Deploy a production instance

In production, AskOmics is deployed with docker and docker-compose. We provide docker-compose.yml templates to deploy your instance.

Prerequisites

Install git

# Debian/Ubuntu
apt install -y git
# Fedora
dnf install -y git

Install docker:

Install docker-compose:

# Debian/Ubuntu
apt install -y docker-compose
# Fedora
dnf install -y docker-compose

Deployment

Download templates

First, clone the flaskomics-docker-compose repository. It contain template files to deploy your AskOmics instance.

git clone https://github.com/askomics/flaskomics-docker-compose.git

This repo contains several directories, depending on your needs

cd flaskomics-docker-compose
ls -1

Two directories are used for production deployment

  • standalone: deploy AskOmics with all its dependencies for a standalone usage
  • federated: deploy AskOmics with all its dependencies for a federated usage (Ask external endpoint such as NeXtProt)

Choose one of this directory depending of your needs

cd federated

Configure

First, edit the docker-compose.yml file. You can change the following entries:

  • services > askomics > image: Use the latest image tag. Example: askomics/flaskomics:3.2.1
  • services > virtuoso > image: Use the latest image tag. Example: askomics/virtuoso:7.2.5.1
  • services > nginx > ports: You can change the default port if 80 is already used on your machine. Example: "8080:80"
Virtuoso

Then, configure virtuoso by editing virtuoso.env

Edit VIRT_Parameters_NumberOfBuffers and VIRT_Parameters_MaxDirtyBuffers following rules described here.

Warning

Change the DBA_PASSWORD if you plan to expose the virtuoso endpoint.

Nginx (web proxy)

Nginx is used to manage web redirection. Nginx configuration is in two files: nginx.conf and nginx.env. If you want to access the virtuoso endpoint, uncomment the virtuoso section in nginx.conf

AskOmics

AskOmics configuration is set using enviroment variables. This variables are set in askomics.env. All entry if the askomics.ini file can be overrided in this file using

All properties defined in askomics.ini can be configured via the environment variables in askomics.env. The environment variable should be prefixed with ASKO_ and have a format like ASKO_$SECTION_$KEY. $SECTION and $KEY are case sensitive. E.g. property footer_message in the askomics section should be configured as ASKO_askomics_footer_message=Welcome to my AskOmics!

Warning

Change ASKO_flask_secret_key and ASKO_askomics_password_salt to random string

Configuration

AskOmics configuration is stored in config/askomics.ini file.

  • flask

    • debug (true or false): Set to true if you run AskOmics in development mode, or for debug purpose
    • secret_key (string): AskOmics secret key for session.
    • session_timeout (int): timeout for the session cookie (in minutes)

  • celery

    • broker_url (url): Redis or RabitMQ url
    • result_backend (url): Redis or RabitMQ url

  • askomics

    • debug (true or false): Display debug log in console
    • debug_ttl (true or false): Keep converted rdf file. Set the to true can fill you disk, active only for debug purpose
    • reverse_proxy_path (string): proxy path if AskOmics is accessible under a subpath
    • subtitle (string): Subtitle, displayed on the browser tab
    • footer_message (string): Custom message displayed on the AskOmics footer
    • display_commit_hash (true or false): diplay the commit hash of the current version in the AskOmics footer
    • data_directory (path): where AskOmics store the data
    • database_path (path): Path to the sqlite database
    • npreview (int): Number of line displayed during integration
    • password_salt (string): Password salt
    • default_locked_account (true or false): Lock new account
    • disable_integration (true or false): Disable integration to non admin users
    • quota (size): Default quota for new users

  • virtuoso

    • triplestore (string): Triplestore used. Can be virtuoso, fuseki or corese
    • endpoint (url): Triplestore endpoint url
    • updatepoint (url): Triplestore updatepoint url
    • fuseki_upload_url (url): If triplestore is fuseki, set the fuseki upload url
    • username (string): Triplestore credential: username
    • password (string): Triplestore credential: password
    • load_url (url): AskOmics url accessible from the triplestore
    • upload_method (string): upload method fir virtuoso. Can be load or insert
    • chunk_size (int): Number of RDF triples to upload in one time
    • block_size (int): Size of location bocksize for positionable entities
    • serialization_format (string): RDF serialization format. Can be nt, turtle or xml
    • default_graph (string): Triplestore default graph
    • users_graph (string): User base graph
    • prefix (url): Default AskOmics prefix
    • namespace (url): Default AskOmics namespace
    • preview_limit (int): Number of line to be previewed in the results page
    • result_set_max_rows (int): Triplestore max row. Must be the same as SPARQL[ResultSetMaxRows] in virtuoso.ini config

  • federation

    • query_engine (string): Query engine to use, can be corese or fedx
    • endpoint (url): Federated query engine endpoint url
    • local_endpoint (url): Triplestore url, accessible from the federated query engine

  • sentry

    • server_dsn (url): Sentry url for the server
    • frontend_dsn (url): Sentry url for the frontend