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docker-compose-dev.yml
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# This is for spinning up core services as single hosts in the DEV environment
version: "3.6"
name: dev-cms
services:
medcat-snomed:
extends:
file: ./docker-compose.yml
service: medcat-snomed
labels:
- org.cogstack.model-serve.dev=true
build:
context: ./
dockerfile: ./docker/medcat-snomed/Dockerfile
args:
- CMS_MODEL_NAME=SNOMED MedCAT model
- CMS_UID=${CMS_UID:-1000}
- CMS_GID=${CMS_GID:-1000}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=$NO_PROXY
image: local-cms-medcat-snomed:do-not-push
environment:
- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
- AWS_ACCESS_KEY_ID=
- AWS_SECRET_ACCESS_KEY=
- MLFLOW_S3_ENDPOINT_URL=
- MLFLOW_TRACKING_URI=${MLFLOW_TRACKING_URI:-file:/tmp/mlruns}
- MLFLOW_TRACKING_USERNAME=
- MLFLOW_TRACKING_PASSWORD=
- MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING=${MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING:-false}
- GELF_INPUT_URI=
- AUTH_USER_ENABLED=${AUTH_USER_ENABLED:-false}
- AUTH_JWT_SECRET=$AUTH_JWT_SECRET
- AUTH_ACCESS_TOKEN_EXPIRE_SECONDS=${AUTH_ACCESS_TOKEN_EXPIRE_SECONDS:-3600}
- AUTH_DATABASE_URL=${AUTH_DATABASE_URL:-sqlite+aiosqlite:///./cms-users.db}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=localhost
- http_proxy=$HTTP_PROXY
- https_proxy=$HTTPS_PROXY
- no_proxy=localhost
medcat-icd10:
extends:
file: ./docker-compose.yml
service: medcat-icd10
labels:
- org.cogstack.model-serve.dev=true
build:
context: ./
dockerfile: ./docker/medcat-icd10/Dockerfile
args:
- CMS_MODEL_NAME=ICD-10 MedCAT model
- CMS_UID=${CMS_UID:-1000}
- CMS_GID=${CMS_GID:-1000}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=$NO_PROXY
image: local-cms-medcat-icd10:do-not-push
environment:
- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
- AWS_ACCESS_KEY_ID=
- AWS_SECRET_ACCESS_KEY=
- MLFLOW_S3_ENDPOINT_URL=
- MLFLOW_TRACKING_URI=${MLFLOW_TRACKING_URI:-file:/tmp/mlruns}
- MLFLOW_TRACKING_USERNAME=
- MLFLOW_TRACKING_PASSWORD=
- MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING=${MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING:-false}
- GELF_INPUT_URI=
- AUTH_USER_ENABLED=${AUTH_USER_ENABLED:-false}
- AUTH_JWT_SECRET=$AUTH_JWT_SECRET
- AUTH_ACCESS_TOKEN_EXPIRE_SECONDS=${AUTH_ACCESS_TOKEN_EXPIRE_SECONDS:-3600}
- AUTH_DATABASE_URL=${AUTH_DATABASE_URL:-sqlite+aiosqlite:///./cms-users.db}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=localhost
- http_proxy=$HTTP_PROXY
- https_proxy=$HTTPS_PROXY
- no_proxy=localhost
medcat-deid:
extends:
file: ./docker-compose.yml
service: medcat-deid
labels:
- org.cogstack.model-serve.dev=true
build:
context: ./
dockerfile: ./docker/medcat-deid/Dockerfile
args:
- CMS_MODEL_NAME=De-Identification MedCAT model
- CMS_UID=${CMS_UID:-1000}
- CMS_GID=${CMS_GID:-1000}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=$NO_PROXY
image: local-cms-medcat-deid:do-not-push
environment:
- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
- AWS_ACCESS_KEY_ID=
- AWS_SECRET_ACCESS_KEY=
- MLFLOW_S3_ENDPOINT_URL=
- MLFLOW_TRACKING_URI=${MLFLOW_TRACKING_URI:-file:/tmp/mlruns}
- MLFLOW_TRACKING_USERNAME=
- MLFLOW_TRACKING_PASSWORD=
- MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING=${MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING:-false}
- GELF_INPUT_URI=
- AUTH_USER_ENABLED=${AUTH_USER_ENABLED:-false}
- AUTH_JWT_SECRET=$AUTH_JWT_SECRET
- AUTH_ACCESS_TOKEN_EXPIRE_SECONDS=${AUTH_ACCESS_TOKEN_EXPIRE_SECONDS:-3600}
- AUTH_DATABASE_URL=${AUTH_DATABASE_URL:-sqlite+aiosqlite:///./cms-users.db}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=localhost
- http_proxy=$HTTP_PROXY
- https_proxy=$HTTPS_PROXY
- no_proxy=localhost
medcat-umls:
extends:
file: ./docker-compose.yml
service: medcat-umls
labels:
- org.cogstack.model-serve.dev=true
build:
context: ./
dockerfile: ./docker/medcat-umls/Dockerfile
args:
- CMS_MODEL_NAME=UMLS MedCAT model
- CMS_UID=${CMS_UID:-1000}
- CMS_GID=${CMS_GID:-1000}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=$NO_PROXY
image: local-cms-medcat-umls:do-not-push
environment:
- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
- AWS_ACCESS_KEY_ID=
- AWS_SECRET_ACCESS_KEY=
- MLFLOW_S3_ENDPOINT_URL=
- MLFLOW_TRACKING_URI=${MLFLOW_TRACKING_URI:-file:/tmp/mlruns}
- MLFLOW_TRACKING_USERNAME=
- MLFLOW_TRACKING_PASSWORD=
- MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING=${MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING:-false}
- GELF_INPUT_URI=
- AUTH_USER_ENABLED=${AUTH_USER_ENABLED:-false}
- AUTH_JWT_SECRET=$AUTH_JWT_SECRET
- AUTH_ACCESS_TOKEN_EXPIRE_SECONDS=${AUTH_ACCESS_TOKEN_EXPIRE_SECONDS:-3600}
- AUTH_DATABASE_URL=${AUTH_DATABASE_URL:-sqlite+aiosqlite:///./cms-users.db}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=localhost
- http_proxy=$HTTP_PROXY
- https_proxy=$HTTPS_PROXY
- no_proxy=localhost
huggingface-ner:
extends:
file: ./docker-compose.yml
service: huggingface-ner
labels:
- org.cogstack.model-serve.dev=true
build:
context: ./
dockerfile: ./docker/huggingface-ner/Dockerfile
args:
- CMS_MODEL_NAME=HuggingFace NER model
- CMS_UID=${CMS_UID:-1000}
- CMS_GID=${CMS_GID:-1000}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=$NO_PROXY
image: local-cms-huggingface-ner:do-not-push
restart: always
networks:
- cms
environment:
- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
- AWS_ACCESS_KEY_ID=
- AWS_SECRET_ACCESS_KEY=
- MLFLOW_S3_ENDPOINT_URL=
- MLFLOW_TRACKING_URI=${MLFLOW_TRACKING_URI:-file:/tmp/mlruns}
- MLFLOW_TRACKING_USERNAME=
- MLFLOW_TRACKING_PASSWORD=
- MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING=${MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING:-false}
- GELF_INPUT_URI=
- AUTH_USER_ENABLED=${AUTH_USER_ENABLED:-false}
- AUTH_JWT_SECRET=$AUTH_JWT_SECRET
- AUTH_ACCESS_TOKEN_EXPIRE_SECONDS=${AUTH_ACCESS_TOKEN_EXPIRE_SECONDS:-3600}
- AUTH_DATABASE_URL=${AUTH_DATABASE_URL:-sqlite+aiosqlite:///./cms-users.db}
- HTTP_PROXY=$HTTP_PROXY
- HTTPS_PROXY=$HTTPS_PROXY
- NO_PROXY=localhost
- http_proxy=$HTTP_PROXY
- https_proxy=$HTTPS_PROXY
- no_proxy=localhost
volumes:
retrained-models:
driver: local
networks:
cms:
driver: bridge