build: use standalone executable to avoid dotnet runtime (#2928)

* build: use standalone executable to avoid dotnet runtime

* style: newlines are nice

* fix: cmd args

* fix: remove debug cmd

* fix: update tag

* fix: back to branch :(

* fix: debugging

* fix: remove debug stuff

* update tag

containers/ecr-viewer/seed-scripts/docker-compose-seed.yml

@@ -4,6 +4,7 @@ include:
   - ../docker-compose.yml
 services:
   fhir-converter-service:
+    platform: linux/amd64
     build:
       context: ../../fhir-converter/
     ports:

containers/fhir-converter/Dockerfile

@@ -1,39 +1,31 @@
 FROM mcr.microsoft.com/dotnet/sdk:6.0 AS build
 
 # Download FHIR-Converter
-RUN git clone https://github.com/skylight-hq/FHIR-Converter.git --branch v7.0-skylight-9 --single-branch /build/FHIR-Converter
+RUN git clone https://github.com/skylight-hq/FHIR-Converter.git --branch v7.0-skylight-11 --single-branch /build/FHIR-Converter
 
 WORKDIR /build/FHIR-Converter
 
-RUN pwd && ls -la
-
 RUN echo test > src/Microsoft.Health.Fhir.TemplateManagement.UnitTests/TestData/DecompressedFiles/VXU_V04.liquid
 RUN if [ -f src/Microsoft.Health.Fhir.TemplateManagement.UnitTests/TestData/DecompressedFiles/.wh.VXU_V04.liquid ]; then rm src/Microsoft.Health.Fhir.TemplateManagement.UnitTests/TestData/DecompressedFiles/.wh.VXU_V04.liquid; fi
-RUN mkdir bin && \
-  wget https://github.com/deislabs/oras/releases/download/v0.12.0/oras_0.12.0_windows_amd64.tar.gz -O ./bin/oras.tar.gz && \
-  tar -xvf ./bin/oras.tar.gz -C ./bin
 
 # Build Microsoft FHIR Converter
-RUN dotnet build -c Release -o output
+RUN dotnet clean
+RUN dotnet publish \
+  src/Microsoft.Health.Fhir.Liquid.Converter.Tool/Microsoft.Health.Fhir.Liquid.Converter.Tool.csproj \
+  -c Release \
+  -r linux-x64 \
+  --self-contained true \
+  -o output
 
-FROM mcr.microsoft.com/dotnet/runtime:6.0 AS runtime
+# Set up python Server
+FROM python:3.10-slim AS runtime
 
 # Copy FHIR-Converter binary from build stage
 COPY --from=build /build/FHIR-Converter/output /build/FHIR-Converter/output
 COPY --from=build /build/FHIR-Converter/data/Templates /build/FHIR-Converter/data/Templates
 
-ENV PYTHONUNBUFFERED=1
-
-# Install python via pyenv
-RUN apt-get update && apt-get install -y curl git jq build-essential libreadline-dev libncursesw5-dev  libssl-dev  libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev libffi-dev zlib1g-dev
-RUN curl https://pyenv.run | bash
-RUN export PYENV_ROOT="$HOME/.pyenv"
-RUN export PATH="$PYENV_ROOT/bin:$PATH"
-RUN eval "$(pyenv init -)"
-RUN /root/.pyenv/bin/pyenv install 3.10.13
-RUN /root/.pyenv/bin/pyenv global 3.10.13
-
-RUN /root/.pyenv/shims/pip install --no-cache --upgrade pip setuptools
+# # Install python via pyenv
+RUN apt-get update && apt-get install -y curl jq libicu-dev
 
 # Get an up to date copy of active rxnorm codes and names
 RUN rm /build/FHIR-Converter/output/rxnorm.csv
@@ -44,13 +36,16 @@ RUN curl 'https://rxnav.nlm.nih.gov/REST/allstatus.json?status=active' \
 # Install requirements
 WORKDIR /code
 
+# Set --build-arg CACHBUSTSERVICE=<random number here> to only invalidate the python code installation
+ARG CACHEBUSTSERVICE=1
+
 COPY requirements.txt .
-RUN /root/.pyenv/shims/pip install -r requirements.txt
+RUN pip install -r requirements.txt
 
 # Copy FastAPI app
 COPY app /code/app
 COPY assets /code/assets
 COPY README.md /code/README.md
 
 EXPOSE 8080
-CMD /root/.pyenv/shims/uvicorn app.main:app --host 0.0.0.0 --port 8080
+CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "8080"]

containers/fhir-converter/Makefile

@@ -42,4 +42,8 @@ build-image:
 
 build-image-no-cache:
 	@echo "Building Docker image for the FHIR Converter service without cache..."
-	docker compose build --no-cache 
+	docker compose build --no-cache
+
+build-image-no-cache-service:
+	@echo "Building Docker image for the FHIR Converter service without cache..."
+	docker compose build --build-arg CACHEBUSTSERVICE=$(shell date +%s)

containers/fhir-converter/README.md

@@ -149,7 +149,7 @@ For local development, you may prefer to run the service directly from Python. T
 4. Make a fresh virtual environment with `python -m venv .venv`.
 5. Activate the virtual environment with `source .venv/bin/activate` (MacOS and Linux), `venv\Scripts\activate` (Windows Command Prompt), or `.venv\Scripts\Activate.ps1` (Windows PowerShell).
 5. Install all of the Python dependencies for the ingestion service with `pip install -r requirements.txt` into your virtual environment.
-6. Run the FHIR Converter on `localhost:8080` with `FHIR_CONVERTER_TOOl_PATH=~/fully/qualified/path/to/Microsoft.Health.Fhir.Liquid.Converter.Tool.dll python -m uvicorn app.main:app --host 0.0.0.0 --port 8080`. 
+6. Run the FHIR Converter on `localhost:8080` with `FHIR_CONVERTER_TOOl_PATH=~/fully/qualified/path/to/Microsoft.Health.Fhir.Liquid.Converter.Tool python -m uvicorn app.main:app --host 0.0.0.0 --port 8080`. 
 
 ### Building the Docker Image
 

containers/fhir-converter/app/service.py

@@ -91,7 +91,7 @@ def convert_to_fhir(
     # Setup path variables
     converter_project_path = os.getenv(
         "FHIR_CONVERTER_TOOL_PATH",
-        "/build/FHIR-Converter/output/Microsoft.Health.Fhir.Liquid.Converter.Tool.dll",
+        "/build/FHIR-Converter/output/Microsoft.Health.Fhir.Liquid.Converter.Tool",
     )
     if input_type == "vxu" or input_type == "elr":
         template_directory_path = "/build/FHIR-Converter/data/Templates/Hl7v2"
@@ -110,7 +110,7 @@ def convert_to_fhir(
 
     # Formulate command for the FHIR Converter.
     fhir_conversion_command = [
-        f"dotnet {converter_project_path} ",
+        f"{converter_project_path} ",
         "convert -- ",
         f"--TemplateDirectory {template_directory_path} ",
         f"--RootTemplate {root_template.value} ",
@@ -127,6 +127,7 @@ def convert_to_fhir(
         capture_output=True,
         text=True,
     )
+
     # Print the standard output
     dev_mode = os.getenv("DEV_MODE", "false").lower()
     if dev_mode == "true":