UCSD-E4E / Pyrenote

Pyrenote, the Audio Labeling System for Acoustics Specifies Identification Project, is built to generate human moment-to-moment labels on audio files. At present, being used to label bird audio data. Derived from the open source repo Audino

Pyrenote, The E4E Manual Audio Labeling System

This project, Pyrenote, creates moment to moment or strong labels for audio data. Pyrenote and much of this README are based on heavily on Audino as well as Wavesurfer.js. The name is a combination of Py, Lyrebird, and note (such as making a note on a label).

If you want to use Pyrenote, use the following to get started!

NOTE: Before making any changes to the code, make sure to create a branch to safely make changes. Never commit directly to main or production branch. Read github_procedures.md for more detailed information before contributing to the repo.

Usage

Note: Before getting the project set up, message project leads for env file. This file should be put in /audino. Make sure the file is never pushed to the github

Please install the following dependencies to run Pyrenote on your system:

1. git [tested on v2.23.0]
2. docker [tested on v19.03.8, build afacb8b]
3. docker-compose [tested on v1.25.5, build 8a1c60f6]

Clone the repository

$ git clone https://github.com/UCSD-E4E/Pyrenote.git
$ cd audino

Note for Windows users: Please configure git to handle line endings correctly as services might throw an error and not come up. You can do this by cloning the project this way:

$ git clone https://github.com/UCSD-E4E/Pyrenote.git --config core.autocrlf=input

For Development (Note this is the one we will test on and use)

Similar to production setup, you need to use development configuration for working on the project, fixing bugs and making contributions. Note: Before proceeding further, you might need to give docker sudo access or run the commands listed below as sudo.

To build the services (do this when you first start it), run:
Note: Remember to cd into audino before starting

$ docker-compose -f docker-compose.dev.yml build

To bring up the services, run:

$ docker-compose -f docker-compose.dev.yml up

Then, in browser, go to http://localhost:3000/ to view the application.

To bring down the services, run:

$ docker-compose -f docker-compose.dev.yml down

Troubleshooting for starting docker

1. Docker containers do not even get a chance to start

• Make sure docker is set up properly
• Make sure docker itself has started. On Windows, check the system tray and hover over the icon to see the current status. Restart it if necessary

2. Backend crashes

• For this error, check the top of the log. It should be complaining about /r characters in the run-dev.sh files
• The backend will crash if the endline characters are set to CRLF rather than LF
• On VSCode, you can swap this locally via going into the file and changing the CRLF icon in the bottom right to LF
• Do this for frontend/scripts/run-dev.sh and backend/scripts/run-dev.sh

3. Database migration issues

• If the backend complains about compiler issues while the database migration is occurring go into backend/scripts/run-dev.sh
• On line 25, check and make sure that the stamp command is pointing to the right migration for the database
  • Ask for help on this one

Getting Started

At this point, the docker should have gotten everything set up. After going to http://localhost:3000/ you should be able to log into the docker

To access the site, sign in with the username of admin and password of password. On logging in, navigate to the admin-portal to create your first project. Make sure to make a label group and some labels for the project!

After creating a project, get the API key by returning to the admin portal. You can use the API key to add data to a project. Create a new terminal (while docker is running the severs) and cd into audino/backend/scripts. Here use the following command:

python upload_mass.py --username admin.test --is_marked_for_review True --audio_file C:\REPLACE\THIS\WITH\FOLDER\PATH\TO\AUDIO\DATA --host localhost --port 5000 --api_key REPLACE_THIS_WITH_API_KEY

Make sure to have a folder with the audio data ready to be added. For testing purposes, get a folder with about 20 clips.

Once that runs, you are ready to start testing!

For Production (Don't use on windows)

You can either run the project on default configuration or modify them to your need.
Note: Before proceeding further, you might need to give docker sudo access or run the commands listed below as sudo.
Note: Remember to cd into audino before starting

To build the services, run:

$ docker-compose -f docker-compose.prod.yml build

To bring up the services, run:

$ docker-compose -f docker-compose.prod.yml up

Then, in browser, go to http://0.0.0.0/ to view the application.

To bring down the services, run:

$ docker-compose -f docker-compose.prod.yml down

For Dev Team:

Features should be turned on and off by admins for individual projects. When adding a new feature to either a project's data page or annotation page, make sure to do the following:

1. Go to .\audino\frontend\src\containers\forms\featureForm.js
2. Add a new item in the featuresEnabled directory. This will be the name of the feature_toggle variable.
3. Return to the page you are working on.

• For example, if you are working on the annotation page, navigate to the componentDidMount() method
• about 20 lines down in the setState callback, add to the list SOME_VAR: response.data.features_list['VARIABLE_NAMED_IN_STEP_2'].