I'm wondering if jupyter_client is able to return code sent in to the execute function as HTML somehow?
I'm also wondering if I can do the same with stdout and stderr, as well as markdown?
If jupyter_client cannot do this, is there a jupyter library that does?
Adapting the solution from here might help. This adaptation takes the request of 1+1 or msg_id=c.execute('1+1') and returns the result formatted in html as bold red text with this display(HTML('<div style="color:Red;"><b>' + res + '</b></div>')) using IPython's display module. The kernel info status has been commented out but left for reference.
from subprocess import PIPE
from jupyter_client import KernelManager
from IPython.display import display, HTML
from queue import Empty
km = KernelManager(kernel_name='python3')
km.start_kernel()
# print(km.is_alive())
try:
c = km.client()
msg_id=c.execute('1+1')
state='busy'
data={}
while state!='idle' and c.is_alive():
try:
msg=c.get_iopub_msg(timeout=1)
if not 'content' in msg: continue
content = msg['content']
if 'data' in content:
data=content['data']
if 'execution_state' in content:
state=content['execution_state']
except Empty:
pass
res = data['text/plain']
# print(data)
display(HTML('<div style="color:Red;"><b>' + res + '</b></div>'))
except KeyboardInterrupt:
pass
finally:
km.shutdown_kernel()
# print(km.is_alive())
Also see here for more info.
Related
I'm executing the Dagster tutorial, and I got stuck at the Multiple and Conditional Outputs step.
In the solid definitions, it asks to declare (among other things):
output_defs=[
OutputDefinition(
name="hot_cereals", dagster_type=DataFrame, is_required=False
),
OutputDefinition(
name="cold_cereals", dagster_type=DataFrame, is_required=False
),
],
But there's no information where the DataFrame cames from.
Firstly I have tried with pandas.DataFrame but I faced the error: {dagster_type} is not a valid dagster type. It happens when I try to submit it via $ dagit -f multiple_outputs.py.
Then I installed the dagster_pyspark and gave a try with the dagster_pyspark.DataFrame. This time I managed to summit the DAG to the UI. However, when I run it from the UI, I got the following error:
dagster.core.errors.DagsterTypeCheckDidNotPass: Type check failed for step output hot_cereals of type PySparkDataFrame.
File "/Users/bambrozio/.local/share/virtualenvs/dagster-tutorial/lib/python3.7/site-packages/dagster/core/execution/plan/execute_plan.py", line 210, in _dagster_event_sequence_for_step
for step_event in check.generator(step_events):
File "/Users/bambrozio/.local/share/virtualenvs/dagster-tutorial/lib/python3.7/site-packages/dagster/core/execution/plan/execute_step.py", line 273, in core_dagster_event_sequence_for_step
for evt in _create_step_events_for_output(step_context, user_event):
File "/Users/bambrozio/.local/share/virtualenvs/dagster-tutorial/lib/python3.7/site-packages/dagster/core/execution/plan/execute_step.py", line 298, in _create_step_events_for_output
for output_event in _type_checked_step_output_event_sequence(step_context, output):
File "/Users/bambrozio/.local/share/virtualenvs/dagster-tutorial/lib/python3.7/site-packages/dagster/core/execution/plan/execute_step.py", line 221, in _type_checked_step_output_event_sequence
dagster_type=step_output.dagster_type,
Does anyone know how to fix it? Thanks for the help!
As Arthur pointed out, the full tutorial code is available on Dagster's github.
However, you do not need dagster_pandas, rather, the key lines missing from your code are:
if typing.TYPE_CHECKING:
DataFrame = list
else:
DataFrame = PythonObjectDagsterType(list, name="DataFrame") # type: Any
The reason for the above structure is to achieve MyPy compliance, see the Types & Expectations section of the tutorial.
See also the documentation on Dagster types.
I was stuck here, too, but luckily I found the updated source code.
They have updated the docs so that the OutputDefinition is defined beforehand.
Update your code before sorting and pipeline like below:
import csv
import os
from dagster import (
Bool,
Field,
Output,
OutputDefinition,
execute_pipeline,
pipeline,
solid,
)
#solid
def read_csv(context, csv_path):
lines = []
csv_path = os.path.join(os.path.dirname(__file__), csv_path)
with open(csv_path, "r") as fd:
for row in csv.DictReader(fd):
row["calories"] = int(row["calories"])
lines.append(row)
context.log.info("Read {n_lines} lines".format(n_lines=len(lines)))
return lines
#solid(
config_schema={
"process_hot": Field(Bool, is_required=False, default_value=True),
"process_cold": Field(Bool, is_required=False, default_value=True),
},
output_defs=[
OutputDefinition(name="hot_cereals", is_required=False),
OutputDefinition(name="cold_cereals", is_required=False),
],
)
def split_cereals(context, cereals):
if context.solid_config["process_hot"]:
hot_cereals = [cereal for cereal in cereals if cereal["type"] == "H"]
yield Output(hot_cereals, "hot_cereals")
if context.solid_config["process_cold"]:
cold_cereals = [cereal for cereal in cereals if cereal["type"] == "C"]
yield Output(cold_cereals, "cold_cereals")
You can also find the whole lines of codes from here.
Try first to install the dagster pandas integration:
pip install dagster_pandas
Then do:
from dagster_pandas import DataFrame
You can find the code from the tutorial here.
How can I use Asynchronous Widgets on jupyter lab?
I'm trying to reproduce the official Asynchronous Widgets-Example on jupyter lab, but the await never continues.
Setup / reproduction
docker run --rm -p 8888:8888 -e JUPYTER_ENABLE_LAB=yes jupyter/datascience-notebook start-notebook.sh --NotebookApp.token=''
firefox 0.0.0.0:8888
create a new python3 notebook
create a cell and enter the code below
run cell
move slider
code for the cell
%gui asyncio
import asyncio
def wait_for_change(widget, value):
future = asyncio.Future()
def getvalue(change):
# make the new value available
future.set_result(change.new)
widget.unobserve(getvalue, value)
widget.observe(getvalue, value)
return future
from ipywidgets import IntSlider
slider = IntSlider()
async def f():
for i in range(10):
print('did work %s'%i)
#x = await asyncio.sleep(1)
x = await wait_for_change(slider, 'value')
print('async function continued with value %s'%x)
asyncio.ensure_future(f())
#task = asyncio.create_task(f())
slider
Expected result
The cell outputs
did work 0
async function continued with value 1
did work 1
async function continued with value 2
[...]
Actual output
nothing after the first did work 0
Notes
I'm specifically talking about jupyter lab and not about regular jupyter notebooks
There is no error-message or anything. The expected output just doesn't happen
The minimal asyncio-example does work in jupyter lab:
import asyncio
async def main():
print('hello')
await asyncio.sleep(1)
print('world')
await main()
when you leave out the -e JUPYTER_ENABLE_LAB=yes, then you get a regular jupyter notebook without jupyter lab and the expected result happens.
this is not a duplicate of ipywidgets widgets values not changing or Jupyter Interactive Widget not executing properly, because these questions nether include jupyter lab nor asyncio
Actually it works, but jupyter lose print output.
Try this code:
from IPython.display import display
import ipywidgets as widgets
out = widgets.Output()
import asyncio
def wait_for_change(widget, value):
future = asyncio.Future()
def getvalue(change):
# make the new value available
future.set_result(change.new)
widget.unobserve(getvalue, value)
widget.observe(getvalue, value)
return future
from ipywidgets import IntSlider
slider = IntSlider()
# Now the key: the container is displayed (while empty) in the main thread
async def f():
for i in range(10):
out.append_stdout('did work %s'%i)
x = await wait_for_change(slider, 'value')
out.append_stdout('async function continued with value %s'%x)
asyncio.ensure_future(f())
display(slider)
display(out)
You can find more details here: https://github.com/jupyter-widgets/ipywidgets/issues/2567#issuecomment-535971252
I've had luck with jupyter-ui-poll to synchronize widget activity with the Jupyter Python kernal:
https://github.com/Kirill888/jupyter-ui-poll
In particular I used it here:
https://github.com/AaronWatters/jp_doodle/blob/master/jp_doodle/auto_capture.py
Works for me.
Hope that helps!
I'm trying to use the below mail function for python3 which is throwing error NameError: name 'file' is not defined which its works perfectly for python2.
I got to know file() is not supported in Python 3 what will be substitute of file.
#!/usr/bin/env python3
from subprocess import Popen, PIPE
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
import os
############ File comparison & sendmail part starts here ########
def ps_Mail():
filename = "/tmp/ps_msg"
f = file(filename)
if os.path.exists(filename) and os.path.getsize(filename) > 0:
mailp = Popen(["/usr/sbin/sendmail", "-t", "-oi"], stdin=PIPE)
msg = MIMEMultipart('alternative')
msg['To'] = "sam#seemac.com"
msg['Subject'] = "Uhh!! Unsafe process seen"
msg['From'] = "psCheck#seemac.com"
msg1 = MIMEText(filename.read(), 'text')
msg.attach(msg1)
mailp.communicate(msg.as_string())
ps_Mail()
I have edited your code and this should work, please try this...
There are two key things to change universal_newlines=True and use open() instead of file().
#!/usr/bin/env python3
from subprocess import Popen, PIPE
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
import os
############ File comparison & sendmail part starts here ########
def ps_Mail():
filename = "/tmp/ps_msg"
f = open(filename)
if os.path.exists(filename) and os.path.getsize(filename) > 0:
mailp = Popen(["/usr/sbin/sendmail", "-t", "-oi"], stdin=PIPE, universal_newlines=True)
msg = MIMEMultipart('alternative')
msg['To'] = "sam#seemac.com"
msg['Subject'] = "Uhh!! Unsafe process seen"
msg['From'] = "psCheck#seemac.com"
msg1 = MIMEText(filename.read(), 'text')
msg.attach(msg1)
mailp.communicate(msg.as_string())
ps_Mail()
For more details....
What is the difference between using universal_newlines=True (with bufsize=1) and using default arguments with Popen
The default values are: universal_newlines=False (meaning input/output is accepted as bytes, not Unicode strings plus the universal newlines mode handling (hence the name of the parameter though text_mode might have been a better name here) is disabled -- you get binary data as is (unless POSIX layer on Windows messes it up) and bufsize=-1 (meaning the streams are fully buffered -- the default buffer size is used).
universal_newlines=True uses locale.getpreferredencoding(False) character encoding to decode bytes (that may be different from ascii encoding used in your code).
If universal_newlines=False then for line in Robocopy.stdout: iterates over b'\n'-separated lines. If the process uses non-ascii encoding e.g., UTF-16 for its output then even if os.linesep == '\n' on your system; you may get a wrong result. If you want to consume text lines, use the text mode: pass universal_newlines=True or use io.TextIOWrapper(process.stdout) explicitly.
The second version does include universal_newlines and therefore I specify a bufsize.
In general, It is not necessary to specify bufsize if you use universal_newlines (you may but it is not required). And you don't need to specify bufsize in your case. bufsize=1 enables line-bufferred mode (the input buffer is flushed automatically on newlines if you would write to process.stdin) otherwise it is equivalent to the default bufsize=-1.
My app interfaces with the IPython Qt shell with code something like this:
from IPython.core.interactiveshell import ExecutionResult
shell = self.kernelApp.shell # ZMQInteractiveShell
code = compile(script, file_name, 'exec')
result = ExecutionResult()
shell.run_code(code, result=result)
if result:
self.show_result(result)
The problem is: how can show_result show the traceback resulting from exceptions in code?
Neither the error_before_exec nor the error_in_exec ivars of ExecutionResult seem to give references to the traceback. Similarly, neither sys nor shell.user_ns.namespace.get('sys') have sys.exc_traceback attributes.
Any ideas? Thanks!
Edward
IPython/core/interactiveshell.py contains InteractiveShell._showtraceback:
def _showtraceback(self, etype, evalue, stb):
"""Actually show a traceback. Subclasses may override..."""
print(self.InteractiveTB.stb2text(stb), file=io.stdout)
The solution is to monkey-patch IS._showtraceback so that it writes to sys.stdout (the Qt console):
from __future__ import print_function
...
shell = self.kernelApp.shell # ZMQInteractiveShell
code = compile(script, file_name, 'exec')
def show_traceback(etype, evalue, stb, shell=shell):
print(shell.InteractiveTB.stb2text(stb), file=sys.stderr)
sys.stderr.flush() # <==== Oh, so important
old_show = getattr(shell, '_showtraceback', None)
shell._showtraceback = show_traceback
shell.run_code(code)
if old_show: shell._showtraceback = old_show
Note: there is no need to pass an ExecutionResult object to shell.run_code().
EKR
I'm creating a fork of my Plone site (which has not been forked for a long time). This site has a special catalog object for user profiles (a special Archetypes-based object type) which is called portal_user_catalog:
$ bin/instance debug
>>> portal = app.Plone
>>> print [d for d in portal.objectMap() if d['meta_type'] == 'Plone Catalog Tool']
[{'meta_type': 'Plone Catalog Tool', 'id': 'portal_catalog'},
{'meta_type': 'Plone Catalog Tool', 'id': 'portal_user_catalog'}]
This looks reasonable because the user profiles don't have most of the indexes of the "normal" objects, but have a small set of own indexes.
Since I found no way how to create this object from scratch, I exported it from the old site (as portal_user_catalog.zexp) and imported it in the new site. This seemed to work, but I can't add objects to the imported catalog, not even by explicitly calling the catalog_object method. Instead, the user profiles are added to the standard portal_catalog.
Now I found a module in my product which seems to serve the purpose (Products/myproduct/exportimport/catalog.py):
"""Catalog tool setup handlers.
$Id: catalog.py 77004 2007-06-24 08:57:54Z yuppie $
"""
from Products.GenericSetup.utils import exportObjects
from Products.GenericSetup.utils import importObjects
from Products.CMFCore.utils import getToolByName
from zope.component import queryMultiAdapter
from Products.GenericSetup.interfaces import IBody
def importCatalogTool(context):
"""Import catalog tool.
"""
site = context.getSite()
obj = getToolByName(site, 'portal_user_catalog')
parent_path=''
if obj and not obj():
importer = queryMultiAdapter((obj, context), IBody)
path = '%s%s' % (parent_path, obj.getId().replace(' ', '_'))
__traceback_info__ = path
print [importer]
if importer:
print importer.name
if importer.name:
path = '%s%s' % (parent_path, 'usercatalog')
print path
filename = '%s%s' % (path, importer.suffix)
print filename
body = context.readDataFile(filename)
if body is not None:
importer.filename = filename # for error reporting
importer.body = body
if getattr(obj, 'objectValues', False):
for sub in obj.objectValues():
importObjects(sub, path+'/', context)
def exportCatalogTool(context):
"""Export catalog tool.
"""
site = context.getSite()
obj = getToolByName(site, 'portal_user_catalog', None)
if tool is None:
logger = context.getLogger('catalog')
logger.info('Nothing to export.')
return
parent_path=''
exporter = queryMultiAdapter((obj, context), IBody)
path = '%s%s' % (parent_path, obj.getId().replace(' ', '_'))
if exporter:
if exporter.name:
path = '%s%s' % (parent_path, 'usercatalog')
filename = '%s%s' % (path, exporter.suffix)
body = exporter.body
if body is not None:
context.writeDataFile(filename, body, exporter.mime_type)
if getattr(obj, 'objectValues', False):
for sub in obj.objectValues():
exportObjects(sub, path+'/', context)
I tried to use it, but I have no idea how it is supposed to be done;
I can't call it TTW (should I try to publish the methods?!).
I tried it in a debug session:
$ bin/instance debug
>>> portal = app.Plone
>>> from Products.myproduct.exportimport.catalog import exportCatalogTool
>>> exportCatalogTool(portal)
Traceback (most recent call last):
File "<console>", line 1, in <module>
File ".../Products/myproduct/exportimport/catalog.py", line 58, in exportCatalogTool
site = context.getSite()
AttributeError: getSite
So, if this is the way to go, it looks like I need a "real" context.
Update: To get this context, I tried an External Method:
# -*- coding: utf-8 -*-
from Products.myproduct.exportimport.catalog import exportCatalogTool
from pdb import set_trace
def p(dt, dd):
print '%-16s%s' % (dt+':', dd)
def main(self):
"""
Export the portal_user_catalog
"""
g = globals()
print '#' * 79
for a in ('__package__', '__module__'):
if a in g:
p(a, g[a])
p('self', self)
set_trace()
exportCatalogTool(self)
However, wenn I called it, I got the same <PloneSite at /Plone> object as the argument to the main function, which didn't have the getSite attribute. Perhaps my site doesn't call such External Methods correctly?
Or would I need to mention this module somehow in my configure.zcml, but how? I searched my directory tree (especially below Products/myproduct/profiles) for exportimport, the module name, and several other strings, but I couldn't find anything; perhaps there has been an integration once but was broken ...
So how do I make this portal_user_catalog work?
Thank you!
Update: Another debug session suggests the source of the problem to be some transaction matter:
>>> portal = app.Plone
>>> puc = portal.portal_user_catalog
>>> puc._catalog()
[]
>>> profiles_folder = portal.some_folder_with_profiles
>>> for o in profiles_folder.objectValues():
... puc.catalog_object(o)
...
>>> puc._catalog()
[<Products.ZCatalog.Catalog.mybrains object at 0x69ff8d8>, ...]
This population of the portal_user_catalog doesn't persist; after termination of the debug session and starting fg, the brains are gone.
It looks like the problem was indeed related with transactions.
I had
import transaction
...
class Browser(BrowserView):
...
def processNewUser(self):
....
transaction.commit()
before, but apparently this was not good enough (and/or perhaps not done correctly).
Now I start the transaction explicitly with transaction.begin(), save intermediate results with transaction.savepoint(), abort the transaction explicitly with transaction.abort() in case of errors (try / except), and have exactly one transaction.commit() at the end, in the case of success. Everything seems to work.
Of course, Plone still doesn't take this non-standard catalog into account; when I "clear and rebuild" it, it is empty afterwards. But for my application it works well enough.