Skip to content
Snippets Groups Projects

Labkey api

Merged BIOPZ-Börsch Anastasiya requested to merge labkey_api into master
1 file
+ 36
21
Compare changes
  • Side-by-side
  • Inline
+ 36
21
This is the description how to connect to the LabKey through API:
1. Create a file named ".netrc" in your home directory. This file must include the following three lines:
machine "remote-instance-of-labkey-server"
login "user-email"
password "user-password"
E.g.:
machine labkey.scicore.unibas.ch
login eva.pujadas@unibas.ch
password xxxxx
To secure the file, set permissions in a way that only you can see the content of the file:
$ chmod 400 .netrc
2. For running the script labkey_api.py libraries "labkey" and "pandas" are required. Either you install them and run the script with the standard python or you use the module "labkey-api-python/1.1.0-foss-2018b-Python-3.6.6" provided by SciCore. Execute the following command:
python labkey_api.py arg1 arg2
Here, arg1 stands for the project name, arg2 stands for the name of the LabKey table.
E.g.:
In order to connect to the LabKey through API, you will first need to create a file `.netrc` in your home directory:
```bash
touch ${HOME}/.netrc
Add the following lines to the file:
```console
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:
```bash
chmod 400 .netrc
```
Install the `labkey` and `pandas` packages, ideally from a virtual environment (e.g., `virtualenv` or `conda`):
```bash
pip install labkey pandas
```
Run the LabKey API client script:
```bash
python labkey_api.py project_name labkey_table_nane
```
Example:
```bash
python labkey_api.py TEST_ABOERSCH RNA_Seq_data_template
```
The script outputs the complete LabKey table in the form of pandas data frame.
The script outputs the requested LabKey table in the form of a pandas data frame.
Loading