fix

costateixeira · Sep 21, 2024 · 0d2eaa9 · 0d2eaa9
1 parent 701d5ce
commit 0d2eaa9
Show file tree

Hide file tree

Showing 19 changed files with 277 additions and 140 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:24.04 as builder
+FROM ubuntu:24.04 AS builder
 
 ENV DEBIAN_FRONTEND=noninteractive
 
@@ -46,8 +46,8 @@ 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/config/default_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 && \
@@ -56,18 +56,26 @@ RUN cd /work/fhirserver && \
     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_bare.sh /work/fhirserver/exec/install/bin/start.sh && \
+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/config/config.ini       /work/fhirserver/exec/install/config/config && \
-    cp /work/fhirserver/config/config_bare.json /work/fhirserver/exec/install/config/config/config.json && \
-    cp /work/fhirserver/config/config.ini       /work/fhirserver/exec/install/config/default_config && \
-    cp /work/fhirserver/config/config_bare.json /work/fhirserver/exec/install/config/default_config/config.json && \
+
+
+    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
@@ -78,9 +86,9 @@ 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=
@@ -92,7 +100,7 @@ ENV DEBIAN_FRONTEND=
 
 
 # Runtime stage
-FROM ubuntu:24.04 as runtime
+FROM ubuntu:24.04 AS runtime
 
 ENV DEBIAN_FRONTEND=noninteractive
 ENV TZ=UTC
@@ -132,7 +140,7 @@ WORKDIR /fhirserver/install
 ##
 
 # 1. Run the installation script for a blank, clean install
-RUN chmod a+x ./install.sh && ./install.sh -nodaemon 
+RUN chmod a+x ./install.sh && ./install.sh
 
 # OR
 
@@ -144,6 +152,7 @@ RUN chmod a+x ./install.sh && ./install.sh -nodaemon
 ##
 ####################################################################
 
+WORKDIR /root/fhirserver
 
 # Define entrypoint and command
 CMD ["bash", "-c", "cd ~/fhirserver/ && ./start.sh"]

diff --git a/Dockerfile prev b/Dockerfile prev
@@ -0,0 +1,152 @@
+FROM ubuntu:22.04 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 binutils
+
+# Download and build OpenSSL 1.1.1w
+WORKDIR /tmp
+RUN 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 \
+    && make \
+    && make test \
+    && make install
+
+RUN ls -la /usr/local/lib/
+
+# Set the timezone
+RUN echo "UTC" > /etc/timezone
+
+RUN cd /tmp && \
+    wget https://dev.mysql.com/get/Downloads/Connector-ODBC/8.0/mysql-connector-odbc-8.0.26-linux-glibc2.12-x86-64bit.tar.gz && \
+    tar -xzvf mysql-connector-odbc-8.0.26-linux-glibc2.12-x86-64bit.tar.gz && \
+    cp -r mysql-connector-odbc-8.0.26-linux-glibc2.12-x86-64bit/lib/* /usr/local/lib && \
+    cp -r mysql-connector-odbc-8.0.26-linux-glibc2.12-x86-64bit/bin/* /usr/local/bin && \
+    rm -rf mysql-connector-odbc-8.0.26-linux-glibc2.12-x86-64bit  && \
+    rm -rf mysql-connector-odbc-8.0.26-linux-glibc2.12-x86-64bit.tar.gz && \
+    myodbc-installer -a -d -n "MySQL ODBC 8.0 Driver" -t "Driver=/usr/local/lib/libmyodbc8w.so" && \
+    myodbc-installer -a -d -n "MySQL ODBC 8.0" -t "Driver=/usr/local/lib/libmyodbc8a.so"
+
+COPY build/linux-toolchain.sh build/linux-libraries.sh /work/bootstrap/
+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 cp exec/install/* exec/64
+
+RUN mkdir -p /work/fhirserver/exec/install/bin
+RUN mkdir -p /work/fhirserver/exec/install/x86_64
+RUN mkdir -p /work/fhirserver/exec/install/content
+RUN mkdir -p /work/fhirserver/exec/install/config
+RUN mkdir -p /work/fhirserver/exec/install/config/config
+RUN mkdir -p /work/fhirserver/exec/install/web
+
+RUN cd /work/fhirserver
+RUN cp /work/fhirserver/exec/64/fhirserver /work/fhirserver/exec/install/bin
+RUN cp /work/fhirserver/exec/64/FHIRToolkit /work/fhirserver/exec/install/bin
+RUN cp /work/fhirserver/exec/64/FHIRConsole /work/fhirserver/exec/install/bin
+RUN 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
+RUN cp /work/fhirserver/exec/pack/linux/install.sh /work/fhirserver/exec/install
+RUN cp /work/fhirserver/exec/pack/linux/get-openssl.sh /work/fhirserver/exec/install
+RUN cp /tmp/openssl-1.1.1w/*.so* /work/fhirserver/exec/install/x86_64
+RUN cp /work/fhirserver/exec/pack/*.properties /work/fhirserver/exec/install/content
+RUN cp /work/fhirserver/exec/pack/*.dat /work/fhirserver/exec/install/content
+RUN cp /work/fhirserver/exec/pack/fhirserver.cfg /work/fhirserver/exec/install/config
+RUN cp /work/fhirserver/exec/64/web.ini /work/fhirserver/exec/install/config
+RUN cp /work/fhirserver/config/config.ini /work/fhirserver/exec/install/config/config
+RUN mkdir -p /work/fhirserver/exec/install/web
+RUN cp -r /work/fhirserver/server/web/* /work/fhirserver/exec/install/web
+
+RUN 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 \
+  CMD curl -f http://localhost:${PORT}/fhir/metadata || exit 1
+
+# Set the environment variables
+ENV DISPLAY :99
+ENV PORT 80
+ENV TERMINOLOGY_CACHE /terminology
+VOLUME /terminology
+
+ENV DEBIAN_FRONTEND=
+
+RUN printf '#!/bin/bash \n\
+    set -e \n\
+    start_xvfb() { \n\
+        Xvfb :99 -screen 0 1024x768x8 -nolisten tcp & \n\
+    } \n\
+    stop_xvfb() { \n\
+        killall Xvfb || true \n\
+    } \n\
+    trap stop_xvfb SIGTERM \n\
+    rm -f /tmp/.X99-lock \n\
+    start_xvfb \n\
+    echo "[web]" > /work/fhirserver/exec/64/web.ini; \n\
+    echo "http=${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"]
+
+
+
+# Runtime stage
+FROM ubuntu:22.04 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 install -y wget tzdata xvfb libgtk2.0-0 libsqlite3-dev \
+    && 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
+
+# Run the installation script
+RUN ./install.sh -nodaemon 
+                          # -zero=https://storage.googleapis.com/tx-fhir-org/config.json
+### Uncomment and append this line above to the install script, to allow the initial tx config to be loaded
+
+
+# Define entrypoint and command
+CMD ["bash", "-c", "cd ~/fhirserver/ && ./start.sh"]
+
+# Expose the necessary port
+EXPOSE 80
diff --git a/FastMM4_AVX512.obj b/FastMM4_AVX512.obj
diff --git a/config/config.ini b/config/config.ini
@@ -1,5 +1,5 @@
 [config]
-zero=file:/root/fhirserver/config
+zero=file:/root/fhirserver/default_config
 version=*
 local=/var/cache/txcache
 user=gg

diff --git a/config/config.json 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/config/config_bare.json b/config/config_bare.json
diff --git a/exec/pack/fhirserver.web b/exec/pack/fhirserver.web