Backend for Historical Manuscripts Indexing

Requirements

• Git
• Make
• Python 3.10+
• pip
• virtualenvwrapper
• Docker 24+
• mkcert
• GeoDjango system dependencies: sudo apt install binutils libproj-dev gdal-bin

Setup for developers

You'll also need the Arkindex frontend to be able to develop on the whole platform.

git clone git@gitlab.teklia.com:arkindex/backend.git
git clone git@gitlab.teklia.com:arkindex/frontend.git
cd backend
mkvirtualenv ark -a . -p /usr/bin/python3.10
pip install -e .[test]

The Arkindex backend relies on some open-source services to store data and communicate to asynchronous workers. To run all the required services, please run in a dedicated shell:

make services

On a first run, you'll need to:

1. Configure the instance by enabling the sample configuration.
2. Populate the database structure.
3. Initialize some fields in the database.
4. Create an administration account.

All of these steps are done through:

cp config.yml.sample arkindex/config.yml
arkindex migrate
arkindex bootstrap
arkindex createsuperuser

Finally, you can run the backend:

arkindex runserver

At this stage, you can use http://localhost:8000/admin to access the administration interface.

Asycnhronous tasks

To run asynchronous tasks, run in another shell:

make worker

Dockerized stack

It is also possible to run the whole Arkindex stack through Docker containers. This is useful to quickly test the platform.

This command will build all the required Docker images (backend & frontend) and run them as Docker containers:

make stack

You'll be able to access the platform at the url https://ark.localhost.

Local configuration

For development purposes, you can customize the Arkindex settings by adding a YAML file as arkindex/config.yml. This file is not tracked by Git; if it exists, any configuration directive set in this file will be used for exposed settings from settings.py. You can view the full list of settings on the wiki.

Another way to customize your Arkindex instance is to add a Python file in arkindex/project/local_settings.py. Here you are not limited to exposed settings, and can customize any setting, or even load Python dependencies at boot time. This is not recommended, as your customization may not be available to real-world Arkindex instances.

Local image server

Arkindex splits up image URLs in their image server and the image path. For example, a IIIF server at http://iiif.irht.cnrs.fr/iiif/ and an image at /Paris/JJ042/1.jpg would be represented as an ImageServer instance holding one Image. Since Arkindex has a local IIIF server for image uploads and thumbnails, a special instance of ImageServer is required to point to this local server. In local development, this server should be available at https://ark.localhost/iiif. You will therefore need to create an ImageServer via the Django admin or the Django shell with this URL. To set the local server ID, you can add a custom setting in arkindex/config.yml:

local_imageserver_id: 999

Here is how to quickly create the ImageServer using the shell:

$ arkindex shell
>>> from arkindex.images.models import ImageServer
>>> ImageServer.objects.create(id=1, display_name='local', url='https://ark.localhost/iiif')

Note that this local server will only work inside Docker.

Usage

Makefile

At the root of the repository is a Makefile that provides commands for common operations:

• make or make all: Clean and build;
• make base: Create and push the arkindex-base Docker image that is used to build the arkindex-app image;
• make clean: Cleanup the Python package build and cache files;
• make clean-docker: Deletes all running containers to avoid naming and network ports conflicts;
• make build: Build the arkindex Python package and recreate the arkindex-app:latest without pushing to the GitLab container registry;
• make test-fixtures: Create the unit tests fixtures on a temporary PostgreSQL database and save them to the data.json file used by most Django unit tests.

Django commands

Aside from the usual Django commands, some custom commands are available via arkindex:

• build_fixtures: Create a set of database elements designed for use by unit tests in a fixture (see make test-fixtures).
• delete_corpus: Delete a big corpus using an RQ task.
• reindex: Reindex elements into Solr.
• move_lines_to_parents: Moves element children to their geographical parents.

See arkindex <command> --help to view more details about a specific command.

Code validation

Once your code appears to be working on a local server, a few checks have to be performed:

• Migrations: Ensure that all migrations have been created by typing arkindex makemigrations.
• Unit tests: Run arkindex test to perform unit tests.
  • Use arkindex test module_name to perform tests on a single module, if you wish to spend less time waiting for all tests to complete.

Linting

We use pre-commit to check the Python source code syntax of this project.

To be efficient, you should run pre-commit before committing (hence the name...).

To do that, run once:

pip install pre-commit
pre-commit install

The linting workflow will now run on modified files before committing, and may fix issues for you.

If you want to run the full workflow on all the files: pre-commit run -a.

Debugging tools

Run pip install ipython django-debug-toolbar django_extensions to install all the available optional dev tools for the backend.

IPython will give you a nicer shell with syntax highlighting, auto reloading and much more via arkindex shell.

Django Debug Toolbar provides you with a neat debug sidebar that will help diagnosing slow API endpoints or weird template bugs. Since the Arkindex frontend is completely decoupled from the backend, you will need to browse to an API endpoint to see the debug toolbar.

Django Extensions adds a lot of arkindex commands ; the most important one is arkindex shell_plus which runs the usual shell but with all the available models pre-imported. You can add your own imports with the local_settings.py file. Here is an example that imports some of the backend's enums and some special QuerySet features:

SHELL_PLUS_POST_IMPORTS = [
    ('django.db.models', ('Value', )),
    ('django.db.models.functions', '*'),
    ('arkindex.documents.models', (
        'ElementType',
        'Right',
    )),
    ('arkindex.process.models', (
        'ProcessMode',
    )),
    ('arkindex.project.aws', (
        'S3FileStatus',
    ))
]

Asynchronous tasks

We use rq, integrated via django-rq, to run tasks without blocking an API request or causing timeouts. To call them in Python code, you should use the trigger methods in arkindex.project.triggers; those will do some safety checks to make catching some errors easier in dev. The actual tasks are in arkindex.documents.tasks, or in other tasks modules within each Django app. The following tasks exist:

• Delete a corpus: corpus_delete
• Delete a list of elements: element_trash
• Delete worker results (transcriptions, classifications, etc. of a worker version): worker_results_delete
• Move an element to another parent: move_element
• Create WorkerActivity instances for all elements of a process: initialize_activity
• Delete a process and its worker activities: process_delete
• Export a corpus to an SQLite database: export_corpus

To run them, use make worker to start a RQ worker. You will need to have Redis running; make services will provide it. make stack also provides an RQ worker running in Docker from a binary build.

Metrics

The application serves metrics for Prometheus under the /metrics prefix. A specific port can be used by setting the PROMETHEUS_METRICS_PORT environment variable, thus separating the application from the metrics API.

Migration from architecture setup

If you were using the architecture repository previously to run Arkindex, you'll need to migrate MinIO data from a static path on your computer towards a new docker volume.

docker volume create arkindex_miniodata
mv /usr/share/arkindex/s3/data/iiif /var/lib/docker/volumes/arkindex_miniodata/_data/uploads
mv /usr/share/arkindex/s3/data/{export,iiif-cache,ponos-logs,ponos-artifacts,staging,thumbnails,training} /var/lib/docker/volumes/arkindex_miniodata/_data/

You will also need to setup mkcert as we do not use Teklia development Certificate Authority anymore. mkcert will take care of SSL certificates automatically, updating your browsers and system certificate store !

Finally, you can remove the architecture project from your work folder, as it's now archived and could be confusing.