container.puml

@startuml
title Galaxy Container Architecture
agent user as "User Agent"

frame "Ansible" {
  artifact playbook_webserver as "webserver.playbook.yml"
  artifact playbook_application as "application.playbook.yml"
  artifact playbook_worker as "worker.playbook.yml"
}

frame "Container Registry" {
  artifact image_postgres as "PostGRES"
  artifact image_slurm as "SLURM"
  artifact image_minio as "MinIO"

  folder brinkman_containers_registry as "Brinkman Lab"
  folder "Biocontainers" {
    artifact tools as "Various analysis tool dependencies"
  }
}

rectangle brinkman_containers as "Brinkman Lab Containers" {
  package container_webserver as "Front end" {
    component nginx
    folder "/srv/galaxy" {
      file "static content"
    }
    folder "/etc/nginx/nginx.conf.d/" {
      file "galaxy.conf"
    }
  }

  package container_application as "Galaxy application" {
    component uwsgi_application as "UWSGI Daemon"
    folder "/srv/galaxy/lib" {
      file "Galaxy codebase"
    }
    folder "/srv/galaxy/config" {
      file "galaxy.yml"
      file "job_conf.xml"
      file "object_store_conf.xml"
    }
  }

  package container_worker as "Galaxy worker" {
    component uwsgi_worker as "UWSGI Daemon"
  }

}

cloud cc as "External resource" {
  queue slurm_cluster as "SLURM Cluster"
  entity pulsar as "Galaxy Pulsar service"
}

cloud k8s as "Kubernetes" {
  storage user_data [
    User data object store
    ====
    ----
  ]
  database galaxy_state [
    Galaxy state
    ----
    ----
  ]
  database service_registry as "Service Registry"
  entity kubernetes_controller as "Kubernetes controller"

  entity loadbalancer [
    Load-balancer replicate 1
    Load-balancer replicate 2
  ]
  node instance_webserver [
    Web server replicate 1
    ----
    Web server replicate 2
    ----
    Web server replicate 3
    ----
    ...
    Web server replicate n
  ]
  node instance_application [
    Galaxy application replicate 1
    ----
    Galaxy application replicate 2
    ----
    Galaxy application replicate 3
    ----
    ...
    Galaxy application replicate n
  ]
  node instance_worker [
    Galaxy worker replicate 1
    ----
    Galaxy worker replicate 2
    ----
    Galaxy worker replicate 3
    ----
    ...
    Galaxy worker replicate n
  ]
  node tool_invocation as "Various tool container invocations"
}

user -0)-> instance_webserver : "via load-balancer"

playbook_webserver ~~o container_webserver
playbook_application ~~o container_application
playbook_worker ~~o container_worker

instance_webserver ..> container_webserver : "instance of"
instance_webserver --> instance_application : "proxies to"
instance_application ..> container_application : "instance of"
instance_application -(0-> galaxy_state
instance_worker ..> container_worker : "instance of"
instance_worker -(0-> galaxy_state
instance_worker --* kubernetes_controller : "schedules jobs"
instance_worker --* pulsar
instance_worker -(0-> user_data : "uploads to"
kubernetes_controller --> tool_invocation
tool_invocation ..> tools : "instance of"
tool_invocation -(0-> user_data : "stages from"
galaxy_state ..> image_postgres : "instance of"
user_data ..> image_minio : "instance of"


brinkman_containers_registry --> brinkman_containers
container_worker --0 container_application : extends

pulsar --> slurm_cluster : "schedules"
pulsar --> user_data : "stages from"

@enduml