Merge pull request #2818 from IBM/issue-2798

Add Automation for ibm-fhir-term-graph-loader and ibm-fhir-bucket-tool

README.md

@@ -8,7 +8,10 @@ The server can be packaged as a set of jar files, a web application archive (war
 ### Running the IBM FHIR Server
 The IBM FHIR Server is available from the [Releases tab](https://github.com/IBM/FHIR/releases) as a zip file with installation scripts for Mac/Linux and Windows or as a docker image at https://hub.docker.com/r/ibmcom/ibm-fhir-server.
 
-Note: The Docker image [ibmcom/ibm-fhir-schematool](https://hub.docker.com/r/ibmcom/ibm-fhir-schematool) is an early technology preview and is experimental.
+Note:
+1. The Docker image [ibmcom/ibm-fhir-schematool](https://hub.docker.com/r/ibmcom/ibm-fhir-schematool) is an early technology preview and is experimental.
+2. The Docker image [ibmcom/ibm-fhir-bucket-tool](https://hub.docker.com/r/ibmcom/ibm-fhir-bucket-tool) is an early technology preview and is experimental.
+3. The Docker image [ibmcom/ibm-fhir-term-loader](https://hub.docker.com/r/ibmcom/ibm-fhir-term-loader) is an early technology preview and is experimental.
 
 More information on installing and running the server is available in the User Guide at https://ibm.github.io/FHIR/guides/FHIRServerUsersGuide.
 

build/release/bin/30_release/1_dockerhub.sh

@@ -14,6 +14,10 @@ docker login -u "${DOCKERHUB_USERNAME}" -p "${DOCKERHUB_TOKEN}"
 export WORKSPACE=$(pwd)
 bash ${WORKSPACE}/fhir-install/src/main/docker/ibm-fhir-schematool/build.sh
 
+bash ${WORKSPACE}/fhir-install/src/main/docker/ibm-fhir-term-graph-loader/build.sh
+
+bash ${WORKSPACE}/fhir-install/src/main/docker/ibm-fhir-bucket-tool/build.sh
+
 # create and remove a 1 GB file to make sure we have the room needed later
 df -h
 dd if=/dev/urandom oflag=direct of=balloon.dat bs=1024k count=1000

fhir-install/src/main/docker/ibm-fhir-bucket-tool/.gitignore

@@ -0,0 +1 @@
+target/

fhir-install/src/main/docker/ibm-fhir-bucket-tool/DEVELOPMENT.md

@@ -0,0 +1,50 @@
+---
+layout: default
+title:  IBM FHIR Server - Bucket Tool - Development
+date:   2021-10-14
+permalink: /ibm-fhir-bucket-tool-development/
+---
+
+# Development
+
+The document helps developers setup the development environment for the IBM FHIR Server - Bucket Tool. 
+
+1. Build the `fhir-examples` and `fhir-parent`
+
+``` shell
+export WORKSPACE=`pwd`
+cd fhir-install/src/main/docker/ibm-fhir-bucket-tool
+mvn clean install -DskipTests -f ${WORKSPACE}/fhir-examples/
+mvn clean install -DskipTests -f ${WORKSPACE}/fhir-parent/
+```
+
+2. Change to the `fhir-install/src/main/docker/ibm-fhir-bucket-tool` directory
+
+3. Prep the contents
+
+``` shell
+mkdir -p target
+cp ${WORKSPACE}/fhir-bucket/target/fhir-bucket-*-cli.jar target/
+cp ${WORKSPACE}/LICENSE target/LICENSE
+```
+
+4. Build the bucket tool. 
+
+``` shell
+docker build --build-arg FHIR_VERSION=4.10.0 -t ibm-fhir-bucket-tool:4.10.0 .
+```
+
+5. Run
+
+``` shell
+time docker run ibmcom/ibm-fhir-bucket-tool:latest $ARGS | tee out.log
+```
+
+# Run a Shell Check 
+
+Sanity check of the Shell Script
+
+```
+brew install shellcheck
+shellcheck run.sh
+```

fhir-install/src/main/docker/ibm-fhir-bucket-tool/Dockerfile

@@ -0,0 +1,63 @@
+# ----------------------------------------------------------------------------
+# (C) Copyright IBM Corp. 2021
+#
+# SPDX-License-Identifier: Apache-2.0
+# ----------------------------------------------------------------------------
+# Stage: Base
+
+# IBM Semeru Runtimes provides Non-official docker images. These are maintained by IBM.
+# The link to Semeru is at https://hub.docker.com/r/ibmsemeruruntime/open-11-jdk
+FROM ibmsemeruruntime/open-11-jdk:ubi_min-jre-latest as base
+
+# Create the base working directory
+RUN mkdir -p /opt/ibm/fhir/bucket/workarea
+
+# Copy in the relevant artifacts in a single command
+COPY ./run.sh ./target/fhir-bucket-*-cli.jar ./target/LICENSE /opt/ibm/fhir/bucket/
+
+# ----------------------------------------------------------------------------
+# Stage: Runnable
+
+FROM registry.access.redhat.com/ubi8/ubi-minimal
+
+ARG FHIR_VERSION=4.10.0
+
+# The following labels are required: 
+LABEL name='IBM FHIR Server - Bucket Tool'
+LABEL vendor='IBM'
+LABEL version="$FHIR_VERSION"
+LABEL summary="Image for IBM FHIR Server - Bucket Tool with OpenJ9 and UBI 8"
+LABEL description="The IBM FHIR Server - Bucket Tool manages the IBM FHIR Server operations and generates synthetic load."
+
+# Environment variables
+ENV SKIP false
+ENV TOOL_INPUT false
+
+ENV LANG='en_US.UTF-8'
+ENV LANGUAGE='en_US:en'
+ENV LC_ALL='en_US.UTF-8'
+ENV TZ 'UTC'
+
+WORKDIR /opt/ibm/fhir/bucket/workarea
+
+COPY --chown=1001:0 --from=base /opt/ /opt/
+
+RUN chmod -R 755 /opt/ibm/fhir/bucket/run.sh && \
+    mkdir -p /licenses && \
+    mv /opt/ibm/fhir/bucket/LICENSE /licenses && \
+    microdnf update -y && \
+    microdnf install -y nc tzdata openssl curl ca-certificates fontconfig glibc-langpack-en gzip tar findutils shadow-utils && \
+    groupadd -r fhirbucketadmin -g 1001 && \
+    useradd -u 1001 -r -g 1001 -m -d /opt/ibm/fhir/bucket/home -s /sbin/nologin fhirbucketadmin && \
+    chmod -R 755 /opt/ibm/fhir/bucket/ && \
+    rm -rf /var/cache/yum && \
+    rm -f /@System.solv && \
+    microdnf clean all && \
+    rm -rf /var/tmp/* && \
+    rm -rf /tmp/* && \
+    mkdir -p /opt/ibm/fhir/bucket/workarea && \
+    chmod -R 775 /opt/ibm/fhir/bucket/workarea
+
+USER 1001
+
+ENTRYPOINT ["/opt/ibm/fhir/bucket/run.sh"]

fhir-install/src/main/docker/ibm-fhir-bucket-tool/README.md

@@ -0,0 +1,11 @@
+# IBM FHIR Server - Bucket Tool
+
+The image wraps the IBM FHIR Server Bucket Tool which wraps the module - `fhir-bucket`.
+
+************
+# **License**
+
+The IBM FHIR Server - Bucket Tool is licensed under the Apache 2.0 license. Full license text is available at [LICENSE](https://github.com/IBM/FHIR/blob/master/LICENSE).
+
+FHIR® is the registered trademark of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.
+IBM and the IBM logo are trademarks of International Business Machines Corporation, registered in many jurisdictions worldwide. Other product and service names might be trademarks of IBM or other companies. A current list of IBM trademarks is available on [https://ibm.com/trademark](https://ibm.com/trademark).

fhir-install/src/main/docker/ibm-fhir-bucket-tool/build.sh

@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+
+# ----------------------------------------------------------------------------
+# (C) Copyright IBM Corp. 2021
+#
+# SPDX-License-Identifier: Apache-2.0
+# ----------------------------------------------------------------------------
+
+##############################################################################
+
+if [ -z "${WORKSPACE}" ]
+then
+    echo "The WORKSPACE is not set" 
+    exit 10;
+fi
+
+if [ -z "${BUILD_ID}" ]
+then
+    echo "The Build ID is not set"
+    exit 11;
+fi
+
+# docker login is already complete at this point.
+
+pushd $(pwd)
+
+cd ${WORKSPACE}/fhir-install/src/main/docker/ibm-fhir-bucket-tool/
+
+# Copy the files over
+mkdir -p target/
+cp ${WORKSPACE}/fhir-bucket/target/fhir-bucket-*cli.jar target/
+cp ${WORKSPACE}/LICENSE target/
+
+docker build --build-arg FHIR_VERSION=${BUILD_ID} -t ibm-fhir-bucket-tool:latest .
+DOCKER_IMAGE=$(docker images --filter=reference='ibm-fhir-bucket-tool:latest' --format "{{.ID}}")
+echo "Docker Image is:  ${DOCKER_IMAGE}"
+
+docker tag ${DOCKER_IMAGE} ibmcom/ibm-fhir-bucket-tool:${BUILD_ID}
+docker tag ${DOCKER_IMAGE} ibmcom/ibm-fhir-bucket-tool:latest
+docker push ibmcom/ibm-fhir-bucket-tool:${BUILD_ID}
+docker push ibmcom/ibm-fhir-bucket-tool:latest
+
+popd > /dev/null
+
+# EOF

fhir-install/src/main/docker/ibm-fhir-bucket-tool/run.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+# ----------------------------------------------------------------------------
+# (C) Copyright IBM Corp. 2021
+#
+# SPDX-License-Identifier: Apache-2.0
+# ----------------------------------------------------------------------------
+
+/opt/java/openjdk/bin/java -jar /opt/ibm/fhir/bucket/fhir-bucket-*-cli.jar "$@"
+# EOF

fhir-install/src/main/docker/ibm-fhir-schematool/build.sh

@@ -6,8 +6,6 @@
 # SPDX-License-Identifier: Apache-2.0
 # ----------------------------------------------------------------------------
 
-set -e -o pipefail
-
 ##############################################################################
 
 if [ -z "${WORKSPACE}" ]

fhir-install/src/main/docker/ibm-fhir-term-graph-loader/.gitignore

@@ -0,0 +1 @@
+target/

fhir-install/src/main/docker/ibm-fhir-term-graph-loader/DEVELOPMENT.md

@@ -0,0 +1,62 @@
+---
+layout: default
+title:  IBM FHIR Term Graph Loader Tool - Development
+date:   2021-10-04
+permalink: /ibm-fhir-term-graph-loader-tool-development/
+---
+
+# Development
+
+The document helps developers setup the development environment for the IBM FHIR Server - Term Graph Loader Tool. 
+
+1. Build the `fhir-examples` and `fhir-parent`
+
+``` shell
+export WORKSPACE=`pwd`
+cd fhir-install/src/main/docker/ibm-fhir-term-graph-loader
+mvn clean install -DskipTests -f ${WORKSPACE}/fhir-examples/
+mvn clean install -DskipTests -f ${WORKSPACE}/fhir-parent/
+```
+
+2. Change to the `fhir-install/src/main/docker/ibm-fhir-term-graph-loader` directory
+
+3. Prep the contents
+
+``` shell
+mkdir -p target
+cp ${WORKSPACE}/term/fhir-term-graph-loader/target/fhir-term-graph-loader-*-cli.jar target/
+cp ${WORKSPACE}/LICENSE target/LICENSE
+```
+
+4. Build the tool. 
+
+``` shell
+docker build --tag ibm-fhir-term-loader:latest .
+```
+
+or 
+
+``` shell
+docker build --build-arg FHIR_VERSION=4.10.0 -t ibm-fhir-term-loader:4.10.0 .
+```
+
+5. Run the shell. (You may have to edit the corresponding examples)
+
+``` shell
+time docker run --rm -e LOAD_UMLS=true ibmcom/ibm-fhir-term-loader:latest| tee out.log
+```
+
+``` shell
+time docker run --rm -e LOAD_MAP=true ibmcom/ibm-fhir-term-loader:latest| tee out.log
+```
+
+You'll also have to mount a config properties and pass in a configuration environment variable.
+
+# Run a Shell Check 
+
+Sanity check of the Shell Script
+
+```
+brew install shellcheck
+shellcheck run.sh
+```

fhir-install/src/main/docker/ibm-fhir-term-graph-loader/Dockerfile

@@ -4,25 +4,63 @@
 # SPDX-License-Identifier: Apache-2.0
 # ----------------------------------------------------------------------------
 
-# Build stage
-FROM maven:3.6.0-jdk-11-slim AS build
-COPY . /
+# Stage: Base
 
-RUN mvn -B org.apache.maven.plugins:maven-dependency-plugin:3.1.2:go-offline -f /fhir-examples -DexcludeReactor=true -Dmaven.wagon.http.retryHandler.count=3
-RUN mvn -B org.apache.maven.plugins:maven-dependency-plugin:3.1.2:resolve-plugins -f /fhir-examples -DexcludeReactor=true -Dmaven.wagon.http.retryHandler.count=3
-RUN mvn -f /fhir-examples/pom.xml install -DskipTests=true
+# IBM Semeru Runtimes provides Non-official docker images. These are maintained by IBM.
+# The link to Semeru is at https://hub.docker.com/r/ibmsemeruruntime/open-11-jdk
+FROM ibmsemeruruntime/open-11-jdk:ubi_min-jre-latest as base
 
-RUN mvn -B org.apache.maven.plugins:maven-dependency-plugin:3.1.2:go-offline -f /fhir-parent -DexcludeReactor=true -Dmaven.wagon.http.retryHandler.count=3
-RUN mvn -B org.apache.maven.plugins:maven-dependency-plugin:3.1.2:resolve-plugins -f /fhir-parent -DexcludeReactor=true -Dmaven.wagon.http.retryHandler.count=3
-RUN mvn -f /fhir-parent/pom.xml install -DskipTests=true -pl ../fhir-term-graph -am
+# Create the base working directory
+RUN mkdir -p /opt/ibm/fhir/graph/loader/workarea
 
-RUN mvn org.apache.maven.plugins:maven-dependency-plugin:3.2.0:copy-dependencies -f /fhir-parent -pl ../fhir-term-graph -am -DoutputDirectory=target/ftg
+# Copy in the relevant artifacts in a single command
+# the cli is a shaded jar with all dependencies
+COPY ./run.sh ./target/fhir-term-graph-loader-*-cli.jar ./target/LICENSE /opt/ibm/fhir/graph/loader/
 
-# Package stage
-FROM openjdk:11-jre-slim
+# ----------------------------------------------------------------------------
+# Stage: Runnable
+
+FROM registry.access.redhat.com/ubi8/ubi-minimal
+
+ARG FHIR_VERSION=4.10.0
+
+# The following labels are required: 
+LABEL name='IBM FHIR Server - Term Loader Tool'
+LABEL vendor='IBM'
+LABEL version="$FHIR_VERSION"
+LABEL summary="Image for IBM FHIR Server - Term Loader Tool with OpenJ9 and UBI 8"
+LABEL description="The IBM FHIR Server - Term Loader Tool is designed to load the terminology graph."
+
+# Environment variables
+ENV SKIP false
+ENV TOOL_INPUT false
+
+ENV LANG='en_US.UTF-8'
+ENV LANGUAGE='en_US:en'
+ENV LC_ALL='en_US.UTF-8'
+ENV TZ 'UTC'
+
+WORKDIR /opt/ibm/fhir/graph/loader/
+
+COPY --chown=1001:0 --from=base /opt/ /opt/
+
+RUN chmod -R 755 /opt/ibm/fhir/graph/loader/run.sh && \
+    mkdir -p /licenses && \
+    mv /opt/ibm/fhir/graph/loader/LICENSE /licenses && \
+    microdnf update -y && \
+    microdnf install -y nc tzdata openssl curl ca-certificates fontconfig glibc-langpack-en gzip tar findutils shadow-utils && \
+    groupadd -r fhirgraphadmin -g 1001 && \
+    useradd -u 1001 -r -g 1001 -m -d /opt/ibm/fhir/graph/loader/home -s /sbin/nologin fhirgraphadmin && \
+    chmod -R 755 /opt/ibm/fhir/graph/loader && \
+    rm -rf /var/cache/yum && \
+    rm -f /@System.solv && \
+    microdnf clean all && \
+    rm -rf /var/tmp/* && \
+    rm -rf /tmp/* && \
+    mkdir -p /opt/ibm/fhir/graph/loader/workarea && \
+    chmod -R 775 /opt/ibm/fhir/graph/loader/workarea
 
-COPY --from=build run.sh /opt/
-COPY --from=build /fhir-term-graph/target/*.jar /opt/lib/
-COPY --from=build /fhir-term-graph/target/ftg/*.jar /opt/lib/
+USER 1001
 
-ENTRYPOINT ["/opt/run.sh"]
+ENTRYPOINT ["/opt/ibm/fhir/graph/loader/run.sh"]
+# EOF

fhir-install/src/main/docker/ibm-fhir-term-graph-loader/README.md

@@ -0,0 +1,11 @@
+# IBM FHIR Term Graph Loader Tool
+
+The image wraps the IBM FHIR Server Term Graph Loader tool.
+
+************
+# **License**
+
+The IBM FHIR Server - Term Graph Loader Tool is licensed under the Apache 2.0 license. Full license text is available at [LICENSE](https://github.com/IBM/FHIR/blob/master/LICENSE).
+
+FHIR® is the registered trademark of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.
+IBM and the IBM logo are trademarks of International Business Machines Corporation, registered in many jurisdictions worldwide. Other product and service names might be trademarks of IBM or other companies. A current list of IBM trademarks is available on [https://ibm.com/trademark](https://ibm.com/trademark).