Nextcode-sdk is a python package for interfacing with Wuxi Nextcode services.
$ pip install nextcode-sdk -U$ pip install nextcode-sdk[jupyter] -Uimport nextcode
client = nextcode.Client(api_key="xxx")
qry = client.service("query")
qry.status()
qry.get_queries()
qry.get_query(query_id)
qry.list_templates()To start using the python sdk in Jupyter Notebooks you will first need to install it using the jupyter extras and then load the gor % magic extension.
! pip install nextcode-sdk[jupyter] -U
%load_ext nextcode.gorJupyter notebooks running on the Wuxi Nextcode servers are preconfigured with a GOR_API_KEY and GOR_PROJECT. If you are running outside such an environment you will need to configure your environment accordingly:
%env GOR_API_KEY="***"
%env GOR_API_PROJECT="test_project"
# optionally set the LOG_QUERY environment variable to get more information about running queries.
%env LOG_QUERY=1Now you can run gor with the following syntax:
# simple one-liner
%gor gor #dbsnp# | top 100
# one-liner which outputs to local variable as a pandas dataframe
results = %gor gor #dbsnp# | top 100
# multi-line statement
%%gor
gor #dbsnp#
| top 100
# multi-line statement which writes results into project folder
%%gor user_data/results.tsv <<
nor #dbsnp#
| top 100
# output results to local variable as a pandas dataframe
%%gor myvar <<
nor #dbsnp#
| top 100
# read from a pandas dataframe in a local variable
%%gor
nor [var:myvar]
| top 100
# reference a local variable
num = 10
%%gor
nor [var:myvar]
| top $num