mavroudo/siesta-preprocess repository overview

The preprocessing component of SIESTA is integrated with a REST API to allow easy access to its functionalities.

⁠How to use this image

docker run --name siesta-preprocess -p8000:8000 mavroudo/siesta-preprocess

Once the application starts, the user can access all available endpoints at http://localhost:8000/docs⁠. Note that to execute the application, a database is required to store the computed indices. Currently, the supported databases are Apache Cassandra and S3. A docker-compose file that deploys the entire SIESTA infrastructure, along with an instance of both databases, can be found in the preprocessing repository on GitHub (https://github.com/mavroudo/SequenceDetectionPreprocess⁠).

This application utilizes a variety of environmental variables to facilitate database connectivity. For connecting to a Cassandra database, the following parameters are used:

• cassandra_host: Specifies the hostname or IP address of the Cassandra server.
• cassandra_port: Defines the port number on which Cassandra is listening.
• cassandra_user: The username for authenticating with the Cassandra database.
• cassandra_pass: The password associated with the specified Cassandra user.
• cassandra_replication_factor: Sets the number of replicas of data in the cluster.
• cassandra_gc_grace_seconds: Sets the time in seconds for garbage collection grace period in Cassandra.

For connecting to an S3-compatible storage service, these parameters are utilized:

• s3accessKeyAws: The access key for authenticating with the S3 service.
• s3ConnectionTimeout: Sets the timeout duration for S3 connections.
• s3endPointLoc: Specifies the endpoint URL of the S3 service.
• s3secretKeyAws: The secret key corresponding to the S3 access key for authentication.

However, despite the default values given for the parameters, users have the option to change them before submitting a job.