sipist-workspace

This repository provides containerized applications and microservices for the Information Processing and Retrieval Course @ Instituto Superior Técnico

This guide helps setting up a workspace environment for completing lab classes, which includes a search server and other auxiliary services.

Services provided include:

• Elasticsearch Elasticsearch is a search engine based on the Lucene library.
• sipist/notebook Jupyter Notebook Intelligent Retrieval Systems Stack

Prerequisites

Install Docker Desktop

Docker Desktop is an application for MacOS, Linux, and Windows machines for the building and sharing of containerized applications and microservices.

Install Docker Desktop on Mac, Windows or Linux

Install Git

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

Install Git on Mac Windows or Linux

Your first time launching the Workspace

1. Open Terminal.

2. Change the current working directory to the location where you want the cloned directory.

3. Run the following command to create your local clone

   git clone https://github.com/sipist/sipist-workspace.git

   Press Enter

   Cloning into 'sipist-workspace'...
   remote: Enumerating objects: 297, done.
   remote: Counting objects: 100% (80/80), done.
   remote: Compressing objects: 100% (65/65), done.
   remote: Total 297 (delta 41), reused 38 (delta 14), pack-reused 217
   Receiving objects: 100% (297/297), 733.65 KiB | 501.00 KiB/s, done.
   Resolving deltas: 100% (136/136), done.

4. Change the current working directory to the location of the cloned directory.

   cd sipist-workspace/

5. From the cloned directory, start up sipist-workspace by running

   docker compose up

   Note: The services are attached to this Terminal, so the logs for all the services provided will be printed on its window. Quitting this Terminal window quits all the services abruptly. To shutdown safely you will need to issue CTRL+C in the Terminal window and wait until all the services stop gracefuly. You can close the Terminal window after all services are stopped.

Using the Jupyter Notebook (Docs)

The Jupyter Notebook service runs on the non-stardard 10001 port. Token authentication is enabled.

1. You need to find your Authentication Token to login every time the sipist-workspace is launched (e.g., after a reboot)

2. Find the section of the logs towards the bottom of the Terminal window that look like this excerpt:

   sipist-workspace-notebook-1  |     Or copy and paste one of these URLs:
   sipist-workspace-notebook-1  |         http://7fd8c38e99bd:10001/lab?token=f83ee982668ebe66bee2dbeb5875d14131a1d118d1e0fa12
   sipist-workspace-notebook-1  |         http://127.0.0.1:10001/lab?token=f83ee982668ebe66bee2dbeb5875d14131a1d118d1e0fa12
   

   Note: You can also view the logs for the sipist-workspace-notebook-1 in the Containers tab in the Docker Desktop application.

3. Follow the link printed last with host 127.0.0.1. The authentication token is embedded in the URL.

FAQ and Troubleshooting

How do I update my workspace?

1. Firstly, from the project directory run

   git pull

   This updates sipist-workspace to the latest version.

2. Secondly, from the project directory run

   docker compose pull

   This updates container images to the latest version.

3. Lastly, from the project directory run

   docker compose up --build --force-recreate --remove-orphans

   This starts up the sipist-workspace and cleans up unused images.

I get Permission Errors and/or the notebook Save Button is disabled

You need to set the owner of every directory under /home/jovyan/ to the user jovyan and groups users. This is the default username and group for the user in the notebook container.

You only need to run this once.

1. Open Terminal.

2. Run this to reset the permissions for files and folders under home/jovyan/.

   chown -R jovyan:users /home/jovyan/

If this still does not solve the issue with permissions then follow this recipe:

1. Open Terminal.

2. Run this do access the notebook container as administrator (root):

   docker compose exec -e GRANT_SUDO=yes --user root notebook /bin/bash

3. Run this to reset the permissions for files and folders under home/jovyan/.

   chown -R jovyan:users /home/jovyan/

Issues

Please use GitHub Issues to report any issues you might have with sipist-workspace.

Credits

Flavio Martins