"]["traceback"]))
else:
logging.info("Cell returned")
outs = list()
while True:
try:
msg = self.iopub.get_msg(timeout=1)
if msg["msg_type"] == "status":
if msg["content"]["execution_state"] == "idle":
break
except Empty:
# execution state should return to idle before the queue becomes empty,
# if it doesn't, something bad has happened
raise
content = msg["content"]
msg_type = msg["msg_type"]
out = NotebookNode(output_type=msg_type)
if "execution_count" in content:
cell["prompt_number"] = content["execution_count"]
out.prompt_number = content["execution_count"]
if msg_type in ["status", "pyin"]:
continue
elif msg_type == "stream":
out.stream = content["name"]
out.text = content["data"]
# print(out.text, end='')
elif msg_type in ("display_data", "pyout"):
for mime, data in content["data"].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError("unhandled mime type: %s" % mime)
setattr(out, attr, data)
# print(data, end='')
elif msg_type == "pyerr":
out.ename = content["ename"]
out.evalue = content["evalue"]
out.traceback = content["traceback"]
# logging.error('\n'.join(content['traceback']))
else:
raise NotImplementedError("unhandled iopub message: %s" % msg_type)
outs.append(out)
cell["outputs"] = outs
if status == "error":
raise Exception(json.dumps(out))
def _process_execute_ok(self, msg):
""" Process a reply for a successful execution request.
"""
payload = msg['content']['payload']
for item in payload:
if not self._process_execute_payload(item):
warning = 'Warning: received unknown payload of type %s'
print(warning % repr(item['source']))
content = msg['content']
msg_type = msg['msg_type']
# IPython 3.0.0-dev writes pyerr/pyout in the notebook format but uses
# error/execute_result in the message spec. This does the translation
# needed for tests to pass with IPython 3.0.0-dev
notebook3_format_conversions = {
'error': 'pyerr',
'execute_result': 'pyout'
}
msg_type = notebook3_format_conversions.get(msg_type, msg_type)
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
self._current_cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type in ('status', 'pyin', 'execute_input'):
return
elif msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
# Is this handled in _handle_execute_result?
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
setattr(out, attr, data)
return
elif msg_type == 'pyerr':
# Is this handled in _handle_execute_errror?
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
return
elif msg_type == 'clear_output':
self._current_cell['outputs'] = []
return
elif msg_type == 'execute_reply':
pass
else:
raise NotImplementedError('unhandled iopub message: %s' % msg_type)
self._current_cell['outputs'].append(out)
def _process_execute_ok(self, msg):
""" Process a reply for a successful execution request.
"""
payload = msg['content']['payload']
for item in payload:
if not self._process_execute_payload(item):
warning = 'Warning: received unknown payload of type %s'
print(warning % repr(item['source']))
content = msg['content']
msg_type = msg['msg_type']
# IPython 3.0.0-dev writes pyerr/pyout in the notebook format but uses
# error/execute_result in the message spec. This does the translation
# needed for tests to pass with IPython 3.0.0-dev
notebook3_format_conversions = {
'error': 'pyerr',
'execute_result': 'pyout'
}
msg_type = notebook3_format_conversions.get(msg_type, msg_type)
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
self._current_cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type in ('status', 'pyin', 'execute_input'):
return
elif msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
# Is this handled in _handle_execute_result?
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
setattr(out, attr, data)
return
elif msg_type == 'pyerr':
# Is this handled in _handle_execute_errror?
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
return
elif msg_type == 'clear_output':
self._current_cell['outputs'] = []
return
elif msg_type == 'execute_reply':
pass
else:
raise NotImplementedError('unhandled iopub message: %s' % msg_type)
self._current_cell['outputs'].append(out)
def run_cell(self, cell):
'''
Run a notebook cell and update the output of that cell in-place.
'''
logging.info('Running cell:\n%s\n', cell.input)
self.shell.execute(cell.input)
reply = self.shell.get_msg()
status = reply['content']['status']
if status == 'error':
traceback_text = 'Cell raised uncaught exception: \n' + \
'\n'.join(reply['content']['traceback'])
logging.info(traceback_text)
else:
logging.info('Cell returned')
outs = list()
while True:
try:
msg = self.iopub.get_msg(timeout=1)
if msg['msg_type'] == 'status':
if msg['content']['execution_state'] == 'idle':
break
except Empty:
# execution state should return to idle before the queue becomes empty,
# if it doesn't, something bad has happened
raise
content = msg['content']
msg_type = msg['msg_type']
# IPython 3.0.0-dev writes pyerr/pyout in the notebook format but uses
# error/execute_result in the message spec. This does the translation
# needed for tests to pass with IPython 3.0.0-dev
notebook3_format_conversions = {
'error': 'pyerr',
'execute_result': 'pyout'
}
msg_type = notebook3_format_conversions.get(msg_type, msg_type)
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type in ('status', 'pyin', 'execute_input'):
continue
elif msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
#print(out.text, end='')
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
setattr(out, attr, data)
#print(data, end='')
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
#logging.error('\n'.join(content['traceback']))
elif msg_type == 'clear_output':
outs = list()
continue
else:
raise NotImplementedError('unhandled iopub message: %s' % msg_type)
outs.append(out)
cell['outputs'] = outs
if status == 'error':
raise NotebookError(traceback_text)
while True:
try:
msg = iopub.get_msg(timeout=0.2)
except Empty:
break
msg_type = msg['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outs = []
continue
content = msg['content']
# print msg_type, content
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].iteritems():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = content['execution_count']
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
def run_cell(kc, cell, collect_outputs=True):
"""
Run contents of a cell in a kernel client.
If collect_outputs is True, return the outputs as a list.
"""
shell = kc.shell_channel
iopub = kc.iopub_channel
outputs = []
shell.execute(cell.input)
# wait for finish, maximum 20s
try:
msg = shell.get_msg(timeout=10)
except Empty:
return []
reply = msg['content']
if reply['status'] == 'error':
print("\nFAILURE:")
print(cell.input)
print('-----')
print("raised:")
print('\n'.join(reply['traceback']))
if collect_outputs:
outputs = []
while True:
try:
reply = iopub.get_msg(timeout=0.5)
except Empty:
break
content = reply['content']
msg_type = reply['msg_type']
if msg_type in ('status', 'pyin'):
continue
elif msg_type == 'clear_output':
outputs = []
continue
out = NotebookNode(output_type=msg_type)
if msg_type == 'stream':
out.stream = content['name']
out.text = content['data']
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].iteritems():
attr = mime.split('/')[-1].lower()
# this gets most right, but fix svg+html, plain
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'pyout':
out.prompt_number = cell.prompt_number
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
print("unhandled iopub msg:", msg_type)
outputs.append(out)
return outputs
return []
def runtest(self):
"""
Run all the cell tests in one kernel without restarting.
It is very common for ipython notebooks to run through assuming a
single kernel.
"""
# Execute the code from the current cell and get the msg_id
# of the shell process.
msg_id = self.parent.kernel.execute_cell_input(self.cell.input,
allow_stdin=False)
# Time for the reply of the cell execution
timeout = 2000
# This list stores the output information for the entire cell
outs = []
# Wait for the execution reply (we can see this in the msg_type)
# This execution produces a dictionary where a status string can be
# obtained: 'ok' OR 'error' OR 'abort'
# We can also get how many cells have been executed
# until here, with the 'execution_count' entry
#self.parent.kernel.kc.get_shell_msg(timeout=timeout)
while True:
"""
The messages from the cell contain information such
as input code, outputs generated
and other messages. We iterate through each message
until we reach the end of the cell.
"""
try:
# Get one message at a time, per code block inside the cell
msg = self.parent.get_kernel_message(timeout=1.)
except Empty:
# This is not working: ! The code will not be checked
# if the time is out (when the cell stops to be executed?)
# raise NbCellError("Timeout of %d seconds exceeded"
# " executing cell: %s" (timeout,
# self.cell.input))
# Just break the loop when the output is empty
break
"""
Now that we have the output from a piece of code
inside the cell,
we want to compare the outputs of the messages
to a reference output (the ones that are present before
the notebook was executed)
"""
# Firstly, get the msg type from the cell to know if
# the output comes from a code
# It seems that the type 'stream' is irrelevant
msg_type = msg['msg_type']
# REF:
# execute_input: To let all frontends know what code is
# being executed at any given time, these messages contain a
# re-broadcast of the code portion of an execute_request,
# along with the execution_count.
if msg_type in ('status', 'execute_input'):
continue
# If there is no more output, continue with the executions
# (it will break if it is empty, with the previous statements)
#
# REF:
# This message type is used to clear the output that is
# visible on the frontend
# elif msg_type == 'clear_output':
# outs = []
# continue
# I added the msg_type 'idle' condition (when the cell stops)
# so we get a complete cell output
# REF:
# When the kernel starts to execute code, it will enter the 'busy'
# state and when it finishes, it will enter the 'idle' state.
# The kernel will publish state 'starting' exactly
# once at process startup.
elif (msg_type == 'clear_output'
and msg_type['execution_state'] == 'idle'):
outs = []
continue
# WE COULD ADD HERE a condition for the 'error' message type
# Making the test to fail
"""
Now we get the reply from the piece of code executed
and analyse the outputs
"""
reply = msg['content']
out = NotebookNode(output_type=msg_type)
# Now check what type of output it is
if msg_type == 'stream':
out.stream = reply['name']
out.text = reply['text']
elif msg_type in ('display_data', 'execute_result'):
# REF:
# data and metadata are identical to a display_data message.
# the object being displayed is that passed to the display
# hook, i.e. the *result* of the execution.
out['metadata'] = reply['metadata']
for mime, data in reply['data'].iteritems():
attr = mime.split('/')[-1].lower()
attr = attr.replace('+xml', '').replace('plain', 'text')
setattr(out, attr, data)
if msg_type == 'execute_result':
out.prompt_number = reply['execution_count']
else:
print("unhandled iopub msg:", msg_type)
outs.append(out)
"""
This message is the last message of the cell, which contains no output.
It only indicates whether the entire cell ran successfully or if there
was an error.
"""
reply = msg['content']
failed = False
# THIS COMPARISON IS ONLY WHEN THE OUTPUT DICTIONARIES
# ARE DIFFERENT, WHICH IS A DIFFERENT ERROR, not
# from the output in the notebook
#
# SINCE WE SANITIZE AND COMPARE, IF THERE ARE DIFFERENT
# NUMBER OF LINES, this error will be reported
#
# Compare if the outputs have the same number of lines
# and throw an error if it fails
# if len(outs) != len(self.cell.outputs):
# self.diff_number_outputs(outs, self.cell.outputs)
# failed = True
# If the outputs are the same, compare them line by line
# else:
# for out, ref in zip(outs, self.cell.outputs):
if not self.compare_outputs(outs, self.cell.outputs):
failed = True
# if reply['status'] == 'error':
# Traceback is only when an error is raised (?)
# We usually get an exception because traceback is not defined
if failed: # Use this to make the test fail
"""
The pytest exception will be raised if there are any
errors in the notebook cells. Now we check that
the outputs produced from running each cell
matches the outputs in the existing notebook.
This code is taken from [REF].
"""
raise NbCellError(
self.cell_num,
# Still needs correction. We could
# add a description
"Error with cell",
self.cell.input,
# Here we must put the traceback output:
'\n'.join(self.comparisons))
def run_cell(self, shell, iopub, cell):
msg_id = shell.execute(cell.input)
self.log.debug("Executing cell:\n%s", cell.input)
# wait for finish, with timeout
while True:
try:
msg = shell.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 = iopub.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']
out = NotebookNode(
output_type=self.msg_type_map.get(msg_type, msg_type))
# set the prompt number for the input and the output
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type == 'status':
if content['execution_state'] == 'idle':
break
else:
continue
elif msg_type in {'execute_input', 'pyin'}:
continue
elif msg_type == 'clear_output':
outs = []
continue
if msg_type == 'stream':
out.stream = content['name']
out.text = content['text']
elif msg_type in ('display_data', 'execute_result'):
out['metadata'] = content['metadata']
for mime, data in content['data'].items():
# map mime-type keys to nbformat v3 keys
# this will be unnecessary in nbformat v4
key = self.mime_map.get(mime, mime)
out[key] = data
elif msg_type == 'error':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
else:
self.log.error("unhandled iopub msg: " + msg_type)
outs.append(out)
return outs
def run_cell(self, cell):
'''
Run a notebook cell and update the output of that cell in-place.
'''
logging.info('Running cell:\n%s\n', cell.input)
self.kc.execute(cell.input)
reply = self.kc.get_shell_msg()
status = reply['content']['status']
if status == 'error':
traceback_text = 'Cell raised uncaught exception: \n' + \
'\n'.join(reply['content']['traceback'])
logging.info(traceback_text)
else:
logging.info('Cell returned')
outs = list()
while True:
try:
msg = self.kc.get_iopub_msg(timeout=1)
if msg['msg_type'] == 'status':
if msg['content']['execution_state'] == 'idle':
break
except Empty:
# execution state should return to idle before the queue becomes empty,
# if it doesn't, something bad has happened
raise
content = msg['content']
msg_type = msg['msg_type']
# IPython 3.0.0-dev writes pyerr/pyout in the notebook format but uses
# error/execute_result in the message spec. This does the translation
# needed for tests to pass with IPython 3.0.0-dev
notebook3_format_conversions = {
'error': 'pyerr',
'execute_result': 'pyout'
}
msg_type = notebook3_format_conversions.get(msg_type, msg_type)
out = NotebookNode(output_type=msg_type)
if 'execution_count' in content:
cell['prompt_number'] = content['execution_count']
out.prompt_number = content['execution_count']
if msg_type in ('status', 'pyin', 'execute_input'):
continue
elif msg_type == 'stream':
out.stream = content['name']
# in msgspec 5, this is name, text
# in msgspec 4, this is name, data
if 'text' in content:
out.text = content['text']
else:
out.text = content['data']
#print(out.text, end='')
elif msg_type in ('display_data', 'pyout'):
for mime, data in content['data'].items():
try:
attr = self.MIME_MAP[mime]
except KeyError:
raise NotImplementedError('unhandled mime type: %s' % mime)
setattr(out, attr, data)
#print(data, end='')
elif msg_type == 'pyerr':
out.ename = content['ename']
out.evalue = content['evalue']
out.traceback = content['traceback']
#logging.error('\n'.join(content['traceback']))
elif msg_type == 'clear_output':
outs = list()
continue
else:
raise NotImplementedError('unhandled iopub message: %s' % msg_type)
outs.append(out)
cell['outputs'] = outs
if status == 'error':
raise NotebookError(traceback_text)
