I am looking to clean up the normal python unittest output. I want to the console output to still be
test_isupper (__main__.TestStringMethods) ... ok
test_split (__main__.TestStringMethods) ... ok
test_upper (__main__.TestStringMethods) ... ok
test_fail (__main__.TestFail) ... ERROR
----------------------------------------------------------------------
Ran 4 tests in 0.001s
OK
But for the fail tests I want to capture the detailed output, and put that in a log file. So instead of it being inline with the console output...
======================================================================
FAIL: test_fail (__main__.TestFail)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test.py", line x
self.assertTrue(False)
AssertionError: False is not True
======================================================================
Gets logged to a file for further investigation, along with any debug level logger output. Is there a way to overload the logger in the unittest.testcase to do what I want?
I should mention I am still very new to python...
I ended up being able to get close enough results to what I wanted by using the testResult object. From that object I was able to get tuples with data on different tests that had passed, failed, or had errors. Then it was a simple create a "prettyPrint" method to take this object and print out the contents nicely.
The exact recipe was:
suite = unittest.TestLoader().loadTestsFromModule( className )
testResult = unittest.TextTestRunner(verbosity=3).run( suite )
Hopefully this helps anyone else looking to do something similar.
The TextTestRunner output can be redirected to a file by providing a stream argument to constructor. Later then, using run() on the suite will return TextTestResult, which you can pretty print. Something like this:
logs_filename = 'logs.txt'
def print_test_results_summary(result):
n_failed = len(result.failures) + len(result.unexpectedSuccesses)
n_crashed = len(result.errors)
n_succeeded = result.testsRun - n_failed - n_crashed
print(f'''See for details {logs_filename} file.
Results: Total: {result.testsRun}, Crashed: {n_crashed}, Failed: {n_failed}, Succeeded: {n_succeeded}''')
with open(logs_filename, 'w') as log_file:
suite = unittest.defaultTestLoader.loadTestsFromModule(className)
testResult = unittest.TextTestRunner(log_file, verbosity=3).run(suite)
print_test_results_summary(testResult)
Related
I am trying to make a simple feedback loop in my nextflow script. I am getting a weird error message that I do not know how to debug. My attempt is modeled after the NextFlow design pattern described here. I need a value to be calculated from a python3 script that operates on an image but pass that value on to subsequent executions of the script. At this stage I just want to get the structure right by adding numbers but I cannot get that to work yet.
my script
feedback_ch = Channel.create()
input_ch = Channel.from(feedback_ch)
process test {
echo true
input:
val chan_a from Channel.from(1,2,3)
val feedback_val from input_ch
output:
stdout output_val into feedback_ch
shell:
'''
#!/usr/bin/python3
new_val = !{chan_a} + !{feedback_val}
print(new_val)
'''
}
The error message I get
Error executing process > 'test (1)'
Caused by:
Process `test (1)` terminated with an error exit status (1)
Command executed:
#!/usr/bin/python3
new_val = 1 + DataflowQueue(queue=[])
print(new_val)
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File ".command.sh", line 3, in <module>
new_val = 1 + DataflowQueue(queue=[])
NameError: name 'DataflowQueue' is not defined
Work dir:
executor > local (1)
[cd/67768e] process > test (1) [100%] 1 of 1, failed: 1 ✘
Error executing process > 'test (1)'
Caused by:
Process `test (1)` terminated with an error exit status (1)
Command executed:
#!/usr/bin/python3
new_val = 1 + DataflowQueue(queue=[])
print(new_val)
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File ".command.sh", line 3, in <module>
new_val = 1 + DataflowQueue(queue=[])
NameError: name 'DataflowQueue' is not defined
Work dir:
/home/cv_proj/work/cd/67768e706f50d7675ae93645a0ce6e
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Anyone have any ideas?
The problem you have says, that you are passing empty DataflowQueue object with input_ch. Nextflow tries to execute it, so it substitutes your python code with variables, resulting in:
#!/usr/bin/python3
new_val = 1 + DataflowQueue(queue=[])
print(new_val)
What is nonsense (You want some number instead of DataflowQueue(queue=[]), don't you?).
Second problem is, that you don't have channels mixed, what seems to be important in this pattern. Anyway, I fixed it, to have proof of concept, working solution:
condition = { it.trim().toInteger() > 10 } // As your output is stdout, you need to trim() to get rid of newline. Then cast to Integer to compare.
feedback_ch = Channel.create()
input_ch = Channel.from(1,2,3).mix( feedback_ch.until(condition) ) // Mixing channel, so we have feedback
process test {
input:
val chan_a from input_ch
output:
stdout output_val into feedback_ch
shell:
var output_val_trimmed = chan_a.toString().trim()
// I am using double quotes, so nextflow interpolates variable above.
"""
#!/usr/bin/python3
new_val = ${output_val_trimmed} + ${output_val_trimmed}
print(new_val)
"""
}
I hope, that it at least set you on right track :)
#!/usr/bin/env python3
import subprocess
import os
if False:
# create log file.
kfd = os.open( 'kk.log', os.O_WRONLY )
# redirect stdout & err to a log file.
os.close(1)
os.dup(kfd)
os.close(2)
os.dup(kfd)
subprocess.run([ "echo", "hello world"], check=True )
% ./kk.py
hello world
%
The above works fine, but if you try edit file, and replace False with true:
% ./kk.py
% more kk.log
Traceback (most recent call last):
File "./kk.py", line 16, in <module>
subprocess.run([ "echo", "hello world"], check=True )
File "/usr/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['echo', 'hello world']' returned
non-zero exit status 1.
%
We don't get the output, and the process error exits...
I would have expected it to just work, writing to kk.log.
You probably want to say something like this instead:
#!/usr/bin/env python3
import subprocess
import os
if True:
# create log file.
kfd = os.open( 'kk.log', os.O_WRONLY | os.O_CREAT )
# redirect stdout & err to a log file.
os.dup2(kfd, 1)
os.dup2(kfd, 2)
subprocess.run([ "echo", "hello world"], check=True )
Notice the use of os.dup2. There are two reasons for that. First and foremost, resulting file descriptors are inheritable. Your echo had no open stdout/-err actually and hence failed (You can run the following in shell to echo with just stdout closed to check out the behavior: /bin/echo hello world 1>&-). Also note, it may not always hold true that if I closed stdout (1), the lowest descriptor (and result of os.dup) is 1. Someone could have closed your stdin (0) before running the script (same goes for stderr).
The background story to file descriptors inheritance is in the PEP-446.
I've also added os.O_CREAT, since my first failure trying to reproduce your problem was non-existing kk.log.
Needless to say, unless trying to play with interfaces into the os (perhaps as a an exercise), I guess you should normally stick to subprocess itself.
I'm running pytest to check a function that uses pdfminer to convert PDF to text. The function works when doing $ python function.py and the result is what I expect it to be. I should also point out that I'm using a stream when parsing the file (io.BytesIO) and this stream is the reason my test fails.
Running pytest the function fails with a PDFSyntaxError.
# function.py
...
from pdfminer.pdfparser import PDFParser
from pdfminer.document import PDFDocument
req = requests.get(url_pointing_to_pdf_file)
pdf = io.BytesIO(req.content)
parser = PDFParser(pdf)
document = PDFDocument(parser, password=None) # this fails
...
pytest calls the init method in pdfdocument.py (part of the pdfminer library) and stops here:
for xref in xrefs:
trailer = xref.get_trailer()
...
if 'Root' in trailer:
self.catalog = dict_value(trailer['Root'])
break
else:
raise PDFSyntaxError('No /Root object! - Is this really a PDF?')
...
And this is what pytest shows when testing the function fails:
tests/test_function.py:11:
----------------------------------------------------
.../function.py:157: in function
**document = PDFDocument(parser, password=None)**
...
E pdfminer.pdfparser.PDFSyntaxError: No /Root object! - Is this really a PDF?
lib/python3.6/site-packages/pdfminer/pdfdocument.py:583:PDFSyntaxError
Running the test with a PDF file stored in the same directory as function.py is successful, so the culprit is the io.BytesIO format of the downloaded PDF file. Since I want to use a stream with function.py I would like to know if there is a better way to do this.
I'm porting some code from perl (log4perl) and java (slf4j). All is fine except for logging.critical() does not dump stacktrace and die like it does in the other frameworks, need to add a lot of extra code, logger.exception() also only writes error.
Today I do:
try:
errmsg = "--id={} not found on --host={}".format(args.siteid, args.host)
raise GX8Exception(errmsg)
except GX8Exception as e:
log.exception(e)
sys.exit(-1)
This produces:
2018-01-10 10:09:56,814 [ERROR ] root --id=7A4A7845-7559-4F89-B678-8ADFECF5F7C3 not found on --host=welfare-qa
Traceback (most recent call last):
File "./gx8-controller.py", line 85, in <module>
raise GX8Exception(errmsg)
GX8Exception: --id=7A4A7845-7559-4F89-B678-8ADFECF5F7C3 not found on --host=welfare-qa
Is there a way to config pythonmodule logger to do this, or any other framework to do the same:
log.critical("--id={} not found on --host={}".format(args.siteid, args.host))
One approach would be to create a custom Handler that does nothing but pass log messages on to its super and then exit if the log level is high enough:
import logging
class ExitOnExceptionHandler(logging.StreamHandler):
def emit(self, record):
super().emit(record)
if record.levelno in (logging.ERROR, logging.CRITICAL):
raise SystemExit(-1)
logging.basicConfig(handlers=[ExitOnExceptionHandler()], level=logging.DEBUG)
logger = logging.getLogger('MYTHING')
def causeAProblem():
try:
raise ValueError("Oh no!")
except Exception as e:
logger.exception(e)
logger.warning('Going to try something risky...')
causeAProblem()
print("This won't get printed")
Output:
rat#pandion:~$ python test.py
ERROR:root:Oh no!
Traceback (most recent call last):
File "test.py", line 14, in causeAProblem
raise ValueError("Oh no!")
ValueError: Oh no!
rat#pandion:~$ echo $?
255
However, this could cause unexpected behavior for users of your code. It would be much more straightfoward, if you want to log an exception and exit, to simply leave the exception uncaught. If you want to log a traceback and exit wherever the code is currently calling logging.critical, change it to raise an exception instead.
I inherited some code where I could not change the handler class. I resorted to run time patching of the handler which is a variation on the solution by #nathan-vērzemnieks:
import types
def patch_logging_handler(logger):
def custom_emit(self, record):
self.orig_emit(record)
if record.levelno == logging.FATAL:
raise SystemExit(-1)
handler = logger.handlers[0]
setattr(handler, 'orig_emit', handler.emit)
setattr(handler, 'emit', types.MethodType(custom_emit, handler))
Nathans anwser is great! Been looking for this for a long time,
will just add that you can also do:
if record.levelno >= logging.ERROR:
instead of
if record.levelno in (logging.ERROR, logging.CRITICAL):
to set the minimum level that would cause an exit.
I've got a Python 3 script that gets some JSON from a URL, processes it, and notifies me if there's any significant changes to the data I get. I've tried using notify2 and PyGObject's libnotify bindings (gi.repository.Notify) and get similar results with either method. This script works a-ok when I run it from a terminal, but chokes when cron tries to run it.
import notify2
from gi.repository import Notify
def notify_pygobject(new_stuff):
Notify.init('My App')
notify_str = '\n'.join(new_stuff)
print(notify_str)
popup = Notify.Notification.new('Hey! Listen!', notify_str,
'dialog-information')
popup.show()
def notify_notify2(new_stuff):
notify2.init('My App')
notify_str = '\n'.join(new_stuff)
print(notify_str)
popup = notify2.Notification('Hey! Listen!', notify_str,
'dialog-information')
popup.show()
Now, if I create a script that calls notify_pygobject with a list of strings, cron throws this error back at me via the mail spool:
Traceback (most recent call last):
File "/home/p0lar_bear/Documents/devel/notify-test/test1.py", line 3, in <module>
main()
File "/home/p0lar_bear/Documents/devel/notify-test/test1.py", line 4, in main
testlib.notify(notify_projects)
File "/home/p0lar_bear/Documents/devel/notify-test/testlib.py", line 8, in notify
popup.show()
File "/usr/lib/python3/dist-packages/gi/types.py", line 113, in function
return info.invoke(*args, **kwargs)
gi._glib.GError: Error spawning command line `dbus-launch --autolaunch=776643a88e264621544719c3519b8310 --binary-syntax --close-stderr': Child process exited with code 1
...and if I change it to call notify_notify2() instead:
Traceback (most recent call last):
File "/home/p0lar_bear/Documents/devel/notify-test/test2.py", line 3, in <module>
main()
File "/home/p0lar_bear/Documents/devel/notify-test/test2.py", line 4, in main
testlib.notify(notify_projects)
File "/home/p0lar_bear/Documents/devel/notify-test/testlib.py", line 13, in notify
notify2.init('My App')
File "/usr/lib/python3/dist-packages/notify2.py", line 93, in init
bus = dbus.SessionBus(mainloop=mainloop)
File "/usr/lib/python3/dist-packages/dbus/_dbus.py", line 211, in __new__
mainloop=mainloop)
File "/usr/lib/python3/dist-packages/dbus/_dbus.py", line 100, in __new__
bus = BusConnection.__new__(subclass, bus_type, mainloop=mainloop)
File "/usr/lib/python3/dist-packages/dbus/bus.py", line 122, in __new__
bus = cls._new_for_bus(address_or_type, mainloop=mainloop)
dbus.exceptions.DBusException: org.freedesktop.DBus.Error.NotSupported: Unable to autolaunch a dbus-daemon without a $DISPLAY for X11
I did some research and saw suggestions to put a PATH= into my crontab, or to export $DISPLAY (I did this within the script by calling os.system('export DISPLAY=:0')) but neither resulted in any change...
You are in the right track. This behavior is because cron is run in a multiuser headless environment (think of it as running as root in a terminal without GUI, kinda), so he doesn't know to what display (X Window Server session) and user target to. If your application open, for example, windows or notification to some user desktop, then this problems is raised.
I suppose you edit your cron with crontab -e and the entry looks like this:
m h dom mon dow command
Something like:
0 5 * * 1 /usr/bin/python /home/foo/myscript.py
Note that I use full path to Python, is better if this kind of situation where PATH environment variable could be different.
Then just change to:
0 5 * * 1 export DISPLAY=:0 && /usr/bin/python /home/foo/myscript.py
If this still doesn't work you need to allow your user to control the X Windows server:
Add to your .bash_rc:
xhost +si:localuser:$(whoami)
If you want to set the DISPLAY from within python like you attempted with os.system('export DISPLAY=:0'), you can do something like this
import os
if not 'DISPLAY' in os.environ:
os.environ['DISPLAY'] = ':0'
This will respect any DISPLAY that users may have on a multi-seat box, and fall back to the main head :0.
If ur notify function, regardless of Python version or notify library, does not track the notify id [in a Python list] and deleting the oldest before the queue is completely full or on error, then depending on the dbus settings (in Ubuntu it's 21 notification max) dbus will throw an error, maximum notifications reached!
from gi.repository import Notify
from gi.repository.GLib import GError
# Normally implemented as class variables.
DBUS_NOTIFICATION_MAX = 21
lstNotify = []
def notify_show(strSummary, strBody, strIcon="dialog-information"):
try:
# full queue, delete oldest
if len(lstNotify)==DBUS_NOTIFICATION_MAX:
#Get oldest id
lngOldID = lstNotify.pop(0)
Notify.Notification.clear(lngOldID)
del lngOldID
if len(lstNotify)==0:
lngLastID = 0
else:
lngLastID = lstNotify[len(lstNotify) -1] + 1
lstNotify.append(lngLastID)
notify = Notify.Notification.new(strSummary, strBody, strIcon)
notify.set_property('id', lngLastID)
print("notify_show id %(id)d " % {'id': notify.props.id} )
#notify.set_urgency(Notify.URGENCY_LOW)
notify.show()
except GError as e:
# Most likely exceeded max notifications
print("notify_show error ", e )
finally:
if notify is not None:
del notify
Although it may somehow be possible to ask dbus what the notification queue max limit is. Maybe someone can help ... Improve this until perfection.
Plz
Cuz gi.repository complete answers are spare to come by.