Merge branch 'master' of https://github.com/HealthIntersections/fhirs…

…erver into HealthIntersections-master

.github/workflows/linux-docker-build.yml

@@ -1,27 +1,36 @@
+name: Build and Push Docker Image to GHCR
+
 on:
-  # Trigger the workflow on push or pull request,
-  # but only for the main branch
+  # Trigger the workflow on push or pull request for the main branch
   push:
-    branches:
-#  pull_request:
+  pull_request:
+
 jobs:
   Build-Docker-Image:
     runs-on: ubuntu-latest
+
     steps:
+    # Step 1: Check out the repository code
     - name: Check out repository code
       uses: actions/checkout@v2
-#    -
-#      name: Login to Docker Hub
-#      uses: docker/login-action@v2
-#      with:
-#        username: ${{ secrets.DOCKERHUB_USERNAME }}
-#        password: ${{ secrets.DOCKERHUB_TOKEN }}      
+
+    # Step 2: Log in to GitHub Container Registry (GHCR)
+    - name: Log in to GitHub Container Registry
+      uses: docker/login-action@v2
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }} # Automatically provided by GitHub
+
+    # Step 3: Cache terminology files (optional, to avoid re-downloading terminology files)
     - name: Cache terminology files
       uses: actions/cache@v2
       with:
         path: ~/terminology
         key: terminology-${{ github.sha }}
         restore-keys: terminology-
+
+    # Step 4: Setup MySQL for the build
     - name: Setup MySQL
       run: |
         docker network create gh
@@ -33,15 +42,13 @@ jobs:
           -e MYSQL_PASSWORD=test \
           -e MYSQL_DATABASE=test \
           -d mysql:8
+
+    # Step 5: Build the Docker image and tag it for GitHub Container Registry (GHCR)
     - name: Docker Build
       run: |
-        docker  build \
-          --tag fhirserver \
-        .
-#    - name: Scan Code
-#      run: |
-#        export DISPLAY=0:0
-#        docker run --entrypoint /work/fhirserver/utilities/codescan/codescan fhirserver /work/bootstrap
+        docker build --tag ghcr.io/${{ github.repository_owner }}/fhirserver:nightly .
+
+    # Step 6: Prepare ini file for your FHIR Server with environment variables
     - name: Prepare ini file
       env:
         FHIRSERVER_LOCATIONS_CLONE_PATH: /work/fhirserver
@@ -58,29 +65,15 @@ jobs:
         FHIRSERVER_SSL_PASSWORD: password
       run: |
         cat fixtures/test-settings.ini.template | envsubst > ~/test-settings.ini
+
+    # Step 7: Ensure SNOMED cache is present
     - name: Ensure SNOMED cache is present
       run: |
         mkdir -p ~/terminology/fhir-server
         wget -q --no-clobber https://storage.googleapis.com/ig-build/snomed.test.cache -O ~/terminology/fhir-server/snomed.test.cache || true
-        ls  ~/terminology/fhir-server/snomed.test.cache
-#    - name: Run tests in docker
-#      run: |
-#        docker images --all
-#        docker run \
-#          --network gh \
-#          -v ~/terminology:/terminology \
-#          -v ~/test-settings.ini:/work/fhirserver/exec/64/test-settings.ini \
-#          fhirserver -tests
+        ls ~/terminology/fhir-server/snomed.test.cache
 
-    - name: Tag and push Docker image
+    # Step 8: Push the Docker image to GitHub Container Registry (GHCR)
+    - name: Push Docker image to GHCR
       run: |
-        # Extract the FHIR server version from the library/version.inc file
-        FHIR_VERSION=$(grep -oP "FHIR_CODE_FULL_VERSION = '\K[^']+" library/version.inc)
-
-        # Tag the Docker image with the extracted version and "latest"
-        docker tag fhirserver ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:$FHIR_VERSION
-        docker tag fhirserver ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:latest
-
-        # Push both tagged images to Docker Hub
-        docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:$FHIR_VERSION
-        docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:latest
+        docker push ghcr.io/${{ github.repository_owner }}/fhirserver:nightly

Dockerfile

@@ -135,21 +135,9 @@ RUN tar -xzvf install.tgz
 WORKDIR /fhirserver/install
 
 
-### Choose your flavour / uncomment one of the following lines ###:
-##
-##
-
-# 1. Run the installation script for a blank, clean install
+# Run the installation script for a blank, clean install
 RUN chmod a+x ./install.sh && ./install.sh
 
-# OR
-
-# 2. Run the installation script With Zero  Config as tx.fhir.org
-# RUN chmod a+x ./install.sh && ./install.sh -nodaemon -zero=https://storage.googleapis.com/tx-fhir-org/config.json
-
-##
-##
-##
 ####################################################################
 
 WORKDIR /root/fhirserver

README-docker.md

@@ -0,0 +1,113 @@
+# FHIR Server Docker Installation
+
+This  Dockerfile and necessary scripts build and run a FHIR Server environment on Ubuntu 24.04. The Dockerfile is split into two stages: a **builder** stage where the FHIR server is built and packaged, and a **runtime** stage where the server is executed. Below are the details of the build and installation process.
+
+## Dockerfile Overview
+
+### 1. **Builder Stage**
+In the builder stage, the Dockerfile performs the following tasks:
+- Installs the necessary dependencies, including `git`, `curl`, `openssl`, `unixODBC`, and other libraries required for building the server.
+- Downloads and compiles **OpenSSL 1.1.1w**.
+- Installs **MySQL ODBC Connector 8.0.26**.
+- Copies toolchain and library scripts from the host machine (`build/linux-toolchain.sh` and `build/linux-libraries.sh`) and executes them to prepare the build environment.
+- Builds the FHIR server in `/work/fhirserver` using the `linux-fhirserver.sh` script.
+- Copies all necessary files (binaries, libraries, properties files, etc.) to the installation directory: `/work/fhirserver/exec/install`.
+- Packages the installation files into a tarball (`install.tgz`) located in `/work/fhirserver/exec/install.tgz`.
+
+### 2. **Runtime Stage**
+In the runtime stage, the Dockerfile:
+- Installs necessary runtime dependencies like `xvfb`, `libgtk2.0`, `libsqlite3`, and others required to run the FHIR server.
+- Creates directories for configuration, package cache, and terminology cache:
+  - Configuration directory: `/root/fhirserver/config`
+  - Terminology cache: `/var/cache/txcache`
+- Extracts the tarball (`install.tgz`) into `/root/fhirserver/install`.
+- Runs the installation script (`install.sh`) to set up the FHIR server environment.
+- Exposes port `80` for the FHIR server.
+
+## Paths
+
+### 1. **Installation Paths**
+The software is installed by default into the following directories:
+- **Binary files** (executables): `/root/fhirserver/install/bin/`
+- **Libraries**: `/root/fhirserver/install/x86_64/`
+- **Configuration files**: `/root/fhirserver/install/config/`
+- **Default configuration files**: `/root/fhirserver/install/default_config/`
+- **Content files (such as `.properties` and `.dat` files)**: `/root/fhirserver/install/content/`
+- **Web assets**: `/root/fhirserver/install/web/`
+
+### 2. **Cache and Configuration**
+- **Terminology cache**: `/var/cache/txcache`
+  - This directory is used for caching terminology data during FHIR operations.
+- **Configuration**:
+  - The main configuration files for the FHIR server are stored in `/root/fhirserver/install/config/`. If configuration files are not available, default configurations from `/root/fhirserver/install/default_config/` will be used.
+
+### 3. **Tarball Location**
+The final packaged installation tarball is created in `/root/fhirserver/install.tgz`. This tarball contains all the necessary files to deploy and run the FHIR server.
+
+## Health Check
+The Dockerfile includes a health check to verify if the FHIR server is running. It sends a request to `http://localhost:80/fhir/metadata` every minute. If the server fails to respond, the container is considered unhealthy.
+
+```bash
+HEALTHCHECK --interval=1m --timeout=10s --retries=5 \
+  CMD curl -f http://localhost:${PORT}/fhir/metadata || exit 1
+```
+
+
+
+## Environment Variables
+
+- `DISPLAY=:99`: Xvfb is used for the graphical environment. This environment variable sets the display.
+- `PORT=80`: The default port for the FHIR server.
+- `TERMINOLOGY_CACHE=/var/cache/txcache`: The directory used to cache terminology data during runtime.
+
+## Installation Process
+
+The installation is done by running the installer after ensuring the needed permissions are set:
+
+```bash
+RUN chmod a+x ./install.sh && ./install.sh
+```
+
+
+## Usage Instructions
+
+### Build the Docker Image
+
+To build the Docker image, use the following command:
+
+```bash
+docker build -t fhirserver-image .
+```
+
+
+### Run the Docker Container
+
+#### Default configuration
+To run the container with the default configuration:
+
+```bash
+docker run -d -p 80:80 --name fhirserver fhirserver-image`
+```
+This command will run the FHIR server on port 80 of your host machine.
+
+#### Customizing Configuration
+
+You can customize the configuration of the FHIR server by mapping local directory to the respective Docker container directory (`/root/fhirserver/config`). This can be done using Docker volume mapping.
+
+For example, to override the default configuration by mapping a local folder to the FHIR server's configuration folder:
+```yaml
+version: '3.3'  
+services: 
+  fhirserver:  
+    image: zeora/fhirserver:nightly
+  volumes: 
+  - ./config:/root/fhirserver/config        
+```
+
+You can also map a local terminology cache to `/var/cache/txcache` to persist it between container restarts.
+
+
+### Access the FHIR Server
+
+Once the container is running, you can access the FHIR server at http://localhost
+

build/linux-fhirserver.sh

@@ -57,4 +57,4 @@ $BUILD/tools/lazarus/lazbuild toolkit2/fhirtoolkit.lpr --build-mode=linux -q -q
 echo "## compile server"
 $BUILD/tools/lazarus/lazbuild server/fhirserver.lpr --build-mode=linux -q -q --build-all
 
-find ./exec/64 -type f ! -name "*.*" -exec strip {} \;
+find ./exec/64 -type f ! -name "*.*" -exec strip {} \;

clean.sh

@@ -1,2 +1,2 @@
-find . -name "*.ppu" -exec rm '{}' +
-find . -name "*.o" -exec rm '{}' +
+find . -name "*.ppu" -exec rm '{}' +
+find . -name "*.o" -exec rm '{}' +

dependencies/Indy10/Protocols/IdHL7.pas

@@ -79,9 +79,7 @@
 
     Original author Grahame Grieve
 
-    This code was donated by HL7Connect.com
-    For more HL7 open source code see
-    http://www.hl7connect.com/tools
+    This code was donated by Kestral Computing
 
   This unit implements support for the Standard HL7 minimal Lower Layer
   protocol. For further details, consult the HL7 standard (www.hl7.org).

exec/pack/Messages.properties

@@ -13,7 +13,9 @@ Attempt_to_a_slice_an_element_that_does_not_repeat__from__in_ = Attempt to a sli
 Attempt_to_replace_element_name_for_a_nonchoice_type=Attempt to replace element name for a non-choice type
 Attempt_to_use_Terminology_server_when_no_Terminology_server_is_available = Attempt to use Terminology server when no Terminology server is available
 Attempt_to_use_a_snapshot_on_profile__as__before_it_is_generated = Attempt to use a snapshot on profile ''{0}'' as {1} before it is generated
-BINDING_ADDITIONAL = {0} specified in an additional binding
+BINDING_ADDITIONAL_D = {0} specified in an additional binding
+BINDING_ADDITIONAL_UC = {0} specified in an additional binding which applies because {1}
+BINDING_ADDITIONAL_USAGE = {0} = {1}
 BINDING_MAX = {0} specified in the max binding
 BUNDLE_BUNDLE_ENTRY_FOUND_MULTIPLE = Found {0} matches for ''{1}'' in the bundle ({2})
 BUNDLE_BUNDLE_ENTRY_FOUND_MULTIPLE_FRAGMENT = Found {0} matches for fragment {2} in resource ''{1}'' in the bundle ({3})
@@ -1029,7 +1031,7 @@ VALUESET_SUPPLEMENT_MISSING_one = Required supplement not found: {1}
 VALUESET_SUPPLEMENT_MISSING_other = Required supplements not found: {1}
 VALUESET_TOO_COSTLY = The value set ''{0}'' expansion has too many codes to display ({1})
 VALUESET_TOO_COSTLY_COUNT = The value set ''{0}'' expansion has {2} codes, which is too many to display ({1})
-VALUESET_TOO_COSTLY_TIME = The value set ''{0}'' expansion took too long to process (>{1}sec)
+VALUESET_TOO_COSTLY_TIME = The value set ''{0}'' {2} took too long to process (>{1}sec)
 VALUESET_UNC_SYSTEM_WARNING = Unknown System ''{0}'' specified, so Concepts and Filters can''t be checked (Details: {1})
 VALUESET_UNC_SYSTEM_WARNING_VER = Unknown System/Version ''{0}'' specified, so Concepts and Filters can''t be checked (Details: {1})
 VALUESET_UNKNOWN_FILTER_PROPERTY = The property ''{0}'' is not known for the system ''{1}'', so may not be understood by the terminology ecosystem. Known properties for this system: {2}
@@ -1138,6 +1140,12 @@ TYPE_SPECIFIC_CHECKS_DT_XHTML_LITERAL_HREF = Hyperlink scheme ''{3}'' in ''{0}''
 SM_TARGET_TYPE_UNKNOWN = The type of the target variable is not known: {0}
 XHTML_XHTML_ATTRIBUTE_XML_SPACE = The attribute 'xml:space' is legal but has a fixed value of 'preserve'. It''s use is discouraged
 VALIDATION_HL7_PUBLISHER_MULTIPLE_WGS = This resource has more than workgroup extension (http://hl7.org/fhir/StructureDefinition/structuredefinition-wg)
-NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG = Wrong Display Name ''{0}'' for {1}#{2}. There are no valid display names found for language(s) ''{3}''. Default display is ''{4}''
+NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG_OK = There are no valid display names found for the code {1}#{2} for language(s) ''{3}''. The display is ''{4}'' the default language display
+NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG_ERR = Wrong Display Name ''{0}'' for {1}#{2}. There are no valid display names found for language(s) ''{3}''. Default display is ''{4}''
 NO_VALID_DISPLAY_AT_ALL = Cannot validate display Name ''{0}'' for {1}#{2}: No displays are known
-
+SD_BASE_EXPERIMENTAL = The definition builds on ''{0}'' which is experimental, but this definition is not labeled as experimental
+SD_ED_EXPERIMENTAL_BINDING = The definition for the element ''{0}'' binds to the value set ''{1}'' which is experimental, but this structure is not labeled as experimental
+VALIDATION_NO_EXPERIMENTAL_CONTENT = Experimental content is not allowed in this context
+SD_ED_ADDITIONAL_BINDING_USAGE_UNKNOWN = The Usage Context {0}#{1} is not recognised and may not be correct
+SD_ED_ADDITIONAL_BINDING_USAGE_INVALID_ELEMENT = The Usage Context {0}#{1} is a reference to an element that does not exist
+SD_ED_ADDITIONAL_BINDING_USAGE_INVALID_TYPE = The Usage Context value must be of type {1} not {0}