Thu, 06 May 2021 13:49:05 Desmond Driver v2.3
Traceback (most recent call last):
File "/opt/schrodinger2021-1/internal/bin/desmond_driver.py", line 294, in <module>
main(sys.argv[1:])
File "/opt/schrodinger2021-1/internal/bin/desmond_driver.py", line 279, in main
driver_model = get_driver_model(option.destrier_flag, backend)(args,
File "/opt/schrodinger2021-1/internal/bin/drivermodel.py", line 426, in __init__
DriverModel.__init__(self, args, backend)
File "/opt/schrodinger2021-1/internal/bin/drivermodel.py", line 118, in __init__
self._config_cuda()
File "/opt/schrodinger2021-1/internal/bin/drivermodel.py", line 175, in _config_cuda
tmp_dir = fileutils.get_directory_path(fileutils.TEMP)
File "/opt/schrodinger2021-1/internal/lib/python3.8/site-packages/schrodinger/utils/fileutils.py", line 669, in get_directory_path
return mm.get_schrodinger_temp_dir()
**RuntimeError: could not get username from env**
Hi there, I tried to install a molecular dynamic package on collab called Desmond. The installation looks fine, even the -h flag shows a good return. but when I try to run some real job, there the error showed up saying could not get the username from env. Not sure what is going on, please help if you have any ideas, many thanks.
try this
import getpass
getpass.getuser()
The current user name will be returned by this.
eg
>>> import getpass
>>> print(getpass.getuser())
root
>>>
I just figured it out after two months!
The trick is, unlike a local computer or an HPC cluster, the way of cloud platform does not define the USER environment variable, yes, it is as simple as the error shows to some extent.
Just do: （take the Baidu AI studio as example）
echo “export USER=aistudio” >> ~/.bashrc
source ~/.bashrc
that’s it, and then, desmond will be able to up and running, I believe on Google Colab, the solution should be very similar.
The best way to find the correct USER value for your system is use "printenv" and look for the $HOME variable, your username should be as part of $HOME, then you just copy that name and give it to the new $USER variable.
Related
Python Version = 3.9,
Foreman Version = 2.5.4
I'm using the Python Foreman (python-foreman) module to connect to Foreman to do a bunch of automation tasks, however as soon as i'm connecting to Foreman as below:
from foreman.client import Foreman
f = Foreman('http://foreman-url.com/api/hosts', ('admin', 'password'), api_version = 2)
I'm getting a bunch of conflicting statements as below and eventually erroring out.
There is a conflict trying to redefine a method for a foreign resource (foreman_tasks_index):
resource:
apipie_resource: foreman_tasks
new_api: <resource:, name:foreman_tasks_index>
new_url: /foreman_tasks/api/tasks/:parent_task_id/sub_tasks
old_api: <resource:, name:foreman_tasks_index>
old_url: /foreman_tasks/api/tasks
There is a conflict trying to redefine a method for a foreign resource (sync_plans_rganizations):
resource:
apipie_resource: sync_plans
new_api: <resource:organizations, name:sync_plans_rganizations>
new_url: /katello/api/organizations/:organization_id/sync_plans/:id/add_products
old_api: <resource:organizations, name:sync_plans_rganizations>
old_url: /katello/api/organizations/:organization_id/sync_plans/:id
Eventually the script is erroring out at this:
Traceback (most recent call last):
File "", line 1, in
File "/data/sfreport/python3.9/lib/python3.9/site-packages/foreman/client.py", line 619, in init
self._generate_api_defs(use_cache, strict_cache)
File "/data/sfreport/python3.9/lib/python3.9/site-packages/foreman/client.py", line 820, in generate_api_defs
new_resource, extra_foreign_methods = parse_resource_definition(
File "/data/sfreport/python3.9/lib/python3.9/site-packages/foreman/client.py", line 375, in parse_resource_definition
functions[api.name] = api.generate_func()
File "/data/sfreport/python3.9/lib/python3.9/site-packages/foreman/client.py", line 282, in generate_func
six.exec(code)
File "", line 1
def lifecycle_environments_update(self, id, organization_id=None, new_name=None, description=None, registry_name_pattern=None, registry_unauthenticated_pull=None, async=None):
^
SyntaxError: invalid syntax
Can you pls help with this or let me know the best way to connect to Foreman API via Python to carry out the automations?
The error message you are getting states that (sine Python 3.5) async is a reserved keyword, and cannot be a variable name. This means that the version of Foreman you are using is incompatible with Python 3.9. Try updating Foreman, downgrading Python, or (if you are comfortable doing it) try to fix the issue yourself (changing the variable name from async to something else, and hoping it works).
I am not sure whether the offending code comes directly from Foreman. Try to search your code (and libraries) for async=None pattern, as it may also not be Foreman's fault.
I am currently working with the Instabot API for python and I ran across the following issue:
I wrote a small program:
from instabot import Bot
bot = Bot()
bot.login(username = "[my username]", password = "[my passowrd]")
bot.follow("lego")
which worked fine after running it for the very first time. However, after running the program for a second time, this time following another account, it raised an error ("KeyError: ds_user").
This error can be fixed by deleting the config folder inside the project folder. Unfortunately, this isn't a very sustainable solution, as it makes working on the code really arduous. I therefore would like to know if there is any solution for getting the program to run multiple times without having to delete the config folder over and over again.
I am receiving the following traceback (code is running in an anaconda environment called "Instagram Automation"):
Traceback (most recent call last):
File "e:/Programme/OneDrive/Dokumente/Projekte/Instagram Automation/main.py", line 4, in <module>
bot.login(username = "[my username]", password = "[my password]")
File "E:\Programme\Anaconda\envs\Instagram Automation\lib\site-packages\instabot\bot\bot.py", line 443, in login
if self.api.login(**args) is False:
File "E:\Programme\Anaconda\envs\Instagram Automation\lib\site-packages\instabot\api\api.py", line 240, in login
self.load_uuid_and_cookie(load_cookie=use_cookie, load_uuid=use_uuid)
File "E:\Programme\Anaconda\envs\Instagram Automation\lib\site-packages\instabot\api\api.py", line 199, in load_uuid_and_cookie
return load_uuid_and_cookie(self, load_uuid=load_uuid, load_cookie=load_cookie)
File "E:\Programme\Anaconda\envs\Instagram Automation\lib\site-packages\instabot\api\api_login.py", line 352, in load_uuid_and_cookie
cookie_username = self.cookie_dict["ds_user"]
KeyError: 'ds_user'
As far as I can see, the only way on your side to fight the symptoms is to always delete the JSON file in the config folder, e.g:
import os
if os.path.isfile("path/to/config/file.json"):
os.remove("path/to/config/file.json")
import instabot
# rest of your code goes here
The developers of instabot should fix the source of the problem, for example by using self.cookie_dict.get("ds_user", "some default value") instead of self.cookie_dict["ds_user"]
The whois.whois function always gets a timed out error.
At first, I thought it was because my project is written in Python 2.7 but I also checked in 3.7 and got the same error.
I checked the address on the online website that uses whois and the link worked and didn't get this error.
Anyone knows why this is happening?
import whois
w = whois.whois("https://stackoverflow.com")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Program Files\Python37\lib\site-packages\whois\__init__.py", line 43, in whois
text = nic_client.whois_lookup(None, domain.encode('idna'), flags)
File "C:\Program Files\Python37\lib\site-packages\whois\whois.py", line 264, in whois_lookup
result = self.whois(query_arg, nichost, flags)
File "C:\Program Files\Python37\lib\site-packages\whois\whois.py", line 142, in whois
s.connect((hostname, 43))
socket.timeout: timed out
Your code has at least two problems, and you may have a network problem also.
However, there is no reason for it not to work on Python2.
About the code
This works perfectly fine:
In [7]: import whois
In [8]: print whois.query('stackoverflow.com').expiration_date
2020-02-02 11:59:59
Note two things:
whois is about domain names, not URLs; so you should pass a domain name; note more generally that for new endeavors you should have a look at RDAP instead of whois since you will get a far better experience
you need to use whois.query not whois.whois (you are not saying which version of the library you use, but at its documentation page on https://pypi.org/project/whois/ you can clearly see it is whois.query so I do not know where your whois.whois` comes from).
About the network
You show a network error. It is not 100% clear but you may or may not have access to the whois servers you want to query.
Easy way to test: just use the command line whois from the same box as your code (but again use a domain name, not a URL as parameter) and you will see what is happening.
You can even do directly a telnet on port 43 as whois does nothing else.
$ echo 'stackoverflow.com' | nc whois.verisign-grs.com 43 | grep 'Expiry'
Registry Expiry Date: 2020-02-02T11:59:59Z
During my pandas/Google Analytics API setup, I basically did everything as described in this link:
http://blog.yhathq.com/posts/pandas-google-analytics.html
The client_secrets.json is in the pandas/io folder. When i now try to execute a statement of the form
>>>from pandas.io import ga
>>>df = ga.read_ga(metrics, dimensions, start_date)
the following error occurs:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "\Anaconda\lib\site-packages\pandas\io\ga.py", line 110, in read_ga
reader = GAnalytics(**reader_kwds)
File "\Anaconda\lib\site-packages\pandas\io\ga.py", line 179, in __init__
self._service = self._init_service(secrets)
File "\Anaconda\lib\site-packages\pandas\io\ga.py", line 191, in _init_service
http = self.authenticate(secrets)
File "\Anaconda\lib\site-packages\pandas\io\ga.py", line 151, in authenticate
return auth.authenticate(flow, self.token_store)
File "\Anaconda\lib\site-packages\pandas\io\auth.py", line 108, in authenticate
credentials = tools.run(flow, storage)
AttributeError: 'module' object has no attribute 'run'
According to the yhat link, my browser should open for authentication.
Note: I did not not create the Client ID for "installed application", since I did not have this choice in the menu when creating the ID. Instead, i chose "other". This shouldn't be the cause of the error, though.
Second Note: I recently updated my pandas to 0.17.1. When importing pandas.io.ga, i got the message that the .ga module is deprecated. Furthermore, i manually installed the gflags module, because it was needed when I tried to import .io.ga the first time.
Either file a ticket with the owners of Pandas to change (currently) line 108 of pandas/io/auth.py from run() to run_flow(), or make the fix yourself and file a PR. (Yes, it would've been nice if Google had just made run_flow() and alias of run(), but as you can imagine, this is not how this change evolved, so we have to live with it.)
For other developers running into this error: If you have the latest version (as of Feb 2016) of the Google APIs Client Library for Python, just rename your call from tools.run() to tools.run_flow(), and you should be good-to-go. More about this change in a PSA (public service announcement) blogpost I wrote back in mid-2015 but update periodically to stay current.
The fastest way to upgrade your Client Library is with:
pip install -U google-api-python-client # or pip3 for 3.x
The following code:
gb = self.request.form['groupby']
typ = self.request.form['type']
tbl = self.request.form['table']
primary = self.request.form.get('primary', None)
if primary is not None:
create = False
else:
create = True
mdb = tempfile.NamedTemporaryFile()
mdb.write(self.request.form['mdb'].read())
mdb.seek(0)
csv = tempfile.TemporaryFile()
conversion = subprocess.Popen(("/Users/jondoe/development/mdb-export", mdb.name, tbl,),stdout=csv)
Causes the this error when calling the last line i.e. 'conversion =' in OS X.
Traceback (innermost last):
Module ZPublisher.Publish, line 119, in publish
Module ZPublisher.mapply, line 88, in mapply
Module ZPublisher.Publish, line 42, in call_object
Module circulartriangle.mdbtoat.mdb, line 62, in __call__
Module subprocess, line 543, in __init__
Module subprocess, line 975, in _execute_child
OSError: [Errno 13] Permission denied
I've tried chmod 777 /Users/jondoe/development/mdb-export - what else might be required?
Assuming that permissions on parent folders are correct (i.e. all parent folders should have +x permission), try adding:
shell=True
to the Popen command such as:
subprocess.Popen(("/Users/jondoe/development/mdb-export", mdb.name, tbl,), stdout=csv, shell=True)
It seems the 'Permissions denied error' was orginally coming from Popen trying to execute mdb-export from the wrong location (and to compound things, with the wrong permissions).
If mdbtools is installed, the following works fine and inherits the correct permissions without the need for sudo etc.
subprocess.Popen(("mdb-export", mdb.name, tbl,),stdout=csv)
(Worth noting, I got myself into a muddle for a while, having forgotten that Popen is for opening executables, not folders or non-exectable files in folders)
Thanks for all your responses, they all made for interesting reading regardless :)
Can you feed "sudo" to subprocess? See this SO thread.
#Jon Hadley, from the interpreter:
>>> import subprocess
>>> p = subprocess.call(['sudo','/usr/bin/env'])
PASSWORD:
[snip]
USER=root
USERNAME=root
SUDO_COMMAND=/usr/bin/env
SUDO_USER=telliott99
SUDO_UID=501
SUDO_GID=20
From Terminal on OS X, I have to do sudo when I run the script:
$ sudo python test.py
then this (in test.py) gives the same output as before:
import subprocess
p = subprocess.Popen('/usr/bin/env')
Getting subprocess to directly handle the authentication from a script is probably not a good idea, since it hides the privilege escalation. But you could look at pexpect and this SO answer.
You also need to ensure read and execute permissions for the user running that code on the directories up the chain - /Users, /Users/jondoe and /Users/jondoe/development.