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Add TOSCA radiomics example
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@micafer
micafer committed Jun 27, 2023
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tosca_definitions_version: tosca_simple_yaml_1_0

imports:
- ec3_custom_types: https://raw.githubusercontent.com/grycap/ec3/tosca/tosca/custom_types.yaml

description: Launch full Radiomics workflow as OSCAR functions

topology_template:
inputs:
os_image:
type: string
description: OS Image
default: "one://ramses.i3m.upv.es/1396"

cluster_name:
type: string
description: Cluster Name
default: "oscar-radiomics"
domain_name:
type: string
description: Domain Name
default: "im.grycap.net"

wn_num:
type: integer
description: Number of WNs in the oscar cluster
default: 4
required: yes

fe_cpus:
type: integer
description: Number of CPUs for the front-end node
default: 4
required: yes
fe_mem:
type: scalar-unit.size
description: Amount of Memory for the front-end node
default: 4 GB
required: yes
fe_instance_type:
type: string
description: Flavor name of the front-end node. Only required in case of special flavors (i.e. with GPUs)
default: ""
wn_cpus:
type: integer
description: Number of CPUs for the WNs
default: 8
required: yes
wn_mem:
type: scalar-unit.size
description: Amount of Memory for the WNs
default: 8 GB
required: yes
wn_instance_type:
type: string
description: Flavor name of the WN node. Only required in case of special flavors (i.e. with GPUs)
default: ""

storage_size:
type: string
description: Size of the extra HD added to the instance
default: 30 GB
required: yes

admin_token:
type: string
description: Access Token for the Kubernetes admin user
default: xxxxxxxxxx
oscar_password:
type: string
description: OSCAR password
default: xxxxxxxxxx
minio_password:
type: string
description: MinIO password (8 characters min.)
default: xxxxxxxxxx
constraints:
- min_length: 8
cert_user_email:
type: string
description: Email to be used in the Let's Encrypt issuer
default: "[email protected]"


node_templates:

radiomicsanon_service:
type: tosca.nodes.aisprint.FaaS.Function
properties:
name: radiomicsanon
memory: 128 MB
script: |
FILE_NAME=$(basename $INPUT_FILE_PATH)
OUTPUT_FILE=$TMP_OUTPUT_DIR/A_$FILE_NAME
python anonymise.py -i $INPUT_FILE_PATH -o $OUTPUT_FILE
cpu: 1
image: grycap/radiomics:anonymise_arm64_v2
input:
- storage_provider: minio.default
path: radiomicsin
output:
- storage_provider: minio.oscar-radiomics
path: anonymise
storage_providers:
minio:
oscar-radiomics:
access_key: minio
endpoint: https://minio.oscar-radiomics.im.grycap.net
region: us-east-1
secret_key: xxxxxxxxxx

radiomicsprep_service:
type: tosca.nodes.aisprint.FaaS.Function
properties:
name: radiomicsprep
memory: 0.9 GB
script: |
FILE_NAME=$(basename $INPUT_FILE_PATH)
OUTPUT_FILE=$TMP_OUTPUT_DIR/P_$FILE_NAME
python doppler_segmentation.py -i $INPUT_FILE_PATH -o $OUTPUT_FILE
cpu: 1
image: grycap/radiomics:preparation
input:
- storage_provider: minio.default
path: anonymise
output:
- storage_provider: s3.scar
path: scar-micafer/input
storage_providers:
s3:
scar:
access_key: AK
region: us-east-1
secret_key: xxxxxxxxxx
requirements:
- host: oscar

radiomicsanalysis_service:
type: tosca.nodes.aisprint.FaaS.Function
properties:
name: micafer-radiomics
memory: 1 GB
script: script.sh
image: 974349055189.dkr.ecr.us-east-1.amazonaws.com/scar-radiomics-analysis
input:
- storage_provider: s3
path: scar-micafer/input
output:
- storage_provider: s3
path: scar-micafer/output

oscar:
type: tosca.nodes.indigo.OSCAR
properties:
minio_secretkey: { get_input: minio_password }
password: { get_input: oscar_password }
dns_host: { concat: [ get_input: cluster_name, '.', get_input: domain_name ] }
minio_dns_host: { concat: [ "minio.", get_input: cluster_name, '.', get_input: domain_name ] }
minio_dns_host_console: { concat: [ "console.minio.", get_input: cluster_name, '.', get_input: domain_name ] }
oidc_enable: false
capabilities:
endpoint:
properties:
ports:
http_port:
protocol: tcp
source: 80
https_port:
protocol: tcp
source: 443
minio_port:
protocol: tcp
source: 30300
requirements:
- host: lrms_front_end

lrms_front_end:
type: tosca.nodes.indigo.LRMS.FrontEnd.Kubernetes
capabilities:
endpoint:
properties:
port: 30443
protocol: tcp
properties:
admin_username: kubeuser
admin_token: { get_input: admin_token }
install_kubeapps: false
install_metrics: true
install_nfs_client: true
install_ingress: true
version: 1.23.6
cert_manager: true
cert_user_email: { get_input: cert_user_email }
public_dns_name: { concat: [ get_input: cluster_name, '.', get_input: domain_name ] }
cri_runtime: containerd
requirements:
- host: front

front:
type: tosca.nodes.indigo.Compute
capabilities:
endpoint:
properties:
dns_name: kubeserver
additional_dns_names:
- { concat: [ get_input: cluster_name, '@', get_input: domain_name ] }
- { concat: [ "minio.", get_input: cluster_name, '@', get_input: domain_name ] }
- { concat: [ "console.minio.", get_input: cluster_name, '@', get_input: domain_name ] }
network_name: PUBLIC
host:
properties:
num_cpus: { get_input: fe_cpus }
mem_size: { get_input: fe_mem }
instance_type: { get_input: fe_instance_type }
os:
properties:
distribution: ubuntu
type: linux
image: { get_input: os_image }
requirements:
- local_storage:
node: my_block_storage
capability: tosca.capabilities.Attachment
relationship:
type: tosca.relationships.AttachesTo
properties:
location: /pv
device: hdb

my_block_storage:
type: tosca.nodes.BlockStorage
properties:
size: { get_input: storage_size }

wn_node:
type: tosca.nodes.indigo.LRMS.WorkerNode.Kubernetes
properties:
front_end_ip: { get_attribute: [ front, private_address, 0 ] }
version: 1.23.6
cri_runtime: containerd
requirements:
- host: wn

wn:
type: tosca.nodes.indigo.Compute
capabilities:
scalable:
properties:
count: { get_input: wn_num }
host:
properties:
num_cpus: { get_input: wn_cpus }
mem_size: { get_input: wn_mem }
instance_type: { get_input: wn_instance_type }
os:
properties:
distribution: ubuntu
type: linux
image: { get_input: os_image }

outputs:
dashboard_endpoint:
value: { concat: [ 'https://', get_input: cluster_name, '.', get_input: domain_name , '/dashboard/' ] }
local_oscarui_endpoint:
value: { concat: [ 'https://', get_input: cluster_name, '.', get_input: domain_name , '/' ] }
minio_endpoint:
value: { concat: [ 'https://minio.', get_input: cluster_name, '.', get_input: domain_name, '/' ] }
console_minio_endpoint:
value: { concat: [ 'https://console.minio.', get_input: cluster_name, '.', get_input: domain_name, '/' ] }

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