From 4025844001b4fc8509ee943c7aaace53631d5032 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Sun, 22 Sep 2024 09:26:56 +0200
Subject: [PATCH 01/16] strip linux binaries

---
 .github/workflows/linux-docker-build.yml | 1 -
 build/linux-fhirserver.sh                | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index e2f26081b..4ca51f6aa 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -3,7 +3,6 @@ on:
   # but only for the main branch
   push:
     branches:
-      - master
 #  pull_request:
 jobs:
   Build-Docker-Image:
diff --git a/build/linux-fhirserver.sh b/build/linux-fhirserver.sh
index aa5c863a6..29b6404e7 100755
--- a/build/linux-fhirserver.sh
+++ b/build/linux-fhirserver.sh
@@ -57,3 +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 {} \;

From 94b6da901459d7492b3d1e61d2774307f45354b3 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Sun, 22 Sep 2024 09:30:31 +0200
Subject: [PATCH 02/16] docker linux build

---
 Dockerfile                     | 148 ++++++++++++++++++++++++++-------
 config/config.ini              |   3 +-
 config/config.json             |  19 +++++
 exec/pack/linux/get-openssl.sh |  30 +++++++
 exec/pack/linux/install.sh     |  73 ++++++++++++++++
 exec/pack/linux/start.sh       |  61 ++++++++++++++
 exec/pack/web.ini              |   2 +
 7 files changed, 304 insertions(+), 32 deletions(-)
 create mode 100644 config/config.json
 create mode 100644 exec/pack/linux/get-openssl.sh
 create mode 100644 exec/pack/linux/install.sh
 create mode 100644 exec/pack/linux/start.sh
 create mode 100644 exec/pack/web.ini

diff --git a/Dockerfile b/Dockerfile
index c04ad593b..2c275e098 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,9 +1,9 @@
-FROM ubuntu:22.04 as builder
+FROM ubuntu:24.04 AS builder
 
 ENV DEBIAN_FRONTEND=noninteractive
 
 
-RUN apt update && apt install -y tzdata wget git unixodbc-dev libgtk2.0-dev xvfb sqlite3 libsqlite3-dev build-essential curl
+RUN apt update && apt-get upgrade -y && apt install -y tzdata wget git unixodbc-dev libgtk2.0-dev xvfb sqlite3 libsqlite3-dev build-essential curl binutils && apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # Download and build OpenSSL 1.1.1w
 WORKDIR /tmp
@@ -15,7 +15,7 @@ RUN wget https://www.openssl.org/source/openssl-1.1.1w.tar.gz \
     && make test \
     && make install
 
-RUN ls -la /usr/local/lib/
+# RUN ls -la /usr/local/lib/
 
 # Set the timezone
 RUN echo "UTC" > /etc/timezone
@@ -36,40 +36,126 @@ RUN /work/bootstrap/linux-toolchain.sh /work/bootstrap
 WORKDIR /work/fhirserver
 COPY . /work/fhirserver
 
-RUN /work/bootstrap/linux-libraries.sh /work/bootstrap
-RUN cp /usr/local/lib/*.so* /usr/lib/
-RUN /work/fhirserver/build/linux-fhirserver.sh /work/bootstrap
-RUN cp exec/pack/*.properties exec/64
+RUN /work/bootstrap/linux-libraries.sh /work/bootstrap && \
+    cp /usr/local/lib/*.so* /usr/lib/ && \
+    /work/fhirserver/build/linux-fhirserver.sh /work/bootstrap && \
+    cp exec/pack/*.properties exec/64
+# RUN cp exec/install/* exec/64
+
+RUN mkdir -p /work/fhirserver/exec/install/bin && \
+    mkdir -p /work/fhirserver/exec/install/x86_64 && \
+    mkdir -p /work/fhirserver/exec/install/content && \
+    mkdir -p /work/fhirserver/exec/install/config && \
+    # mkdir -p /work/fhirserver/exec/install/config/config && \
+    mkdir -p /work/fhirserver/exec/install/default_config && \
+    mkdir -p /work/fhirserver/exec/install/web
+
+RUN cd /work/fhirserver && \
+    cp /work/fhirserver/exec/64/fhirserver /work/fhirserver/exec/install/bin && \
+    cp /work/fhirserver/exec/64/FHIRToolkit /work/fhirserver/exec/install/bin && \
+    cp /work/fhirserver/exec/64/FHIRConsole /work/fhirserver/exec/install/bin && \
+    cp /work/fhirserver/exec/pack/linux/*so* /work/fhirserver/exec/install/x86_64
+
+RUN cp /work/fhirserver/exec/pack/linux/start.sh /work/fhirserver/exec/install/bin/start.sh && \
+    cp /work/fhirserver/exec/pack/linux/install.sh /work/fhirserver/exec/install && \
+    cp /work/fhirserver/exec/pack/linux/get-openssl.sh /work/fhirserver/exec/install && \
+    cp /tmp/openssl-1.1.1w/*.so* /work/fhirserver/exec/install/x86_64 && \
+    cp /work/fhirserver/exec/pack/*.properties /work/fhirserver/exec/install/content && \
+    cp /work/fhirserver/exec/pack/*.dat /work/fhirserver/exec/install/content && \
+
+    cp /work/fhirserver/exec/pack/fhirserver.cfg /work/fhirserver/exec/install/config && \
+    cp /work/fhirserver/exec/pack/web.ini /work/fhirserver/exec/install/config && \
+
+
+    cp /work/fhirserver/exec/pack/web.ini /work/fhirserver/exec/install/default_config && \
+    cp /work/fhirserver/exec/pack/fhirserver.cfg /work/fhirserver/exec/install/default_config && \
+    cp /work/fhirserver/config/config.ini /work/fhirserver/exec/install/default_config/config.ini && \
+    cp /work/fhirserver/config/config.json /work/fhirserver/exec/install/default_config/config.json && \
+    # cp /work/fhirserver/config/config.ini /work/fhirserver/exec/install/config/config.ini && \
+
+    # cp /work/fhirserver/config/config_bare.json /work/fhirserver/exec/install/default_config/config.json && \
+    # cp /work/fhirserver/config/config.ini       /work/fhirserver/exec/install/config/default_config && \
+    
+    mkdir -p /work/fhirserver/exec/install/web && \
+    cp -r /work/fhirserver/server/web/* /work/fhirserver/exec/install/web && \
+    cd /work/fhirserver/exec && tar -czvf ./install.tgz ./install/  && ls -la /work/fhirserver/exec
+
 
 # Set the health check
-HEALTHCHECK --interval=1m --timeout=10s --retries=5 \
+HEALTHCHECK --interval=1m --timeout=10s --retries=5 \ 
   CMD curl -f http://localhost:${PORT}/fhir/metadata || exit 1
 
 # Set the environment variables
-ENV DISPLAY :99
-ENV PORT 80
-ENV TERMINOLOGY_CACHE /terminology
+ENV DISPLAY=:99
+ENV PORT=80
+ENV TERMINOLOGY_CACHE=/terminology
 VOLUME /terminology
 
 ENV DEBIAN_FRONTEND=
 
-RUN printf '#!/bin/bash \n\
-    set -e \n\
-    start_xvfb() { \n\
-        Xvfb :99 -screen 0 1024x768x8 -nolisten tcp & \n\
-    } \n\
-    stop_xvfb() { \n\
-        killall Xvfb || true \n\
-    } \n\
-    trap stop_xvfb SIGTERM \n\
-    rm -f /tmp/.X99-lock \n\
-    start_xvfb \n\
-    echo "[web]" > /work/fhirserver/exec/64/web.ini; \n\
-    echo "http=${PORT}" >> /work/fhirserver/exec/64/web.ini; \n\
-    /work/fhirserver/exec/64/fhirserver $(eval echo "$@")' > /bin/entrypoint.sh && \
-    chmod +x /bin/entrypoint.sh
-
-
-ENTRYPOINT ["/bin/entrypoint.sh"]
-
-CMD ["-cmd",  "exec",  "-cfg", "/config/config.ini", "-local", "$TERMINOLOGY_CACHE"]
+# ENTRYPOINT ["/bin/entrypoint.sh"]
+
+# CMD ["-cmd",  "exec",  "-cfg", "/config/config.ini", "-local", "$TERMINOLOGY_CACHE"]
+
+
+
+# Runtime stage
+FROM ubuntu:24.04 AS runtime
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=UTC
+# Set up environment variables
+# ENV HOME=~/
+ENV DISPLAY=:99
+ENV PORT=80
+ENV TERMINOLOGY_CACHE=/var/cache/txcache
+
+# Install runtime dependencies
+RUN apt-get update && apt-get upgrade -y && apt-get install -y wget tzdata xvfb libgtk2.0-0 libsqlite3-dev curl && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && mkdir -p $HOME/fhirserver/config $TERMINOLOGY_CACHE /fhirserver \
+    && chmod -R 777 $TERMINOLOGY_CACHE \
+    && chmod -R 777 /fhirserver
+
+# Copy necessary files from the builder stage
+COPY --from=builder /work/fhirserver/exec/install.tgz /fhirserver/install.tgz
+
+# RUN cd /fhirserver \
+#     && tar -xzvf install.tgz \
+#     && cd ./install \
+#     && ./install.sh > install.log 2>&1
+
+# Assuming /fhirserver is your working directory
+WORKDIR /fhirserver
+
+# Extract the contents of the tar file
+RUN tar -xzvf install.tgz
+
+# Change working directory to the extracted folder
+WORKDIR /fhirserver/install
+
+
+### Choose your flavour / uncomment one of the following lines ###:
+##
+##
+
+# 1. 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
+
+# Define entrypoint and command
+CMD ["bash", "-c", "cd ~/fhirserver/ && ./start.sh"]
+
+# Expose the necessary port
+EXPOSE 80
diff --git a/config/config.ini b/config/config.ini
index 4ded9d3ac..a051cb8a6 100644
--- a/config/config.ini
+++ b/config/config.ini
@@ -1,6 +1,7 @@
 [config]
-zero=https://storage.googleapis.com/tx-fhir-org
+zero=file:/root/fhirserver/default_config
 version=*
+local=/var/cache/txcache
 user=gg
 
 [web]
diff --git a/config/config.json b/config/config.json
new file mode 100644
index 000000000..302dc0314
--- /dev/null
+++ b/config/config.json
@@ -0,0 +1,19 @@
+{
+  "content" : {
+    "uv" : {
+      "packages" : {
+        "r4" : [
+          "hl7.terminology.r4",
+          "fhir.tx.support.r4"
+        ]
+      }
+    }
+  },
+  "endpoints" : {
+    "cache" : {
+      "path" : "/post/tx-cache",
+      "type" : "folder",
+      "folder": "/var/cache/txcache"
+    }
+  }
+}
diff --git a/exec/pack/linux/get-openssl.sh b/exec/pack/linux/get-openssl.sh
new file mode 100644
index 000000000..43a156fc9
--- /dev/null
+++ b/exec/pack/linux/get-openssl.sh
@@ -0,0 +1,30 @@
+OPENSSL_DIR=${OPENSSL_DIR:-"/tmp/openssl"}
+
+apt update && apt install -y libgtk2.0-0 
+
+
+# Check if OpenSSL is not installed
+if [ ! -d $OPENSSL_DIR ]; then
+    echo "OpenSSL not found in $OPENSSL_DIR. Installing..."
+    apt install -y build-essential 
+
+    # Download and build OpenSSL 1.1.1w
+    pushd /tmp
+    wget https://www.openssl.org/source/openssl-1.1.1w.tar.gz
+    tar -xf openssl-1.1.1w.tar.gz
+    cd openssl-1.1.1w
+
+    ./config --prefix=$OPENSSL_DIR --openssldir=$OPENSSL_DIR
+    make
+    make test
+    make install
+    popd
+
+    echo "OpenSSL installation completed."
+else
+    echo "OpenSSL is already installed in $OPENSSL_DIR."
+fi
+
+    cp $OPENSSL_DIR/lib/*.so* .
+
+
diff --git a/exec/pack/linux/install.sh b/exec/pack/linux/install.sh
new file mode 100644
index 000000000..47f6130e1
--- /dev/null
+++ b/exec/pack/linux/install.sh
@@ -0,0 +1,73 @@
+#!/bin/bash
+cd "$(dirname "$0")"
+
+# Detect architecture
+ARCH=$(uname -m)
+
+INSTALL_PATH=${INSTALL_PATH:-"$HOME/fhirserver"}
+CACHE_FOLDER=${CACHE_FOLDER:-"/var/cache/txcache"}
+ARM_FILES=./arm_64
+X86_64_FILES=./x86_64
+
+set -x
+
+# Function to run commands with sudo only if not root
+run_as_root() {
+    if [ "$(id -u)" -ne 0 ]; then
+        sudo "$@"
+    else
+        "$@"
+    fi
+}
+
+run_as_root apt update && run_as_root apt install -y wget tzdata xvfb libgtk2.0-0 libsqlite3-dev curl
+
+mkdir -p $INSTALL_PATH
+mkdir -p $INSTALL_PATH/config
+mkdir -p $INSTALL_PATH/default_config
+run_as_root mkdir -p $CACHE_FOLDER
+run_as_root chmod 1777 $CACHE_FOLDER
+
+cp bin/* $INSTALL_PATH 
+cp content/* $INSTALL_PATH 
+# cp -r config/* $INSTALL_PATH 
+# cp -r config/config/* $INSTALL_PATH/config 
+cp -r config/* $INSTALL_PATH/config 
+cp -r default_config/* $INSTALL_PATH/default_config 
+cp -r web $INSTALL_PATH
+
+# Files based on architecture
+case $ARCH in
+    x86_64)
+        cp $X86_64_FILES/* $INSTALL_PATH
+        ;;
+    arm*)
+        cp $ARM_FILES/* $INSTALL_PATH
+        ;;
+    *)
+        echo "Unsupported architecture: $ARCH"
+        exit 1
+        ;;
+esac
+
+# Create link so that the server can be started from anywhere
+ln -s $INSTALL_PATH/start.sh /usr/local/bin/fhirserver
+
+# Copy the default configuration file
+cp "$INSTALL_PATH/default_config/config.json" "$INSTALL_PATH/default_config/config.json"
+
+# Prepare and install the systemd service file but do not enable or start it
+SERVICE_FILE="/etc/systemd/system/fhirserver.service"
+echo "[Unit]
+Description=FHIR Server
+
+[Service]
+ExecStart=$INSTALL_PATH/fhirserver
+# Add other service configurations as needed
+
+[Install]
+WantedBy=multi-user.target" | run_as_root tee $SERVICE_FILE > /dev/null
+
+echo "Installation to $INSTALL_PATH completed."
+
+cd $INSTALL_PATH
\ No newline at end of file
diff --git a/exec/pack/linux/start.sh b/exec/pack/linux/start.sh
new file mode 100644
index 000000000..f7e4aedba
--- /dev/null
+++ b/exec/pack/linux/start.sh
@@ -0,0 +1,61 @@
+#!/bin/bash
+set -e
+
+# Determine the directory where this script is located (this will be $HOME/fhirserver)
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SERVICE_FILE="/etc/systemd/system/fhirserver.service"
+
+# Function to start Xvfb
+start_xvfb() {
+    Xvfb :99 -screen 0 1024x768x8 -nolisten tcp &
+    sleep 2  # Give some time for Xvfb to start
+}
+
+# Function to stop Xvfb
+stop_xvfb() {
+   pkill Xvfb || true
+}
+
+trap stop_xvfb EXIT
+
+rm -f /tmp/.X99-lock
+start_xvfb
+export DISPLAY=:99
+
+# Parse command-line arguments
+DAEMON_MODE=""
+
+for arg in "$@"; do
+    case $arg in
+        -daemon)
+            DAEMON_MODE="enable"
+            ;;
+        -nodaemon)
+            DAEMON_MODE="disable"
+            ;;
+    esac
+done
+
+# Determine which config.ini to use
+if [ -f "$SCRIPT_DIR/config/config.ini" ]; then
+    CONFIG_FILE="$SCRIPT_DIR/config/config.ini"
+else
+    CONFIG_FILE="$SCRIPT_DIR/default_config/config.ini"
+fi
+
+if [ ! -f "$SCRIPT_DIR/config/config.json" ]; then
+    cp "$SCRIPT_DIR/default_config/config.json" "$SCRIPT_DIR/config/config.json"
+    echo "File copied successfully."
+fi
+
+# Handle daemon management
+if [ "$DAEMON_MODE" == "enable" ]; then
+    sudo systemctl enable fhirserver.service
+    sudo systemctl start fhirserver.service
+elif [ "$DAEMON_MODE" == "disable" ]; then
+    sudo systemctl stop fhirserver.service || true
+    sudo systemctl disable fhirserver.service || true
+fi
+
+# Start the FHIR server using the determined config file
+exec "$SCRIPT_DIR/fhirserver" -cmd exec -cfg "$CONFIG_FILE"
diff --git a/exec/pack/web.ini b/exec/pack/web.ini
new file mode 100644
index 000000000..c40ba4601
--- /dev/null
+++ b/exec/pack/web.ini
@@ -0,0 +1,2 @@
+[web]
+htttp=80

From 11f51c3c5e4021a0cf6b062f172b47f157c87d4e Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Sun, 22 Sep 2024 09:36:02 +0200
Subject: [PATCH 03/16] typos

---
 server/endpoint_storage.pas | 2 +-
 server/fhirserver.lpi       | 4 ++--
 server/web/diagnostics.html | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/server/endpoint_storage.pas b/server/endpoint_storage.pas
index 0ac18de11..6ea060582 100644
--- a/server/endpoint_storage.pas
+++ b/server/endpoint_storage.pas
@@ -1080,7 +1080,7 @@ function TStorageWebEndpoint.SecureRequest(AContext: TIdContext; ip: String;
     else if request.Document = PathNoSlash then
     begin
       result := 'Home Page';
-      ReturnProcessedFile(request, response, Session, '/hompage.html', Common.SourceProvider.AltFile('/homepage.html', PathNoSlash), true)
+      ReturnProcessedFile(request, response, Session, '/homepage.html', Common.SourceProvider.AltFile('/homepage.html', PathNoSlash), true)
     end
     else
     begin
diff --git a/server/fhirserver.lpi b/server/fhirserver.lpi
index df50389d1..a6da9954e 100644
--- a/server/fhirserver.lpi
+++ b/server/fhirserver.lpi
@@ -130,7 +130,7 @@
           </Target>
           <SearchPaths>
             <IncludeFiles Value="$(ProjOutDir);..\library"/>
-            <Libraries Value="\usr\local\lib64\"/>
+            <Libraries Value="\usr\local\lib64"/>
             <OtherUnitFiles Value="..\library\fsl\tests;..\library\fhir\tests;..\library\fhir4\tests;..\library\fhir4b\tests;..\library\fhir5\tests;..\library\ftx\tests;..\library\fxver\tests;..\library\cda\tests;..\library\v2\tests;..\library\fdb\tests;modules;tests;admin;..\library\fcomp\tests;tx"/>
             <UnitOutputDirectory Value="lib\$(BuildMode)"/>
           </SearchPaths>
@@ -323,7 +323,7 @@
           </Target>
           <SearchPaths>
             <IncludeFiles Value="$(ProjOutDir);../library"/>
-            <Libraries Value="/usr/local/lib64/;/tmp/openssl/lib/;/tmp/openssl/"/>
+            <Libraries Value="/usr/local/lib64;/tmp/openssl/lib;/tmp/openssl"/>
             <OtherUnitFiles Value="../library/fsl/tests;../library/fhir/tests;../library/fhir4/tests;../library/fhir4b/tests;../library/fhir5/tests;../library/ftx/tests;../library/fxver/tests;../library/cda/tests;../library/v2/tests;../library/fdb/tests;modules;tests;admin;../library/fcomp/tests;tx"/>
             <UnitOutputDirectory Value="lib/$(BuildMode)"/>
           </SearchPaths>
diff --git a/server/web/diagnostics.html b/server/web/diagnostics.html
index f952b91c8..34db99e18 100644
--- a/server/web/diagnostics.html
+++ b/server/web/diagnostics.html
@@ -15,7 +15,7 @@ <h3>Current Activity</h3>
 <ul>
   <li>Background Thread: [%status.thread%]</li>
   <li>CDS client instances: [%status.cds.client%]</li>
-<li>[%status.web-total-count%] total requests for [%status.web-total-time%]ms. [%status.web-rest-count%] REST requests for [%status.web-rest-time%]ms. [%status.run-time%] since starting ({%status.run-time.ms%]ms)</li>
+<li>[%status.web-total-count%] total requests for [%status.web-total-time%]ms. [%status.web-rest-count%] REST requests for [%status.web-rest-time%]ms. [%status.run-time%] since starting ([%status.run-time.ms%] ms)</li>
 </ul>
 
 [%status.web%]

From 077ea2ea0fb28851892b85d8dcfd09f06bd20fd8 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Sun, 22 Sep 2024 09:54:53 +0200
Subject: [PATCH 04/16] clean up

---
 server/endpoint_txsvr.pas | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/server/endpoint_txsvr.pas b/server/endpoint_txsvr.pas
index b45b2df3a..7792d5d48 100644
--- a/server/endpoint_txsvr.pas
+++ b/server/endpoint_txsvr.pas
@@ -1418,10 +1418,7 @@ procedure TTerminologyFhirServerStorage.loadPackage(pid: String; ignoreEmptyCode
 begin
   i := 0;
 
-
-//  FEndPoint.
-fileToLoad := filePath([FServerContext.pcm.folder,pid]) ;
-
+  fileToLoad := filePath([FServerContext.pcm.folder,pid]) ;
 
   if (FileExists(fileToLoad)) then
     try

From 46eb07d8c8e6213d459ca190254c1ab6689620b2 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Mon, 23 Sep 2024 15:18:21 +0200
Subject: [PATCH 05/16] CRLF to LF + add readme for docker

---
 Dockerfile       | 14 +-------
 README-docker.md | 93 ++++++++++++++++++++++++++++++++++++++++++++++++
 clean.sh         |  4 +--
 3 files changed, 96 insertions(+), 15 deletions(-)
 create mode 100644 README-docker.md

diff --git a/Dockerfile b/Dockerfile
index 2c275e098..ecb8e0092 100644
--- a/Dockerfile
+++ b/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
diff --git a/README-docker.md b/README-docker.md
new file mode 100644
index 000000000..935122856
--- /dev/null
+++ b/README-docker.md
@@ -0,0 +1,93 @@
+# 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
+
+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.
+
+### Access the FHIR Server
+
+Once the container is running, you can access the FHIR server metadata endpoint by opening http://localhost/fhir/metadata
+
diff --git a/clean.sh b/clean.sh
index 3de0aa50c..d8c610b8d 100644
--- a/clean.sh
+++ b/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 '{}' +

From e148eed14af52b6239aebecec49a448d8e1af5d5 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Mon, 23 Sep 2024 16:05:43 +0200
Subject: [PATCH 06/16] upload docker image

---
 .github/workflows/linux-docker-build.yml | 172 +++++++++++------------
 1 file changed, 86 insertions(+), 86 deletions(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index 4ca51f6aa..63503dcf7 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -1,86 +1,86 @@
-on:
-  # Trigger the workflow on push or pull request,
-  # but only for the main branch
-  push:
-    branches:
-#  pull_request:
-jobs:
-  Build-Docker-Image:
-    runs-on: ubuntu-latest
-    steps:
-    - 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: ${{ secrets.DOCKERHUB_TOKEN }}      
-    - name: Cache terminology files
-      uses: actions/cache@v2
-      with:
-        path: ~/terminology
-        key: terminology-${{ github.sha }}
-        restore-keys: terminology-
-    - name: Setup MySQL
-      run: |
-        docker network create gh
-        docker run \
-          --network gh \
-          --name mysql \
-          -e MYSQL_ROOT_PASSWORD=test \
-          -e MYSQL_USER=test \
-          -e MYSQL_PASSWORD=test \
-          -e MYSQL_DATABASE=test \
-          -d mysql:8
-    - 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
-    - name: Prepare ini file
-      env:
-        FHIRSERVER_LOCATIONS_CLONE_PATH: /work/fhirserver
-        FHIRSERVER_LOCATIONS_TEST_CASES_CLONE_PATH: /work/bootstrap/source/fhir-test-cases
-        FHIRSERVER_LOCATIONS_MARKDOWN_CLONE_PATH: /work/bootstrap/source/delphi-markdown
-        FHIRSERVER_LOCATIONS_SNOMED_CACHE_PATH: /terminology/fhir-server/snomed.test.cache
-        FHIRSERVER_MYSQL_SERVER: mysql
-        FHIRSERVER_EMAIL_SENDER: fhir-server@healthintersections.com.au
-        FHIRSERVER_EMAIL_DESTINATION: fhirservertests@gmail.com
-        FHIRSERVER_EMAIL_PASSWORD: ${{ secrets.FHIRSERVER_EMAIL_PASSWORD }}
-        FHIRSERVER_SSL_CERT_PATH: /work/fhirserver/fixtures/domain.crt
-        FHIRSERVER_SSL_KEY_PATH: /work/fhirserver/fixtures/domain.key
-        FHIRSERVER_SSL_CACERT_PATH: /work/fhirserver/fixtures/rootCA.crt
-        FHIRSERVER_SSL_PASSWORD: password
-      run: |
-        cat fixtures/test-settings.ini.template | envsubst > ~/test-settings.ini
-    - name: Ensure SNOMED cache is present
-      run: |
-        mkdir -p ~/terminology/fhir-server
-        wget -q --no-clobber https://storage.googleapis.com/ig-build/snomed.test.cache -O ~/terminology/fhir-server/snomed.test.cache || true
-        ls  ~/terminology/fhir-server/snomed.test.cache
-    - name: Run tests in docker
-      run: |
-        docker images --all
-        docker run \
-          --network gh \
-          -v ~/terminology:/terminology \
-          -v ~/test-settings.ini:/work/fhirserver/exec/64/test-settings.ini \
-          fhirserver -tests
-
-#    - name: Tag and push Docker image
-#      run: |
-#        # Extract the FHIR server version from the library/version.inc file
-#        FHIR_VERSION=$(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
+on:
+  # Trigger the workflow on push or pull request,
+  # but only for the main branch
+  push:
+    branches:
+#  pull_request:
+jobs:
+  Build-Docker-Image:
+    runs-on: ubuntu-latest
+    steps:
+    - 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: ${{ secrets.DOCKERHUB_TOKEN }}      
+
+    - name: Cache terminology files
+      uses: actions/cache@v2
+      with:
+        path: ~/terminology
+        key: terminology-${{ github.sha }}
+        restore-keys: terminology-
+    - name: Setup MySQL
+      run: |
+        docker network create gh
+        docker run \
+          --network gh \
+          --name mysql \
+          -e MYSQL_ROOT_PASSWORD=test \
+          -e MYSQL_USER=test \
+          -e MYSQL_PASSWORD=test \
+          -e MYSQL_DATABASE=test \
+          -d mysql:8
+    - 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
+
+    - name: Prepare ini file
+      env:
+        FHIRSERVER_LOCATIONS_CLONE_PATH: /work/fhirserver
+        FHIRSERVER_LOCATIONS_TEST_CASES_CLONE_PATH: /work/bootstrap/source/fhir-test-cases
+        FHIRSERVER_LOCATIONS_MARKDOWN_CLONE_PATH: /work/bootstrap/source/delphi-markdown
+        FHIRSERVER_LOCATIONS_SNOMED_CACHE_PATH: /terminology/fhir-server/snomed.test.cache
+        FHIRSERVER_MYSQL_SERVER: mysql
+        FHIRSERVER_EMAIL_SENDER: fhir-server@healthintersections.com.au
+        FHIRSERVER_EMAIL_DESTINATION: fhirservertests@gmail.com
+        FHIRSERVER_EMAIL_PASSWORD: ${{ secrets.FHIRSERVER_EMAIL_PASSWORD }}
+        FHIRSERVER_SSL_CERT_PATH: /work/fhirserver/fixtures/domain.crt
+        FHIRSERVER_SSL_KEY_PATH: /work/fhirserver/fixtures/domain.key
+        FHIRSERVER_SSL_CACERT_PATH: /work/fhirserver/fixtures/rootCA.crt
+        FHIRSERVER_SSL_PASSWORD: password
+      run: |
+        cat fixtures/test-settings.ini.template | envsubst > ~/test-settings.ini
+    - name: Ensure SNOMED cache is present
+      run: |
+        mkdir -p ~/terminology/fhir-server
+        wget -q --no-clobber https://storage.googleapis.com/ig-build/snomed.test.cache -O ~/terminology/fhir-server/snomed.test.cache || true
+        ls  ~/terminology/fhir-server/snomed.test.cache
+    - name: Run tests in docker
+      run: |
+        docker images --all
+        docker run \
+          --network gh \
+          -v ~/terminology:/terminology \
+          -v ~/test-settings.ini:/work/fhirserver/exec/64/test-settings.ini \
+          fhirserver -tests
+
+   - name: Tag and push Docker image
+     run: |
+       # Extract the FHIR server version from the library/version.inc file
+       FHIR_VERSION=$(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:nightly
+
+       # Push both tagged images to Docker Hub
+       docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:nightly

From 9c5061dca2eabed2e3c858f1acee3c8b9b81abec Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Mon, 23 Sep 2024 18:06:03 +0200
Subject: [PATCH 07/16] Update linux-docker-build.yml

---
 .github/workflows/linux-docker-build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index 63503dcf7..a815e574e 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -10,7 +10,7 @@ jobs:
     steps:
     - name: Check out repository code
       uses: actions/checkout@v2
-   -
+    -
      name: Login to Docker Hub
      uses: docker/login-action@v2
      with:

From 1c597e6f634fd5118d89f46bb274b7542f3679bf Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Mon, 23 Sep 2024 18:06:22 +0200
Subject: [PATCH 08/16] Update linux-docker-build.yml

---
 .github/workflows/linux-docker-build.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index a815e574e..0c7f7c323 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -11,11 +11,11 @@ jobs:
     - 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 }}      
+      name: Login to Docker Hub
+      uses: docker/login-action@v2
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}      
 
     - name: Cache terminology files
       uses: actions/cache@v2

From 17e2d6e1eea4fe9f35615399bb68184242d6bc2a Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Tue, 24 Sep 2024 01:12:59 +0200
Subject: [PATCH 09/16] Update linux-docker-build.yml

---
 .github/workflows/linux-docker-build.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index 0c7f7c323..326584fd3 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -3,7 +3,8 @@ on:
   # but only for the main branch
   push:
     branches:
-#  pull_request:
+  pull_request:
+
 jobs:
   Build-Docker-Image:
     runs-on: ubuntu-latest

From 319c86919c446cc53a177e6e22ee16931701080b Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Tue, 24 Sep 2024 01:34:38 +0200
Subject: [PATCH 10/16] Update linux-docker-build.yml

---
 .github/workflows/linux-docker-build.yml | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index 326584fd3..bb3f41b2b 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -11,13 +11,11 @@ jobs:
     steps:
     - name: Check out repository code
       uses: actions/checkout@v2
-    -
-      name: Login to Docker Hub
+    - name: Login to Docker Hub
       uses: docker/login-action@v2
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
         password: ${{ secrets.DOCKERHUB_TOKEN }}      
-
     - name: Cache terminology files
       uses: actions/cache@v2
       with:
@@ -75,13 +73,13 @@ jobs:
           -v ~/test-settings.ini:/work/fhirserver/exec/64/test-settings.ini \
           fhirserver -tests
 
-   - name: Tag and push Docker image
-     run: |
+    - name: Tag and push Docker image
+      run: |
        # Extract the FHIR server version from the library/version.inc file
-       FHIR_VERSION=$(grep -oP "FHIR_CODE_FULL_VERSION = '\K[^']+" library/version.inc)
+        FHIR_VERSION=$(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:nightly
+        docker tag fhirserver ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:nightly
 
        # Push both tagged images to Docker Hub
-       docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:nightly
+        docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:nightly

From e4748d0ada0c2069417e0c82a6c408095bb91a46 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Tue, 24 Sep 2024 02:08:02 +0200
Subject: [PATCH 11/16] skip tests

---
 .github/workflows/linux-docker-build.yml | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index bb3f41b2b..df0dd56fa 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -64,14 +64,15 @@ jobs:
         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
+
+#    - 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
 
     - name: Tag and push Docker image
       run: |

From 6936f03f2561da897d78c8c02ed06fed41c6f878 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Tue, 24 Sep 2024 15:17:42 +0200
Subject: [PATCH 12/16] Update README-docker.md

---
 README-docker.md | 206 ++++++++++++++++++++++++++---------------------
 1 file changed, 113 insertions(+), 93 deletions(-)

diff --git a/README-docker.md b/README-docker.md
index 935122856..640de6024 100644
--- a/README-docker.md
+++ b/README-docker.md
@@ -1,93 +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
-
-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.
-
-### Access the FHIR Server
-
-Once the container is running, you can access the FHIR server metadata endpoint by opening http://localhost/fhir/metadata
-
+# 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
+

From dd89c5caacc0ed8f859930674fa4279d44f8cbeb Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Thu, 26 Sep 2024 21:55:49 +0200
Subject: [PATCH 13/16] Update linux-docker-build.yml

---
 .github/workflows/linux-docker-build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index df0dd56fa..1013bd91e 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -83,4 +83,4 @@ jobs:
         docker tag fhirserver ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:nightly
 
        # Push both tagged images to Docker Hub
-        docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:nightly
+        docker push ghcr.io/${{ github.repository_owner }}/fhirserver:nightly

From abdef7f17a3521f2e8bb3e0220d4f349a2bfa2f3 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Thu, 26 Sep 2024 22:13:39 +0200
Subject: [PATCH 14/16] Update linux-docker-build.yml

---
 .github/workflows/linux-docker-build.yml | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index 1013bd91e..e38c57364 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -35,13 +35,9 @@ jobs:
           -d mysql:8
     - 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 .
+
 
     - name: Prepare ini file
       env:
@@ -76,11 +72,4 @@ jobs:
 
     - name: Tag and push Docker image
       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 ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:nightly
-
-       # Push both tagged images to Docker Hub
         docker push ghcr.io/${{ github.repository_owner }}/fhirserver:nightly

From 2878d2b0a35f34623f3c93fda648456889354ada Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Thu, 26 Sep 2024 23:08:11 +0200
Subject: [PATCH 15/16] Update linux-docker-build.yml

---
 .github/workflows/linux-docker-build.yml | 46 ++++++++++++++----------
 1 file changed, 27 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index e38c57364..c43322772 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -1,27 +1,40 @@
+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:
+      - main
   pull_request:
+    branches:
+      - main
 
 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
+
+    # Step 2: Log in to GitHub Container Registry (GHCR)
+    - name: Log in to GitHub Container Registry
       uses: docker/login-action@v2
       with:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_TOKEN }}      
+        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
@@ -33,12 +46,13 @@ 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 ghcr.io/${{ github.repository_owner }}/fhirserver:nightly .
-
+        docker build --tag ghcr.io/${{ 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
@@ -55,21 +69,15 @@ 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: |
         docker push ghcr.io/${{ github.repository_owner }}/fhirserver:nightly

From 25a676440a75a1ccc02921e7702f5d7cc2a3a756 Mon Sep 17 00:00:00 2001
From: Jose Costa Teixeira <jose.a.teixeira@gmail.com>
Date: Thu, 26 Sep 2024 23:14:20 +0200
Subject: [PATCH 16/16] Update linux-docker-build.yml

---
 .github/workflows/linux-docker-build.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
index c43322772..514815176 100644
--- a/.github/workflows/linux-docker-build.yml
+++ b/.github/workflows/linux-docker-build.yml
@@ -3,11 +3,7 @@ name: Build and Push Docker Image to GHCR
 on:
   # Trigger the workflow on push or pull request for the main branch
   push:
-    branches:
-      - main
   pull_request:
-    branches:
-      - main
 
 jobs:
   Build-Docker-Image: