labkey_api.md

NOTE: Include this info in the main doc in the root directory once available

In order to connect to the LabKey through API, you will first need to create a file .netrc in your home directory:

touch ${HOME}/.netrc

Add the following lines to the file:

machine <remote-instance-of-labkey-server>  
login <user-email>
password <user-password>  

To secure the file, set permissions in a way that only you can see the content of the file:

chmod 400 .netrc

Install the labkey and pandas packages, ideally from a virtual environment (e.g., virtualenv or conda):

pip install labkey pandas

Run the LabKey API client script:

python labkey_api.py project_name labkey_table_nane  

Example:

python labkey_api.py TEST_ABOERSCH RNA_Seq_data_template  

Right now the script prints a representation of a pandas data frame containing the requested LabKey table the the screen. For further processing the current script could be included in another script, or it could be modified to write out the data in a desired file format (e.g., TSV).