After setting up my netrc file according to the instructions, I have not been able to pull any data from labkey. Instead am receiving a "ServerContextError" when using the python export script that labkey provides. Is there anything wrong with the following script?
import labkey
server_context = labkey.utils.create_server_context('52.36.10.100', 'home/db_test', use_ssl=True)
my_results = labkey.query.select_rows(
server_context=server_context,
schema_name='study',
query_name='db_test'
)
The ServerContextError is somewhat vague, so any advice on how to resolve this issue would be greatly appreciated! |
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| Jon (LabKey DevOps) responded: |
2016-07-18 19:51 |
Hi James,
Have you checked our docs here? https://github.com/LabKey/labkey-api-python
Your script looks semi-complete since I'm seeing "import labkey" instead of:
from labkey.utils import create_server_context
from labkey.query import select_rows
Mind you, this is assuming you're using the latest version of our Python API. Do you know what version of the Python API you're using?
Also, is there a query or table called "db_test"? I checked the IP address and from what I'm seeing, you just have a table called "Database":
https://52.36.10.100/study/home/db_test/dataset.view?datasetId=5001
Regards,
Jon |
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| james skane 93089 responded: |
2016-07-18 21:59 |
Hi Jon,
Thanks for your response. db_test was a table that was made earlier during our attempts to pull data with labkey. I am using version 0.4.2. After changing the imports above and the table name I am still receiving the same ServerContextError. Here is the script below:
from labkey.query import select_rows
from labkey.utils import create_server_context
server_context = create_server_context('52.36.10.100', 'home/db_test', use_ssl=True)
my_results = select_rows(
server_context=server_context,
schema_name='study',
query_name='Database'
)
And below is the error:
Traceback (most recent call last):
File "/Users/...", line 11, in <module>
query_name='Database'
File "/Users/...", line 274, in select_rows
select_rows_response = _make_request(server_context, url, payload, timeout=timeout)
File "/Users/...", line 310, in _make_request
raise ServerContextError(e)
labkey.exceptions.ServerContextError
Is there anything I am missing that might be causing this error?
Sincerely,
James |
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| Brian Connolly responded: |
2016-07-19 09:12 |
James,
The problem is with your SSL certificate. You can see this by catching the error from your select_rows call. For example, if you change your script to
from labkey.query import select_rows
from labkey.utils import create_server_context
server_context = create_server_context('52.36.10.100', 'home/db_test', use_ssl=True)
try:
my_results = select_rows(
server_context=server_context,
schema_name='study',
query_name='Database'
)
except labkey.exceptions.ServerContextError as e:
print "Exception Code: " + str(e.exception)
print "Error Message: " + str(e.message)
You will see the error messages
Exception Code: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:581)
Error Message: Failed to match server SSL configuration. Ensure the server_context is configured correctly.
You are running into two SSL problems. The first is that the Common Name in the SSL certificate does not match the hostname you are using in the create_server_context call (in your example code, you are using the IP address of 52.36.10.100, which does not match the Common Name of your SSL certificate which is "William Bosl"). The second is that the SSL certificate is self-signed.
If you fix both of these problem with the SSL certificate then I believe the Python api will work correctly. |
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