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JRC JJ1000 + dronekit >> ERROR:dronekit.mavlink:Exception in MAVLink input loop

I am trying to connect JRC JJ1000 drone using dronekit + python.
when executing the connect command:
dronekit.connect('com3', baud=115200, heartbeat_timeout=30)
I am getting the following error:
ERROR:dronekit.mavlink:Exception in MAVLink input loop
Traceback (most recent call last):
File "C:\Python37\lib\site-packages\dronekit\mavlink.py", line 211, in mavlink_thread_in
fn(self)
File "C:\Python37\lib\site-packages\dronekit\__init__.py", line 1371, in listener
self._heartbeat_error)
dronekit.APIException: No heartbeat in 5 seconds, aborting.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Python37\lib\site-packages\dronekit\__init__.py", line 3166, in connect
vehicle.initialize(rate=rate, heartbeat_timeout=heartbeat_timeout)
File "C:\Python37\lib\site-packages\dronekit\__init__.py", line 2275, in initialize
raise APIException('Timeout in initializing connection.')
dronekit.APIException: Timeout in initializing connection.
I left no store unturned but no progress. I also tried both Python 2.7 and 3.7 with same result.

I have been getting the same error. I am using some custom code in a docker container to run simulations with dronekit and ArduPilot. The error is intermittent. So far it seems like the only way to get the error to stop is to:
Close all docker containers.
Open windows task manager and wait for vmmem to lower memory usage (5-10m).
Try again.
Maybe the problems are related somehow. To me it seems like the connection might be in use by a previous instance and it was not properly close. Since waiting for vmmem to free up resources appears to fix it. I would prefer a better solution if anyone finds one!
We are using python code like this to connect:
from dronekit import connect
...
# try to connect 5 times
while connected == False and fails < 5:
try:
vehicle = connect(connection_string, wait_ready=True)
except:
fails += 1
time.sleep(3)
print("Failed to connect to local mavlink sleeping for 3 seconds")
else:
connected = True
Where the connection_string is of the form:
"tcp:host:port"
Also, the documentation states "If the baud rate is not set correctly, connect may fail with a timeout error. It is best to set the baud rate explicitly." Are you sure that you have the correct baud rate?

psutil.AccessDenied when using StanfordCoreNLP in Pycharm? [duplicate]

This question already has answers here:
psutil.AccessDenied Error while trying to load StanfordCoreNLP
(3 answers)
Closed 2 years ago.
# coding=utf-8
from stanfordcorenlp import StanfordCoreNLP
nlp = StanfordCoreNLP(r'/Users/silas/stanford-corenlp/', lang='zh')
sentence = '清华大学位于北京。'
print nlp.word_tokenize(sentence)
print nlp.pos_tag(sentence)
print nlp.ner(sentence)
print nlp.parse(sentence)
print nlp.dependency_parse(sentence)
nlp.close()
I'm using Mac. Java, NLKT, and Stanforcorenlp toolkit are all ready. When I'm testing the project, the error came out.
Traceback (most recent call last):
line 5, in <module>
nlp = StanfordCoreNLP(r'/Users/silas/stanford-corenlp/', lang='zh')
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/stanfordcorenlp/corenlp.py", line 79, in __init__
if port_candidate not in [conn.laddr[1] for conn in psutil.net_connections()]:
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/psutil/__init__.py", line 2120, in net_connections
return _psplatform.net_connections(kind)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/psutil/_psosx.py", line 255, in net_connections
cons = Process(pid).connections(kind)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/psutil/_psosx.py", line 347, in wrapper
raise AccessDenied(self.pid, self._name)
psutil._exceptions.AccessDenied: psutil.AccessDenied (pid=25422)
I guess it is because the Pycharm project isn't running under a root user. But how can I configure the IDE to fix the problem?

Unfortunately, if you look at the psutil project in _psosx.py, under net_connections, line 243 says..
Note: on macOS this will fail with AccessDenied unless the process is owned by root.
That means that you'll need to run as root by doing something like sudo pycharm.sh.
If you don't want to run your entire IDE as root, there's a few examples on SO on how you can run a specific script with super-user privileges. For instance see Debugging in pyCharm with sudo privileges.

This problem seems to be specific to Mac OS X which would not allow Python to check the current port.
Comment this portion of code of corenlp.py file:
if self.port is None:
for port_candidate in range(9000, 65535):
if port_candidate not in [conn.laddr[1] for conn in psutil.net_connections()]:
self.port = port_candidate
break
if self.port in [conn.laddr[1] for conn in psutil.net_connections()]:
raise IOError('Port ' + str(self.port) + ' is already in use.')
Replace by this line:
self.port = 9999
Source: https://github.com/Lynten/stanford-corenlp/issues/26#issuecomment-445507811
Another solution is to run StanfordCoreNLP with a sudo command line.

How to install packages with python scripts

I want to install a package with a python script. I have read the documentation about PackageManager API (http://doc.aldebaran.com/2-4/naoqi/core/packagemanager-api.html):
So I have packaged the app with choregraphe as it is described in http://doc.aldebaran.com/2-4/naoqi/core/packagemanager.html and I have tried to install it with a python script that looks like:
import qi
import sys
if __name__ == '__main__':
ip = "11.1.11.111"
port = 9559
session = qi.Session()
try:
session.connect("tcp://" + ip + ":" + str(port))
except RuntimeError:
print ("Can't connect to Naoqi at ip \"" + ip + "\" on port " + str(port))
sys.exit(1)
service = session.service("PackageManager")
package = "C:\\test_package_handlers_01-835a92-1.0.0.pkg"
# this is to see if the problem is that python can not locate the file
with open(package) as f:
print f
service.install(package)
And here is what I receive as an error:
# provided package could be opened
<open file 'C:\\test_package_handlers_01-835a92-1.0.0.pkg', mode 'r' at 0x02886288>
Traceback (most recent call last):
File "C:/test.py", line 24, in <module>
service.install(package)
RuntimeError: C:\test_package_handlers_01-835a92-1.0.0.pkg: no such file
I guess this is because the package must be uploaded on the robot and the package file path must be the one that is on the robot.
EDITED
I have added the package to a choreographe blank project and run this blank project on the robot. This way the package was saved to the robot with path /home/nao/.local/share/PackageManager/apps/.lastUploadedChoregrapheBehavior/test_package_handlers_01-835a92-1.0.0.pkg and when I have changed the path in my script ("C:\\test_package_handlers_01-835a92-1.0.0.pkg" with "/home/nao/.local/share/PackageManager/apps/.lastUploadedChoregrapheBehavior/test_package_handlers_01-835a92-1.0.0.pkg") the script worked as it was intended and the package was installed on the robot.
So is there a way to install packages from my PC without uploading them to the robot, because otherwise it is better to use Choregraphe to upload projects.
Maybe it is good to give the following explanation of what I want to achieve:
I have a folder on my PC with 20 packages for example
I want to install all those 20 packages with one python script
There is a python script that installs all the packages from the folder when it is invoked like this:
python package_installer.py path_to_packages_folder
EDITED_2
import qi
import ftplib
import os
ROBOT_URL = "10.80.129.90"
print "Uploading PKG"
pkg_file = "my-application-0.0.1.pkg"
pkg_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), pkg_file)
ftp = ftplib.FTP(ROBOT_URL)
ftp.login("nao", "nao")
with open(pkg_path) as pkg:
ftp.storbinary("STOR "+pkg_file, pkg)
print "Connecting NAOqi session"
app = qi.Application(url='tcp://'+ROBOT_URL+':9559')
app.start()
session = app.session
print "Installing app"
packagemgr = session.service("PackageManager")
packagemgr.install("/home/nao/"+pkg_file)
print "Cleaning robot"
ftp.delete(pkg_file)
ftp.quit()
print "End"
app.stop()
This piece of code ftp = ftplib.FTP(ROBOT_URL) throws the following exception:
Traceback (most recent call last):
File "C:/Stefan/DSK_PEPPER_clode_2/PythonScripts/_local_testing/uploading_and_installing_package.py", line 11, in <module>
ftp = ftplib.FTP(ROBOT_URL)
File "C:\Python27\lib\ftplib.py", line 120, in __init__
self.connect(host)
File "C:\Python27\lib\ftplib.py", line 135, in connect
self.sock = socket.create_connection((self.host, self.port), self.timeout)
File "C:\Python27\lib\socket.py", line 575, in create_connection
raise err
socket.error: [Errno 10061] No connection could be made because the target machine actively refused it
Also when I connect to the robot with username 'nao' and pass 'nao' as described in http://doc.aldebaran.com/2-5/dev/tools/opennao.html and then try to create a folder in /home/nao/.local/share/PackageManager/apps/ with sudo mkdir it informs me that: Sorry, user nao is not allowed to execute '/bin/mkdir dasdas' as root on Pepper.. If I use only mkdir here is what it tells me: mkdir: cannot create directory 'new_folder': Permission denied

Using qibuild, you can also directly install using:
qipkg deploy-package /path/to/my-package.pkg --url nao#10.10.23.45

You indeed need to upload the file before. You can use scp or sftp to do this. Once the .pkg is on the robot then you can use PackageManager.install.
Imagine something like:
import qi
import paramiko
import os
ROBOT_URL = "10.80.129.90"
print "Uploading PKG"
pkg_file = "my-application-0.0.1.pkg"
pkg_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), pkg_file)
transport = paramiko.Transport((ROBOT_URL, 22))
transport.connect(username="nao", password="nao")
sftp = paramiko.SFTPClient.from_transport(transport)
sftp.put(pkg_path, pkg_file)
print "Connecting NAOqi session"
app = qi.Application(url='tcp://'+ROBOT_URL+':9559')
app.start()
session = app.session
print "Installing app"
packagemgr = session.service("PackageManager")
packagemgr.install("/home/nao/"+pkg_file)
print "Cleaning robot"
sftp.remove(pkg_file)
sftp.close()
transport.close()
print "End"
app.stop()

Using nmap library in Python program

I have a simple Python program which uses nmap library to do port scanning.
from optparse import OptionParser
import nmap
from threading import *
screenLock=Semaphore(value=1)
def nmapScan(thost,tport):
x=nmap.PortScanner()
x.scan(thost,tport)
state=x[thost]['tcp'][int(tport)]['state']
print "[*]" + thost + "tcp/"+tport+" "+state
def main():
parser=OptionParser('usage %prog -H <target host> -p <target port>')
parser.add_option('-H',dest='thost',type='string',help='specify target host')
parser.add_option('-p',dest='tports',type='string',help='specify target port[s] seperated by comma')
(options,args)=parser.parse_args()
thost=options.thost
tports=options.tports
tports=tports.split(',')
if (thost==None)|(tports==None):
print parser.usage
exit(0)
for i in tports:
nmapScan(thost,i)
main()
When i run the program, i get the following error.
akshayrajmacbookpro$ python nmapScanner.py -H 192.168.1.60 -p 80,443
Traceback (most recent call last):
File "nmapScanner.py", line 28, in <module>
main()
File "nmapScanner.py", line 26, in main
nmapScan(thost,i)
File "nmapScanner.py", line 10, in nmapScan
state=x[thost]['tcp'][int(tport)]['state']
File "build/bdist.macosx-10.11-intel/egg/nmap/nmap.py", line 555, in __getitem__
KeyError: '192.168.1.60'
I tried using url instead of ip in the command line. But I get the same error. Being new to Python, I am not able to understand and resolve this.

x (instance of nmap.PortScanner) does not contain those keys. To be able to iterate the scan results you can do this:
for host, result in x._scan_result['scan'].items():
print "[*]" + thost + "tcp/" + tport + " " + result['status']['state']
It's best if you looked at the docs or source code of python-nmap to see what other useful info is available e.g. Service name and version that is listening on that port.
More info here: https://bitbucket.org/xael/python-nmap/src/f368486a2cf12ce2bf3d5978614586e89c49c417/nmap/nmap.py?at=default&fileviewer=file-view-default#nmap.py-381

The host does not exist in the result of the scan as a "Key" for the Dictionary that forms a part of the data thrown up by scan data. That is probably, in my opinion, the reason for the error. Thanks

UART in python on raspberry pi doesn't receive data

I am trying to implement data sending in Python 3 on a raspberryPi (as a part of a bigger project) and cannot receive data when I connect the Rx and Tx pins. Regardless of using Python 2 or 3 (as far as I understand this API allows Python 3 programming) I either get Received: b'\n' response or such an exception:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/serial/serialposix.py", line 471, in write
n = os.write(self.fd, d)
OSError: [Errno 5] Input/output error
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./uart.py", line 12, in <module>
port.write(bytearray(input_data, 'utf-8'))
File "/usr/lib/python3/dist-packages/serial/serialposix.py", line 485, in write
raise SerialException('write failed: %s' % (v,))
serial.serialutil.SerialException: write failed: [Errno 5] Input/output error
I can't write anything except from buffered reader though.
The code I've made is here:
#!/usr/bin/env python3
import serial
port = serial.Serial("/dev/ttyAMA0", baudrate=9600)
while True:
input_data = input("Say sth: ")
if input_data != 'exit':
port.write(bytearray(input_data, 'utf-8'))
print('Sent: {0}'.format(bytearray(input_data, 'ASCII')))
output_data = port.readline()
print('Received: {0}\n'.format(str(output_data)))
else:
break
port.close()
I want to use ASCII encoding since it will be further connected to an microcontroller with code in C. I've also checked whether any data is written into the buffer (and it is), I've tried out laying the programme to sleep for a second after sending data, I've tried using port.read(port.inWaiting()) and port.read(in_waiting) (no attribute found in the latter case) and nothing seems to be helpful.
I've also tried this example; I am sure correct pins are connected and I have updated and upgraded my raspbian by using sudo apt-get update and sudo apt-get upgrade and when I typed sudo apt-get install python3-serial I was told that I already have newest version installed.

I am posting this answear to close the topic and to help anyone who might come across similar difficulties.
Since the processor is of different architecture trying to set up ports with setserial was pointles, however this was exactly the problem.
pi#raspberrypi ~ $ sudo setserial -g /dev/ttyAMA0
/dev/ttyAMA0, UART: undefined, Port: 0x0000, IRQ: 83
The answear I found here solved all the problems.