issue #1708 merge with master and handle NPE when search param is fil…

…tered out

Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>

build/release/docker-push.sh

@@ -8,6 +8,11 @@
 
 # Assumes that fhir-install has already been built
 docker login -u ${DOCKERHUB_USERNAME} -p ${DOCKERHUB_TOKEN}
+
+# Executes the build for the ibm-fhir-schematool
+# This build runs first so that the FAILURE comes before and stops the subsequent builds/releases.
+${WORKSPACE}/fhir-install/src/main/docker/ibm-fhir-schematool/build.sh
+
 mvn dockerfile:build -f fhir-install -Dmaven.wagon.http.retryHandler.count=3
 mvn dockerfile:tag@tag-version -f fhir-install -Dmaven.wagon.http.retryHandler.count=3
 mvn dockerfile:push@push-version -f fhir-install -Dmaven.wagon.http.retryHandler.count=3

docs/src/pages/guides/FHIRServerUsersGuide.md

@@ -974,6 +974,8 @@ It is also possible to configure a set of profiles, one or more of which a resou
  * Validate that all profiles specified in the resource's `meta.profile` element are supported by the FHIR server
  * Validate that the resource's data conforms to all profiles specified in the resource's `meta.profile` element
 
+If a profile in the list specified by the configuration parameter contains a version, for example `http://ibm.com/fhir/profile/partner|1.0`, then a profile of the same name specified in the resource's `meta.profile` element will only be considered a match if it contains exactly the same version. However, if a profile in the list specified by the configuration parameter does not contain a version, for example `http://ibm.com/fhir/profile/partner`, then a profile of the same name specified in the resource's `meta.profile` element will be considered a match whether it contains a version or not.
+
 If this configuration parameter is not set or is set to an empty list, then the FHIR server will perform its standard validation. 
 
 The IBM FHIR Server pre-packages all conformance resources from the core specification.

fhir-install/licenses/LICENSE

@@ -0,0 +1 @@
+../../LICENSE

fhir-install/src/main/docker/ibm-fhir-schematool/.gitignore

@@ -0,0 +1,3 @@
+target/
+fhirschema.log
+out.log

fhir-install/src/main/docker/ibm-fhir-schematool/DESIGN.md

@@ -0,0 +1,77 @@
+---
+layout: default
+title:  IBM FHIR Server - Schema Tool - Development
+date:   2020-11-11
+permalink: /ibm-fhir-server-schema-tool-development/
+---
+
+# **Design**
+
+The IBM FHIR Schema Tool provides an Docker image that wraps the `fhir-persistence-schema` executable jar. The tool is state machine which take a single configuration to establish a current and running state of the IBM FHIR Server.
+
+The design is such that it COULD, but does not support multiple input files at this time.
+
+When the container is started, the container process one of two flows:
+
+* Schema Onboarding - creates and updates a schema and apply grants
+* Schema Offboarding - deletes a tenant (Db2) and removes data if there are no tenants left.
+
+**Schema Onboarding Flow**
+
+The schema onboarding flow setup add a new tenant or update the database to the latest schema levels. 
+
+1. Check if set to **skip**: 
+    1. If `SKIP['true']`, stop and exit cleanly. 
+    1. If `SKIP['false']`, proceed.
+1. Check if **BEHAVIOR** set to ONBOARD:
+    1. If not `BEHAVIOR['ONBOARD']`, skip. 
+    1. If `BEHAVIOR['ONBOARD']`, proceed.
+1. Create the database configuration file
+1. Check connectivity: 
+    1. If connectivity fails, stop and exit in error. 
+    1. If connectivity succeeds, proceed.
+1. Create the schema
+1. Update the Schema 
+1. Check if Db2:
+    1. If Db2, allocate tenant and save output.
+    1. If Db2, test the allocated tenant
+    1. If not Db2, proceed.
+1. Grant permissions to the IBM FHIR Server database user
+
+**Schema Offboarding Flow**
+
+The schema offboarding flow offboards the current schema, while preserving the schema for multiple tenants (if supported by the database type).
+
+1. Check if set to **SKIP**: 
+    1. If `SKIP['true']`, stop and exit cleanly. 
+    1. If `SKIP['false']`, proceed.
+1. Check if **BEHAVIOR** set to OFFBOARD:
+    1. If not `BEHAVIOR['OFFBOARD']`, skip. 
+    1. If `BEHAVIOR['OFFBOARD']`, proceed.
+1. Check if Db2: 
+    1. If Db2, then deallocate tenant
+    1. If not Db2, then proceed.
+1. If (Db2 and no more tenants) or Postgres, then proceed:
+    1. Drop FHIR Schema
+    1. Drop Java Batch
+    1. Drop OAuth
+
+# **Implementation Details**
+
+## Configuration
+
+The configuration is drived primarily from a working directory, and in alternative circumstances backed by an Environment variable with the input.
+
+The configuration data is mounted to `/ibm-fhir-schematool/workarea/input`.
+
+## Logging
+1. Logging - The logging is to standard error and standard out. 
+ - The logs data is put into the `/ibm-fhir-schematool/workarea/output` folder.
+2. Must Gather Flow - Each execution generates a new set of log files to the `/ibm-fhir-schematool/workarea/output` folder.
+
+## Docker 
+The design is to use as few layers as possible starting with `adoptopenjdk/openjdk11-openj9:ubi-minimal-jre`. 
+
+The build uses multiple layers to avoid a bloated image after the necessary updates. Using a single image results in a 500M image (per docker history ibm-fhir-schematool), versus 167M.
+
+The DockerHub repository is at `ibmcom/ibm-fhir-schematool` and the team that manages it is the IBM FHIR Server team (Docker team: fhir).

fhir-install/src/main/docker/ibm-fhir-schematool/DEVELOPMENT.md

@@ -0,0 +1,80 @@
+---
+layout: default
+title:  IBM FHIR Server - Schema Tool - Development
+date:   2020-11-11
+permalink: /ibm-fhir-server-schema-tool-development/
+---
+
+# Development
+
+The document helps developers setup the development environment for the IBM FHIR Server Schema Tool. 
+
+1. Build the `fhir-examples` and `fhir-parent`
+
+``` shell
+export WORKSPACE=`pwd`
+cd fhir-install/src/main/docker/ibm-fhir-schematool
+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-schematool` directory
+
+3. Prep the contents
+
+``` shell
+mkdir -p target
+cp ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar target/
+cp ${WORKSPACE}/LICENSE target/LICENSE
+```
+
+4. Build the schema tool. 
+
+``` shell
+docker build --tag ibm-fhir-schematool:latest .
+```
+
+or 
+
+``` shell
+docker build --build-arg FHIR_VERSION=4.5.0 -t ibm-fhir-schematool:4.5.0 .
+```
+
+5. For Db2, change run. (You may have to edit the corresponding examples)
+
+* onboard
+``` shell
+time docker run  --env ENV_TOOL_INPUT=`cat examples/db2/persistence-offboard-example.json |base64` ibm-fhir-schematool:latest | tee out.log
+```
+
+* offboard
+``` shell
+time docker run  --env ENV_TOOL_INPUT=`cat examples/db2/persistence-onboard-example.json |base64` ibm-fhir-schematool:latest | tee out.log
+```
+
+6. For Postgres, run. (You may have to edit the corresponding examples)
+
+* onboard
+``` shell
+time docker run  --env ENV_TOOL_INPUT=`cat examples/postgres/persistence-offboard-example.json |base64` ibm-fhir-schematool:latest | tee out.log
+```
+
+* offboard
+``` shell
+time docker run  --env ENV_TOOL_INPUT=`cat examples/postgres/persistence-onboard-example.json |base64` ibm-fhir-schematool:latest | tee out.log
+```
+
+7. Confirm you see your changes work, and the Deployment works.
+
+    * Schema is created, or deleted
+    * No Error Logs (at least unexpected)
+    * Output is as expected
+
+# Run a Shell Check 
+
+Sanity check of the Shell Script
+
+```
+brew install shellcheck
+shellcheck run.sh
+```