I am trying to use the biomaRt package to access the data from Ensembl, however I got error message when using the useDataset() function. My codes are shown below.
library(httr)
listMarts()
ensembl = useMart("ENSEMBL_MART_ENSEMBL")
listDatasets(ensemble)
ensembl = useDataset("hsapiens_gene_ensembl",mart = ensemble)
When I type useDataset function i got error message like this:
> ensembl = useDataset("hsapiens_gene_ensembl",mart = ensembl)
Ensembl site unresponsive, trying asia mirror
Error in textConnection(text, encoding = "UTF-8") :
invalid 'text' argument
and sometimes another different error message showed as:
> ensembl = useDataset("hsapiens_gene_ensembl",mart = ensembl)
Ensembl site unresponsive, trying asia mirror
Error in textConnection(bmResult) : invalid 'text' argument
it seems like that the mirror automatically change to asia OR useast OR uswest, but the error message still shows up over and over again, and i don't know what to do.
So if anyone could help me with this? I will be very grateful for any help or suggestion.
Kind regards Riley Qiu, Dongguan, China
I am trying to generate custom result file which will contain system information gathered using python psutil library.I searched, followed the documentation but couldn't get the answer. All I want to do is, I have written code to collect system information in python psutil library, this code should run along with malware file in cuckoo sandbox and result should be saved in ubuntu host machine.
I don't know where should i put my code and how to save the results.
Here is my code to collect system information
import psutil
pids = psutil.pids()
max_pid = max(pids)
total_id = len(pids)
psutil.cpu_times_percent()
cputimes = psutil.cpu_times_percent(0.1)
usertime = cputimes.user
systemtime = cputimes.system
memuse = psutil.virtual_memory().used
swapuse = psutil.swap_memory().used
net = psutil.net_io_counters()
packsent = net.packets_sent
packrecv = net.packets_recv
bytessent = net.bytes_sent
bytesrecv = net.bytes_recv
result={"maxpid":max_pip,"totalid":total_id,"usertime":usertime,"systemtime":systemtime,"memuse":memuse,"swapuse":swapuse,"packsent":packsent,"packrecv":packrecv,"bytessent":bytessent,"bytesrecv":bytesrecv}
I want to save this result dictionary to be saved in json file in host machine.
I have this block of code that basically translates text from one language to another using the cloud translate API. The problem is that this code always throws the error: "Caller's project doesn't match parent project". What could be the problem?
translation_separator = "translated_text: "
language_separator = "detected_language_code: "
translate_client = translate.TranslationServiceClient()
# parent = translate_client.location_path(
# self.translate_project_id, self.translate_location
# )
os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = (
os.getcwd()
+ "/translator_credentials.json"
)
# Text can also be a sequence of strings, in which case this method
# will return a sequence of results for each text.
try:
result = str(
translate_client.translate_text(
request={
"contents": [text],
"target_language_code": self.target_language_code,
"parent": f'projects/{self.translate_project_id}/'
f'locations/{self.translate_location}',
"model": self.translate_model
}
)
)
print(result)
except Exception as e:
print("error here>>>>>", e)
Your issue seems to be related to the authentication method that you are using on your application, please follow the guide for authention methods with the translate API. If you are trying to pass the credentials using code, you can explicitly point to your service account file in code with:
def explicit():
from google.cloud import storage
# Explicitly use service account credentials by specifying the private key
# file.
storage_client = storage.Client.from_service_account_json(
'service_account.json')
Also, there is a codelab for getting started with the translation API with Python, this is a great step by step getting started guide for running the translate API with Python.
If the issue persists, you can try creating a Public Issue Tracker for Google Support
I need to find out for a script I'm writing who is the true owner of a file in an smb share (mounted using mount -t cifs of course on my server and using net use through windows machines).
Turns out it is a real challenge finding this information out using python on a linux server.
I tried using many many smb libraries (such as smbprotocol, smbclient and others), nothing worked.
I find few solutions for windows, they all use pywin32 or another windows specific package.
And I also managed to do it from bash using smbcalcs but couldn't do it cleanly but using subprocess.popen('smbcacls')..
Any idea on how to solve it?
This was unbelievably not a trivial task, and unfortunately the answer isn't simple as I hoped it would be..
I'm posting this answer if someone will be stuck with this same problem in the future, but hope maybe someone would post a better solution earlier
In order to find the owner I used this library with its examples:
from smb.SMBConnection import SMBConnection
conn = SMBConnection(username='<username>', password='<password>', domain=<domain>', my_name='<some pc name>', remote_name='<server name>')
conn.connect('<server name>')
sec_att = conn.getSecurity('<share name>', r'\some\file\path')
owner_sid = sec_att.owner
The problem is that pysmb package will only give you the owner's SID and not his name.
In order to get his name you need to make an ldap query like in this answer (reposting the code):
from ldap3 import Server, Connection, ALL
from ldap3.utils.conv import escape_bytes
s = Server('my_server', get_info=ALL)
c = Connection(s, 'my_user', 'my_password')
c.bind()
binary_sid = b'....' # your sid must be in binary format
c.search('my_base', '(objectsid=' + escape_bytes(binary_sid) + ')', attributes=['objectsid', 'samaccountname'])
print(c.entries)
But of course nothing will be easy, it took me hours to find a way to convert a string SID to binary SID in python, and in the end this solved it:
# posting the needed functions and omitting the class part
def byte(strsid):
'''
Convert a SID into bytes
strdsid - SID to convert into bytes
'''
sid = str.split(strsid, '-')
ret = bytearray()
sid.remove('S')
for i in range(len(sid)):
sid[i] = int(sid[i])
sid.insert(1, len(sid)-2)
ret += longToByte(sid[0], size=1)
ret += longToByte(sid[1], size=1)
ret += longToByte(sid[2], False, 6)
for i in range(3, len(sid)):
ret += cls.longToByte(sid[i])
return ret
def byteToLong(byte, little_endian=True):
'''
Convert bytes into a Python integer
byte - bytes to convert
little_endian - True (default) or False for little or big endian
'''
if len(byte) > 8:
raise Exception('Bytes too long. Needs to be <= 8 or 64bit')
else:
if little_endian:
a = byte.ljust(8, b'\x00')
return struct.unpack('<q', a)[0]
else:
a = byte.rjust(8, b'\x00')
return struct.unpack('>q', a)[0]
... AND finally you have the full solution! enjoy :(
I'm adding this answer to let you know of the option of using smbprotocol; as well as expand in case of misunderstood terminology.
SMBProtocol Owner Info
It is possible to get the SID using the smbprotocol library as well (just like with the pysmb library).
This was brought up in the github issues section of the smbprotocol repo, along with an example of how to do it. The example provided is fantastic and works perfectly. An extremely stripped down version
However, this also just retrieves a SID and will need a secondary library to perform a lookup.
Here's a function to get the owner SID (just wrapped what's in the gist in a function. Including here in case the gist is deleted or lost for any reason).
import smbclient
from ldap3 import Server, Connection, ALL,NTLM,SUBTREE
def getFileOwner(smb: smbclient, conn: Connection, filePath: str):
from smbprotocol.file_info import InfoType
from smbprotocol.open import FilePipePrinterAccessMask,SMB2QueryInfoRequest, SMB2QueryInfoResponse
from smbprotocol.security_descriptor import SMB2CreateSDBuffer
class SecurityInfo:
# 100% just pulled from gist example
Owner = 0x00000001
Group = 0x00000002
Dacl = 0x00000004
Sacl = 0x00000008
Label = 0x00000010
Attribute = 0x00000020
Scope = 0x00000040
Backup = 0x00010000
def guid2hex(text_sid):
"""convert the text string SID to a hex encoded string"""
s = ['\\{:02X}'.format(ord(x)) for x in text_sid]
return ''.join(s)
def get_sd(fd, info):
""" Get the Security Descriptor for the opened file. """
query_req = SMB2QueryInfoRequest()
query_req['info_type'] = InfoType.SMB2_0_INFO_SECURITY
query_req['output_buffer_length'] = 65535
query_req['additional_information'] = info
query_req['file_id'] = fd.file_id
req = fd.connection.send(query_req, sid=fd.tree_connect.session.session_id, tid=fd.tree_connect.tree_connect_id)
resp = fd.connection.receive(req)
query_resp = SMB2QueryInfoResponse()
query_resp.unpack(resp['data'].get_value())
security_descriptor = SMB2CreateSDBuffer()
security_descriptor.unpack(query_resp['buffer'].get_value())
return security_descriptor
with smbclient.open_file(filePath, mode='rb', buffering=0,
desired_access=FilePipePrinterAccessMask.READ_CONTROL) as fd:
sd = get_sd(fd.fd, SecurityInfo.Owner | SecurityInfo.Dacl)
# returns SID
_sid = sd.get_owner()
try:
# Don't forget to convert the SID string-like object to a string
# or you get an error related to "0" not existing
sid = guid2hex(str(_sid))
except:
print(f"Failed to convert SID {_sid} to HEX")
raise
conn.search('DC=dell,DC=com',f"(&(objectSid={sid}))",SUBTREE)
# Will return an empty array if no results are found
return [res['dn'].split(",")[0].replace("CN=","") for res in conn.response if 'dn' in res]
to use:
# Client config is required if on linux, not if running on windows
smbclient.ClientConfig(username=username, password=password)
# Setup LDAP session
server = Server('mydomain.com',get_info=ALL,use_ssl = True)
# you can turn off raise_exceptions, or leave it out of the ldap connection
# but I prefer to know when there are issues vs. silently failing
conn = Connection(server, user="domain\username", password=password, raise_exceptions=True,authentication=NTLM)
conn.start_tls()
conn.open()
conn.bind()
# Run the check
fileCheck = r"\\shareserver.server.com\someNetworkShare\someFile.txt"
owner = getFileOwner(smbclient, conn, fileCheck)
# Unbind ldap session
# I'm not clear if this is 100% required, I don't THINK so
# but better safe than sorry
conn.unbind()
# Print results
print(owner)
Now, this isn't super efficient. It takes 6 seconds for me to run this one a SINGLE file. So if you wanted to run some kind of ownership scan, then you probably want to just write the program in C++ or some other low-level language instead of trying to use python. But for something quick and dirty this does work. You could also setup a threading pool and run batches. The piece that takes longest is connecting to the file itself, not running the ldap query, so if you can find a more efficient way to do that you'll be golden.
Terminology Warning, Owner != Creator/Author
Last note on this. Owner != File Author. Many domain environments, and in particular SMB shares, automatically alter ownership from the creator to a group. In my case the results of the above is:
What I was actually looking for was the creator of the file. File creator and modifier aren't attributes which windows keeps track of by default. An administrator can enable policies to audit file changes in a share, or auditing can be enabled on a file-by-file basis using the Security->Advanced->Auditing functionality for an individual file (which does nothing to help you determine the creator).
That being said, some applications store that information for themselves. For example, if you're looking for Excel this answer provides a method for which to get the creator of any xls or xlsx files (doesn't work for xlsb due to the binary nature of the files). Unfortunately few files store this kind of information. In my case I was hoping to get that info for tblu, pbix, and other reporting type files. However, they don't contain this information (which is good from a privacy perspective).
So in case anyone finds this answer trying to solve the same kind of thing I did - Your best bet (to get actual authorship information) is to work with your domain IT administrators to get auditing setup.
So I'm following the NCBI instructions available here: https://www.ncbi.nlm.nih.gov/books/NBK52640/
and I can't for the life of me understand what's wrong here.
Here's my PATH and BLASTDB:
And the error message:
And my blastdb directory:
And here's my Python code:
from Bio.Blast.Applications import NcbipsiblastCommandline
import subprocess
psi_cline = NcbipsiblastCommandline('psiblast', db = 'refseq_protein.00',\
query = "results.fasta", evalue = 10 , \
out = "out_psi.xml", outfmt = 7, \
out_pssm ="pssm-results_pssm")
print(psi_cline)
I had this very problem today and it turns out that my blast-database was corrupted in some manner. I recreated my database with makeblastdb and this error went away.