Contains sample scripts and code to be used with LabKey Server
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docker
ops
python
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LICENSE.txt
README.md

README.md

samples

This repository contains scripts and tools which can be used to manage and/or work with data stored in a LabKey Server.

The scripts and tools that you find here are either in development or have not yet been merged into the LabKey Server subversion repository (more information)

Available Scripts and Tools

Python Scripts

Located in the /python folder

The LabKey Server Python API provides ways for you to access the data in your LabKey Server programmatically with Python. The LabKey Server Python API does not cover all the functionality of the LabKey Server. These scripts will provide examples for working the LabKey Server Python API and sample scripts for interacting with your LabKey Server in ways not currently covered by the API.

  • upload_file.py: Use this script to upload a file to your LabKey Server using WEBDAV.
    • Before using the script, goto the Variables section of the script and change the URL, Project and Folder Path to point to your LabKey Server.
    • Requires the Poster package
    • This script is not officially supported by LabKey.
  • download_study_archive: Use this script to create a Study Archive and download the resulting archive to your computer.
    • Before using the script, goto the Variables section of the script and change the URL, Project and Folder Path to point to your LabKey Server.
    • Requires the Poster package
    • This script is not officially supported by LabKey.

Installation and Upgrade

Located in the /ops folder

  • install-windows-manual.bat: Use script to install the LabKey Server binaries on Windows. This should only be used if you are performing at manual installation.
    • This should only be used if you are performing at manual installation on a Windows server.
    • This script is not officially supported by LabKey.
  • upgrade-windows-manual.bat: Use script to upgrade a LabKey Server running on Windows, which was manually installed.
    • Instruction
    • Do not use this script if you installed your LabKey Server using the Windows Installer. Please use the Windows Installer to upgrade your server
    • This script is not officially supported by LabKey, but it is used by a number of labs and institutions running LabKey Server on Windows.
    • If you have questions or need support, please post a message on the LabKey Server Community Forum.
  • upgrade-remote-pipeline.sh: Use script to upgrade a LabKey Remote Pipeline Server running on *nix operating system.
    • This script is not officially supported by LabKey and there is currently no documentation for it. However, I regularly use a modified version of this on my test servers.
    • If you have questions or need support, please post a message on the LabKey Server Community Forum.
  • upgrade-remote-pipeline.bat: Use script to upgrade a LabKey Remote Pipeline Server running on Windows that was installed manually.
    • This script is not officially supported by LabKey and there is currently no documentation for it. However, I regularly use a modified version of this on my test servers.
    • Do not use this script if you installed your LabKey Remote Pipeline Server using the Windows Installer. Please use the Windows Installer to upgrade your server.
    • If you have questions or need support, please post a message on the LabKey Server Community Forum.
  • labkey-database-backup-sample-script.bat: This script can be used to perform a nightly backup (using pg_dump) of databases on a PostgreSQL server instance.
    • This script is not officially supported by LabKey and there is currently no documentation for it.
    • See blog entry for more information on using the script.

Docker

Located in the /docker folder

  • labkey-standalone: Dockerfile and other source files needed for building a Docker image that runs LabKey Server.
    • See the README file for information on building your own image or
    • See bconn/labkey-standalone on DockerHub.
    • This script is not officially supported by LabKey.

Support

If you need support using these scripts/tools or for the LabKey Server in general, please post message to LabKey Server Community Forum. Or send me a message on twitter(@bdconnolly).