remove dibbs container (#2888)

* add dibbs directly into ingestion

* add dibbs directly into message-parser

* add dibbs directly into message-refiner

* add dibbs directly into orchestration

* add dibbs directly into record linkage

* add dibbs directly into trigger-code-reference

* add dibbs directly into validation

* remove containers/dibbs

* update github workflows

* update base_service.py

* update tests to use pyproject.toml as source of truth

* add toml as dev requirement

* update pyproject path

* remove first character from version

* remove duplicate deps

* remove dupe reqs

* fix snyk

* fix requirements pin

.github/codecov.yml

@@ -15,9 +15,6 @@ coverage:
         flags:
           - sdk
 flags:
-  dibbs:
-    paths:
-      - "containers/dibbs"
   ecr-viewer:
     paths:
       - "containers/ecr-viewer"

.github/workflows/container-ingestion.yaml

@@ -6,7 +6,6 @@ on:
       - "**"
     paths:
       - containers/ingestion/**
-      - containers/dibbs/**
       - containers/fhir-converter/**
   merge_group:
     types:

.github/workflows/container-message-parser.yaml

@@ -6,7 +6,6 @@ on:
       - "**"
     paths:
       - containers/message-parser/**
-      - containers/dibbs/**
       - containers/fhir-converter/**
   merge_group:
     types:

.github/workflows/container-message-refiner.yaml

@@ -6,7 +6,6 @@ on:
       - "**"
     paths:
       - containers/message-refiner/**
-      - containers/dibbs/**
       - containers/fhir-converter/**
   merge_group:
     types:

.github/workflows/container-record-linkage.yaml

@@ -6,7 +6,6 @@ on:
       - "**"
     paths:
       - containers/record-linkage/**
-      - containers/dibbs/**
   merge_group:
     types:
       - checks_requested

.github/workflows/container-trigger-code-reference.yaml

@@ -6,7 +6,6 @@ on:
       - "**"
     paths:
       - containers/trigger-code-reference/**
-      - containers/dibbs/**
   merge_group:
     types:
       - checks_requested

.github/workflows/container-validation.yaml

@@ -6,7 +6,6 @@ on:
       - "**"
     paths:
       - containers/validation/**
-      - containers/dibbs/**
       - containers/fhir-converter/**
   merge_group:
     types:

containers/ecr-viewer/package.json

@@ -12,6 +12,7 @@
     "lint": "next lint",
     "test": "TZ=America/New_York jest",
     "test:watch": "TZ=America/New_York jest --watch",
+    "clear-local": "docker compose -f ./docker-compose.yml --profile \"*\" down -v",
     "convert-seed-data": "npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./docker-compose.yml --profile ${SOURCE} --profile ${METADATA_DATABASE_TYPE} --profile ecr-viewer up -d && docker compose -f ./seed-scripts/docker-compose-seed.yml up --abort-on-container-exit && docker compose -f ./docker-compose.yml --profile \"*\" down && docker compose -f ./seed-scripts/docker-compose-seed.yml --profile \"*\" down'",
     "convert-seed-data:build": "npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./docker-compose.yml --profile ${SOURCE} --profile ${METADATA_DATABASE_TYPE} --profile ecr-viewer up -d --build && docker compose -f ./seed-scripts/docker-compose-seed.yml up --abort-on-container-exit --build && docker compose -f ./docker-compose.yml --profile \"*\" down && docker compose -f ./seed-scripts/docker-compose-seed.yml --profile \"*\" down'",
     "update-cypress-data": "docker compose -f ./seed-scripts/docker-compose-create-sql.yml up --build --abort-on-container-exit",

containers/ingestion/Dockerfile

@@ -1,4 +1,9 @@
-FROM ghcr.io/cdcgov/phdi/dibbs
+FROM python:3.11-slim
+
+RUN apt-get update && \
+    apt-get upgrade -y
+
+RUN pip install --upgrade pip
 
 WORKDIR /code
 

containers/dibbs/dibbs/base_service.py → containers/ingestion/app/base_service.py

@@ -1,4 +1,3 @@
-from importlib import metadata
 from pathlib import Path
 from typing import Literal
 
@@ -69,7 +68,7 @@ def __init__(
         self.include_health_check_endpoint = include_health_check_endpoint
         self.app = FastAPI(
             title=service_name,
-            version=metadata.version("dibbs"),
+            version="1.7.1",
             contact=DIBBS_CONTACT,
             license_info=LICENSES[license_info],
             description=description,

containers/ingestion/app/main.py

@@ -1,7 +1,6 @@
 from pathlib import Path
 
-from dibbs.base_service import BaseService
-
+from app.base_service import BaseService
 from app.config import get_settings
 from app.routers import cloud_storage
 from app.routers import fhir_geospatial

containers/ingestion/dev-requirements.txt

@@ -1,3 +1,4 @@
 pytest
 rich     
-testcontainers[compose]==3.7.1
+testcontainers[compose]==3.7.1
+toml

containers/ingestion/requirements.txt

@@ -1,4 +1,6 @@
-../dibbs
+pydantic==1.10.13
+fastapi>=0.109.1
+uvicorn
 azure-identity
 azure-keyvault-secrets
 azure-storage-blob

containers/ingestion/tests/test_base_service.py

@@ -1,12 +1,16 @@
-from importlib import metadata
 from pathlib import Path
 
-from dibbs.base_service import BaseService
-from dibbs.base_service import DIBBS_CONTACT
-from dibbs.base_service import LICENSES
+import toml
+from app.base_service import BaseService
+from app.base_service import DIBBS_CONTACT
+from app.base_service import LICENSES
 from fastapi.testclient import TestClient
 
-default_app_version = metadata.version("dibbs")
+with open(
+    Path(__file__).parent.parent.parent.parent / "pyproject.toml"
+) as project_config_file:
+    project_config = toml.load(project_config_file)
+    default_app_version = project_config["tool"]["poetry"]["version"][1:]
 
 
 def test_base_service():

containers/message-parser/Dockerfile

@@ -1,4 +1,9 @@
-FROM ghcr.io/cdcgov/phdi/dibbs
+FROM python:3.11-slim
+
+RUN apt-get update && \
+    apt-get upgrade -y
+
+RUN pip install --upgrade pip
 
 WORKDIR /code