mirror of
https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit.git
synced 2025-09-17 14:25:02 +00:00
V4.1 Prep
Build Path options added Candle Added Custom
This commit is contained in:
parent
f1478561c1
commit
6ae0e56118
@ -2,57 +2,130 @@
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setlocal enabledelayedexpansion
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REM --- Configuration ---
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set REPO_URL=https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
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set CLONE_DIR=hapi-fhir-jpaserver
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set REPO_URL_HAPI=https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
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set REPO_URL_CANDLE=https://github.com/FHIR/fhir-candle.git
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set CLONE_DIR_HAPI=hapi-fhir-jpaserver
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set CLONE_DIR_CANDLE=fhir-candle
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set SOURCE_CONFIG_DIR=hapi-fhir-setup
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set CONFIG_FILE=application.yaml
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REM --- Define Paths ---
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set SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%
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set DEST_CONFIG_PATH=%CLONE_DIR%\target\classes\%CONFIG_FILE%
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set DEST_CONFIG_PATH=%CLONE_DIR_HAPI%\target\classes\%CONFIG_FILE%
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REM === CORRECTED: Prompt for Version ===
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REM --- NEW: Define a variable for the custom FHIR URL and server type ---
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set "CUSTOM_FHIR_URL_VAL="
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set "SERVER_TYPE="
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set "CANDLE_FHIR_VERSION="
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REM === MODIFIED: Prompt for Installation Mode ===
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:GetModeChoice
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SET "APP_MODE=" REM Clear the variable first
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echo.
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echo Select Installation Mode:
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echo 1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)
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echo 2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)
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CHOICE /C 12 /N /M "Enter your choice (1 or 2):"
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echo 1. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)
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echo 2. Custom URL (Uses a custom FHIR Server - No Git/Maven/Dotnet needed)
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echo 3. Hapi (Includes local HAPI FHIR Server - Requires Git & Maven)
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echo 4. Candle (Includes local FHIR Candle Server - Requires Git & Dotnet)
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CHOICE /C 1234 /N /M "Enter your choice (1, 2, 3, or 4):"
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IF ERRORLEVEL 4 (
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SET APP_MODE=standalone
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SET SERVER_TYPE=candle
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goto :GetCandleFhirVersion
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)
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IF ERRORLEVEL 3 (
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SET APP_MODE=standalone
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SET SERVER_TYPE=hapi
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goto :ModeSet
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)
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IF ERRORLEVEL 2 (
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SET APP_MODE=standalone
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goto :GetCustomUrl
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)
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IF ERRORLEVEL 1 (
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SET APP_MODE=lite
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goto :ModeSet
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)
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IF ERRORLEVEL 1 (
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SET APP_MODE=standalone
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goto :ModeSet
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)
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REM If somehow neither was chosen (e.g., Ctrl+C), loop back
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echo Invalid input. Please try again.
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goto :GetModeChoice
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:GetCustomUrl
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set "CONFIRMED_URL="
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:PromptUrlLoop
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echo.
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set /p "CUSTOM_URL_INPUT=Please enter the custom FHIR server URL: "
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echo.
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echo You entered: !CUSTOM_URL_INPUT!
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set /p "CONFIRM_URL=Is this URL correct? (Y/N): "
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if /i "!CONFIRM_URL!" EQU "Y" (
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set "CONFIRMED_URL=!CUSTOM_URL_INPUT!"
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goto :ConfirmUrlLoop
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) else (
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goto :PromptUrlLoop
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)
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:ConfirmUrlLoop
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echo.
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echo Please re-enter the URL to confirm it is correct:
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set /p "CUSTOM_URL_INPUT=Re-enter URL: "
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if /i "!CUSTOM_URL_INPUT!" EQU "!CONFIRMED_URL!" (
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set "CUSTOM_FHIR_URL_VAL=!CUSTOM_URL_INPUT!"
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echo.
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echo Custom URL confirmed: !CUSTOM_FHIR_URL_VAL!
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goto :ModeSet
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) else (
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echo.
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echo URLs do not match. Please try again.
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goto :PromptUrlLoop
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)
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:GetCandleFhirVersion
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echo.
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echo Select the FHIR version for the Candle server:
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echo 1. R4 (4.0)
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echo 2. R4B (4.3)
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echo 3. R5 (5.0)
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CHOICE /C 123 /N /M "Enter your choice (1, 2, or 3):"
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IF ERRORLEVEL 3 (
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SET CANDLE_FHIR_VERSION=r5
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goto :ModeSet
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)
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IF ERRORLEVEL 2 (
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SET CANDLE_FHIR_VERSION=r4b
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goto :ModeSet
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)
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IF ERRORLEVEL 1 (
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SET CANDLE_FHIR_VERSION=r4
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goto :ModeSet
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)
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echo Invalid input. Please try again.
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goto :GetCandleFhirVersion
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:ModeSet
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IF "%APP_MODE%"=="" (
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echo Invalid choice detected after checks. Exiting.
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goto :eof
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)
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echo Selected Mode: %APP_MODE%
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echo Server Type: %SERVER_TYPE%
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echo.
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REM === END CORRECTION ===
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REM === END MODIFICATION ===
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REM === Conditionally Execute HAPI Setup ===
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IF "%APP_MODE%"=="standalone" (
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echo Running Standalone setup including HAPI FHIR...
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REM === Conditionally Execute Server Setup ===
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IF "%SERVER_TYPE%"=="hapi" (
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echo Running Hapi server setup...
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echo.
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REM --- Step 0: Clean up previous clone (optional) ---
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echo Checking for existing directory: %CLONE_DIR%
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if exist "%CLONE_DIR%" (
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echo Checking for existing directory: %CLONE_DIR_HAPI%
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if exist "%CLONE_DIR_HAPI%" (
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echo Found existing directory, removing it...
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rmdir /s /q "%CLONE_DIR%"
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rmdir /s /q "%CLONE_DIR_HAPI%"
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if errorlevel 1 (
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echo ERROR: Failed to remove existing directory: %CLONE_DIR%
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echo ERROR: Failed to remove existing directory: %CLONE_DIR_HAPI%
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goto :error
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)
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echo Existing directory removed.
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@ -62,8 +135,8 @@ IF "%APP_MODE%"=="standalone" (
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echo.
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REM --- Step 1: Clone the HAPI FHIR server repository ---
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echo Cloning repository: %REPO_URL% into %CLONE_DIR%...
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git clone "%REPO_URL%" "%CLONE_DIR%"
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echo Cloning repository: %REPO_URL_HAPI% into %CLONE_DIR_HAPI%...
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git clone "%REPO_URL_HAPI%" "%CLONE_DIR_HAPI%"
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if errorlevel 1 (
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echo ERROR: Failed to clone repository. Check Git installation and network connection.
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goto :error
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@ -72,10 +145,10 @@ IF "%APP_MODE%"=="standalone" (
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echo.
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REM --- Step 2: Navigate into the cloned directory ---
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echo Changing directory to %CLONE_DIR%...
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cd "%CLONE_DIR%"
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echo Changing directory to %CLONE_DIR_HAPI%...
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cd "%CLONE_DIR_HAPI%"
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if errorlevel 1 (
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echo ERROR: Failed to change directory to %CLONE_DIR%.
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echo ERROR: Failed to change directory to %CLONE_DIR_HAPI%.
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goto :error
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)
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echo Current directory: %CD%
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@ -92,7 +165,7 @@ IF "%APP_MODE%"=="standalone" (
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)
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echo Maven build completed successfully. ErrorLevel: %errorlevel%
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echo.
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REM --- Step 4: Copy the configuration file ---
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echo ===> "Starting file copy (Step 4)..."
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echo Copying configuration file...
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@ -118,47 +191,141 @@ IF "%APP_MODE%"=="standalone" (
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echo Current directory: %CD%
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echo.
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) ELSE (
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echo Running Lite setup, skipping HAPI FHIR build...
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REM Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen after a standalone attempt
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if exist "%CLONE_DIR%" (
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echo Found existing HAPI directory in Lite mode. Removing it to avoid build issues...
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rmdir /s /q "%CLONE_DIR%"
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) ELSE IF "%SERVER_TYPE%"=="candle" (
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echo Running FHIR Candle server setup...
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echo.
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REM --- Step 0: Clean up previous clone (optional) ---
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echo Checking for existing directory: %CLONE_DIR_CANDLE%
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if exist "%CLONE_DIR_CANDLE%" (
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echo Found existing directory, removing it...
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rmdir /s /q "%CLONE_DIR_CANDLE%"
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if errorlevel 1 (
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echo ERROR: Failed to remove existing directory: %CLONE_DIR_CANDLE%
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goto :error
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)
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echo Existing directory removed.
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) else (
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echo Directory does not exist, proceeding with clone.
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)
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REM Create empty target directories expected by Dockerfile COPY, even if not used
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mkdir "%CLONE_DIR%\target\classes" 2> nul
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mkdir "%CLONE_DIR%\custom" 2> nul
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REM Create a placeholder empty WAR file to satisfy Dockerfile COPY
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echo. > "%CLONE_DIR%\target\ROOT.war"
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echo. > "%CLONE_DIR%\target\classes\application.yaml"
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echo.
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REM --- Step 1: Clone the FHIR Candle server repository ---
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echo Cloning repository: %REPO_URL_CANDLE% into %CLONE_DIR_CANDLE%...
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git clone "%REPO_URL_CANDLE%" "%CLONE_DIR_CANDLE%"
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if errorlevel 1 (
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echo ERROR: Failed to clone repository. Check Git and Dotnet installation and network connection.
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goto :error
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)
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echo Repository cloned successfully.
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echo.
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REM --- Step 2: Navigate into the cloned directory ---
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echo Changing directory to %CLONE_DIR_CANDLE%...
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cd "%CLONE_DIR_CANDLE%"
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if errorlevel 1 (
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echo ERROR: Failed to change directory to %CLONE_DIR_CANDLE%.
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goto :error
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)
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echo Current directory: %CD%
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echo.
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REM --- Step 3: Build the FHIR Candle server using Dotnet ---
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echo ===> "Starting Dotnet build (Step 3)...""
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dotnet publish -c Release -f net9.0 -o publish
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echo ===> Dotnet command finished. Checking error level...
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if errorlevel 1 (
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echo ERROR: Dotnet build failed. Check Dotnet SDK installation.
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cd ..
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goto :error
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)
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echo Dotnet build completed successfully. ErrorLevel: %errorlevel%
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echo.
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REM --- Step 4: Navigate back to the parent directory ---
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echo ===> "Changing directory back (Step 4)..."
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cd ..
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if errorlevel 1 (
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echo ERROR: Failed to change back to the parent directory. ErrorLevel: %errorlevel%
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goto :error
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)
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echo Current directory: %CD%
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echo.
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) ELSE (
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echo Running Lite setup, skipping server build...
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REM Ensure the server directories don't exist in Lite mode
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if exist "%CLONE_DIR_HAPI%" (
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echo Found existing HAPI directory in Lite mode. Removing it to avoid build issues...
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rmdir /s /q "%CLONE_DIR_HAPI%"
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)
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if exist "%CLONE_DIR_CANDLE%" (
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echo Found existing Candle directory in Lite mode. Removing it to avoid build issues...
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rmdir /s /q "%CLONE_DIR_CANDLE%"
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)
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REM Create empty placeholder files to satisfy Dockerfile COPY commands in Lite mode.
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mkdir "%CLONE_DIR_HAPI%\target\classes" 2> nul
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mkdir "%CLONE_DIR_HAPI%\custom" 2> nul
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echo. > "%CLONE_DIR_HAPI%\target\ROOT.war"
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echo. > "%CLONE_DIR_HAPI%\target\classes\application.yaml"
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mkdir "%CLONE_DIR_CANDLE%\publish" 2> nul
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echo. > "%CLONE_DIR_CANDLE%\publish\fhir-candle.dll"
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echo Placeholder files created for Lite mode build.
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echo.
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)
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REM === Modify docker-compose.yml to set APP_MODE ===
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echo Updating docker-compose.yml with APP_MODE=%APP_MODE%...
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REM === MODIFIED: Update docker-compose.yml to set APP_MODE and HAPI_FHIR_URL ===
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echo Updating docker-compose.yml with APP_MODE=%APP_MODE% and HAPI_FHIR_URL...
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(
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echo version: '3.8'
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echo services:
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echo fhirflare:
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echo build:
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echo context: .
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echo dockerfile: Dockerfile
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IF "%SERVER_TYPE%"=="hapi" (
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echo dockerfile: Dockerfile.hapi
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) ELSE IF "%SERVER_TYPE%"=="candle" (
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echo dockerfile: Dockerfile.candle
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) ELSE (
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echo dockerfile: Dockerfile.lite
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)
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echo ports:
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echo - "5000:5000"
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echo - "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
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IF "%SERVER_TYPE%"=="candle" (
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echo - "5000:5000"
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echo - "5001:5826"
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) ELSE (
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echo - "5000:5000"
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echo - "8080:8080"
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)
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echo volumes:
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echo - ./instance:/app/instance
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echo - ./static/uploads:/app/static/uploads
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echo - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
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IF "%SERVER_TYPE%"=="hapi" (
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echo - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
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)
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echo - ./logs:/app/logs
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IF "%SERVER_TYPE%"=="hapi" (
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echo - ./hapi-fhir-jpaserver/target/ROOT.war:/usr/local/tomcat/webapps/ROOT.war
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echo - ./hapi-fhir-jpaserver/target/classes/application.yaml:/usr/local/tomcat/conf/application.yaml
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) ELSE IF "%SERVER_TYPE%"=="candle" (
|
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echo - ./fhir-candle/publish/:/app/fhir-candle-publish/
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)
|
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echo environment:
|
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echo - FLASK_APP=app.py
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||||
echo - FLASK_ENV=development
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echo - NODE_PATH=/usr/lib/node_modules
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echo - APP_MODE=%APP_MODE%
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echo - APP_BASE_URL=http://localhost:5000
|
||||
echo - HAPI_FHIR_URL=http://localhost:8080/fhir
|
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IF DEFINED CUSTOM_FHIR_URL_VAL (
|
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echo - HAPI_FHIR_URL=!CUSTOM_FHIR_URL_VAL!
|
||||
) ELSE (
|
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IF "%SERVER_TYPE%"=="candle" (
|
||||
echo - HAPI_FHIR_URL=http://localhost:5826/fhir/%CANDLE_FHIR_VERSION%
|
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echo - ASPNETCORE_URLS=http://0.0.0.0:5826
|
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) ELSE (
|
||||
echo - HAPI_FHIR_URL=http://localhost:8080/fhir
|
||||
)
|
||||
)
|
||||
echo command: supervisord -c /etc/supervisord.conf
|
||||
) > docker-compose.yml.tmp
|
||||
|
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@ -208,4 +375,4 @@ exit /b 1
|
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|
||||
:eof
|
||||
echo Script execution finished.
|
||||
pause
|
||||
pause
|
||||
|
||||
15
Dockerfile
15
Dockerfile
@ -3,13 +3,16 @@ FROM tomcat:10.1-jdk17
|
||||
|
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# Install build dependencies, Node.js 18, and coreutils (for stdbuf)
|
||||
RUN apt-get update && apt-get install -y --no-install-recommends \
|
||||
python3 python3-pip python3-venv curl coreutils \
|
||||
python3 python3-pip python3-venv curl coreutils git \
|
||||
&& curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
|
||||
&& apt-get install -y --no-install-recommends nodejs \
|
||||
&& rm -rf /var/lib/apt/lists/*
|
||||
|
||||
# ADDED: Install the Dotnet SDK for the FHIR Candle server
|
||||
# This makes the image a universal base for either server type
|
||||
RUN apt-get update && apt-get install -y dotnet-sdk-6.0
|
||||
|
||||
# Install specific versions of GoFSH and SUSHI
|
||||
# REMOVED pip install fhirpath from this line
|
||||
RUN npm install -g gofsh fsh-sushi
|
||||
|
||||
# ADDED: Download the latest HL7 FHIR Validator CLI
|
||||
@ -24,7 +27,6 @@ RUN chmod 755 validator_cli.jar
|
||||
# Change back to the main app directory for the next steps
|
||||
WORKDIR /app
|
||||
# Set up Python environment
|
||||
WORKDIR /app
|
||||
RUN python3 -m venv /app/venv
|
||||
ENV PATH="/app/venv/bin:$PATH"
|
||||
|
||||
@ -55,6 +57,9 @@ COPY hapi-fhir-jpaserver/target/classes/application.yaml /app/config/application
|
||||
COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/webapps/app/config/application.yaml
|
||||
COPY hapi-fhir-jpaserver/custom/ /usr/local/tomcat/webapps/custom/
|
||||
|
||||
# ADDED: Copy pre-built Candle DLL files
|
||||
COPY fhir-candle/publish/ /app/fhir-candle-publish/
|
||||
|
||||
# Install supervisord
|
||||
RUN pip install supervisor
|
||||
|
||||
@ -62,7 +67,7 @@ RUN pip install supervisor
|
||||
COPY supervisord.conf /etc/supervisord.conf
|
||||
|
||||
# Expose ports
|
||||
EXPOSE 5000 8080
|
||||
EXPOSE 5000 8080 5001
|
||||
|
||||
# Start supervisord
|
||||
CMD ["supervisord", "-c", "/etc/supervisord.conf"]
|
||||
CMD ["supervisord", "-c", "/etc/supervisord.conf"]
|
||||
|
||||
62
Dockerfile.candle
Normal file
62
Dockerfile.candle
Normal file
@ -0,0 +1,62 @@
|
||||
# Base image with Python and Dotnet
|
||||
FROM mcr.microsoft.com/dotnet/sdk:9.0
|
||||
|
||||
# Install build dependencies, Node.js 18, and coreutils (for stdbuf)
|
||||
RUN apt-get update && apt-get install -y --no-install-recommends \
|
||||
python3 python3-pip python3-venv curl coreutils git \
|
||||
&& curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
|
||||
&& apt-get install -y --no-install-recommends nodejs \
|
||||
&& rm -rf /var/lib/apt/lists/*
|
||||
|
||||
# Install specific versions of GoFSH and SUSHI
|
||||
RUN npm install -g gofsh fsh-sushi
|
||||
|
||||
# ADDED: Download the latest HL7 FHIR Validator CLI
|
||||
RUN mkdir -p /app/validator_cli
|
||||
WORKDIR /app/validator_cli
|
||||
# Download the validator JAR and a separate checksum file for verification
|
||||
RUN curl -L -o validator_cli.jar "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar"
|
||||
|
||||
# Set permissions for the downloaded file
|
||||
RUN chmod 755 validator_cli.jar
|
||||
|
||||
# Change back to the main app directory for the next steps
|
||||
WORKDIR /app
|
||||
# Set up Python environment
|
||||
RUN python3 -m venv /app/venv
|
||||
ENV PATH="/app/venv/bin:$PATH"
|
||||
|
||||
# ADDED: Uninstall old fhirpath just in case it's in requirements.txt
|
||||
RUN pip uninstall -y fhirpath || true
|
||||
# ADDED: Install the new fhirpathpy library
|
||||
RUN pip install --no-cache-dir fhirpathpy
|
||||
|
||||
# Copy Flask files
|
||||
COPY requirements.txt .
|
||||
# Install requirements (including Pydantic - check version compatibility if needed)
|
||||
RUN pip install --no-cache-dir -r requirements.txt
|
||||
COPY app.py .
|
||||
COPY services.py .
|
||||
COPY forms.py .
|
||||
COPY package.py .
|
||||
COPY templates/ templates/
|
||||
COPY static/ static/
|
||||
COPY tests/ tests/
|
||||
|
||||
# Ensure /tmp, /app/h2-data, /app/static/uploads, and /app/logs are writable
|
||||
RUN mkdir -p /tmp /app/h2-data /app/static/uploads /app/logs && chmod 777 /tmp /app/h2-data /app/static/uploads /app/logs
|
||||
|
||||
# Copy pre-built Candle DLL files
|
||||
COPY fhir-candle/publish/ /app/fhir-candle-publish/
|
||||
|
||||
# Install supervisord
|
||||
RUN pip install supervisor
|
||||
|
||||
# Configure supervisord
|
||||
COPY supervisord.conf /etc/supervisord.conf
|
||||
|
||||
# Expose ports
|
||||
EXPOSE 5000 5001
|
||||
|
||||
# Start supervisord
|
||||
CMD ["supervisord", "-c", "/etc/supervisord.conf"]
|
||||
66
Dockerfile.hapi
Normal file
66
Dockerfile.hapi
Normal file
@ -0,0 +1,66 @@
|
||||
# Base image with Python, Java, and Maven
|
||||
FROM tomcat:10.1-jdk17
|
||||
|
||||
# Install build dependencies, Node.js 18, and coreutils (for stdbuf)
|
||||
RUN apt-get update && apt-get install -y --no-install-recommends \
|
||||
python3 python3-pip python3-venv curl coreutils git maven \
|
||||
&& curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
|
||||
&& apt-get install -y --no-install-recommends nodejs \
|
||||
&& rm -rf /var/lib/apt/lists/*
|
||||
|
||||
# Install specific versions of GoFSH and SUSHI
|
||||
RUN npm install -g gofsh fsh-sushi
|
||||
|
||||
# ADDED: Download the latest HL7 FHIR Validator CLI
|
||||
RUN mkdir -p /app/validator_cli
|
||||
WORKDIR /app/validator_cli
|
||||
# Download the validator JAR and a separate checksum file for verification
|
||||
RUN curl -L -o validator_cli.jar "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar"
|
||||
|
||||
# Set permissions for the downloaded file
|
||||
RUN chmod 755 validator_cli.jar
|
||||
|
||||
# Change back to the main app directory for the next steps
|
||||
WORKDIR /app
|
||||
# Set up Python environment
|
||||
RUN python3 -m venv /app/venv
|
||||
ENV PATH="/app/venv/bin:$PATH"
|
||||
|
||||
# ADDED: Uninstall old fhirpath just in case it's in requirements.txt
|
||||
RUN pip uninstall -y fhirpath || true
|
||||
# ADDED: Install the new fhirpathpy library
|
||||
RUN pip install --no-cache-dir fhirpathpy
|
||||
|
||||
# Copy Flask files
|
||||
COPY requirements.txt .
|
||||
# Install requirements (including Pydantic - check version compatibility if needed)
|
||||
RUN pip install --no-cache-dir -r requirements.txt
|
||||
COPY app.py .
|
||||
COPY services.py .
|
||||
COPY forms.py .
|
||||
COPY package.py .
|
||||
COPY templates/ templates/
|
||||
COPY static/ static/
|
||||
COPY tests/ tests/
|
||||
|
||||
# Ensure /tmp, /app/h2-data, /app/static/uploads, and /app/logs are writable
|
||||
RUN mkdir -p /tmp /app/h2-data /app/static/uploads /app/logs && chmod 777 /tmp /app/h2-data /app/static/uploads /app/logs
|
||||
|
||||
# Copy pre-built HAPI WAR and configuration
|
||||
COPY hapi-fhir-jpaserver/target/ROOT.war /usr/local/tomcat/webapps/
|
||||
COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/conf/
|
||||
COPY hapi-fhir-jpaserver/target/classes/application.yaml /app/config/application.yaml
|
||||
COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/webapps/app/config/application.yaml
|
||||
COPY hapi-fhir-jpaserver/custom/ /usr/local/tomcat/webapps/custom/
|
||||
|
||||
# Install supervisord
|
||||
RUN pip install supervisor
|
||||
|
||||
# Configure supervisord
|
||||
COPY supervisord.conf /etc/supervisord.conf
|
||||
|
||||
# Expose ports
|
||||
EXPOSE 5000 8080
|
||||
|
||||
# Start supervisord
|
||||
CMD ["supervisord", "-c", "/etc/supervisord.conf"]
|
||||
58
Dockerfile.lite
Normal file
58
Dockerfile.lite
Normal file
@ -0,0 +1,58 @@
|
||||
# Base image with Python and Node.js
|
||||
FROM python:3.9-slim
|
||||
|
||||
# Install Node.js 18 and npm
|
||||
RUN apt-get update && apt-get install -y --no-install-recommends \
|
||||
curl coreutils git \
|
||||
&& curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
|
||||
&& apt-get install -y --no-install-recommends nodejs \
|
||||
&& rm -rf /var/lib/apt/lists/*
|
||||
|
||||
# Install specific versions of GoFSH and SUSHI
|
||||
RUN npm install -g gofsh fsh-sushi
|
||||
|
||||
# ADDED: Download the latest HL7 FHIR Validator CLI
|
||||
RUN mkdir -p /app/validator_cli
|
||||
WORKDIR /app/validator_cli
|
||||
# Download the validator JAR and a separate checksum file for verification
|
||||
RUN curl -L -o validator_cli.jar "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar"
|
||||
|
||||
# Set permissions for the downloaded file
|
||||
RUN chmod 755 validator_cli.jar
|
||||
|
||||
# Change back to the main app directory for the next steps
|
||||
WORKDIR /app
|
||||
# Set up Python environment
|
||||
RUN python3 -m venv /app/venv
|
||||
ENV PATH="/app/venv/bin:$PATH"
|
||||
|
||||
# ADDED: Uninstall old fhirpath just in case it's in requirements.txt
|
||||
RUN pip uninstall -y fhirpath || true
|
||||
# ADDED: Install the new fhirpathpy library
|
||||
RUN pip install --no-cache-dir fhirpathpy
|
||||
|
||||
# Copy Flask files
|
||||
COPY requirements.txt .
|
||||
RUN pip install --no-cache-dir -r requirements.txt
|
||||
COPY app.py .
|
||||
COPY services.py .
|
||||
COPY forms.py .
|
||||
COPY package.py .
|
||||
COPY templates/ templates/
|
||||
COPY static/ static/
|
||||
COPY tests/ tests/
|
||||
|
||||
# Ensure necessary directories are writable
|
||||
RUN mkdir -p /app/static/uploads /app/logs && chmod 777 /app/static/uploads /app/logs
|
||||
|
||||
# Install supervisord
|
||||
RUN pip install supervisor
|
||||
|
||||
# Configure supervisord
|
||||
COPY supervisord.conf /etc/supervisord.conf
|
||||
|
||||
# Expose ports
|
||||
EXPOSE 5000
|
||||
|
||||
# Start supervisord
|
||||
CMD ["supervisord", "-c", "/etc/supervisord.conf"]
|
||||
@ -3,14 +3,13 @@ services:
|
||||
fhirflare:
|
||||
build:
|
||||
context: .
|
||||
dockerfile: Dockerfile
|
||||
dockerfile: Dockerfile.lite
|
||||
ports:
|
||||
- "5000:5000"
|
||||
- "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
|
||||
- "8080:8080"
|
||||
volumes:
|
||||
- ./instance:/app/instance
|
||||
- ./static/uploads:/app/static/uploads
|
||||
- ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
|
||||
- ./logs:/app/logs
|
||||
environment:
|
||||
- FLASK_APP=app.py
|
||||
@ -18,5 +17,5 @@ services:
|
||||
- NODE_PATH=/usr/lib/node_modules
|
||||
- APP_MODE=standalone
|
||||
- APP_BASE_URL=http://localhost:5000
|
||||
- HAPI_FHIR_URL=https://fhir.hl7.org.au/aucore/fhir/DEFAULT/
|
||||
- HAPI_FHIR_URL=https://fhir.hl7.org.au/aucore/fhir/DEFAULT/
|
||||
command: supervisord -c /etc/supervisord.conf
|
||||
|
||||
414
setup_linux.sh
414
setup_linux.sh
@ -1,18 +1,21 @@
|
||||
#!/bin/bash
|
||||
|
||||
# --- Configuration ---
|
||||
REPO_URL="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
|
||||
CLONE_DIR="hapi-fhir-jpaserver"
|
||||
SOURCE_CONFIG_DIR="hapi-fhir-Setup" # Assuming this is relative to the script's parent
|
||||
REPO_URL_HAPI="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
|
||||
REPO_URL_CANDLE="https://github.com/FHIR/fhir-candle.git"
|
||||
CLONE_DIR_HAPI="hapi-fhir-jpaserver"
|
||||
CLONE_DIR_CANDLE="fhir-candle"
|
||||
SOURCE_CONFIG_DIR="hapi-fhir-Setup"
|
||||
CONFIG_FILE="application.yaml"
|
||||
|
||||
# --- Define Paths ---
|
||||
# Note: Adjust SOURCE_CONFIG_PATH if SOURCE_CONFIG_DIR is not a sibling directory
|
||||
# This assumes the script is run from a directory, and hapi-fhir-setup is at the same level
|
||||
SOURCE_CONFIG_PATH="../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}"
|
||||
DEST_CONFIG_PATH="${CLONE_DIR}/target/classes/${CONFIG_FILE}"
|
||||
DEST_CONFIG_PATH="${CLONE_DIR_HAPI}/target/classes/${CONFIG_FILE}"
|
||||
|
||||
APP_MODE=""
|
||||
CUSTOM_FHIR_URL_VAL=""
|
||||
SERVER_TYPE=""
|
||||
CANDLE_FHIR_VERSION=""
|
||||
|
||||
# --- Error Handling Function ---
|
||||
handle_error() {
|
||||
@ -20,25 +23,39 @@ handle_error() {
|
||||
echo "An error occurred: $1"
|
||||
echo "Script aborted."
|
||||
echo "------------------------------------"
|
||||
# Removed 'read -p "Press Enter to exit..."' as it's not typical for non-interactive CI/CD
|
||||
exit 1
|
||||
}
|
||||
|
||||
# === Prompt for Installation Mode ===
|
||||
# === MODIFIED: Prompt for Installation Mode ===
|
||||
get_mode_choice() {
|
||||
echo ""
|
||||
echo "Select Installation Mode:"
|
||||
echo "1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)"
|
||||
echo "2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)"
|
||||
echo "1. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)"
|
||||
echo "2. Custom URL (Uses a custom FHIR Server - No Git/Maven/Dotnet needed)"
|
||||
echo "3. Hapi (Includes local HAPI FHIR Server - Requires Git & Maven)"
|
||||
echo "4. Candle (Includes local FHIR Candle Server - Requires Git & Dotnet)"
|
||||
|
||||
while true; do
|
||||
read -r -p "Enter your choice (1 or 2): " choice
|
||||
read -r -p "Enter your choice (1, 2, 3, or 4): " choice
|
||||
case "$choice" in
|
||||
1)
|
||||
APP_MODE="standalone"
|
||||
APP_MODE="lite"
|
||||
break
|
||||
;;
|
||||
2)
|
||||
APP_MODE="lite"
|
||||
APP_MODE="standalone"
|
||||
get_custom_url_prompt
|
||||
break
|
||||
;;
|
||||
3)
|
||||
APP_MODE="standalone"
|
||||
SERVER_TYPE="hapi"
|
||||
break
|
||||
;;
|
||||
4)
|
||||
APP_MODE="standalone"
|
||||
SERVER_TYPE="candle"
|
||||
get_candle_fhir_version
|
||||
break
|
||||
;;
|
||||
*)
|
||||
@ -47,156 +64,301 @@ get_mode_choice() {
|
||||
esac
|
||||
done
|
||||
echo "Selected Mode: $APP_MODE"
|
||||
echo "Server Type: $SERVER_TYPE"
|
||||
echo
|
||||
}
|
||||
|
||||
# === NEW: Prompt for Custom URL ===
|
||||
get_custom_url_prompt() {
|
||||
local confirmed_url=""
|
||||
while true; do
|
||||
echo
|
||||
read -r -p "Please enter the custom FHIR server URL: " custom_url_input
|
||||
echo
|
||||
echo "You entered: $custom_url_input"
|
||||
read -r -p "Is this URL correct? (Y/N): " confirm_url
|
||||
if [[ "$confirm_url" =~ ^[Yy]$ ]]; then
|
||||
confirmed_url="$custom_url_input"
|
||||
break
|
||||
else
|
||||
echo "URL not confirmed. Please re-enter."
|
||||
fi
|
||||
done
|
||||
|
||||
while true; do
|
||||
echo
|
||||
read -r -p "Please re-enter the URL to confirm it is correct: " custom_url_input
|
||||
if [ "$custom_url_input" = "$confirmed_url" ]; then
|
||||
CUSTOM_FHIR_URL_VAL="$custom_url_input"
|
||||
echo
|
||||
echo "Custom URL confirmed: $CUSTOM_FHIR_URL_VAL"
|
||||
break
|
||||
else
|
||||
echo
|
||||
echo "URLs do not match. Please try again."
|
||||
confirmed_url="$custom_url_input"
|
||||
fi
|
||||
done
|
||||
}
|
||||
|
||||
# === NEW: Prompt for Candle FHIR version ===
|
||||
get_candle_fhir_version() {
|
||||
echo ""
|
||||
echo "Select the FHIR version for the Candle server:"
|
||||
echo "1. R4 (4.0)"
|
||||
echo "2. R4B (4.3)"
|
||||
echo "3. R5 (5.0)"
|
||||
while true; do
|
||||
read -r -p "Enter your choice (1, 2, or 3): " choice
|
||||
case "$choice" in
|
||||
1)
|
||||
CANDLE_FHIR_VERSION=r4
|
||||
break
|
||||
;;
|
||||
2)
|
||||
CANDLE_FHIR_VERSION=r4b
|
||||
break
|
||||
;;
|
||||
3)
|
||||
CANDLE_FHIR_VERSION=r5
|
||||
break
|
||||
;;
|
||||
*)
|
||||
echo "Invalid input. Please try again."
|
||||
;;
|
||||
esac
|
||||
done
|
||||
}
|
||||
|
||||
|
||||
# Call the function to get mode choice
|
||||
get_mode_choice
|
||||
|
||||
# === Conditionally Execute HAPI Setup ===
|
||||
if [ "$APP_MODE" = "standalone" ]; then
|
||||
echo "Running Standalone setup including HAPI FHIR..."
|
||||
echo
|
||||
# === Conditionally Execute Server Setup ===
|
||||
case "$SERVER_TYPE" in
|
||||
"hapi")
|
||||
echo "Running Hapi server setup..."
|
||||
echo
|
||||
|
||||
# --- Step 0: Clean up previous clone (optional) ---
|
||||
echo "Checking for existing directory: $CLONE_DIR"
|
||||
if [ -d "$CLONE_DIR" ]; then
|
||||
echo "Found existing directory, removing it..."
|
||||
rm -rf "$CLONE_DIR"
|
||||
if [ $? -ne 0 ]; then
|
||||
handle_error "Failed to remove existing directory: $CLONE_DIR"
|
||||
# --- Step 0: Clean up previous clone (optional) ---
|
||||
echo "Checking for existing directory: $CLONE_DIR_HAPI"
|
||||
if [ -d "$CLONE_DIR_HAPI" ]; then
|
||||
echo "Found existing directory, removing it..."
|
||||
rm -rf "$CLONE_DIR_HAPI"
|
||||
if [ $? -ne 0 ]; then
|
||||
handle_error "Failed to remove existing directory: $CLONE_DIR_HAPI"
|
||||
fi
|
||||
echo "Existing directory removed."
|
||||
else
|
||||
echo "Directory does not exist, proceeding with clone."
|
||||
fi
|
||||
echo "Existing directory removed."
|
||||
else
|
||||
echo "Directory does not exist, proceeding with clone."
|
||||
fi
|
||||
echo
|
||||
echo
|
||||
|
||||
# --- Step 1: Clone the HAPI FHIR server repository ---
|
||||
echo "Cloning repository: $REPO_URL into $CLONE_DIR..."
|
||||
git clone "$REPO_URL" "$CLONE_DIR"
|
||||
if [ $? -ne 0 ]; then
|
||||
handle_error "Failed to clone repository. Check Git installation and network connection."
|
||||
fi
|
||||
echo "Repository cloned successfully."
|
||||
echo
|
||||
|
||||
# --- Step 2: Navigate into the cloned directory ---
|
||||
echo "Changing directory to $CLONE_DIR..."
|
||||
cd "$CLONE_DIR" || handle_error "Failed to change directory to $CLONE_DIR."
|
||||
echo "Current directory: $(pwd)"
|
||||
echo
|
||||
|
||||
# --- Step 3: Build the HAPI server using Maven ---
|
||||
echo "===> Starting Maven build (Step 3)..."
|
||||
mvn clean package -DskipTests=true -Pboot
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "ERROR: Maven build failed."
|
||||
cd ..
|
||||
handle_error "Maven build process resulted in an error."
|
||||
fi
|
||||
echo "Maven build completed successfully."
|
||||
echo
|
||||
|
||||
# --- Step 4: Copy the configuration file ---
|
||||
echo "===> Starting file copy (Step 4)..."
|
||||
echo "Copying configuration file..."
|
||||
# Corrected SOURCE_CONFIG_PATH to be relative to the new current directory ($CLONE_DIR)
|
||||
# This assumes the original script's SOURCE_CONFIG_PATH was relative to its execution location
|
||||
# If SOURCE_CONFIG_DIR is ../hapi-fhir-setup relative to script's original location:
|
||||
# Then from within CLONE_DIR, it becomes ../../hapi-fhir-setup
|
||||
# We defined SOURCE_CONFIG_PATH earlier relative to the script start.
|
||||
# So, when inside CLONE_DIR, the path from original script location should be used.
|
||||
# The original script had: set SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%
|
||||
# And then: xcopy "%SOURCE_CONFIG_PATH%" "target\classes\"
|
||||
# This implies SOURCE_CONFIG_PATH is relative to the original script's location, not the $CLONE_DIR
|
||||
# Therefore, we need to construct the correct relative path from *within* $CLONE_DIR back to the source.
|
||||
# Assuming the script is in dir X, and SOURCE_CONFIG_DIR is ../hapi-fhir-setup from X.
|
||||
# So, hapi-fhir-setup is a sibling of X's parent.
|
||||
# If CLONE_DIR is also in X, then from within CLONE_DIR, the path is ../ + original SOURCE_CONFIG_PATH
|
||||
# For simplicity and robustness, let's use an absolute path or a more clearly defined relative path from the start.
|
||||
# The original `SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%` implies
|
||||
# that `hapi-fhir-setup` is a sibling of the directory where the script *is being run from*.
|
||||
|
||||
# Let's assume the script is run from the root of FHIRFLARE-IG-Toolkit.
|
||||
# And hapi-fhir-setup is also in the root, next to this script.
|
||||
# Then SOURCE_CONFIG_PATH would be ./hapi-fhir-setup/target/classes/application.yaml
|
||||
# And from within ./hapi-fhir-jpaserver/, the path would be ../hapi-fhir-setup/target/classes/application.yaml
|
||||
|
||||
# The original batch file sets SOURCE_CONFIG_PATH as "..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%"
|
||||
# And COPIES it to "target\classes\" *while inside CLONE_DIR*.
|
||||
# This means the source path is relative to where the *cd %CLONE_DIR%* happened from.
|
||||
# Let's make it relative to the script's initial execution directory.
|
||||
INITIAL_SCRIPT_DIR=$(pwd)
|
||||
ABSOLUTE_SOURCE_CONFIG_PATH="${INITIAL_SCRIPT_DIR}/../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}" # This matches the ..\ logic
|
||||
|
||||
echo "Source: $ABSOLUTE_SOURCE_CONFIG_PATH"
|
||||
echo "Destination: target/classes/$CONFIG_FILE"
|
||||
|
||||
if [ ! -f "$ABSOLUTE_SOURCE_CONFIG_PATH" ]; then
|
||||
echo "WARNING: Source configuration file not found at $ABSOLUTE_SOURCE_CONFIG_PATH."
|
||||
echo "The script will continue, but the server might use default configuration."
|
||||
else
|
||||
cp "$ABSOLUTE_SOURCE_CONFIG_PATH" "target/classes/"
|
||||
# --- Step 1: Clone the HAPI FHIR server repository ---
|
||||
echo "Cloning repository: $REPO_URL_HAPI into $CLONE_DIR_HAPI..."
|
||||
git clone "$REPO_URL_HAPI" "$CLONE_DIR_HAPI"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "WARNING: Failed to copy configuration file. Check if the source file exists and permissions."
|
||||
handle_error "Failed to clone repository. Check Git installation and network connection."
|
||||
fi
|
||||
echo "Repository cloned successfully."
|
||||
echo
|
||||
|
||||
# --- Step 2: Navigate into the cloned directory ---
|
||||
echo "Changing directory to $CLONE_DIR_HAPI..."
|
||||
cd "$CLONE_DIR_HAPI" || handle_error "Failed to change directory to $CLONE_DIR_HAPI."
|
||||
echo "Current directory: $(pwd)"
|
||||
echo
|
||||
|
||||
# --- Step 3: Build the HAPI server using Maven ---
|
||||
echo "===> Starting Maven build (Step 3)..."
|
||||
mvn clean package -DskipTests=true -Pboot
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "ERROR: Maven build failed."
|
||||
cd ..
|
||||
handle_error "Maven build process resulted in an error."
|
||||
fi
|
||||
echo "Maven build completed successfully."
|
||||
echo
|
||||
|
||||
# --- Step 4: Copy the configuration file ---
|
||||
echo "===> Starting file copy (Step 4)..."
|
||||
echo "Copying configuration file..."
|
||||
INITIAL_SCRIPT_DIR=$(pwd)
|
||||
ABSOLUTE_SOURCE_CONFIG_PATH="${INITIAL_SCRIPT_DIR}/../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}"
|
||||
|
||||
echo "Source: $ABSOLUTE_SOURCE_CONFIG_PATH"
|
||||
echo "Destination: target/classes/$CONFIG_FILE"
|
||||
|
||||
if [ ! -f "$ABSOLUTE_SOURCE_CONFIG_PATH" ]; then
|
||||
echo "WARNING: Source configuration file not found at $ABSOLUTE_SOURCE_CONFIG_PATH."
|
||||
echo "The script will continue, but the server might use default configuration."
|
||||
else
|
||||
echo "Configuration file copied successfully."
|
||||
cp "$ABSOLUTE_SOURCE_CONFIG_PATH" "target/classes/"
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "WARNING: Failed to copy configuration file. Check if the source file exists and permissions."
|
||||
echo "The script will continue, but the server might use default configuration."
|
||||
else
|
||||
echo "Configuration file copied successfully."
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
echo
|
||||
echo
|
||||
|
||||
# --- Step 5: Navigate back to the parent directory ---
|
||||
echo "===> Changing directory back (Step 5)..."
|
||||
cd .. || handle_error "Failed to change back to the parent directory."
|
||||
echo "Current directory: $(pwd)"
|
||||
echo
|
||||
# --- Step 5: Navigate back to the parent directory ---
|
||||
echo "===> Changing directory back (Step 5)..."
|
||||
cd .. || handle_error "Failed to change back to the parent directory."
|
||||
echo "Current directory: $(pwd)"
|
||||
echo
|
||||
;;
|
||||
|
||||
else # APP_MODE is "lite"
|
||||
echo "Running Lite setup, skipping HAPI FHIR build..."
|
||||
# Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen
|
||||
if [ -d "$CLONE_DIR" ]; then
|
||||
echo "Found existing HAPI directory ($CLONE_DIR) in Lite mode. Removing it..."
|
||||
rm -rf "$CLONE_DIR"
|
||||
fi
|
||||
# Create empty target directories expected by Dockerfile COPY, even if not used
|
||||
mkdir -p "${CLONE_DIR}/target/classes"
|
||||
mkdir -p "${CLONE_DIR}/custom" # This was in the original batch, ensure it's here
|
||||
# Create a placeholder empty WAR file and application.yaml to satisfy Dockerfile COPY
|
||||
touch "${CLONE_DIR}/target/ROOT.war"
|
||||
touch "${CLONE_DIR}/target/classes/application.yaml"
|
||||
echo "Placeholder files and directories created for Lite mode build in $CLONE_DIR."
|
||||
echo
|
||||
fi
|
||||
"candle")
|
||||
echo "Running FHIR Candle server setup..."
|
||||
echo
|
||||
|
||||
# --- Step 0: Clean up previous clone (optional) ---
|
||||
echo "Checking for existing directory: $CLONE_DIR_CANDLE"
|
||||
if [ -d "$CLONE_DIR_CANDLE" ]; then
|
||||
echo "Found existing directory, removing it..."
|
||||
rm -rf "$CLONE_DIR_CANDLE"
|
||||
if [ $? -ne 0 ]; then
|
||||
handle_error "Failed to remove existing directory: $CLONE_DIR_CANDLE"
|
||||
fi
|
||||
echo "Existing directory removed."
|
||||
else
|
||||
echo "Directory does not exist, proceeding with clone."
|
||||
fi
|
||||
echo
|
||||
|
||||
# === Modify docker-compose.yml to set APP_MODE ===
|
||||
echo "Updating docker-compose.yml with APP_MODE=$APP_MODE..."
|
||||
# --- Step 1: Clone the FHIR Candle server repository ---
|
||||
echo "Cloning repository: $REPO_URL_CANDLE into $CLONE_DIR_CANDLE..."
|
||||
git clone "$REPO_URL_CANDLE" "$CLONE_DIR_CANDLE"
|
||||
if [ $? -ne 0 ]; then
|
||||
handle_error "Failed to clone repository. Check Git and Dotnet SDK installation and network connection."
|
||||
fi
|
||||
echo "Repository cloned successfully."
|
||||
echo
|
||||
|
||||
# --- Step 2: Navigate into the cloned directory ---
|
||||
echo "Changing directory to $CLONE_DIR_CANDLE..."
|
||||
cd "$CLONE_DIR_CANDLE" || handle_error "Failed to change directory to $CLONE_DIR_CANDLE."
|
||||
echo "Current directory: $(pwd)"
|
||||
echo
|
||||
|
||||
# --- Step 3: Build the FHIR Candle server using Dotnet ---
|
||||
echo "===> Starting Dotnet build (Step 3)..."
|
||||
dotnet publish -c Release -f net9.0 -o publish
|
||||
if [ $? -ne 0 ]; then
|
||||
handle_error "Dotnet build failed. Check Dotnet SDK installation."
|
||||
fi
|
||||
echo "Dotnet build completed successfully."
|
||||
echo
|
||||
|
||||
# --- Step 4: Navigate back to the parent directory ---
|
||||
echo "===> Changing directory back (Step 4)..."
|
||||
cd .. || handle_error "Failed to change back to the parent directory."
|
||||
echo "Current directory: $(pwd)"
|
||||
echo
|
||||
;;
|
||||
|
||||
*) # APP_MODE is Lite, no SERVER_TYPE
|
||||
echo "Running Lite setup, skipping server build..."
|
||||
if [ -d "$CLONE_DIR_HAPI" ]; then
|
||||
echo "Found existing HAPI directory in Lite mode. Removing it to avoid build issues..."
|
||||
rm -rf "$CLONE_DIR_HAPI"
|
||||
fi
|
||||
if [ -d "$CLONE_DIR_CANDLE" ]; then
|
||||
echo "Found existing Candle directory in Lite mode. Removing it to avoid build issues..."
|
||||
rm -rf "$CLONE_DIR_CANDLE"
|
||||
fi
|
||||
mkdir -p "${CLONE_DIR_HAPI}/target/classes"
|
||||
mkdir -p "${CLONE_DIR_HAPI}/custom"
|
||||
touch "${CLONE_DIR_HAPI}/target/ROOT.war"
|
||||
touch "${CLONE_DIR_HAPI}/target/classes/application.yaml"
|
||||
mkdir -p "${CLONE_DIR_CANDLE}/publish"
|
||||
touch "${CLONE_DIR_CANDLE}/publish/fhir-candle.dll"
|
||||
echo "Placeholder files and directories created for Lite mode build."
|
||||
echo
|
||||
;;
|
||||
esac
|
||||
|
||||
# === MODIFIED: Update docker-compose.yml to set APP_MODE and HAPI_FHIR_URL and DOCKERFILE ===
|
||||
echo "Updating docker-compose.yml with APP_MODE=$APP_MODE and HAPI_FHIR_URL..."
|
||||
DOCKER_COMPOSE_TMP="docker-compose.yml.tmp"
|
||||
DOCKER_COMPOSE_ORIG="docker-compose.yml"
|
||||
|
||||
HAPI_URL_TO_USE="https://fhir.hl7.org.au/aucore/fhir/DEFAULT/"
|
||||
if [ -n "$CUSTOM_FHIR_URL_VAL" ]; then
|
||||
HAPI_URL_TO_USE="$CUSTOM_FHIR_URL_VAL"
|
||||
elif [ "$SERVER_TYPE" = "candle" ]; then
|
||||
HAPI_URL_TO_USE="http://localhost:5826/fhir/${CANDLE_FHIR_VERSION}"
|
||||
else
|
||||
HAPI_URL_TO_USE="http://localhost:8080/fhir"
|
||||
fi
|
||||
|
||||
DOCKERFILE_TO_USE="Dockerfile.lite"
|
||||
if [ "$SERVER_TYPE" = "hapi" ]; then
|
||||
DOCKERFILE_TO_USE="Dockerfile.hapi"
|
||||
elif [ "$SERVER_TYPE" = "candle" ]; then
|
||||
DOCKERFILE_TO_USE="Dockerfile.candle"
|
||||
fi
|
||||
|
||||
cat << EOF > "$DOCKER_COMPOSE_TMP"
|
||||
version: '3.8'
|
||||
services:
|
||||
fhirflare:
|
||||
build:
|
||||
context: .
|
||||
dockerfile: Dockerfile
|
||||
dockerfile: ${DOCKERFILE_TO_USE}
|
||||
ports:
|
||||
EOF
|
||||
|
||||
if [ "$SERVER_TYPE" = "candle" ]; then
|
||||
cat << EOF >> "$DOCKER_COMPOSE_TMP"
|
||||
- "5000:5000"
|
||||
- "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
|
||||
- "5001:5826"
|
||||
EOF
|
||||
else
|
||||
cat << EOF >> "$DOCKER_COMPOSE_TMP"
|
||||
- "5000:5000"
|
||||
- "8080:8080"
|
||||
EOF
|
||||
fi
|
||||
|
||||
cat << EOF >> "$DOCKER_COMPOSE_TMP"
|
||||
volumes:
|
||||
- ./instance:/app/instance
|
||||
- ./static/uploads:/app/static/uploads
|
||||
- ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
|
||||
- ./logs:/app/logs
|
||||
EOF
|
||||
|
||||
if [ "$SERVER_TYPE" = "hapi" ]; then
|
||||
cat << EOF >> "$DOCKER_COMPOSE_TMP"
|
||||
- ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
|
||||
- ./hapi-fhir-jpaserver/target/ROOT.war:/usr/local/tomcat/webapps/ROOT.war
|
||||
- ./hapi-fhir-jpaserver/target/classes/application.yaml:/usr/local/tomcat/conf/application.yaml
|
||||
EOF
|
||||
elif [ "$SERVER_TYPE" = "candle" ]; then
|
||||
cat << EOF >> "$DOCKER_COMPOSE_TMP"
|
||||
- ./fhir-candle/publish/:/app/fhir-candle-publish/
|
||||
EOF
|
||||
fi
|
||||
|
||||
cat << EOF >> "$DOCKER_COMPOSE_TMP"
|
||||
environment:
|
||||
- FLASK_APP=app.py
|
||||
- FLASK_ENV=development
|
||||
- NODE_PATH=/usr/lib/node_modules
|
||||
- APP_MODE=${APP_MODE}
|
||||
- APP_BASE_URL=http://localhost:5000
|
||||
- HAPI_FHIR_URL=http://localhost:8080/fhir
|
||||
- HAPI_FHIR_URL=${HAPI_URL_TO_USE}
|
||||
EOF
|
||||
|
||||
if [ "$SERVER_TYPE" = "candle" ]; then
|
||||
cat << EOF >> "$DOCKER_COMPOSE_TMP"
|
||||
- ASPNETCORE_URLS=http://0.0.0.0:5826
|
||||
EOF
|
||||
fi
|
||||
|
||||
cat << EOF >> "$DOCKER_COMPOSE_TMP"
|
||||
command: supervisord -c /etc/supervisord.conf
|
||||
EOF
|
||||
|
||||
|
||||
@ -33,4 +33,18 @@ stdout_logfile_maxbytes=10MB
|
||||
stdout_logfile_backups=5
|
||||
stderr_logfile=/app/logs/tomcat_err.log
|
||||
stderr_logfile_maxbytes=10MB
|
||||
stderr_logfile_backups=5
|
||||
stderr_logfile_backups=5
|
||||
|
||||
[program:candle]
|
||||
command=dotnet /app/fhir-candle-publish/fhir-candle.dll
|
||||
directory=/app/fhir-candle-publish
|
||||
autostart=true
|
||||
autorestart=true
|
||||
startsecs=10
|
||||
stopwaitsecs=10
|
||||
stdout_logfile=/app/logs/candle.log
|
||||
stdout_logfile_maxbytes=10MB
|
||||
stdout_logfile_backups=5
|
||||
stderr_logfile=/app/logs/candle_err.log
|
||||
stderr_logfile_maxbytes=10MB
|
||||
stderr_logfile_backups=5
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user