So I was trying to get Biograkn usecase for BLAST working , following the steps as per this video series. I was able to load the schema , but after that we need to execute python migrate.py to load data into it. I executed the command and i am getting the following error traceback
Traceback (most recent call last):
File "/home/aditya/anaconda3/envs/RD/lib/python3.7/site-packages/grakn/service/Session/TransactionService.py", line 161, in send
response = next(self._response_iterator)
File "/home/aditya/anaconda3/envs/RD/lib/python3.7/site-packages/grpc/_channel.py", line 364, in __next__
return self._next()
File "/home/aditya/anaconda3/envs/RD/lib/python3.7/site-packages/grpc/_channel.py", line 358, in _next
raise self
grpc._channel._Rendezvous: <_Rendezvous of RPC that terminated with:
status = StatusCode.INVALID_ARGUMENT
details = "GraqlSemanticException-label 'database' not found. Please check server logs for the stack trace."
debug_error_string = "{"created":"#1582269484.666990683","description":"Error received from peer","file":"src/core/lib/surface/call.cc","file_line":1017,"grpc_message":"GraqlSemanticException-label 'database' not found. Please check server logs for the stack trace.","grpc_status":3}"
>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "migrate.py", line 92, in <module>
init(data_path="uniprot-asthma-proteins.fasta")
File "migrate.py", line 23, in init
session, q_get_database, q_insert_database, "$db"
File "/home/aditya/Projects/RD/biograkn/blast/util.py", line 14, in insert_if_non_existent
found_list = list(read_transaction.query(get_query))
File "/home/aditya/anaconda3/envs/RD/lib/python3.7/site-packages/grakn/client.py", line 131, in query
return self._tx_service.query(query, infer)
File "/home/aditya/anaconda3/envs/RD/lib/python3.7/site-packages/grakn/service/Session/TransactionService.py", line 49, in query
response = self._communicator.send(request)
File "/home/aditya/anaconda3/envs/RD/lib/python3.7/site-packages/grakn/service/Session/TransactionService.py", line 165, in send
raise GraknError("Server/network error: {0}\n\n generated from request: {1}".format(e, request))
grakn.exception.GraknError.GraknError: Server/network error: <_Rendezvous of RPC that terminated with:
status = StatusCode.INVALID_ARGUMENT
details = "GraqlSemanticException-label 'database' not found. Please check server logs for the stack trace."
debug_error_string = "{"created":"#1582269484.666990683","description":"Error received from peer","file":"src/core/lib/surface/call.cc","file_line":1017,"grpc_message":"GraqlSemanticException-label 'database' not found. Please check server logs for the stack trace.","grpc_status":3}"
>
generated from request: query_req {
query: "match $db isa database, has name \"uniprot\"; get $db;"
}
now this is not understandable why loading is not possible. Hence requesting for assistance.
There appears to already be a problem with the schema, since graql is trying to look for the label "database" but cannot find it.
You can check your schema using workbase:
1. connect to your local server (localhost:48555)
2. select your keyspace ("proteins")
3. click on the hierarchy symbol on the top left next to the grakn logo
If the schema is present, it will be visualized automatically.
Related
I try to connect to Azure Data Lake using Airflow. I use Airflow connection via the Web UI.
When I try to connect using the test button, I get an error Bad Request. As seen below
I use the correct UUIDs. These UUIDs have been verified in other cases. I also checked the firewall.
When I execute the DAG, I use the Azure Data Lake connection id to check if a file exists: If I apply the method as described here: What is the best way to check if a file exists on an Azure Datalake using Apache Airflow?
This is the error I get
[2022-05-06, 17:27:33 UTC] {log.py:127} ERROR - 99ec1d77-e91c-4fd3-a1c7-fa751ca1e779 - OAuth2Client:The token response from the server is unparseable as JSON: ***
Traceback (most recent call last):
File "/opt/airflow/lib/python3.8/site-packages/adal/oauth2_client.py", line 168, in _validate_token_response
wire_response = json.loads(body)
File "/usr/lib/python3.8/json/init.py", line 357, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.8/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.8/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 3 column 1 (char 4)
[2022-05-06, 17:27:33 UTC] {log.py:127} ERROR - 99ec1d77-e91c-4fd3-a1c7-fa751ca1e779 - OAuth2Client:Error validating get token response: ***
Traceback (most recent call last):
File "/opt/airflow/lib/python3.8/site-packages/adal/oauth2_client.py", line 238, in _handle_get_token_response
return self._validate_token_response(body)
File "/opt/airflow/lib/python3.8/site-packages/adal/oauth2_client.py", line 168, in _validate_token_response
Authenticating to Azure Data Lake is by token credentials i.e. add specific credentials (client_id, secret, tenant) and account name to the Airflow connection.
Information about how to set it up can be found in this doc.
You can see code example in the source code test function.
Other method of authentication are currently not supported.
I was trying to get the connection running using the Airflow implementation. My impression was that it was buggy and did not work out well. The above situation happened with Airflow 2.2.5. When I upgraded to Airflow 2.3.0, the test button was grayed out.
The final solution was to use Access Tokens instead.
I am trying to upload a file into a SFTP using a key file. I already configured the connection and I can authenticate without any problem:
{'key_file': '/my_folder/public_key'}
Also I am able to do all the process manually using Cyberduck for example. This is the function that I am calling:
from contextlib import closing
from airflow.contrib.hooks.ssh_hook import SSHHook
# Get connection details
ssh = SSHHook(ssh_conn_id='my conn id')
# Upload the file into sftp
with closing(ssh.get_conn().open_sftp()) as sftp_client:
sftp_client.put('/local_folder/my_file.xlsx', '/sftp_folder/my_file.xlsx')
This is the error I am receiving:
{base_hook.py:80} INFO - Using connection to: xxxxxxx
{transport.py:1687} INFO - Connected (version 2.0, client AWS_SFTP_1.0)
{transport.py:1687} INFO - Authentication (publickey) successful!
PermissionError: [Errno 13] Forbidden
Does anyone have any idea of why this is happening if I am able to do the same manually?
Thank you so much!
The whole stack:
{transport.py:1687} INFO - Authentication (publickey) successful!
{sftp.py:131} INFO - [chan 0] Opened sftp connection (server version 3)
Traceback (most recent call last):
File "/.../airflow/plugins/operators/my_operator.py", line 231, in sftp_upload
client.put(local_path, sftp_path)
File "/.../venv/lib/python3.6/site-packages/paramiko/sftp_client.py", line 727, in put
return self.putfo(fl, remotepath, file_size, callback, confirm)
File "/.../venv/lib/python3.6/site-packages/paramiko/sftp_client.py", line 683, in putfo
with self.file(remotepath, 'wb') as fr:
File "/.../venv/lib/python3.6/site-packages/paramiko/sftp_client.py", line 341, in open
t, msg = self._request(CMD_OPEN, filename, imode, attrblock)
File "/.../venv/lib/python3.6/site-packages/paramiko/sftp_client.py", line 780, in _request
return self._read_response(num)
File "/.../venv/lib/python3.6/site-packages/paramiko/sftp_client.py", line 832, in _read_response
self._convert_status(msg)
File "/.../venv/lib/python3.6/site-packages/paramiko/sftp_client.py", line 863, in _convert_status
raise IOError(errno.EACCES, text)
PermissionError: [Errno 13] Forbidden
The problem I was facing was due to invalid path in sftp folder. Cyberduck was hiding part of the path so I was including an incomplete one into my code. Paramiko was returning Forbidden because probably the path exists but this account doesn't have access to it.
Once I included the full path the code above worked pretty fine!
Thanks!
I am trying to upload a binary file I have to Openstack Swift. This size of this file is 129MB. I am using the Python client for uploading:
swift_client = swiftclient.Connection(preauthurl=swift_public_auth_url,preauthtoken=swift_access_token,auth_version="2.0",insecure=True,tenant_name="admin")
with open("/path/to/file/file.ckpt", 'r') as read_file:
swift_client.put_object(swift_container_name, 'file.ckpt', contents= read_file.read(),content_type='text/plain')
print "done"
This throws the following error:
Traceback (most recent call last):
File "<stdin>", line 2, in <module>
File "/usr/local/lib/python2.7/dist-packages/swiftclient/client.py", line 1824, in put_object
response_dict=response_dict)
File "/usr/local/lib/python2.7/dist-packages/swiftclient/client.py", line 1673, in _retry
service_token=self.service_token, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/swiftclient/client.py", line 1322, in put_object
raise ClientException.from_response(resp, 'Object PUT failed', body)
swiftclient.exceptions.ClientException: Object PUT failed: https://abc.xyz/swift/v1/AUTH_123456789abcdefghijklmn/container/file.ckpt 413 Request Entity Too Large [first 60 chars of response] <html>
<head><title>413 Request Entity Too Large</title></h
However, when I tried replacing test.ckpt with a blank text file test.txt, it got uploaded with the same parameters. I know this error occurs when the file size is greater than 5GB but what can be the problem here?
Found out that the problem was because of configuration on my Nginx proxy server. Got it fixed by increasing client_max_body_size. More details here: https://www.cyberciti.biz/faq/linux-unix-bsd-nginx-413-request-entity-too-large/
I am getting "Error handling request" and I can't really trace this down to a particular problem?
I am using gunicorn+nginx and my gunicorn setup is
gunicorn run:app -w 4 -b 0.0.0.0:8080 --workers=1 --timeout=300
here is the error message
2015-10-14 21:27:11,287 DEBG 'myserver' stderr output:
[2015-10-14 21:27:11 +0000] [26725] [ERROR] Error handling request
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/gunicorn/workers/sync.py", line 130, in handle
self.handle_request(listener, req, client, addr)
File "/usr/local/lib/python2.7/dist-packages/gunicorn/workers/sync.py", line 171, in handle_request
respiter = self.wsgi(environ, resp.start_response)
File "/usr/local/lib/python2.7/dist-packages/flask/app.py", line 1836, in __call__
return self.wsgi_app(environ, start_response)
File "/usr/local/lib/python2.7/dist-packages/flask/app.py", line 1820, in wsgi_app
response = self.make_response(self.handle_exception(e))
File "/usr/local/lib/python2.7/dist-packages/flask/app.py", line 1403, in handle_exception
reraise(exc_type, exc_value, tb)
File "/usr/local/lib/python2.7/dist-packages/flask/app.py", line 1817, in wsgi_app
response = self.full_dispatch_request()
File "/usr/local/lib/python2.7/dist-packages/flask/app.py", line 1478, in full_dispatch_request
response = self.make_response(rv)
File "/usr/local/lib/python2.7/dist-packages/flask/app.py", line 1566, in make_response
raise ValueError('View function did not return a response')
ValueError: View function did not return a response
can anybody give me a hint how to debug this? I don't have much experience with server usage...
thanks
carl
tl;dr: This isn't an issue with gunicorn or nginx. Your view function in your Flask app is not returning a response. Check the return statement in your view function for whatever route you are accessing when you get this error.
Beginning at the Line
Traceback (most recent call last):
You can see the stack trace produced by the python interpreter. The stack trace shows the sequence of nested functions leading up to the point where your code failed. In my limited experience, the python interpreter stack trace has reliably directed me to the fault in my code.
In your case here, the final line:
ValueError: View function did not return a response
provides some more detail about the error and should give you pretty good idea of what went wrong (Your view function didn't return a response).
The next line up from the bottom will show you the function that triggered the error, and its exact location in your code:
File "/usr/local/lib/python2.7/dist-packages/flask/app.py", line 1566, in make_response
raise ValueError('View function did not return a response')
In this case the error is raised by a function in the flask source, so unless you edited that, that is probably not where you need to make a fix. Based on the specific ValueError at the end of the trace, I'd go straight to my views function. In Flask that probably looks something like this (example from Flask tutorial):
#app.route('/')
def show_entries():
cur = g.db.execute('select title, text from entries order by id desc')
entries = [dict(title=row[0], text=row[1]) for row in cur.fetchall()]
return render_template('show_entries.html', entries=entries)
That last line seems like a good place to start in your case, since the error says nothing is being returned.
I am trying to install the latest version of swift following instructions from http://docs.openstack.org/icehouse/install.../general-installation-steps-swift.html. I am able to authenticate with keystone and also able to successfully run the command swift stat. But, when I run the command swift upload myfiles temp, I get the following error
Error trying to create container 'myfiles': 404 Not Found: {"error": {"message": "The
resource could not be found.", "c
Object PUT failed: 9.109.124.109:5000:5000/v2.0/myfiles/temp 400 Bad Request
[first 60 chars of response] {"error": {"message": "Expecting to find application/json
in
In /var/log/syslog, I find the following information:
May 28 18:11:40 datafed3 account-server: ERROR __call__ error with PUT /sdb1/100869
/AUTH_system/myfiles : #012Traceback (most recent call last):#012 File "/usr/lib
/python2.7/dist-packages/swift/account/server.py", line 284, in __call__#012 res =
method(req)#012 File "/usr/lib/python2.7/dist-packages/swift/common/utils.py", line
2217, in wrapped#012 return func(*a, **kw)#012 File "/usr/lib/python2.7/dist-
packages/swift/common/utils.py", line 837, in _timing_stats#012 resp = func(ctrl,
*args, **kwargs)#012 File "/usr/lib/python2.7/dist-packages/swift/account/server.py",
line 128, in PUT#012 req.headers['x-bytes-used'])#012 File "/usr/lib/python2.7/dist-
packages/swift/account/backend.py", line 210, in put_container#012 raise
DatabaseConnectionError(self.db_file, "DB doesn't exist")#012DatabaseConnectionError:
DB connection error (/srv/node/sdb1/accounts/100869/80d/62816079be0fc97a4557f52b3b12380d
/62816079be0fc97a4557f52b3b12380d.db, 0):#012DB doesn't exist
One situation may cause this problem is: when create tenant, one or more storage node is down. then when you upload an object, proxy get 404 from at least one storage node.
On my test, even the storage node are all up after tenant creation, 404 error still exist. So, make sure all storage nodes are up, and create another tenant to test.